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\n© 2023 Author(s). Published under an exclusive license by AIP Publishing.
\n© 2025 The Author(s). Natural Sciences published by Wiley-VCH GmbH. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
\n\nWork at Caltech was supported by the Arnold and Mabel Beckman Foundation. Support at Pomona College was provided by the Howard Hughes Medical Institute Research Program, a Sontag Research Fellowship Award and a Hirsch Research Initiation Grant. Molecular graphics and analyses were performed with UCSF Chimera, UCSF ChimeraX, and PyMOL. UCSF Chimera was developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from NIH P41-GM103311. UCSF ChimeraX was developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases. PyMOL was created and distributed by Schrödinger, LLC.
\n\nSupplementary information. See attached: ntls70012-sup-0001-suppmat.pdf
", "abstract": "In an analysis of the structural stability of the coronavirus main protease (Mpro), we identified regions of the protein that could be disabled by cobalt(III)-cation binding to histidines and cysteines. Here we have extended our work to include copper(II) chelates, which we have docked to HIS 41 and CYS 145 in the Mpro active-site region. We have found stable docked structures where Cu(II) could readily bond to the CYS 145 thiolate, which would be lethal to the enzyme. We investigated the structural basis of Cu(II) Schiff-base chelates as potential Mpro inhibitors in silico. Using induced-fit docking (IFD) and molecular dynamics (MD) simulations, we identified the binding mode and assessed the stability of Mpro inhibition. Our results show that Cu(II) chelates form stable complexes with HIS 41 and CYS 145, with Cu(II) bonding to the CYS 145 thiolate. This irreversible binding is anticipated to effectively inhibit Mpro activity, thereby preventing the proteolytic processing of the SARS-CoV-2 polyprotein into functional proteins necessary for viral activity. Our findings suggest that Cu(II) Schiff-base chelates are promising candidates for the irreversible inhibition of SARS-CoV-2 Mpro.
", "date": "2025-07-22", "date_type": "published", "publication": "Natural Sciences", "volume": "5", "number": "3", "publisher": "American Chemical Society", "pagerange": "e70012", "issn": "2698-6248", "official_url": "https://authors.library.caltech.edu/records/d2re7-r7j59", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "Sontag Foundation" }, { "grant_number": "R01-GM129325" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Chemistry-and-Chemical-Engineering" } ] }, "doi": "10.1002/ntls.70012", "primary_object": { "basename": "Natural Sciences - 2025 - Garza\u2010L\u00f3pez - Copper II Inhibition of the SARS\u2010CoV\u20102 Main Protease.pdf", "url": "https://authors.library.caltech.edu/records/d2re7-r7j59/files/Natural Sciences - 2025 - Garza\u2010L\u00f3pez - Copper II Inhibition of the SARS\u2010CoV\u20102 Main Protease.pdf" }, "related_objects": [ { "basename": "ntls70012-sup-0001-suppmat.pdf", "url": "https://authors.library.caltech.edu/records/d2re7-r7j59/files/ntls70012-sup-0001-suppmat.pdf" } ], "pub_year": "2025", "author_list": "Garza-L\u00f3pez, Roberto A.; Kwak, Liam; et al." }, { "id": "https://authors.library.caltech.edu/records/be5fc-n0n92", "eprint_status": "archive", "datestamp": "2025-05-05 21:27:26", "lastmod": "2025-05-05 21:27:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Kubinski", "given": "Hannah C." } }, { "name": { "family": "Despres", "given": "Hannah W." } }, { "name": { "family": "Johnson", "given": "Bryan A." } }, { "name": { "family": "Schmidt", "given": "Madaline M." } }, { "name": { "family": "Jaffrani", "given": "Sara A." } }, { "name": { "family": "Turner", "given": "Allyson H." } }, { "name": { "family": "Fanuele", "given": "Conor D." } }, { "name": { "family": "Mills", "given": "Margaret G." } }, { "name": { "family": "Lokugamage", "given": "Kumari G." } }, { "name": { "family": "Dumas", "given": "Caroline M." } }, { "name": { "family": "Shirley", "given": "David J." } }, { "name": { "family": "Estes", "given": "Leah K." } }, { "name": { "family": "Pekosz", "given": "Andrew" } }, { "name": { "family": "Crothers", "given": "Jessica W." } }, { "name": { "family": "Roychoudhury", "given": "Pavitra" } }, { "name": { "family": "Greninger", "given": "Alexander L." } }, { "name": { "family": "Jerome", "given": "Keith R." } }, { "name": { "family": "Di Genova", "given": "Bruno Martorelli" } }, { "name": { "family": "Walker", "given": "David H." } }, { "name": { "family": "Ballif", "given": "Bryan A." } }, { "id": "Ladinsky-M-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Menachery", "given": "Vineet D." } }, { "name": { "family": "Bruce", "given": "Emily A." }, "orcid": "0000-0001-8391-370X" } ] }, "title": "Variant mutation G215C in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation", "ispublished": "pub", "full_text_status": "public", "keywords": "Nucleocapsids; SARS CoV 2; Cysteine; Microbial mutation; Dimers; Virions; Viral replication; Transfection", "note": "© 2025 Kubinski et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
\n\nThis study was supported by an American Heart Association predoctoral fellowship (HWD; 10.58275/AHA.23PRE1020524.pc.gr.161030), George Mason University Fast Grant (PJB), NIH (NIAID) Award AI165075 (PJB), NIH (NIAID) Award 1R01AI153602-01 (VDM), Investigators in the Pathogenesis of Infectious Disease, Burroughs Wellcome Fund (VDM), and NIH (NIGMS) award P20GM125498 (EAB) and UVM start-up funds (EAB). The protein mass spectrometry was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103449. The funders played no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
\n\nI have read the journal’s policy and the authors of this manuscript have the following competing interests: HCK, HWD, BAJ, VDM, and EAB have filed a patent on the use of mutations in the nucleocapsid linker as a means of increasing nucleocapsid protein levels. VDM has filed a patent on the reverse genetics system and reporter SARS-CoV-2. Other authors declare no competing interests.
\n\nAll raw sequencing data are available in the NCBI Bioproject ID PRJNA1083584. Individual peptides identified in proteomics experiments are included in S2 Data. Raw proteomics data are available in jPOSTrepo (JPST003506). Plasmids will be provided upon request to the corresponding author, after completion of a material transfer agreement. Infectious virus will be provided after completion of a material transfer agreement and confirmation of suitable BSL-3 facilities and IBC approval to safely handle infectious SARS-CoV-2.
\n\nWe would like to thank Drs Matthew Poynter, Brian Cunniff, Nate Shannon, John Salogiannis, Dimitry Krementsov, and Joyce Oetjen for technical assistance.
\nThe authors thank the Caltech Beckman Institute CryoEM Facility for use and maintenance of the Tecnai T12 TEM.
\n\nS1 Fig. Absence of cysteines in the linker region of Coronaviridae nucleocapsid proteins.
Sequences for the indicated coronavirus nucleocapsid protein sequences were obtained through the NIH Protein Databank and aligned using Clustal Omega from EMBL-EBI (Clustal 0 (1.2.4)). The navy box highlights the linker region (residues 175−247 in SARS-CoV-2). Shown in red is the only cysteine in the displayed sequences, which occurs immediately before the linker region in Erinaceus betacoronavirus.
https://doi.org/10.1371/journal.pbio.3003115.s001
S2 Fig. SARS-CoV-2 N dimer formation.
VeroE6-TMPRSS2 cells were infected, or mock infected, with the indicated SARS-CoV-2 variants (or WA1, termed Wild type) at an MOI of 0.01 for 24 h. (A) Cell lysates were harvested under reducing conditions (10-mM DTT) before visualization by SDS-PAGE and western blot using antibodies recognizing SARS-CoV-2 N (red) and β-actin (green). Alternatively, unreduced lysates from cells infected as above were visualized by SDS-PAGE and western blot using two different antibodies recognizing SARS-CoV-2 N: (B) Invitrogen anti-N mouse antibody (MA5-35943, in green) and (C) Sino Biological anti-N rabbit antibody (40143-R001 in red). (D) Lysates were stained and imaged simultaneously with the two anti-N antibodies and the overlay is shown in yellow. Note minor bands that are seen with the Invitrogen but not the Sino-Biological antibody. The MW of the ~100-kDa band observed in Beta, Delta, and Iota samples under non-reducing conditions is indicated by a *. A representative gel from three (A) or two (C) independent biological replicates is shown. (E) Vero-TMPRSS2 cells were infected with WA1 or Delta SARS-CoV-2 at an MOI of 0.01. Twenty-four hpi cells were harvested, lysed, and N was affinity purified using immunoprecipitation. N and associated proteins were run on an SDS-PAGE gel, and bands corresponding to the monomer and dimer were cut and processed for mass spectrometry. (F) The number of peptides for each SARS-CoV-2 viral protein found in the monomer or dimer portion of the gel, for either WT (WA1) or Delta, is shown. The data underlying this Figure can be found in S1 Data and S2 Data.
https://doi.org/10.1371/journal.pbio.3003115.s002
S3 Fig. Quantification of NEM treatment on N dimer formation.
A) VeroE6-TMPRSS2 cells were infected with WT or the G215C virus at an MOI of 0.01 for 24 h. Cell lysates were harvested in standard triton lysis buffer (lanes 1, 5) or in the presence of increasing concentrations of N-ethylmaleimide (1, 10, 100 mM). (B) A parallel experiment was performed in which cells were pre-treated by incubating for 30 min at 37°C in increasing concentrations (1, 10, 100 mM) of NEM in PBS. Cells were then lysed as in (A), with NEM present in the lysis buffer as well as the pre-incubation. Lysates were visualized by SDS-PAGE and western blot using antibodies to SARS-CoV-2 N and actin. (C and D) Quantification of the N dimer to monomer ratios in (A and B) is shown for two independent experiments. The data underlying this Figure can be found in S1 Data.
|https://doi.org/10.1371/journal.pbio.3003115.s003
S4 Fig. The G215C mutation increases levels of RNA bound to nucleocapsid.VeroE6-TMPRSS2 cells were infected with WT or the G215C viruses at an MOI of 0.01 for 48 h. Clarified viral supernatants were concentrated by binding to PEG and centrifuging at 10,000G for 30 min at 4°C. Concentrated virus was lysed and nucleocapsid proteins from each flask were affinity purified. Western blots were used to verify equal inputs of N from all conditions (inputs), and saturation of the beads (flow-through). The data underlying this Figure can be found in S1 Data.
https://doi.org/10.1371/journal.pbio.3003115.s004
S5 Fig. Antigen staining of lung tissue from infected hamsters.Section of lung tissue from infected hamsters was stained for viral antigen (nucleocapsid). Sections were then blinded and scored on a 4 point scale for parenchyma, airway, and overall staining (A). Each data point represents the average score form two lung section from each hamster in the group (n > 4). Horizontal lines represent the group mean and error bars are ±SD. Significance determined by student T test. (B) Representative images are shown for WT and N:215C infected animals for 2, 4, and 7 dpi. (. [p = 0.05−0.1], * [p < 0.05]). The data underlying this Figure can be found in S1 Data.
https://doi.org/10.1371/journal.pbio.3003115.s005
S6 Fig. The G215S mutation decreases packaging of N and growth in primary differentiated human bronchial cells.(A) VeroE6-TMPRSS2 cells were infected with the WT or N:G21SC viruses at an MOI of 0.0005 for 1 h, viral supernatants were collected at 8, 24, 32, 48, and 72 h post infection and titered by focus forming assay (FFU; focus forming unit). (B) Human bronchial epithelial cells were infected with WT or N:G215S viruses at an MOI of 0.5 for 1 h, apical washes were collected sequentially from the same well at 8, 24, 32, 48, and 72 h post infection and titered by focus forming assay (FFU). (C) High titer viral stocks of the WT or N:G215S viruses were concentrated by binding to 10% polyethylene glycol then centrifugated at 10,000G for 30 min at 4ºC. Unreduced lysates were collected 24 h post transfection directly from the concentrated viral pellet and N and M were visualized by SDS-PAGE. (D) The ratio of N to M is shown, as well as (E) the ratio of N to FFU. Mean ± SEM is plotted, N = 6 from two biological experiments (A), N = 6 (B), and N = 3 (C–E) is shown. Statistical comparisons were conducted using a two-tailed T test, (. [p = 0.05−0.1], * [p < 0.05]). Limit of detection (LoD) is 20 PFU/mL and the y-axis minimum is set as the LoD. The data underlying this Figure can be found in S1 Data.
https://doi.org/10.1371/journal.pbio.3003115.s006
S7 Fig. N:G215C virions are enlarged.Vero-TMPRSS2 cells were infected with WT or N:G215C viruses at an MOI of 0.1. The following day cells were prepared for electron microscopy by high-pressure freezing and freeze-substitution, then sectioned and imaged by dual-axis electron tomography. Virus-containing exit compartments were located in both samples, and 20 virions that had completely separated from cellular membranes were randomly selected and imaged for each virus.
https://doi.org/10.1371/journal.pbio.3003115.s007
S1 Data. The individual datapoints underlying each graph can be found in this dataset.
https://doi.org/10.1371/journal.pbio.3003115.s008
S2 Data. The proteolytic peptides identified in the mass spectrometry experiment in S2 Fig can be found in this dataset.
https://doi.org/10.1371/journal.pbio.3003115.s009\\
S1 Raw Images. The uncropped western blots shown in figures and quantifications can be found in this dataset.
https://doi.org/10.1371/journal.pbio.3003115.s010
The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of spike are not well studied, the entire viral genome is undergoing evolutionary selection, with several variants containing mutations in the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a more stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth both in vitro and in vivo. Mechanistically, we show that the N:G215C mutant has more encapsidation as measured by increased RNA binding to N, N incorporation into virions, and electron microscopy showing that individual virions are larger, with elongated morphologies.
", "date": "2025-04-29", "date_type": "published", "publication": "PLOS Biology", "volume": "23", "number": "4", "publisher": "PLOS", "pagerange": "e3003115", "issn": "1545-7885", "editors": { "items": [ { "name": { "family": "Mehle,", "given": "Andrew" } } ] }, "official_url": "https://authors.library.caltech.edu/records/be5fc-n0n92", "funders": { "items": [ { "grant_number": "10.58275/AHA.23PRE1020524.pc.gr.161030" }, { "grant_number": "Fast Grant" }, { "grant_number": "AI165075" }, { "grant_number": "1R01AI153602-01" }, { "grant_number": "Investigators in the Pathogenesis of Infectious Disease" }, { "grant_number": "P20GM125498" }, { "grant_number": "start-up funds" }, { "agency": "National Institute of General Medical Sciences of the National Institutes of Health", "grant_number": "P20GM103449" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" }, { "id": "COVID-19" } ] }, "doi": "10.1371/journal.pbio.3003115", "primary_object": { "basename": "journal.pbio.3003115.pdf", "url": "https://authors.library.caltech.edu/records/be5fc-n0n92/files/journal.pbio.3003115.pdf" }, "pub_year": "2025", "author_list": "Kubinski, Hannah C.; Despres, Hannah W.; et al." }, { "id": "https://authors.library.caltech.edu/records/555nb-t7q08", "eprint_status": "archive", "datestamp": "2026-04-09 03:41:18", "lastmod": "2026-04-09 03:41:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Agudelo", "given": "Olga L." }, "orcid": "0000-0002-8532-4260" }, { "name": { "family": "Reyes-Loaiza", "given": "Vanessa" } }, { "name": { "family": "Giraldo-Parra", "given": "Lina" }, "orcid": "0000-0002-3558-7249" }, { "name": { "family": "Rosales-Chilama", "given": "Mariana" }, "orcid": "0000-0002-0649-7201" }, { "name": { "family": "Perdomo", "given": "Sammy" }, "orcid": "0000-0001-5802-2702" }, { "name": { "family": "G\u00f3mez", "given": "Mar\u00eda Adelaida" }, "orcid": "0000-0001-8792-1563" }, { "name": { "family": "Rodriguez", "given": "John W." } }, { "name": { "family": "Ortega", "given": "Viviana" }, "orcid": "0000-0001-7927-6082" }, { "name": { "family": "Daza Rivera", "given": "Carlos F." } }, { "name": { "family": "Galindo", "given": "Diana" } }, { "name": { "family": "Valencia", "given": "Drochss P." } }, { "name": { "family": "Quimbaya", "given": "Mauricio" }, "orcid": "0000-0003-2631-270X" }, { "name": { "family": "Plata", "given": "Sim\u00f3n" } }, { "name": { "family": "Bogdanowicz", "given": "Robert" }, "orcid": "0000-0002-7543-2620" }, { "name": { "family": "Rosso", "given": "Fernando" }, "orcid": "0000-0002-2684-9489" }, { "id": "Jaramillo-Botero-Andres", "name": { "family": "Jaramillo-Botero", "given": "Andres" }, "orcid": "0000-0003-2844-0756" } ] }, "title": "Performance assessment of disposable carbon-based immunosensors for the detection of SARS-CoV-2 infections", "ispublished": "pub", "full_text_status": "public", "keywords": "SARS-CoV-2; Biosensor; Immunoassays; Antigen; Spike protein; Point-of-care testing", "note": "© The Author(s) 2025. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nWe gratefully acknowledge all volunteers who participated in this study and donated their samples. This research was partially funded by the Colombian Ministry of Science, Technology, and Innovation (Minciencias) under the Mincienciatón program, which was established to address the COVID-19 pandemic (award #380-2020). Additional support was provided by Wellcome Trust 107595/Z/15/Z and Fundación Restrepo-Barco to MAG. The content of this study is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. The authors would also like to acknowledge contributions of Isabella López, Jhonattan De La Roche, Gabriel Vélez, and Nelson Mancilla, as well as the Secretaria de Salud Departamental del Valle del Cauca—Laboratorio de Salud Pública Departamental in Colombia.
\nO.A. and V.R.-L. contributed to writing (original draft, review and editing), methodology and investigation, L.G.-P. and M.R.-C. contributed to writing (original draft), methodology and investigation, SP contributed to writing (review and editing), methodology, and investigation, JWR contributed to writing (review), methodology and investigation, M.A.G. contributed to writing (original draft, review and editing), conceptualization, methodology, investigation, validation, formal analysis, and funding acquisition, V.O. contributed to writing (editing), methodology and investigation, C.D. and D.G. contributed to writing (review), methodology, resources, and investigation, D.P.V. contributed to writing (review), methodology, and investigation, MQ contributed to writing (review) and methodology, S.Plata. contributed to writing (review), methodology and investigation, R.B. contributed to writing (review) and methodology, F.R. contributed to writing (review), methodology, investigation, and funding acquisition, and A.J.-B. contributed to conceptualization, methodology, investigation, validation, formal analysis, resources, data curation, writing (original draft, review and editing), supervision, administration, and funding acquisition.
\n\nAll clinical and sociodemographic data generated or analyzed during this study are included in this published article (and its Supplementary Information files).
\nWe designed, developed, and clinically tested two rapid antigen-based immunosensors for SARS-CoV-2 detection, enabling diagnosis and viral load quantification for under USD $2. In a first clinical study, a screen-printed disposable carbon-based (SPC) sensor was assessed on prospectively recruited adult participants classified into three study groups: healthy donors (n = 46); SARS-CoV-2-infected symptomatic patients (n = 58); and co-habitants of patients without prior testing (n = 38). Nasopharyngeal aspirates (NA), oropharyngeal swabs (OS), and saliva (SA) samples were obtained from all participants. Performance was measured in terms of clinical sensitivity and specificity against a reference diagnostic RT-qPCR kit and analytical sensitivity (limit of detection, LoD) and specificity using recombinant material in lab tests. A second study was performed using the same sensor design, albeit with laser-induced graphene (LIG) electrodes, using nasopharyngeal swabs (NS) on 224 patient samples obtained at different stages of the pandemic, of which 110 tested negative and 114 positive via RT-qPCR. We find OS was the most informative sample, when compared to NA and SA. The SPC-based sensors had a 93.8% sensitivity and 61.5% specificity with OS samples, while the LIG-based sensors with NS had a lower sensitivity of 68.93%, albeit a significantly higher specificity of 86.17%. We believe specificity values for the SPC sensors were driven by positive results from co-habitants and healthy donors and were affected by the low sensitivity (75.5%) and high LoD (> 20,000 viral copies/mL) of the reference RT-qPCR kit used, and the lower sensitivity of the LIG-based was due to a reduced set of effective antigen-binding sites caused by the non-covalent LIG-mAb ligands used. The immunosensor's LoD to spike protein in phosphate-buffered saline (PBS) for both types of sensors was near 1 fg/mL and showed no cross-reactivity to recombinant structural proteins of Epstein-Barr and Influenza. Performance metrics and time-to-result (5 < 12 min) provide proof-of-principle of the immunosensor's applicability as a low-cost, rapid technology for determining SARS-CoV-2 infections. Changing the working electrode material to LIG, instead of SPC, improved specificity even in the presence of pathogen variants. Discordant results between our two immunosensor versions and RT-qPCR tests are attributed not only to limited antibody effectiveness in the former but also to the quality of RT-qPCR probes used at the height of the pandemic.
", "date": "2025-03-05", "date_type": "published", "publication": "Scientific Reports", "volume": "15", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "7741", "issn": "2045-2322", "official_url": "https://authors.library.caltech.edu/records/555nb-t7q08", "funders": { "items": [ { "grant_number": "380-2020" }, { "grant_number": "107595/Z/15/Z" }, { "agency": "Fundaci\u00f3n Restrepo-Barco" } ] }, "local_group": { "items": [ { "id": "Division-of-Chemistry-and-Chemical-Engineering" }, { "id": "COVID-19" } ] }, "doi": "10.1038/s41598-025-92104-7", "pmcid": "PMC11883031", "primary_object": { "basename": "s41598-025-92104-7.pdf", "url": "https://authors.library.caltech.edu/records/555nb-t7q08/files/s41598-025-92104-7.pdf" }, "related_objects": [ { "basename": "41598_2025_92104_MOESM1_ESM.docx", "url": "https://authors.library.caltech.edu/records/555nb-t7q08/files/41598_2025_92104_MOESM1_ESM.docx" }, { "basename": "41598_2025_92104_MOESM2_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/555nb-t7q08/files/41598_2025_92104_MOESM2_ESM.xlsx" } ], "pub_year": "2025", "author_list": "Agudelo, Olga L.; Reyes-Loaiza, Vanessa; et al." }, { "id": "https://authors.library.caltech.edu/records/eq67h-c9n23", "eprint_status": "archive", "datestamp": "2024-05-07 18:50:35", "lastmod": "2024-05-07 18:50:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dedhe-Abhishek-M", "name": { "family": "Dedhe", "given": "Abhishek M." }, "orcid": "0000-0002-3881-8129" }, { "name": { "family": "Chowkase", "given": "Aakash A." }, "orcid": "0000-0001-6990-4698" }, { "name": { "family": "Gogate", "given": "Niramay V." }, "orcid": "0000-0002-7218-3323" }, { "name": { "family": "Kshirsagar", "given": "Manas M." }, "orcid": "0000-0001-6523-974X" }, { "name": { "family": "Naphade", "given": "Rohan" } }, { "name": { "family": "Naphade", "given": "Atharv" } }, { "id": "Kulkarni-Pranav", "name": { "family": "Kulkarni", "given": "Pranav" }, "orcid": "0000-0002-1461-0948" }, { "name": { "family": "Naik", "given": "Mrunmayi" }, "orcid": "0009-0006-8699-4246" }, { "name": { "family": "Dharm", "given": "Aarya" } }, { "name": { "family": "Raste", "given": "Soham" } }, { "name": { "family": "Patankar", "given": "Shravan" }, "orcid": "0009-0004-3230-2756" }, { "name": { "family": "Jogdeo", "given": "Chinmay M." }, "orcid": "0000-0003-0018-1684" }, { "name": { "family": "Sathe", "given": "Aalok" }, "orcid": "0000-0002-5248-7557" }, { "name": { "family": "Kulkarni", "given": "Soham" } }, { "name": { "family": "Bapat", "given": "Vibha" } }, { "name": { "family": "Joshi", "given": "Rohinee" }, "orcid": "0009-0004-8304-9754" }, { "name": { "family": "Deshmukh", "given": "Kshitij" }, "orcid": "0000-0001-9367-4650" }, { "name": { "family": "Lele", "given": "Subhash" } }, { "name": { "family": "Manke-Miller", "given": "Kody J." }, "orcid": "0000-0002-2485-6538" }, { "name": { "family": "Cantlon", "given": "Jessica F." } }, { "name": { "family": "Pandit", "given": "Pranav S." }, "orcid": "0000-0001-7649-0649" } ] }, "title": "Conventional and frugal methods of estimating COVID-19-related excess deaths and undercount factors", "ispublished": "pub", "full_text_status": "public", "note": "© The Author(s) 2024. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nThis work was partially supported by prize money from the Johns Hopkins Center for Bioengineering Innovation and Design’s COVID-19 Design Challenge 2020 awarded to A.M.D., P.K., S.P., S.R., Dr. Samvid Kurlekar, and Gauri Kapoor. Jnana Prabodhini Foundation’s SurveyMonkey account, that was used to conduct the wisdom of crowds public survey, was partially sponsored by SurveyMonkey’s COVID-19 Support-A-Charity program. Funding for publishing this article open access was provided by the University of California Libraries under a transformative open access agreement with the publisher. This work did not receive any additional funding from grants or other sources. We thank the Pune Knowledge Cluster, a national-level Science and Innovation Cluster set up by the Office of the Principal Scientific Advisor (Government of India), for sharing a dataset about monthly all-cause mortality in Pune from January 2014 through December 2022. Within the Pune Knowledge Cluster, we thank Dr. Raghunath Mashelkar, Dr. L.S. Shashidhara, Dr. Ajit Kembhavi, Dr. Priyanka Nagaraj, and Priyanki Shah for their research support. We thank Nour Al-Zaghloul and Hugo Angulo for laboratory research support at Carnegie Mellon University. Within the Jnana Prabodhini Foundation, we thank Ganesh Kuber, Dr. Swapneeta Date, Revati Desphande, Parnavi Habde, Chinmay Shah, Tejas Shende, Rohan Shinde, Pranav Kajgaonkar, and Pranav A. Kulkarni, as well as Jnana Prabodhini (Pune)'s Educational Resource Centre, Nagari Vasti Abhyas Gat, and Yuvak Vibhag for their research and outreach support. We thank Dr. Suneeta Kulkarni, Dr. Vicki Hegelson, Dr. Joy Monteiro, Dr. Mihir Arjunwadkar, Dr. Murad Banaji, Dr. Wändi Bruine de Bruin, Dr. Bhalchandra Pujari, Joshua de Souza, Aparajita Chandrasekhar, Muhammad Hadi, Dr. Varun Chowdhry, Apoorva Khadilkar, Lakshmi Kumar, Dr. Samvid Kurlekar, Shreyas Chaudhari, Chinmayi Bankar, Bhargavi Patel, Shreyas Gajendragadkar, Rhugwed Ponkshe, Tushar Joshi, Mohit Diwase, Sushant Pawar, and Nachiket Panse for their support and feedback. We are grateful to the participants of our survey. All data analyses were conducted using the Python and R programming languages, Microsoft Excel, and Google Sheets. All figures and tables were created using the R programming language, Microsoft Excel, Google Sheets, and DataWrapper.
\nA.M.D. was the principal investigator of this study. S.L., K.J.M.-M., J.F.C., and P.S.P. were senior faculty investigators in this study. A.M.D., A.A.C., N.V.G., M.M.K., P.K., S.L., K.J.M.-M., J.F.C., and P.S.P. developed the study concept and contributed to the study design. A.M.D., A.A.C., N.V.G., M.M.K., P.K., S.R., S.P., C.M.J., A.S., V.B., and R.J. collected the data. A.M.D., A.A.C., N.V.G., R.N., A.N., P.K., M.N., S.P., S.K., S.L., J.F.C., and P.S.P. performed the data analysis. A.M.D., A.A.C., N.V.G., M.M.K., K.D., J.F.C., and P.S.P. wrote the manuscript. A.M.D., N.V.G., A.D., S.R., and S.K., created the figures. A.M.D. and P.S.P. are the corresponding authors of this study. All authors read the manuscript, discussed the results, and commented on the manuscript.
\n\nAll data generated or analyzed during this study are included in this published article and its supplementary information files.
\nThe authors declare no competing interests.
\nAcross the world, the officially reported number of COVID-19 deaths is likely an undercount. Establishing true mortality is key to improving data transparency and strengthening public health systems to tackle future disease outbreaks. In this study, we estimated excess deaths during the COVID-19 pandemic in the Pune region of India. Excess deaths are defined as the number of additional deaths relative to those expected from pre-COVID-19-pandemic trends. We integrated data from: (a) epidemiological modeling using pre-pandemic all-cause mortality data, (b) discrepancies between media-reported death compensation claims and official reported mortality, and (c) the “wisdom of crowds” public surveying. Our results point to an estimated 14,770 excess deaths [95% CI 9820–22,790] in Pune from March 2020 to December 2021, of which 9093 were officially counted as COVID-19 deaths. We further calculated the undercount factor—the ratio of excess deaths to officially reported COVID-19 deaths. Our results point to an estimated undercount factor of 1.6 [95% CI 1.1–2.5]. Besides providing similar conclusions about excess deaths estimates across different methods, our study demonstrates the utility of frugal methods such as the analysis of death compensation claims and the wisdom of crowds in estimating excess mortality.
\nThe computational studies at Caltech were supported by a grant from the NIH (R01HL155532). J.S. thanks NIH (R35GM137988). Some computational resources for this research were provided by the Anton2 computer at the Pittsburgh National Supercomputing Center (MCB180091P). P.-D.N. thanks Y. Feinstein (University of Arizona) for her assistance in mass spectrometry.
\nS.-K.K. and W.A.G. conceived the study. S.-K.K. performed the docking and virtual screening. S.S. performed the experiments. A.G. assisted with the optical sensing experiments. P.-D.N. performed early experiments and removed the gadolinium ions from gadoversetamide. Y.T. assisted with surface functionalization of the sensor in early experiments. J.S. supervised the experiments. S.S., J.S., and W.A.G. analyzed and interpreted the experiments. S.-K.K. and S.S. wrote the manuscript with inputs from others. Every author has read, edited, and approved the final manuscript. S.-K.K. and S.S. contributed equally to this submission.
\n\nThe authors declare the following competing financial interest(s): J.S. owns a financial stake in Femtorays Technologies which develops label-free molecular sensors.
\n\nThe computational studies at Caltech were supported by a grant from the NIH (R01HL155532). J.S. thanks NIH (R35GM137988). Some computational resources for this research were provided by the Anton2 computer at the Pittsburgh National Supercomputing Center (MCB180091P). P.-D.N. thanks Y. Feinstein (University of Arizona) for her assistance in mass spectrometry.
\nS.-K.K. and W.A.G. conceived the study. S.-K.K. performed the docking and virtual screening. S.S. performed the experiments. A.G. assisted with the optical sensing experiments. P.-D.N. performed early experiments and removed the gadolinium ions from gadoversetamide. Y.T. assisted with surface functionalization of the sensor in early experiments. J.S. supervised the experiments. S.S., J.S., and W.A.G. analyzed and interpreted the experiments. S.-K.K. and S.S. wrote the manuscript with inputs from others. Every author has read, edited, and approved the final manuscript. S.-K.K. and S.S. contributed equally to this submission.
", "abstract": "As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus mutates, finding effective drugs becomes more challenging. In this study, we use ultrasensitive frequency locked microtoroid optical resonators in combination with in silico screening to search for COVID-19 drugs that can stop the virus from attaching to the human angiotensin-converting enzyme 2 (hACE2) receptor in the lungs. We found 29 promising candidates that could block the binding site and selected four of them that were likely to bind very strongly. We tested three of these candidates using frequency locked optical whispering evanescent resonator (FLOWER), a label-free sensing method based on microtoroid resonators. FLOWER has previously been used for sensing single macromolecules. Here we show, for the first time, that FLOWER can provide accurate binding affinities and sense the inhibition effect of small molecule drug candidates without labels, which can be prohibitive in drug discovery. One of the candidates, methotrexate, showed binding to the spike protein 1.8 million times greater than that to the receptor binding domain (RBD) binding to hACE2, making it difficult for the virus to enter cells. We tested methotrexate against different variants of the SARS-CoV-2 virus and found that it is effective against all four of the tested variants. People taking methotrexate for other conditions have also shown protection against the original SARS-CoV-2 virus. Normally, it is assumed that methotrexate inhibits the replication and release of the virus. However, our findings suggest that it may also block the virus from entering cells. These studies additionally demonstrate the possibility of extracting candidate ligands from large databases, followed by direct receptor–ligand binding experiments on the best candidates using microtoroid resonators, thus creating a workflow that enables the rapid discovery of new drug candidates for a variety of applications.
\nBuddhi Pushpawela: Conceptualization (equal); Data curation (equal); Formal analysis (equal); Methodology (equal); Supervision (equal); Writing – original draft (equal). Peter Chea: Formal analysis (equal); Methodology (equal); Writing – original draft (equal). Ryan Ward: Methodology (equal). Richard C. Flagan: Conceptualization (equal); Project administration (equal); Supervision (equal); Writing – review & editing (equal).
\nThe data that support the findings of this study are available from the corresponding author upon request.
\nThe authors have no conflicts to disclose.
\n\u00a9 Te Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nAuthor Contributions: Study design: T.L., J.Z., A.S., N.M., V.D.G., R.K., and R.S.; Data analysis: T.L., J.Z., N.M., and V.D.G.; Data visualization: T.L., S.K., and J.Z.; Manuscript writing: T.L., J.Z., N.M., and V.D.G. Manuscript revisions: all authors.
\n\nAll raw wastewater sequencing data are available via the NCBI Sequence Read Archive under the BioProject ID PRJNA819090. Consensus sequences from clinical and wastewater surveillance are all available on GISAID. Spike-in sequencing data are available via Google cloud (https://console.cloud.google.com/storage/browser/search-reference_data). The UCSD campus dashboard can be accessed at https://returntolearn.ucsd.edu/dashboard/. The SEARCH genomic surveillance dashboard is available at https://searchcovid.info/dashboards/sequencing-statistics/. The wastewater time series features are available to researchers for non-commercial use per request.
\n\nThe code for all analysis involved in this manuscript is hosted publicly on GitHub repository (https://github.com/tuolin123/Wastewater_UCSD).
\n\nThe Institutional Review Board (IRB) of University of California, San Diego provided approval for human subject protection oversight of the data obtained by the EXCITE laboratory for the campus clinical samples. Informed consent was obtained from all participants included in the study, and the appropriate institutional forms have been archived, and any sample identifiers included were de-identified. The wastewater component of this project was discussed with our IRB and was not deemed to be human subject research as it did not record personally identifiable information. All methods were carried out in accordance with relevant guidelines and regulations.
\n\nThe authors declare no competing interests. R.K.'s current conflicts of interest are: Gencirq (stock and SAB member), DayTwo (consultant and SAB member), Cybele (stock and consultant), Biomesense (stock, consultant, SAB member), Micronoma (stock, SAB member, co-founder), and Biota (stock, co-founder).
", "abstract": "During the COVID-19 pandemic, wastewater surveillance of the SARS CoV-2 virus has been demonstrated to be effective for population surveillance at the county level down to the building level. At the University of California, San Diego, daily high-resolution wastewater surveillance conducted at the building level is being used to identify potential undiagnosed infections and trigger notification of residents and responsive testing, but the optimal determinants for notifications are unknown. To fill this gap, we propose a pipeline for data processing and identifying features of a series of wastewater test results that can predict the presence of COVID-19 in residences associated with the test sites. Using time series of wastewater results and individual testing results during periods of routine asymptomatic testing among UCSD students from 11/2020 to 11/2021, we develop hierarchical classification/decision tree models to select the most informative wastewater features (patterns of results) which predict individual infections. We find that the best predictor of positive individual level tests in residence buildings is whether or not the wastewater samples were positive in at least 3 of the past 7 days. We also demonstrate that the tree models outperform a wide range of other statistical and machine models in predicting the individual COVID-19 infections while preserving interpretability. Results of this study have been used to refine campus-wide guidelines and email notification systems to alert residents of potential infections.
", "date": "2023-11-24", "date_type": "published", "publication": "Scientific Reports", "volume": "13", "publisher": "Nature Publishing Group", "pagerange": "20670", "issn": "2045-2322", "official_url": "https://authors.library.caltech.edu/records/tzbmb-zcx74", "funders": { "items": [ { "agency": "UCSD Chancellor's Office Fund" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" }, { "id": "COVID-19" } ] }, "doi": "10.1038/s41598-023-47859-2", "pmcid": "PMC10673837", "primary_object": { "basename": "41598_2023_47859_MOESM1_ESM.docx", "url": "https://authors.library.caltech.edu/records/tzbmb-zcx74/files/41598_2023_47859_MOESM1_ESM.docx" }, "related_objects": [ { "basename": "s41598-023-47859-2.pdf", "url": "https://authors.library.caltech.edu/records/tzbmb-zcx74/files/s41598-023-47859-2.pdf" } ], "pub_year": "2023", "author_list": "Lin, Tuo; Karthikeyan, Smruthi; et al." }, { "id": "https://authors.library.caltech.edu/records/gqd91-2ae97", "eprint_id": 122430, "eprint_status": "archive", "datestamp": "2023-08-22 21:24:23", "lastmod": "2023-12-22 23:32:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rouhani-Nina", "name": { "family": "Rouhani", "given": "Nina" }, "orcid": "0000-0003-2814-0462" }, { "id": "Stanley-Damian", "name": { "family": "Stanley", "given": "Damian" }, "orcid": "0000-0001-9815-913X" }, { "id": "Adolphs-R", "name": { "family": "Adolphs", "given": "Ralph" }, "orcid": "0000-0002-8053-9692" }, { "id": "Alvarez-R-M", "name": { "family": "Alvarez", "given": "R. Michael" }, "orcid": "0000-0002-8113-4451" }, { "id": "Camplisson-Isabella", "name": { "family": "Camplisson", "given": "Isabella" }, "orcid": "0000-0001-9653-2789" }, { "id": "Han-Yanting", "name": { "family": "Han", "given": "Yanting" }, "orcid": "0000-0003-3381-2059" }, { "id": "Harrison-Laura-A", "name": { "family": "Harrison", "given": "Laura A." } }, { "id": "Hien-Denise", "name": { "family": "Hien", "given": "Denise" }, "orcid": "0000-0002-6954-2882" }, { "id": "Hopkins-Amber", "name": { "family": "Hopkins", "given": "Amber" }, "orcid": "0000-0002-8354-565X" }, { "id": "Lan-Tian", "name": { "family": "Lan", "given": "Tian" } }, { "id": "Lawrence-Caroline-V", "name": { "family": "Lawrence", "given": "Caroline" } }, { "id": "Liang-Dehua", "name": { "family": "Liang", "given": "Dehua" }, "orcid": "0000-0003-4794-0270" }, { "id": "Lin-Chujun", "name": { "family": "Lin", "given": "Chujun" }, "orcid": "0000-0002-7605-6508" }, { "id": "L\u00f3pez-Castro-Teresa", "name": { "family": "L\u00f3pez-Castro", "given": "Teresa" }, "orcid": "0000-0003-2521-6329" }, { "id": "Maoz-Uri-M", "name": { "family": "Maoz", "given": "Uri" }, "orcid": "0000-0002-7899-1241" }, { "id": "Nizzi-Marie-Christine", "name": { "family": "Nizzi", "given": "Marie-Christine" }, "orcid": "0000-0002-2062-8992" }, { "id": "Paul-Lynn-K", "name": { "family": "Paul", "given": "Lynn K." }, "orcid": "0000-0002-3128-8313" }, { "id": "Rabkin-Golden-Allison", "name": { "family": "Rabkin Golden", "given": "Allison" } }, { "id": "Rusch-Tessa", "name": { "family": "Rusch", "given": "Tessa" }, "orcid": "0000-0002-5445-6885" }, { "id": "Stanley-Damien-A", "name": { "family": "Stanley", "given": "Damien A." } }, { "id": "Wahle-Iman-A", "name": { "family": "Wahle", "given": "Iman" } } ] }, "title": "Collective events and individual affect shape autobiographical memory", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2023 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY). \n\nWe thank all members of the COVID-Dynamic team (see SI Appendix, section 5 for project description and specific contributions). We also thank Ruben Van Genugten, who developed the Autobiographical Interview NLP tool, Qianying Wu, and James Antony for fruitful discussion. \n\nData, Materials, and Software Availability: All modeling code and output is publicly available, organized by the order of reported results (https://github.com/ninarouhani/2023_RouhaniAdolphs). Anonymized quantitative data/code have been deposited in github (https://github.com/ninarouhani/2023_RouhaniAdolphs) (71). All other data are included in the article and/or supporting information. \n\nAuthor contributions: N.R., D.S., and R.A. designed research; N.R. and C.-D.T. performed research; N.R. analyzed data; and N.R. and R.A. wrote the paper. \n\nThe authors declare no competing interest.\n\nPublished - pnas.2221919120.pdf
Supplemental Material - pnas.2221919120.sapp.pdf
Supplemental Material - pnas.2221919120.sd01.docx
", "abstract": "How do collective events shape how we remember our lives? We leveraged advances in natural language processing as well as a rich, longitudinal assessment of 1,000 Americans throughout 2020 to examine how memory is influenced by two prominent factors: surprise and emotion. Autobiographical memory for 2020 displayed a unique signature: There was a substantial bump in March, aligning with pandemic onset and lockdowns, consistent across three memory collections 1 y apart. We further investigated how emotion, using both immediate and retrieved measures, predicted the amount and content of autobiographical memory: Negative affect increased recall across all measures, whereas its more clinical indices, depression and posttraumatic stress disorder, selectively increased nonepisodic recall. Finally, in a separate cohort, we found pandemic news to be better remembered, surprising, and negative, while lockdowns compressed remembered time. Our work connects laboratory findings to the real world and delineates the effects of acute versus clinical signatures of negative emotion on memory.", "date": "2023-07-18", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "120", "number": "29", "publisher": "National Academy of Sciences", "pagerange": "Art. No. e2221919120", "id_number": "CaltechAUTHORS:20230725-49131000.14", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230725-49131000.14", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "corp_creators": { "items": [ "COVID-Dynamic Team" ] }, "doi": "10.1073/pnas.2221919120", "pmcid": "PMC10629560", "primary_object": { "basename": "pnas.2221919120.pdf", "url": "https://authors.library.caltech.edu/records/gqd91-2ae97/files/pnas.2221919120.pdf" }, "related_objects": [ { "basename": "pnas.2221919120.sapp.pdf", "url": "https://authors.library.caltech.edu/records/gqd91-2ae97/files/pnas.2221919120.sapp.pdf" }, { "basename": "pnas.2221919120.sd01.docx", "url": "https://authors.library.caltech.edu/records/gqd91-2ae97/files/pnas.2221919120.sd01.docx" } ], "pub_year": "2023", "author_list": "Rouhani, Nina; Stanley, Damian; et al." }, { "id": "https://authors.library.caltech.edu/records/aywv3-yy232", "eprint_id": 121457, "eprint_status": "archive", "datestamp": "2023-09-28 11:54:14", "lastmod": "2026-03-27 20:23:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Papini-Santiago", "name": { "family": "Papini", "given": "Santiago" }, "orcid": "0000-0002-8109-4437" }, { "id": "L\u00f3pez-Castro-Teresa", "name": { "family": "L\u00f3pez-Castro", "given": "Teresa" }, "orcid": "0000-0003-2521-6329" }, { "id": "Swarbrick-Margaret", "name": { "family": "Swarbrick", "given": "Margaret" }, "orcid": "0000-0002-8648-0628" }, { "id": "Paul-Lynn-K", "name": { "family": "Paul", "given": "Lynn K." }, "orcid": "0000-0002-3128-8313" }, { "id": "Stanley-Damian-A", "name": { "family": "Stanley", "given": "Damian" }, "orcid": "0000-0001-9815-913X" }, { "id": "Bauer-Alexandria", "name": { "family": "Bauer", "given": "Alexandria" }, "orcid": "0000-0001-9826-9056" }, { "id": "Hien-Denise-A", "name": { "family": "Hien", "given": "Denise A." }, "orcid": "0000-0002-6954-2882" } ] }, "title": "Alcohol, cannabis, and nicotine use have distinct associations with COVID-19 pandemic-related experiences: An exploratory Bayesian network analysis across two timepoints", "ispublished": "pub", "full_text_status": "public", "keywords": "Pharmacology (medical); Psychiatry and Mental health; Pharmacology; Toxicology", "note": "\u00a9 2023 Elsevier. \n\nThis work was supported by grants from the National Institute of Mental Health (2P50MH094258), the Caltech Chen Neuroscience Institute, and the Caltech Merkin Institute (RA), by the Oscar M. Ruebhausen Fund at Yale Law School, the Rutgers Center of Alcohol & Substance Use Studies, the John Templeton Foundation and the Kay Family COVID-19 Rapid Response Research Awards at Chapman University. No other funding sources were declared. The funding sources had no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the article for publication. \n\nWe thank the COVID-Dynamic team (https://coviddynamic.caltech.edu/investigators) for their contributions to the dataset used in this study, including specifically (alphabetical order): Yanting Han, Dehua Liang, Uri Maoz, and Tessa Rusch. We thank the COVID-Dynamic team (https://coviddynamic.caltech.edu/investigators) for their contributions to the dataset used in this study. \n\nCRediT authorship contribution statement. Santiago Papini: Conceptualization, Methodology, Software, Formal Analysis, Validation, Visualization, Writing - Original Draft, Writing - Review & Editing. Teresa L\u00f3pez-Castro: Conceptualization, Funding Acquisition, Project Administration, Writing - Review & Editing. Peggy Swarbrick: Conceptualization, Writing - Original Draft, Writing - Review & Editing. Lynn K. Paul: Data Curation, Investigation, Writing - Original Draft, Writing - Review & Editing. Damian Stanley: Conceptualization, Data Curation, Investigation, Methodology, Project Administration, Validation, Writing - Review & Editing. Alex Bauer: Conceptualization, Writing - Original Draft, Writing - Review & Editing. Denise A. Hien: Conceptualization, Funding Acquisition, Project Administration, Resources, Writing - Original Draft, Writing - Review & Editing. \n\nNo conflict declared.\n\nPublished - main.pdf
Supplemental Material - mmc1.pdf
", "abstract": "Background. Substance use trends during the COVID-19 pandemic have been extensively documented. However, relatively less is known about the associations between pandemic-related experiences and substance use. \n\nMethod. In July 2020 and January 2021, a broad U.S. community sample (N = 1123) completed online assessments of past month alcohol, cannabis, and nicotine use and the 92-item Epidemic-Pandemic Impacts Inventory, a multidimensional measure of pandemic-related experiences. We examined links between substance use frequency, and pandemic impact on emotional, physical, economic, and other key domains, using Bayesian Gaussian graphical networks in which edges represent significant associations between variables (referred to as nodes). Bayesian network comparison approaches were used to assess the evidence of stability (or change) in associations between the two timepoints. \n\nResults. After controlling for all other nodes in the network, multiple significant edges connecting substance use nodes and pandemic-experience nodes were observed across both time points, including positive- (r range 0.07 to 0.23) and negative-associations (r range -0.25 to -0.11). Alcohol was positively associated with social and emotional pandemic impacts and negatively associated with economic impact. Nicotine was positively associated with economic impact and negatively associated with social impact. Cannabis was positively associated with emotional impact. Network comparison suggested these associations were stable across the two timepoints. \n\nConclusion. Alcohol, nicotine, and cannabis use were linked to a few specific domains among a broad range of pandemic-related experiences. Given the cross-sectional nature of these analyses with observational data, further investigation is needed to identify potential causal links.", "date": "2023-07-01", "date_type": "published", "publication": "Drug and Alcohol Dependence", "volume": "248", "publisher": "Elsevier", "pagerange": "Art. No. 109929", "id_number": "CaltechAUTHORS:20230519-1701000.17", "issn": "0376-8716", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230519-1701000.17", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "2P50MH094258" }, { "agency": "Tianqiao and Chrissy Chen Institute for Neuroscience" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "Yale Law School" }, { "agency": "Rutgers University" }, { "agency": "John Templeton Foundation" }, { "agency": "Kay Family Foundation" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" } ] }, "corp_creators": { "items": [ "COVID-Dynamic Team" ] }, "doi": "10.1016/j.drugalcdep.2023.109929", "pmcid": "PMC10186931", "primary_object": { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/aywv3-yy232/files/main.pdf" }, "related_objects": [ { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/aywv3-yy232/files/mmc1.pdf" } ], "pub_year": "2023", "author_list": "Papini, Santiago; L\u00f3pez-Castro, Teresa; et al." }, { "id": "https://authors.library.caltech.edu/records/k79gc-vkp02", "eprint_id": 122011, "eprint_status": "archive", "datestamp": "2023-11-07 23:00:29", "lastmod": "2026-03-28 00:16:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winnett-Alexander-Viloria", "name": { "family": "Winnett", "given": "Alexander Viloria" } }, { "id": "Akana-Reid", "name": { "family": "Akana", "given": "Reid" } }, { "id": "Shelby-Natasha", "name": { "family": "Shelby", "given": "Natasha" } }, { "id": "Davich-Hannah", "name": { "family": "Davich", "given": "Hannah" } }, { "id": "Caldera-Saharai", "name": { "family": "Caldera", "given": "Saharai" } }, { "id": "Yamada-Taikun", "name": { "family": "Yamada", "given": "Taikun" } }, { "id": "Reyna-John-Raymond-B", "name": { "family": "Reyna", "given": "John Raymond B." } }, { "id": "Romano-Anne-E", "name": { "family": "Romano", "given": "Anna E." } }, { "id": "Carter-Alyssa-M", "name": { "family": "Carter", "given": "Alyssa M." } }, { "id": "Kim-Mi-Kyung", "name": { "family": "Kim", "given": "Mi Kyung" } }, { "id": "Thomson-M-W", "name": { "family": "Thomson", "given": "Matt" }, "orcid": "0000-0003-1021-1234" }, { "id": "Tognazzini-Colten", "name": { "family": "Tognazzini", "given": "Colten" } }, { "id": "Feaster-Matthew", "name": { "family": "Feaster", "given": "Matthew" } }, { "id": "Goh-Ying-Ying", "name": { "family": "Goh", "given": "Ying-Ying" } }, { "id": "Chew-Yap-Ching", "name": { "family": "Chew", "given": "Yap Ching" } }, { "id": "Ismagilov-R-F", "name": { "family": "Ismagilov", "given": "Rustem F." }, "orcid": "0000-0002-3680-4399" } ] }, "title": "Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types", "ispublished": "pub", "full_text_status": "public", "keywords": "Infectious Diseases; Cell Biology; Microbiology (medical); Genetics; General Immunology and Microbiology; Ecology; Physiology", "note": "\u00a9 2023 Viloria Winnett et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nWe sincerely thank the study participants for making this work possible. We thank Lauriane Quenee, Grace Fisher-Adams, Junie Hildebrandt, Megan Hayashi, RuthAnne Bevier, Chantal D'Apuzzo, Ralph Adolphs, Victor Rivera, Steve Chapman, Gary Waters, Leonard Edwards, Gaylene Ursua, Cynthia Ramos, and Shannon Yamashita for their assistance and advice on study implementation and/or administration. We thank Jessica Leong, Ojas Pradhan, Si Hyung Jin, Emily Savela, Bridget Yang, Ekta Patel, Hsiuchen Chen, Paresh Samantaray, Zeynep Turan, Cindy Kim, Trinity Lee, Vanessa Mechan, Katherine Stiefel, Rosie Zedan, Rahulijeet Chadha, Minkyo Lee, and Jenny Ji for volunteering their time to help with this study. We thank Prabhu Gounder, Tony Chang, Jennifer Howes, and Nari Shin for their support with recruitment. Finally, we thank all the case investigators and contact tracers at the Pasadena Public Health Department and Caltech Student Wellness Services for their efforts in study recruitment and their work in the pandemic response. \n\nR.F.I. is a cofounder, consultant, and director and has stock ownership of Talis Biomedical Corp. All other authors declare that they have no competing interests. \n\nConceptualization, M.F., Y.-Y.G., R.F.I., N.S., and A.V.W. Methodology, R.A., N.S., and A.V.W. Investigation, R.A., A.M.C., Y.C.C., S.C., H.D., M.K.K., J.R.B.R., A.E.R., N.S., A.V.W., and T.Y. Visualization, R.A., N.S., and A.V.W. Funding acquisition, R.F.I. and A.V.W. Project administration, R.F.I. and N.S. Supervision, Y.C.C. and R.F.I. Writing \u2013 original draft, R.A., N.S., and A.V.W. Writing \u2013 review & editing, R.A., A.M.C., R.F.I., A.E.R., N.S., and A.V.W. Detailed author contributions are given in the supplemental material. \n\nThis work was supported in part by a grant from the Ronald and Maxine Linde Center for New Initiatives at the California Institute of Technology (to R.F.I.) and the Jacobs Institute for Molecular Engineering for Medicine at the California Institute of Technology (to R.F.I.). A.V.W. is supported by a UCLA DGSOM Geffen Fellowship.", "abstract": "In a recent household transmission study of SARS-CoV-2, we found extreme differences in SARS-CoV-2 viral loads among paired saliva, anterior nares swab (ANS), and oropharyngeal swab specimens collected from the same time point. We hypothesized these differences may hinder low-analytical-sensitivity assays (including antigen rapid diagnostic tests [Ag-RDTs]) by using a single specimen type (e.g., ANS) from reliably detecting infected and infectious individuals. We evaluated daily at-home ANS Ag-RDTs (Quidel QuickVue) in a cross-sectional analysis of 228 individuals and a longitudinal analysis (throughout infection) of 17 individuals enrolled early in the course of infection. Ag-RDT results were compared to reverse transcription-quantitative PCR (RT-qPCR) results and high, presumably infectious viral loads (in each, or any, specimen type). The ANS Ag-RDT correctly detected only 44% of time points from infected individuals on cross-sectional analysis, and this population had an inferred limit of detection of 7.6\u2009\u00d7\u200910\u2076 copies/mL. From the longitudinal cohort, daily Ag-RDT clinical sensitivity was very low (<3%) during the early, preinfectious period of the infection. Further, the Ag-RDT detected \u226463% of presumably infectious time points. The poor observed clinical sensitivity of the Ag-RDT was similar to what was predicted based on quantitative ANS viral loads and the inferred limit of detection of the ANS Ag-RDT being evaluated, indicating high-quality self-sampling. Nasal Ag-RDTs, even when used daily, can miss individuals infected with the Omicron variant and even those presumably infectious. Evaluations of Ag-RDTs for detection of infected or infectious individuals should be compared with a composite (multispecimen) infection status to correctly assess performance.\n\nImportance:\nWe reveal three findings from a longitudinal study of daily nasal antigen rapid diagnostic test (Ag-RDT) evaluated against SARS-CoV-2 viral load quantification in three specimen types (saliva, nasal swab, and throat swab) in participants enrolled at the incidence of infection. First, the evaluated Ag-RDT showed low (44%) clinical sensitivity for detecting infected persons at all infection stages. Second, the Ag-RDT poorly detected (\u226463%) time points that participants had high and presumably infectious viral loads in at least one specimen type. This poor clinical sensitivity to detect infectious individuals is inconsistent with the commonly held view that daily Ag-RDTs have near-perfect detection of infectious individuals. Third, use of a combination nasal-throat specimen type was inferred by viral loads to significantly improve Ag-RDT performance to detect infectious individuals.", "date": "2023-07", "date_type": "published", "publication": "Microbiology Spectrum", "volume": "11", "number": "4", "publisher": "American Society for Microbiology", "pagerange": "e01295-23", "id_number": "CaltechAUTHORS:20230628-344482000.1", "issn": "2165-0497", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-344482000.1", "funders": { "items": [ { "agency": "Ronald and Maxine Linde Center for New Initiatives" }, { "agency": "Jacobs Institute for Molecular Engineering for Medicine" }, { "agency": "UCLA" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Jacobs-Institute-for-Molecular-Engineering-for-Medicine" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/spectrum.01295-23", "pmcid": "PMC10434058", "primary_object": { "basename": "spectrum.01295-23.pdf", "url": "https://authors.library.caltech.edu/records/k79gc-vkp02/files/spectrum.01295-23.pdf" }, "related_objects": [ { "basename": "spectrum.01295-23-s0001.pdf", "url": "https://authors.library.caltech.edu/records/k79gc-vkp02/files/spectrum.01295-23-s0001.pdf" } ], "pub_year": "2023", "author_list": "Winnett, Alexander Viloria; Akana, Reid; et al." }, { "id": "https://authors.library.caltech.edu/records/das4e-42g65", "eprint_id": 121455, "eprint_status": "archive", "datestamp": "2023-09-28 11:53:45", "lastmod": "2025-11-22 03:10:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hoffmann-Magnus-A-G", "name": { "family": "Hoffmann", "given": "Magnus A. G." }, "orcid": "0000-0003-4923-9568" }, { "id": "Yang-Zhi", "name": { "family": "Yang", "given": "Zhi" }, "orcid": "0000-0001-8680-3784" }, { "id": "Huey-Tubman-Kathryn-E", "name": { "family": "Huey-Tubman", "given": "Kathryn E." }, "orcid": "0000-0002-4683-8138" }, { "id": "Cohen-Alexander-A", "name": { "family": "Cohen", "given": "Alexander A." }, "orcid": "0000-0002-2818-656X" }, { "id": "Gnanapragasam-Priyanthi-N-P", "name": { "family": "Gnanapragasam", "given": "Priyanthi N. P." } }, { "id": "Nakatomi-Leesa-M", "name": { "family": "Nakatomi", "given": "Leesa M." } }, { "id": "Storm-Kaya-N", "name": { "family": "Storm", "given": "Kaya N." } }, { "id": "Moon-Woohyun-J", "name": { "family": "Moon", "given": "Woohyun J." } }, { "id": "Lin-Paulo-J-C", "name": { "family": "Lin", "given": "Paulo J. C." } }, { "id": "West-Anthony-P-Jr", "name": { "family": "West", "given": "Anthony P., Jr." }, "orcid": "0000-0003-4213-5184" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "ESCRT recruitment to SARS-CoV-2 spike induces virus-like particles that improve mRNA vaccines", "ispublished": "pub", "full_text_status": "public", "keywords": "General Biochemistry, Genetics and Molecular Biology", "note": "\u00a9 2023 The Author(s). Published by Elsevier Under a Creative Commons license Attribution 4.0 International (CC BY 4.0) \n\nWe thank J. Vielmetter and the Caltech Protein Expression Center for assistance with protein production; K. Dam for biotinylated proteins for ELISAs; M. Anaya for a BirA expression plasmid; and J. Bloom (Fred Hutchinson) and P. Bieniasz (Rockefeller University) for neutralization assay reagents. We thank J. Keeffe, Y. Tam (Acuitas Therapeutics), C. Barnes (Stanford), H. Kleanthous (Bill and Melinda Gates Foundation), B. Wold, G. Tolomiczenko, and the Caltech Merkin Institute for Translational Research for helpful discussions. Electron tomography was performed in the Caltech Cryo-EM Center with assistance from S. Chen. We thank Labcorp Drug Development-Antibody Reagents and Vaccines (Denver, PA) (formerly Covance, Inc.) for mouse immunization studies, BIOQUAL, Inc. (Rockville, MD) for PRNT50 assays, and R. Sukhovershin and RNAcore (Houston Methodist Research Institute) for synthesis of mRNAs and helpful discussion. Figures 1A and 3A were created with Biorender.com. This work was supported by the Bill and Melinda Gates Foundation INV-034638 (P.J.B.), the Caltech Merkin Institute (P.J.B.), the George Mason University Fast Grants (P.J.B.), the Rothenberg Innovation Initiative (RI2) (P.J.B.), and Wellcome Leap (P.J.B.). M.A.G.H. was supported by an NIH Director's Early Independence Award (FAIN# DP5OD033362). \n\nAuthor contributions. M.A.G.H. and P.J.B. conceived the study, acquired funding, analyzed the data, and wrote the manuscript with contributions from other authors (Z.Y., P.J.C.L., and A.P.W.). M.A.G.H. and K.E.H.-T. generated, expressed, and evaluated EABR constructs by western blot and flow cytometry analysis. M.A.G.H., K.E.H.-T., P.N.P.G., L.M.N., and K.N.S. evaluated serum antibody responses from immunized mice by ELISA and neutralization assays. Z.Y. performed cryo-ET and interpreted results. A.A.C. prepared S-mi3 immunogens for immunization studies in mice. W.J.M. and P.J.C.L. prepared mRNA-LNP for immunization studies in mice. \n\nInclusion and diversity. We support inclusive, diverse, and equitable conduct of research. \n\nData and code availability. All data are available in the main text or the supplemental information. Materials are available upon request to the corresponding authors with a signed material transfer agreement. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. This paper does not report original code. This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material. \n\nDeclaration of interests. M.A.G.H. and P.J.B. are inventors on a US patent application filed by the California Institute of Technology that covers the EABR technology described in this work. W.J.M. and P.J.C.L. are employees of Acuitas Therapeutics, a company developing LNP delivery technology; P.J.C.L. holds equity in Acuitas Therapeutics.\n\nPublished - main.pdf
", "abstract": "Prime-boost regimens for COVID-19 vaccines elicit poor antibody responses against Omicron-based variants and employ frequent boosters to maintain antibody levels. We present a natural infection-mimicking technology that combines features of mRNA- and protein nanoparticle-based vaccines through encoding self-assembling enveloped virus-like particles (eVLPs). eVLP assembly is achieved by inserting an ESCRT- and ALIX-binding region (EABR) into the SARS-CoV-2 spike cytoplasmic tail, which recruits ESCRT proteins to induce eVLP budding from cells. Purified spike-EABR eVLPs presented densely arrayed spikes and elicited potent antibody responses in mice. Two immunizations with mRNA-LNP encoding spike-EABR elicited potent CD8+ T cell responses and superior neutralizing antibody responses against original and variant SARS-CoV-2 compared with conventional spike-encoding mRNA-LNP and purified spike-EABR eVLPs, improving neutralizing titers >10-fold against Omicron-based variants for 3 months post-boost. Thus, EABR technology enhances potency and breadth of vaccine-induced responses through antigen presentation on cell surfaces and eVLPs, enabling longer-lasting protection against SARS-CoV-2 and other viruses.", "date": "2023-05-25", "date_type": "published", "publication": "Cell", "volume": "186", "number": "11", "publisher": "Cell Press", "pagerange": "2380-2391", "id_number": "CaltechAUTHORS:20230519-1669000.14", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230519-1669000.14", "funders": { "items": [ { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-034638" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "George Mason University" }, { "agency": "Rothenberg Innovation Initiative (RI2)" }, { "agency": "NIH", "grant_number": "DP5OD033362" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cell.2023.04.024", "pmcid": "PMC10121106", "primary_object": { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/das4e-42g65/files/main.pdf" }, "pub_year": "2023", "author_list": "Hoffmann, Magnus A. G.; Yang, Zhi; et al." }, { "id": "https://authors.library.caltech.edu/records/qqhvy-cxb02", "eprint_id": 121373, "eprint_status": "archive", "datestamp": "2023-08-22 20:38:28", "lastmod": "2025-11-22 04:08:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shrock-Ellen-L", "name": { "family": "Shrock", "given": "Ellen L." }, "orcid": "0000-0003-2484-4374" }, { "id": "Timms-Richard-T", "name": { "family": "Timms", "given": "Richard T." }, "orcid": "0000-0001-7275-597X" }, { "id": "Kula-Tomasz", "name": { "family": "Kula", "given": "Tomasz" }, "orcid": "0000-0002-6458-9833" }, { "id": "Mena-Elijah-L", "name": { "family": "Mena", "given": "Elijah L." }, "orcid": "0000-0001-9980-9018" }, { "id": "West-Anthony-P-Jr", "name": { "family": "West", "given": "Anthony P., Jr." }, "orcid": "0000-0003-4213-5184" }, { "id": "Guo-Rui", "name": { "family": "Guo", "given": "Rui" }, "orcid": "0000-0003-4584-1324" }, { "id": "Lee-I-Hsiu", "name": { "family": "Lee", "given": "I-Hsiu" }, "orcid": "0000-0001-7200-7867" }, { "id": "Cohen-Alexander-A", "name": { "family": "Cohen", "given": "Alexander A." }, "orcid": "0000-0002-2818-656X" }, { "id": "McKay-Lindsay-G-A", "name": { "family": "McKay", "given": "Lindsay G. A." }, "orcid": "0000-0003-0369-9067" }, { "id": "Bi-Caihong", "name": { "family": "Bi", "given": "Caihong" } }, { "id": "Rawat-Keerti", "name": { "family": "Rawat", "given": "Keerti" } }, { "id": "Leng-Yumei", "name": { "family": "Leng", "given": "Yumei" }, "orcid": "0000-0003-2512-9284" }, { "id": "Fujimura-Eric", "name": { "family": "Fujimura", "given": "Eric" }, "orcid": "0000-0001-8213-2143" }, { "id": "Horns-Felix", "name": { "family": "Horns", "given": "Felix" }, "orcid": "0000-0001-5872-5061" }, { "id": "Li-Mamie", "name": { "family": "Li", "given": "Mamie" }, "orcid": "0000-0002-7188-1330" }, { "id": "Wesemann-Duane-R", "name": { "family": "Wesemann", "given": "Duane R." }, "orcid": "0000-0002-6690-944X" }, { "id": "Griffiths-Anthony", "name": { "family": "Griffiths", "given": "Anthony" }, "orcid": "0000-0001-5435-8364" }, { "id": "Gewurz-Benjamin-E", "name": { "family": "Gewurz", "given": "Benjamin E." }, "orcid": "0000-0002-3965-3418" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Elledge-Stephen-J", "name": { "family": "Elledge", "given": "Stephen J." }, "orcid": "0000-0001-7923-6283" } ] }, "title": "Germline-encoded amino acid\u2013binding motifs drive immunodominant public antibody responses", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2023 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. This is an article distributed under the terms of the Science Journals Default License. \n\nWe thank L. Vandenberghe, N. Zabaleta, D. Barouch, and A. Chandrashekar for providing sera samples; S. Quake, D. Grishin, J. Bloom, C. O'Leary, C. Glassman, and M. Steffen for helpful discussions; A. Kohlgruber for designing initial versions of the schematics in Fig. 1B, Fig. 2A, and Fig. 4A; C. Araneo and the Immunology Flow Cytometry Facility and A. Ciulla Hurst and the BioPolymers Genomics Core Facility at Harvard Medical School for supporting this work; J. Q. O'Brien for contributing to revision experiments; and R. E. Shrock for reviewing the manuscript. Access to COVID-19 patient samples was facilitated by the MassCPR. We thank the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from NIH P41-GM103311 for help with molecular graphics. Fig. 8 and the print page summary figure were created with BioRender.com. \n\nThis research was supported by the SARS-CoV-2 Viral Variants Program and the Value of Vaccine Research Network to S.J.E.; the MassPCR and the NIH 1P01AI165072 to S.J.E., A.G., and D.R.W.; and the NIH 1R01AI129784 to P.J.B. E.L.S. and T.K. were supported by the NSF Graduate Research Fellows Program. R.T.T. is supported by a Pemberton-Trinity Fellowship and a Sir Henry Wellcome Fellowship (201387/Z/16/Z). E.L.M. is supported by a Jane Coffin Childs Postdoctoral Fellowship. R.G. is supported by an NIH Pathway to Independence Award (K99/R00) K99DE031016. D.R.W. is also supported by AI139538, AI169619, AI170715, and AI170580. B.E.G. is supported by a Burroughs Wellcome Career Award in Medical Sciences. S.J.E. is an Investigator with the Howard Hughes Medical Institute. \n\nAuthor contributions: Conceptualization: S.J.E., E.L.S., and T.K. Formal analysis: E.L.S., R.T.T., T.K., A.P.W., I.L., A.A.C., L.G.A.M., C.B., and K. Investigation: E.L.S., T.K., R.G., A.A.C., L.G.A.M., C.B., K., Y.L., and M.L. Methodology: E.L.S., R.T.T., T.K., E.L.M., and A.P.W. Resources: E.F. and F.H. Supervision: S.J.E., P.J.B., B.E.G., A.G., and D.R.W. Visualization: E.L.S., T.K., E.L.M., I.L., A.A.C., R.G., A.P.W., L.G.A.M., C.B., and K. Writing \u2013 original draft: E.L.S. and S.J.E. Writing \u2013 review and editing: E.L.S., S.J.E., R.T.T., T.K., E.L.M., and P.J.B. \n\nData and materials availability: All data necessary to interpret our findings are available in supplemental tables or on the Harvard Dataverse, digital object identifiers: 10.7910/DVN/AIXWW2; 10.7910/DVN/WZCLMB; 10.7910/DVN/DXWJ2Y. All reasonable requests for materials will be fulfilled. \n\nCompeting interests: S.J.E. and T.K. are founders of TSCAN Therapeutics and ImmuneID. SJ.E. is a founder of MAZE Therapeutics and Mirimus, and serves on the scientific advisory board of Homology Medicines, TSCAN Therapeutics, MAZE Therapeutics, none of which impact this work. E.L.S. was a consultant for ImmuneID. S.J.E., and T.K. are inventors on a patent application filed by the Brigham and Women's Hospital (US20160320406A) that covers the use of the VirScan library to identify pathogen antibodies in blood.\n\nAccepted Version - nihms-1901999.pdf
Supplemental Material - science.adc9498_mdar_reproducibility_checklist.pdf
Supplemental Material - science.adc9498_sm.v2.pdf
Supplemental Material - science.adc9498_tables_s1_to_s17.zip
", "abstract": "INTRODUCTION. Antibodies are generated by a DNA recombination mechanism occurring in the immunoglobulin heavy and light chain genes in which modular VDJ (for heavy) and VJ (for light) gene segments are combinatorially assembled. The vast complexity of the antibody repertoire allows many species to generate antibodies against virtually any protein. However, when different individuals are exposed to a given pathogen they often mount antibody responses to the same precise protein regions\u2014or epitopes\u2014from the pathogen. The mechanisms underlying these recurrent antibody responses to immunodominant \"public epitopes\" are not well understood. \n\nRATIONALE. We set out to identify a collection of immunodominant public epitopes that would allow us to study mechanisms underlying recurrent antibody responses. We employed VirScan\u2014a phage display platform programmed to display peptides covering the entire human virome\u2014to identify the epitopes of antiviral antibodies from a large cohort of individuals in a high-throughput manner. Additionally, we isolated B cell receptors from different individuals that bound to model public epitopes in order to investigate their determinants of specificity. Finally, we performed a systematic analysis of antibody\u2013antigen structures from the Protein Data Bank (PDB) to search for recurrent modes of antigen recognition. \n\nRESULTS. We mapped 376 immunodominant public epitopes from 51 viral species to single-amino-acid resolution. Antibodies from different individuals that recognized the same public epitope often (i) shared light chain isotype (kappa or lambda) and (ii) bound the same precise critical residues in the epitope. Public epitopes showed biased amino acid composition, including a striking enrichment of lysine at the borders of public epitopes recognized by antibodies with lambda light chains. We examined 50 B cell receptors recognizing three model public epitopes in detail and observed conserved V gene segment usage but almost no conservation of heavy chain CDR3 sequences, indicating that key specificity determinants lay within the V gene segments themselves. Structural analysis of antibody\u2013antigen complexes in the PDB uncovered 18 human V gene segments that harbor germline-encoded amino acid\u2013binding (GRAB) motifs that specifically bind to particular amino acids. Among these were a family of six closely related lambda V gene segments with similar GRAB motifs specific for border lysines. We confirmed that the GRAB motifs we identified were critical for antibody recognition of two model public epitopes. Analysis of murine antibody\u2013antigen structures revealed 21 V gene segment\u2013encoded GRAB motifs that only partially overlapped with the human GRAB motifs, which may explain why there is little overlap between the public epitopes recognized across species. Thus, there appears to be a structural basis underlying the notable convergence in humoral immune responses to immunodominant public epitopes across humans and the differing public epitope selection across species. \n\nCONCLUSION. Recurrent antibody responses to immunodominant public epitopes are a general feature of humoral immunity. We propose that they are driven by GRAB motifs, a germline-encoded component of the architecture of the antibody repertoire that predisposes antibodies to recognize particular structures and thus influences epitope selection and composition. Public epitopes likely arise in part because they are best aligned for recognition by GRAB motifs and can thus be bound by a relatively large precursor pool of B cells. GRAB motifs may have evolved to ensure efficient antibody responses to pathogens; the recurrent responses they engender across populations likely exert selective pressure on pathogens and influence host\u2013pathogen coevolution.", "date": "2023-04-07", "date_type": "published", "publication": "Science", "volume": "380", "number": "6640", "publisher": "American Association for the Advancement of Science", "pagerange": "Art. No. eadc9498", "id_number": "CaltechAUTHORS:20230510-349443100.9", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230510-349443100.9", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "SARS-CoV-2 Viral Variants Program" }, { "agency": "Value of Vaccine Research Network" }, { "agency": "MassPCR" }, { "agency": "NIH", "grant_number": "1P01AI165072" }, { "agency": "NIH", "grant_number": "1R01AI129784" }, { "agency": "NSF Graduate Research Fellowship" }, { "agency": "Pemberton-Trinity Fellowship" }, { "agency": "Wellcome Trust", "grant_number": "201387/Z/16/Z" }, { "agency": "Jane Coffin Childs Memorial Fund for Medical Research" }, { "agency": "NIH", "grant_number": "K99DE031016" }, { "agency": "NIH", "grant_number": "AI139538" }, { "agency": "NIH", "grant_number": "AI169619" }, { "agency": "NIH", "grant_number": "AI170715" }, { "agency": "NIH", "grant_number": "AI170580" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/science.adc9498", "pmcid": "PMC10273302", "primary_object": { "basename": "nihms-1901999.pdf", "url": "https://authors.library.caltech.edu/records/qqhvy-cxb02/files/nihms-1901999.pdf" }, "related_objects": [ { "basename": "science.adc9498_mdar_reproducibility_checklist.pdf", "url": "https://authors.library.caltech.edu/records/qqhvy-cxb02/files/science.adc9498_mdar_reproducibility_checklist.pdf" }, { "basename": "science.adc9498_sm.v2.pdf", "url": "https://authors.library.caltech.edu/records/qqhvy-cxb02/files/science.adc9498_sm.v2.pdf" }, { "basename": "science.adc9498_tables_s1_to_s17.zip", "url": "https://authors.library.caltech.edu/records/qqhvy-cxb02/files/science.adc9498_tables_s1_to_s17.zip" } ], "pub_year": "2023", "author_list": "Shrock, Ellen L.; Timms, Richard T.; et al." }, { "id": "https://authors.library.caltech.edu/records/vj28n-5kr25", "eprint_id": 118797, "eprint_status": "archive", "datestamp": "2023-08-22 20:29:54", "lastmod": "2025-11-22 03:11:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Xu-Yang", "name": { "family": "Xu", "given": "Yang" }, "orcid": "0000-0002-9945-7507" }, { "id": "Yao-Yuxing", "name": { "family": "Yao", "given": "Yuxing" }, "orcid": "0000-0003-0337-6372" }, { "id": "Deng-Weichen", "name": { "family": "Deng", "given": "Weichen" } }, { "id": "Fang-Jen-Chun", "name": { "family": "Fang", "given": "Jen-Chun" } }, { "id": "Dupont-Robert-L", "name": { "family": "Dupont", "given": "Robert L." }, "orcid": "0000-0002-1963-6573" }, { "id": "Zhang-Meng", "name": { "family": "Zhang", "given": "Meng" }, "orcid": "0000-0002-9753-0635" }, { "id": "\u010copar-Simon", "name": { "family": "\u010copar", "given": "Simon" }, "orcid": "0000-0002-7566-0260" }, { "id": "Tkalec-Uro\u0161", "name": { "family": "Tkalec", "given": "Uro\u0161" }, "orcid": "0000-0003-0552-0518" }, { "id": "Wang-Xiaoguang", "name": { "family": "Wang", "given": "Xiaoguang" }, "orcid": "0000-0002-4079-9596" } ] }, "title": "Magnetocontrollable droplet mobility on liquid crystal-infused porous surfaces", "ispublished": "pub", "full_text_status": "public", "keywords": "Electrical and Electronic Engineering; General Materials Science; Condensed Matter Physics; Atomic and Molecular Physics, and Optics", "note": "\u00a9 Tsinghua University Press 2022. \n\nX. W. thanks the funding support from the startup fund of the Ohio State University (OSU) and OSU Institute for Materials Research Kickstart Facility Grant. S. \u010c. and U. T. acknowledge support by Slovenian Research Agency (ARRS) under contracts (Nos. P1-0099, P1-0055, and J1-2457).", "abstract": "Magnetocontrollable droplet mobility on surfaces of both solids and simple fluids have been widely used in a wide range of applications. However, little is understood about the effect of the magnetic field on the wettability and mobility of droplets on structured fluids. Here, we report the manipulation of the dynamic behaviors of water droplets on a film of thermotropic liquid crystals (LCs). We find that the static wetting behavior and static friction of water droplets on a 4\u2032-octyl-4-biphenylcarbonitrile (8CB) film strongly depend on the LC mesophases, and that a magnetic field caused no measurable change to these properties. However, we find that the droplet dynamics can be affected by a magnetic field as it slides on a nematic 8CB film, but not on isotropic 8CB, and is dependent on both the direction and strength of the magnetic field. By measuring the dynamic friction of a droplet sliding on a nematic 8CB film, we find that a magnetic field alters the internal orientational ordering of the 8CB which in turn affects its viscosity. We support this interpretation with a scaling argument using the LC magnetic coherence length that includes (i) the elastic energy from the long-range orientational ordering of 8CB and (ii) the free energy from the interaction between 8CB and a magnetic field. Overall, these results advance our understanding of droplet mobility on LC films and enable new designs for responsive surfaces that can manipulate the mobility of water droplets.", "date": "2023-04", "date_type": "published", "publication": "Nano Research", "volume": "16", "number": "4", "publisher": "Springer Verlag", "pagerange": "5098-5107", "id_number": "CaltechAUTHORS:20230113-708423000.13", "issn": "1998-0124", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230113-708423000.13", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ohio State University" }, { "agency": "Slovenian Research Agency", "grant_number": "P1-0099" }, { "agency": "Slovenian Research Agency", "grant_number": "P1-0055" }, { "agency": "Slovenian Research Agency", "grant_number": "J1-2457" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1007/s12274-022-5318-y", "pmcid": "PMC9768411", "pub_year": "2023", "author_list": "Xu, Yang; Yao, Yuxing; et al." }, { "id": "https://authors.library.caltech.edu/records/xe369-15h51", "eprint_id": 120359, "eprint_status": "archive", "datestamp": "2023-08-22 20:24:19", "lastmod": "2026-03-27 20:20:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Braet-Sean-M", "name": { "family": "Braet", "given": "Sean M." }, "orcid": "0000-0003-3782-2262" }, { "id": "Buckley-Theresa-S-C", "name": { "family": "Buckley", "given": "Theresa S. C." }, "orcid": "0009-0005-2897-9630" }, { "id": "Venkatakrishnan-Varun", "name": { "family": "Venkatakrishnan", "given": "Varun" } }, { "id": "Dam-Kim-Marie-A", "name": { "family": "Dam", "given": "Kim-Marie A." }, "orcid": "0000-0002-1416-4757" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Anand-Ganesh-Srinivasan", "name": { "family": "Anand", "given": "Ganesh" }, "orcid": "0000-0001-8995-3067" } ] }, "title": "Timeline of changes in spike conformational dynamics in emergent SARS-CoV-2 variants reveal progressive stabilization of trimer stalk with altered NTD dynamics", "ispublished": "pub", "full_text_status": "public", "keywords": "General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology; General Medicine; General Neuroscience", "note": "\u00a9 2023, Braet, Buckley, Venkatakrishnan et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. \n\nStartup funding from the Pennsylvania State University (PSU) to GSA. We thank Rosa Viner (Thermo Scientific, San Jose, CA) for S glycan analysis. We thank Susan Marqusee (University of California Berkley, CA) for discussions and help with revision. \n\nNo external funding was received for this work. \n\nData availability. We have made raw files, ProteinLynx Global Server 3.0 search outputs, and Dynamx files used for HDXMS analysis available through ProteomeXchange. The dataset can be found in the PRIDE repository with identifier PXD040717.\n\nPublished - elife-82584.pdf
", "abstract": "SARS-CoV-2 emergent variants are characterized by increased viral fitness and each shows multiple mutations predominantly localized to the spike (S) protein. Here, amide hydrogen/deuterium exchange mass spectrometry has been applied to track changes in S dynamics from multiple SARS-CoV-2 variants. Our results highlight large differences across variants at two loci with impacts on S dynamics and stability. A significant enhancement in stabilization first occurred with the emergence of D614G S followed by smaller, progressive stabilization in subsequent variants. Stabilization preceded altered dynamics in the N-terminal domain, wherein Omicron BA.1 S showed the largest magnitude increases relative to other preceding variants. Changes in stabilization and dynamics resulting from S mutations detail the evolutionary trajectory of S in emerging variants. These carry major implications for SARS-CoV-2 viral fitness and offer new insights into variant-specific therapeutic development.", "date": "2023-03-17", "date_type": "published", "publication": "eLife", "volume": "12", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e82584", "id_number": "CaltechAUTHORS:20230322-393072000.2", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230322-393072000.2", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Pennsylvania State University" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/elife.82584", "pmcid": "PMC10049203", "primary_object": { "basename": "elife-82584.pdf", "url": "https://authors.library.caltech.edu/records/xe369-15h51/files/elife-82584.pdf" }, "pub_year": "2023", "author_list": "Braet, Sean M.; Buckley, Theresa S. C.; et al." }, { "id": "https://authors.library.caltech.edu/records/3m90d-t8880", "eprint_id": 119516, "eprint_status": "archive", "datestamp": "2023-10-09 22:02:49", "lastmod": "2026-03-27 20:29:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schulte-Samuel-J", "name": { "family": "Schulte", "given": "Samuel J." }, "orcid": "0000-0001-9982-6504" }, { "id": "Huang-Jining", "name": { "family": "Huang", "given": "Jining" }, "orcid": "0000-0002-3798-4790" }, { "id": "Pierce-N-A", "name": { "family": "Pierce", "given": "Niles A." }, "orcid": "0000-0003-2367-4406" } ] }, "title": "Hybridization Chain Reaction Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing", "ispublished": "pub", "full_text_status": "public", "keywords": "Infectious Diseases", "note": "\u00a9 2023 The Authors. Published by American Chemical Society. Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). \n\nWe thank M. Schwarzkopf and K. S. Lee for performing preliminary studies. We thank M. E. Bronner for reading a draft of the manuscript. We thank M. Schwarzkopf, K. S. Lee, L. M. Hochrein, G. Shin, B. J. Wold, and R. F. Ismagilov for helpful discussions. We thank G. Shin of the Molecular Technologies resource within the Beckman Institute at Caltech for providing HCR reagents. This work was funded by the Shurl and Kay Curci Foundation, by the Richard N. Merkin Institute for Translational Research at Caltech, by the National Aeronautics and Space Administration (Translational Research Institute for Space Health; NNX16AO69A), and by the National Institutes of Health (NIBIB R01EB006192 and NIGMS training grant GM008042 to S.J.S.). \n\nAuthor Contributions. S.J.S. and J.H. contributed equally. \n\nThe authors declare the following competing financial interest(s): Patents, pending patent applications, and the startup company Molecular Instruments.\n\nPublished - acsinfecdis2c00472.pdf
Accepted Version - id2c00472-acc.pdf
Supplemental Material - id2c00472_si_001.pdf
Supplemental Material - id2c00472_si_002.mp4
Supplemental Material - id2c00472_si_003.mp4
", "abstract": "The lateral flow assay format enables rapid, instrument-free, at-home testing for SARS-CoV-2. Due to the absence of signal amplification, this simplicity comes at a cost in sensitivity. Here, we enhance sensitivity by developing an amplified lateral flow assay that incorporates isothermal, enzyme-free signal amplification based on the mechanism of hybridization chain reaction (HCR). The simplicity of the user experience is maintained using a disposable 3-channel lateral flow device to automatically deliver reagents to the test region in three successive stages without user interaction. To perform a test, the user loads the sample, closes the device, and reads the result by eye after 60 min. Detecting gamma-irradiated SARS-CoV-2 virions in a mixture of saliva and extraction buffer, the current amplified HCR lateral flow assay achieves a limit of detection of 200 copies/\u03bcL using available antibodies to target the SARS-CoV-2 nucleocapsid protein. By comparison, five commercial unamplified lateral flow assays that use proprietary antibodies exhibit limits of detection of 500 copies/\u03bcL, 1000 copies/\u03bcL, 2000 copies/\u03bcL, 2000 copies/\u03bcL, and 20,000 copies/\u03bcL. By swapping out antibody probes to target different pathogens, amplified HCR lateral flow assays offer a platform for simple, rapid, and sensitive at-home testing for infectious diseases. As an alternative to viral protein detection, we further introduce an HCR lateral flow assay for viral RNA detection.", "date": "2023-03-10", "date_type": "published", "publication": "ACS Infectious Diseases", "volume": "9", "number": "3", "publisher": "American Chemical Society", "pagerange": "450-458", "id_number": "CaltechAUTHORS:20230227-258668000.1", "issn": "2373-8227", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230227-258668000.1", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Shurl and Kay Curci Foundation" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "NASA", "grant_number": "NNX16AO69A" }, { "agency": "NIH", "grant_number": "R01EB006192" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM008042" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" }, { "id": "Division-of-Engineering-and-Applied-Science" } ] }, "doi": "10.1021/acsinfecdis.2c00472", "pmcid": "PMC9924079", "primary_object": { "basename": "acsinfecdis2c00472.pdf", "url": "https://authors.library.caltech.edu/records/3m90d-t8880/files/acsinfecdis2c00472.pdf" }, "related_objects": [ { "basename": "id2c00472-acc.pdf", "url": "https://authors.library.caltech.edu/records/3m90d-t8880/files/id2c00472-acc.pdf" }, { "basename": "id2c00472_si_001.pdf", "url": "https://authors.library.caltech.edu/records/3m90d-t8880/files/id2c00472_si_001.pdf" }, { "basename": "id2c00472_si_002.mp4", "url": "https://authors.library.caltech.edu/records/3m90d-t8880/files/id2c00472_si_002.mp4" }, { "basename": "id2c00472_si_003.mp4", "url": "https://authors.library.caltech.edu/records/3m90d-t8880/files/id2c00472_si_003.mp4" } ], "pub_year": "2023", "author_list": "Schulte, Samuel J.; Huang, Jining; et al." }, { "id": "https://authors.library.caltech.edu/records/4sxew-1eg60", "eprint_id": 119955, "eprint_status": "archive", "datestamp": "2023-08-22 21:26:50", "lastmod": "2023-10-25 16:48:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fielding-Miller-Rebecca", "name": { "family": "Fielding-Miller", "given": "Rebecca" }, "orcid": "0000-0002-5099-0589" }, { "id": "Karthikeyan-Smruthi", "name": { "family": "Karthikeyan", "given": "Smruthi" }, "orcid": "0000-0001-6226-4536" }, { "name": { "family": "Gaines", "given": "Tommi" } }, { "name": { "family": "Garfein", "given": "Richard S." }, "orcid": "0000-0003-3663-7153" }, { "name": { "family": "Salido", "given": "Rodolfo A." }, "orcid": "0000-0003-0631-2817" }, { "name": { "family": "Kohn", "given": "Laura" } }, { "name": { "family": "Wynn", "given": "Adriane" }, "orcid": "0000-0001-8067-3616" }, { "name": { "family": "Wijaya", "given": "Carrissa" } }, { "name": { "family": "Nguyen", "given": "Megan" } }, { "name": { "family": "Vo", "given": "Anh V." } }, { "name": { "family": "Le", "given": "Tina" } }, { "name": { "family": "Tweeten", "given": "Samantha" } }, { "name": { "family": "Nasamran", "given": "Chanond A." } }, { "name": { "family": "Moshiri", "given": "Niema" }, "orcid": "0000-0003-2209-8128" }, { "name": { "family": "Fisch", "given": "Kathleen M." }, "orcid": "0000-0002-0117-7444" }, { "name": { "family": "Humphrey", "given": "Greg" } }, { "name": { "family": "Valles", "given": "Tommy" } }, { "name": { "family": "Morris", "given": "Justin" } }, { "name": { "family": "Kang", "given": "Jaeyoung" }, "orcid": "0000-0003-1048-1285" }, { "name": { "family": "Khaleghi", "given": "Behnam" }, "orcid": "0000-0002-3655-0501" }, { "name": { "family": "Young", "given": "Colin" }, "orcid": "0000-0002-1907-8276" }, { "name": { "family": "Akel", "given": "Ameen D." } }, { "name": { "family": "Eilert", "given": "Sean" } }, { "name": { "family": "Eno", "given": "Justin" } }, { "name": { "family": "Curewitz", "given": "Ken" } }, { "name": { "family": "Laurent", "given": "Louise C." } }, { "name": { "family": "Rosing", "given": "Tajana" }, "orcid": "0000-0002-6954-997X" }, { "name": { "family": "Knight", "given": "Rob" }, "orcid": "0000-0002-0975-9019" }, { "name": { "family": "Baer", "given": "Nathan A." } }, { "name": { "family": "Barber", "given": "Tom" } }, { "name": { "family": "Chac\u00f3n", "given": "Marisol" } }, { "name": { "family": "Cheung", "given": "Willi" } }, { "name": { "family": "Crescini", "given": "Evelyn S." } }, { "name": { "family": "Eisner", "given": "Emily R." } }, { "name": { "family": "Franco Vargas", "given": "Lizbeth" } }, { "name": { "family": "Hakim", "given": "Abbas" } }, { "name": { "family": "Lastrella", "given": "Alma L." } }, { "name": { "family": "Lawrence", "given": "Elijah S." } }, { "name": { "family": "Matteson", "given": "Nathaniel L." } }, { "name": { "family": "Gangavarapu", "given": "Karthik" } }, { "name": { "family": "Ngo", "given": "Toan T." } }, { "name": { "family": "Seaver", "given": "Phoebe" } }, { "name": { "family": "Smoot", "given": "Elizabeth W." } }, { "name": { "family": "Tsai", "given": "Rebecca" } }, { "name": { "family": "Xia", "given": "Bing" } }, { "name": { "family": "Aigner", "given": "Stefan" } }, { "name": { "family": "Sathe", "given": "Shashank" } }, { "name": { "family": "Andersen", "given": "Kristian G." } }, { "name": { "family": "Kurzban", "given": "Ezra" } } ] }, "title": "Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools", "ispublished": "pub", "full_text_status": "public", "keywords": "Public Health, Environmental and Occupational Health; Internal Medicine; Health Policy", "note": "Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).\n\nWe are deeply grateful to the leadership, staff, students, and families at our partner school districts and school sites across San Diego County. This project would not have been possible without their enthusiasm and generosity. We thank our colleagues at the County of San Diego, Health and Human Services Agency for their vision and support, particularly John Malone, Sarah Stous, and Rorick Luepton. At UCSD, Isabella Cuturrofo, Jeanessa Mendoza, Kristine Ngo, Jessica Ni, and Elizabeth Frost all provided vital support with project implementation. Austin Dahl provided extensive support with data management and visualization. RFM thanks Ms. Esther J. Krohne for inspiring the project.\n\nThe opinions and assertions expressed herein are those of the authors and do not necessarily reflect the official policy or position of the County of San Diego Health and Human Services Agency.\n\nFunding:\n\nCounty of San Diego, Health and Human Services Agency (R.F.-M.). National Institutes of Health Grant K01MH112436 (R.F.-M.). National Institute of Health Grant UL1TR001442. National Institute of Health Grant S10OD026929 (Jepsen). NSF Grants Numbers 1730518, 1826967, 1659104, 2100237, 2112167, 2052809, 2028040 (Rosing). Centers for Disease Control BAA Contract 75D30120C09795 (Andersen). This work was supported in part by CRISP, one of six centers in JUMP, an SRC program sponsored by DARPA (Rosing). \n\nContributors. All authors have read the final version of the manuscript and meet the International Committee for Medical Journal Ethics (ICMJE) criteria for authorship. Dr. Fielding-Miller takes full responsibility for the study. Specific contributions are listed below according to the CRediT roles taxonomy. R.F.-M.: Conceptualization; Methodology; Formal Analysis; Investigation; Writing - original draft; Visualization; Supervision; Funding Acquisition. S.K.: Methodology; Formal Analysis; Investigation; Data curation; Writing - original draft; Visualization. T.G.: Methodology; Formal Analysis; Writing - original draft. R.S.G.: Methodology; Data curation; Writing - original draft; Visualization; Supervision. R.A.S.: Methodology; Formal Analysis; Investigation; Writing - original draft. V.J.C.: Methodology; Formal Analysis; Investigation; Data curation; Writing - original draft. L.K.: Conceptualization; Methodology; Investigation; Data curation; Writing - original draft; Supervision; Project administration; Funding Acquisition. N.K.M.: Methodology; Writing - original draft. A.W.: Methodology; Data curation; Formal Analysis; Writing \u2013 revised draft. C.W.: Supervision; Project administration. M.F.: Investigation; Data curation. V.O.: Investigation; Data curation. A.M.: Investigation; Data curation. P.G.-Z.: Investigation; Supervision. M.N.: Investigation; Data curation. A.V.V.: Investigation; Data curation; Visualization. T.L.: Investigation. D.D.: Investigation. A.H.: Investigation. S.T.: Resources; Supervision; Project administration. K.J.: Methodology; Investigation; Resources. B.H.: Methodology; Investigation. A.H.: Methodology; Investigation. A.B.: Methodology; Investigation. A.M.M.: Methodology; Investigation. C.A.N.: Methodology; Investigation. S.B.R.: Methodology; Investigation. N.M.: Methodology; Investigation. K.M.F.: Methodology; Investigation. G.H.: Investigation; Data curation. S.F.: Investigation; Data curation. H.M.T.: Investigation; Data curation. T.V.: Investigation; Data curation. J.M.: Investigation; Data curation. J.K.: Investigation; Data curation. B.K.: Investigation; Data curation. C.Y.: Investigation; Data curation. A.D.A.: Investigation; Data curation. S.E.: Investigation; Data curation. J.E.: Investigation; Data curation. K.C.: Investigation; Data curation. L.C.L.: Resources. T.R.: Investigation; Data curation. R.K.: Conceptualization; Methodology; Resources; Writing - original draft; Supervision. \n\nData sharing statement. School level environmental, diagnostic, and consent data have been archived in the Dataverse repository and are available at https://doi.org/10.7910/DVN/HD62J4. All wastewater and nasal-swab sequencing data have been deposited to GISAID and their accession details provided in Supplemental File Data S1.\n\nPublished - main.pdf
Supplemental Material - 1-s2.0-S2667193X23000236-mmc1.pdf
", "abstract": "Background. Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. \n\nMethods. The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 to March 2021. \n\nFindings. In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88%\u201398%); 67% were associated with a positive wastewater sample (95% CI: 57%\u201377%), and 40% were associated with a positive surface sample (95% CI: 29%\u201352%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. \n\nInterpretation. Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy.", "date": "2023-03", "date_type": "published", "publication": "Lancet Regional Health - Americas", "volume": "19", "publisher": "Elsevier", "pagerange": "Art. No. 100449", "id_number": "CaltechAUTHORS:20230313-697847000.2", "issn": "2667-193X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230313-697847000.2", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "San Diego County" }, { "agency": "NIH", "grant_number": "K01MH112436" }, { "agency": "NIH", "grant_number": "UL1TR001442" }, { "agency": "NIH", "grant_number": "S10OD026929" }, { "agency": "NSF", "grant_number": "1730518" }, { "agency": "NSF", "grant_number": "OAC-1826967" }, { "agency": "NSF", "grant_number": "OAC-1659104" }, { "agency": "NSF", "grant_number": "CNS-2100237" }, { "agency": "NSF", "grant_number": "OAC-2112167" }, { "agency": "NSF", "grant_number": "EEC-2052809" }, { "agency": "NSF", "grant_number": "DEB-2028040" }, { "agency": "Centers for Disease Control and Prevention", "grant_number": "75D30120C09795" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "contributors": { "items": [ { "name": { "family": "Baer", "given": "Nathan A." } }, { "name": { "family": "Barber", "given": "Tom" } }, { "name": { "family": "Castro-Martinez", "given": "Anelizze" } }, { "name": { "family": "Chac\u00f3n", "given": "Marisol" } }, { "name": { "family": "Cheung", "given": "Willi" } }, { "name": { "family": "Crescini", "given": "Evelyn" } }, { "name": { "family": "Eisner", "given": "Emily R." } }, { "name": { "family": "Franco", "given": "Vargas" } }, { "name": { "family": "Hakim", "given": "Abbas" } }, { "name": { "family": "Hobbs", "given": "Charlotte" } }, { "name": { "family": "Lastrella", "given": "Alma L." } }, { "name": { "family": "Lawrence", "given": "Elijah S." } }, { "name": { "family": "Matteson", "given": "Nathaniel L." } }, { "name": { "family": "Gangavarapu", "given": "Karthik" } }, { "name": { "family": "Ngo", "given": "Toan T." } }, { "name": { "family": "Seaver", "given": "Phoebe" } }, { "name": { "family": "Smoot", "given": "Elizabeth W." } }, { "name": { "family": "Tsai", "given": "Rebecca" } }, { "name": { "family": "Xia", "given": "Bing" } }, { "name": { "family": "Aigner", "given": "Stefan" } }, { "name": { "family": "Anderson", "given": "Catelyn" } }, { "name": { "family": "Belda-Ferre", "given": "Pedro" } }, { "name": { "family": "Sathe", "given": "Shashank" } }, { "name": { "family": "Zeller", "given": "Mark" } }, { "name": { "family": "Andersen", "given": "Kristian" } }, { "name": { "family": "Yeo", "given": "Gene W." } }, { "name": { "family": "Kurzban", "given": "Ezra" } } ] }, "doi": "10.1016/j.lana.2023.100449", "pmcid": "PMC9939935", "primary_object": { "basename": "1-s2.0-S2667193X23000236-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/4sxew-1eg60/files/1-s2.0-S2667193X23000236-mmc1.pdf" }, "related_objects": [ { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/4sxew-1eg60/files/main.pdf" } ], "pub_year": "2023", "author_list": "Fielding-Miller, Rebecca; Karthikeyan, Smruthi; et al." }, { "id": "https://authors.library.caltech.edu/records/8xx2v-fk653", "eprint_id": 120367, "eprint_status": "archive", "datestamp": "2023-08-20 16:38:33", "lastmod": "2026-03-27 19:19:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winnett-Alexander-Viloria", "name": { "family": "Winnett", "given": "Alexander Viloria" }, "orcid": "0000-0002-7338-5605" }, { "id": "Akana-Reid", "name": { "family": "Akana", "given": "Reid" }, "orcid": "0000-0003-4422-587X" }, { "id": "Shelby-Natasha", "name": { "family": "Shelby", "given": "Natasha" }, "orcid": "0000-0001-9097-3663" }, { "id": "Davich-Hannah", "name": { "family": "Davich", "given": "Hannah" }, "orcid": "0000-0001-6880-3086" }, { "id": "Caldera-Saharai", "name": { "family": "Caldera", "given": "Saharai" }, "orcid": "0000-0001-5057-9186" }, { "id": "Yamada-Taikun", "name": { "family": "Yamada", "given": "Taikun" } }, { "id": "Reyna-John-Raymond-B", "name": { "family": "Reyna", "given": "John Raymond B." } }, { "id": "Romano-Anne-E", "name": { "family": "Romano", "given": "Anna E." }, "orcid": "0000-0002-7148-0668" }, { "id": "Carter-Alyssa-M", "name": { "family": "Carter", "given": "Alyssa M." }, "orcid": "0000-0002-2776-9421" }, { "id": "Kim-Mi-Kyung", "name": { "family": "Kim", "given": "Mi Kyung" } }, { "id": "Thomson-M-W", "name": { "family": "Thomson", "given": "Matt" }, "orcid": "0000-0003-1021-1234" }, { "id": "Tognazzini-Colten", "name": { "family": "Tognazzini", "given": "Colten" }, "orcid": "0000-0002-2754-3588" }, { "id": "Feaster-Matthew", "name": { "family": "Feaster", "given": "Matthew" }, "orcid": "0000-0001-9966-2845" }, { "id": "Goh-Ying-Ying", "name": { "family": "Goh", "given": "Ying-Ying" }, "orcid": "0000-0001-5136-7214" }, { "id": "Chew-Yap-Ching", "name": { "family": "Chew", "given": "Yap Ching" }, "orcid": "0000-0002-1686-6541" }, { "id": "Ismagilov-R-F", "name": { "family": "Ismagilov", "given": "Rustem F." }, "orcid": "0000-0002-3680-4399" } ] }, "title": "Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2023. Published by Oxford University Press on behalf of National Academy of Sciences. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nThe authors thank the study participants for making this work possible. The authors thank Lauriane Quenee, Grace Fisher-Adams, Junie Hildebrandt, Megan Hayashi, RuthAnne Bevier, Chantal D'Apuzzo, Ralph Adolphs, Victor Rivera, Steve Chapman, Gary Waters, Leonard Edwards, Gaylene Ursua, Cynthia Ramos, and Shannon Yamashita for their assistance and advice on study implementation and/or administration. They thank Jessica Leong, Ojas Pradhan, Si Hyung Jin, Emily Savela, Bridget Yang, Ekta Patel, Hsiuchen Chen, Paresh Samantaray, Zeynep Turan, Cindy Kim, Trinity Lee, Vanessa Mechan, Katherine Stiefel, Rosie Zedan, Rahulijeet Chadha, Minkyo Lee, and Jenny Ji for volunteering their time to help with this study. The authors thank Prabhu Gounder, Tony Chang, Jennifer Howes, and Nari Shin for their support with recruitment. Finally, the authors thank all the case investigators and contact tracers at the Pasadena Public Health Department and Caltech Student Wellness Services for their efforts in study recruitment and their work in the pandemic response. This manuscript was posted on the preprint server medRxiv at https://www.medrxiv.org/content/10.1101/2022.07.13.22277113v2. \n\nThis work was funded in part by a grant from the Ronald and Maxine Linde Center for New Initiatives at the California Institute of Technology (to RFI), a grant from the Jacobs Institute for Molecular Engineering for Medicine at the California Institute of Technology (to RFI), and a DGSOM Geffen Fellowship at the University of California, Los Angeles (to AVW). \n\nAuthor contributions. Detailed author contributions are in the Supplement. \n\nConceptualization: A.V.W., N.S., M.F., Y-Y.G., R.F.I.; methodology: A.V.W., R.A., N.S.; investigation: A.V.W., R.A., N.S., S.C., H.D., M.K.K., J.R.B.R., T.Y., A.E.R., A.M.C., Y.C.C.; visualization: A.V.W., R.A., N.S.; funding acquisition: A.V.W., R.F.I.; project administration: N.S., R.F.I.; supervision: Y.C.C., R.F.I.; writing\u2014original draft: A.V.W., R.A., N.S. writing\u2014review and editing: A.V.W., R.A., N.S., A.E.R., A.M.C., R.F.I. \n\nData availability. The data underlying the results presented in the study can be accessed at CaltechDATA: https://data.caltech.edu/records/20223. \n\nA.V.W., R.A., and N.S. authors contributed equally to this report. Order of co-first authorship was determined by extent of contributions; see detailed Author Contributions statement in the supplement. \n\nCompeting interest: R.F.I. is a co-founder, consultant, and director for and has stock ownership in Talis Biomedical Corporation. All other authors report no potential conflicts.\n\nPublished - pgad033.pdf
Supplemental Material - pgad033_supplementary_data.zip
", "abstract": "SARS-CoV-2 viral-load measurements from a single-specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus\u2013host interactions. However, measurements from a single-specimen type are implicitly assumed to be representative of other specimen types. We quantified viral-load timecourses from individuals who began daily self-sampling of saliva, anterior-nares (nasal), and oropharyngeal (throat) swabs before or at the incidence of infection with the Omicron variant. Viral loads in different specimen types from the same person at the same timepoint exhibited extreme differences, up to 109 copies/mL. These differences were not due to variation in sample self-collection, which was consistent. For most individuals, longitudinal viral-load timecourses in different specimen types did not correlate. Throat-swab and saliva viral loads began to rise as many as 7 days earlier than nasal-swab viral loads in most individuals, leading to very low clinical sensitivity of nasal swabs during the first days of infection. Individuals frequently exhibited presumably infectious viral loads in one specimen type while viral loads were low or undetectable in other specimen types. Therefore, defining an individual as infectious based on assessment of a single-specimen type underestimates the infectious period, and overestimates the ability of that specimen type to detect infectious individuals. For diagnostic COVID-19 testing, these three single-specimen types have low clinical sensitivity, whereas a combined throat\u2013nasal swab, and assays with high analytical sensitivity, was inferred to have significantly better clinical sensitivity to detect presumed pre-infectious and infectious individuals.", "date": "2023-03", "date_type": "published", "publication": "PNAS Nexus", "volume": "2", "number": "3", "publisher": "Oxford University Press", "pagerange": "pgad033", "id_number": "CaltechAUTHORS:20230323-759607000.4", "issn": "2752-6542", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230323-759607000.4", "funders": { "items": [ { "agency": "Ronald and Maxine Linde Center for New Initiatives" }, { "agency": "Jacobs Institute for Molecular Engineering for Medicine" }, { "agency": "UCLA" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Jacobs-Institute-for-Molecular-Engineering-for-Medicine" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/pnasnexus/pgad033", "pmcid": "PMC10013338", "primary_object": { "basename": "pgad033.pdf", "url": "https://authors.library.caltech.edu/records/8xx2v-fk653/files/pgad033.pdf" }, "related_objects": [ { "basename": "pgad033_supplementary_data.zip", "url": "https://authors.library.caltech.edu/records/8xx2v-fk653/files/pgad033_supplementary_data.zip" } ], "pub_year": "2023", "author_list": "Winnett, Alexander Viloria; Akana, Reid; et al." }, { "id": "https://authors.library.caltech.edu/records/704fk-e7p43", "eprint_id": 119906, "eprint_status": "archive", "datestamp": "2023-10-09 22:02:56", "lastmod": "2023-12-22 23:45:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rusch-Tessa", "name": { "family": "Rusch", "given": "Tessa" }, "orcid": "0000-0002-5445-6885" }, { "id": "Han-Yanting", "name": { "family": "Han", "given": "Yanting" }, "orcid": "0000-0003-3381-2059" }, { "id": "Liang-Dehua", "name": { "family": "Liang", "given": "Dehua" }, "orcid": "0000-0003-4794-0270" }, { "id": "Hopkins-Amber-R", "name": { "family": "Hopkins", "given": "Amber R." } }, { "id": "Lawrence-Caroline-V", "name": { "family": "Lawrence", "given": "Caroline V." } }, { "id": "Maoz-Uri-M", "name": { "family": "Maoz", "given": "Uri" }, "orcid": "0000-0002-7899-1241" }, { "id": "Paul-Lynn-K", "name": { "family": "Paul", "given": "Lynn K." }, "orcid": "0000-0002-3128-8313" }, { "id": "Stanley-Damian-A", "name": { "family": "Stanley", "given": "Damian A." }, "orcid": "0000-0001-5992-8901" }, { "id": "Adolphs-R", "name": { "family": "Adolphs", "given": "Ralph" }, "orcid": "0000-0002-8053-9692" }, { "id": "Alvarez-R-M", "name": { "family": "Alvarez", "given": "R. Michael" }, "orcid": "0000-0002-8113-4451" }, { "id": "Camplisson-Isabella", "name": { "family": "Camplisson", "given": "Isabella" }, "orcid": "0000-0001-9653-2789" }, { "id": "Harrison-Laura-A", "name": { "family": "Harrison", "given": "Laura" } }, { "id": "Hien-Denise", "name": { "family": "Hien", "given": "Denise" }, "orcid": "0000-0002-6954-2882" }, { "id": "Lan-Tian", "name": { "family": "Lan", "given": "Tian" } }, { "id": "Lin-Chujusn", "name": { "family": "Lin", "given": "Chujusn" } }, { "id": "L\u00f3pez-Castro-Teresa", "name": { "family": "Lopez-Castro", "given": "Teresa" }, "orcid": "0000-0003-2521-6329" }, { "id": "Nizzic-Marie-Christine", "name": { "family": "Nizzic", "given": "Marie-Christine" } }, { "id": "Rabkin-Golden-Allison", "name": { "family": "Rabkin Golden", "given": "Allison" } }, { "id": "Wahle-Iman-A", "name": { "family": "Wahle", "given": "Iman" } }, { "id": "Yaffe-Gideon", "name": { "family": "Yaffe", "given": "Gideon" }, "orcid": "0000-0002-9385-3912" } ] }, "title": "COVID-Dynamic:\u00a0a large-scale longitudinal study of socioemotional and behavioral change across the pandemic", "ispublished": "pub", "full_text_status": "public", "keywords": "Library and Information Sciences; Statistics, Probability and Uncertainty; Computer Science Applications; Education; Information Systems; Statistics and Probability", "note": "\u00a9 The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nWe deeply appreciate all COVID-Dynamic participants, whose continued diligence and commitment during this difficult time made this data possible. We thank Jonathan Katz for his expert advice on panel data processing and analysis, and Ruby Basyouni for her help during data collection. Lastly, we are grateful to the various funding sources that supported this work: the National Institute of Mental Health (2P50MH094258), the Caltech Chen Neuroscience Institute, and the Caltech Merkin Institute (RA), by the Oscar M. Ruebhausen Fund at Yale Law School (GY), the Rutgers Center of Alcohol & Substance Use Studies (DH), the John Templeton Foundation and the Kay Family COVID-19 Rapid Response Research Awards at Chapman University (UM), and the Colin Powell School for Civic and Global Leadership, The City College of New York (TLC). The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the funding agencies. \n\nThese authors contributed equally: Tessa Rusch, Yanting Han, Dehua Liang. \n\nThese authors jointly supervised this work: Lynn K. Paul, Damian A. Stanley. \n\nThe authors declare no competing interests.\n\nPublished - 41597_2022_Article_1901.pdf
", "abstract": "The COVID-19 pandemic has caused enormous societal upheaval globally. In the US, beyond the devastating toll on life and health, it triggered an economic shock unseen since the great depression and laid bare preexisting societal inequities. The full impacts of these personal, social, economic, and public-health challenges will not be known for years. To minimize societal costs and ensure future preparedness, it is critical to record the psychological and social experiences of individuals during such periods of high societal volatility. Here, we introduce, describe, and assess the COVID-Dynamic dataset, a within-participant longitudinal study conducted from April 2020 through January 2021, that captures the COVID-19 pandemic experiences of >1000 US residents. Each of 16 timepoints combines standard psychological assessments with novel surveys of emotion, social/political/moral attitudes, COVID-19-related behaviors, tasks assessing implicit attitudes and social decision-making, and external data to contextualize participants' responses. This dataset is a resource for researchers interested in COVID-19-specific questions and basic psychological phenomena, as well as clinicians and policy-makers looking to mitigate the effects of future calamities.", "date": "2023-02-03", "date_type": "published", "publication": "Scientific Data", "volume": "10", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 71", "id_number": "CaltechAUTHORS:20230308-468102500.11", "issn": "2052-4463", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230308-468102500.11", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "2P50MH094258" }, { "agency": "Tianqiao and Chrissy Chen Institute for Neuroscience" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "Yale Law School" }, { "agency": "Rutgers Center of Alcohol & Substance Use Studies" }, { "agency": "John Templeton Foundation" }, { "agency": "Kay Family Foundation" }, { "agency": "City College of New York" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "corp_creators": { "items": [ "COVID-Dynamic Team" ] }, "doi": "10.1038/s41597-022-01901-6", "pmcid": "PMC9897616", "primary_object": { "basename": "41597_2022_Article_1901.pdf", "url": "https://authors.library.caltech.edu/records/704fk-e7p43/files/41597_2022_Article_1901.pdf" }, "pub_year": "2023", "author_list": "Rusch, Tessa; Han, Yanting; et al." }, { "id": "https://authors.library.caltech.edu/records/fxwne-b1949", "eprint_id": 120542, "eprint_status": "archive", "datestamp": "2023-08-22 18:59:01", "lastmod": "2026-03-27 19:38:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sellam-Abdellah-Zakaria", "name": { "family": "Sellam", "given": "Abdellah Zakaria" } }, { "id": "Benlamoudi-Azeddine", "name": { "family": "Benlamoudi", "given": "Azeddine" }, "orcid": "0000-0002-2023-2154" }, { "id": "Cid-Cl\u00e9ment-A", "name": { "family": "Cid", "given": "Cl\u00e9ment Antoine" }, "orcid": "0000-0002-7293-035X" }, { "id": "Dobelle-Leopold", "name": { "family": "Dobelle", "given": "Leopold" } }, { "id": "Slama-Amina", "name": { "family": "Slama", "given": "Amina" } }, { "id": "El-Hillali-Yassin", "name": { "family": "El Hillali", "given": "Yassin" }, "orcid": "0000-0002-3980-9902" }, { "id": "Taleb-Ahmed-Abdelmalik", "name": { "family": "Taleb-Ahmed", "given": "Abdelmalik" }, "orcid": "0000-0001-7218-3799" } ] }, "title": "Deep Learning Solution for Quantification of Fluorescence Particles on a Membrane", "ispublished": "pub", "full_text_status": "public", "keywords": "Electrical and Electronic Engineering; Biochemistry; Instrumentation; Atomic and Molecular Physics, and Optics; Analytical Chemistry", "note": "\u00a9 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). \n\n(This article belongs to the Collection Artificial Intelligence (AI) in Biomedical Imaging).\n\nThe authors would like to thank Jing Li and Sean McBeath for their help with getting microscope and smartphone camera images. \n\nThis research was funded by Bill & Melinda Gates Foundation, Grant INV-030223. \n\nAuthor Contributions. Conceptualization, A.Z.S., A.B. and A.T.-A.; dataset collecting, C.A.C. and L.D.; data annotation, A.Z.S. and C.A.C. software, A.Z.S., A.B. and A.T.-A.; validation, A.B., A.T.-A. and C.A.C.; formal analysis, A.B. and A.S.; investigation, A.T.-A. and A.B.; writing\u2014review and editing, A.T.-A., C.A.C. and Y.E.H.; visualization, A.Z.S., A.B. and A.T.-A.; supervision, A.T.-A.; project administration, A.B. All authors have read and agreed to the published version of the manuscript. \n\nThe authors declare no conflict of interest.\n\nPublished - sensors-23-01794-v2.pdf
", "abstract": "The detection and quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus particles in ambient waters using a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) method can play an important role in large-scale environmental surveillance for early warning of potential outbreaks. However, counting particles or cells in fluorescence microscopy is an expensive, time-consuming, and tedious task that only highly trained technicians and researchers can perform. Although such objects are generally easy to identify, manually annotating cells is occasionally prone to fatigue errors and arbitrariness due to the operator's interpretation of borderline cases. In this research, we proposed a method to detect and quantify multiscale and shape variant SARS-CoV-2 fluorescent cells generated using a portable (mgLAMP) system and captured using a smartphone camera. The proposed method is based on the YOLOv5 algorithm, which uses CSPnet as its backbone. CSPnet is a recently proposed convolutional neural network (CNN) that duplicates gradient information within the network using a combination of Dense nets and ResNet blocks, and bottleneck convolution layers to reduce computation while at the same time maintaining high accuracy. In addition, we apply the test time augmentation (TTA) algorithm in conjunction with YOLO's one-stage multihead detection heads to detect all cells of varying sizes and shapes. We evaluated the model using a private dataset provided by the Linde + Robinson Laboratory, California Institute of Technology, United States. The model achieved a mAP@0.5 score of 90.3 in the YOLOv5-s6.", "date": "2023-02-02", "date_type": "published", "publication": "Sensors", "volume": "23", "number": "4", "publisher": "MDPI", "pagerange": "Art. No. 1794", "id_number": "CaltechAUTHORS:20230328-706203600.35", "issn": "1424-8220", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230328-706203600.35", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-030223" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.3390/s23041794", "pmcid": "PMC9967937", "primary_object": { "basename": "sensors-23-01794-v2.pdf", "url": "https://authors.library.caltech.edu/records/fxwne-b1949/files/sensors-23-01794-v2.pdf" }, "pub_year": "2023", "author_list": "Sellam, Abdellah Zakaria; Benlamoudi, Azeddine; et al." }, { "id": "https://authors.library.caltech.edu/records/tvebq-q9m96", "eprint_id": 118798, "eprint_status": "archive", "datestamp": "2023-10-09 21:19:50", "lastmod": "2025-11-22 02:36:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "L\u00f3pez-Castro-Teresa", "name": { "family": "L\u00f3pez-Castro", "given": "Teresa" }, "orcid": "0000-0003-2521-6329" }, { "id": "Papini-Santiago", "name": { "family": "Papini", "given": "Santiago" }, "orcid": "0000-0002-8109-4437" }, { "id": "Bauer-Alexandria", "name": { "family": "Bauer", "given": "Alexandria" }, "orcid": "0000-0001-9826-9056" }, { "id": "Swarbrick-Margaret", "name": { "family": "Swarbrick", "given": "Margaret" }, "orcid": "0000-0002-8648-0628" }, { "id": "Paul-Lynn-K", "name": { "family": "Paul", "given": "Lynn K." }, "orcid": "0000-0002-3128-8313" }, { "id": "Nizzi-Marie-Christine", "name": { "family": "Nizzi", "given": "Marie-Christine" }, "orcid": "0000-0002-2062-8992" }, { "id": "Stanley-Damian", "name": { "family": "Stanley", "given": "Damian" }, "orcid": "0000-0001-9815-913X" }, { "id": "Hien-Denise", "name": { "family": "Hien", "given": "Denise" }, "orcid": "0000-0002-6954-2882" } ] }, "title": "Posttraumatic stress disorder symptom trajectories in a 16-month COVID-19 pandemic period", "ispublished": "pub", "full_text_status": "public", "keywords": "Psychiatry and Mental health; Clinical Psychology", "note": "\u00a9 2022 International Society for Traumatic Stress Studies.\nThis article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency. \n\nThis work was supported by grants from the National Institute of Mental Health (2P50MH094258), Caltech Chen Neuroscience Institute, Caltech Merkin Institute, Oscar M. Ruebhausen Fund at Yale Law School, Rutgers Center of Alcohol & Substance Use Studies, John Templeton Foundation, and Kay Family Foundation at Chapman University. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the funding agencies. We have no known conflicts of interest to disclose. \n\nCOVID\u2010Dynamic team members associated with this work are as follows: Amber Hopkins, Dehua Liang, Uri Maoz, and Tessa Rusch. A detailed characterization of each author's contribution can be found in Supplementary Table S3. \n\nThis article reported on prespecified aims, hypotheses, and analytic plans (https://osf.io/phwf2/) from a preregistered broader study, the COVID\u2010Dynamic Project. Within the COVID\u2010Dynamic Project in the Open Science F repository, the Introduction to the COVID Dynamic Dataset component (https://osf.io/kex8y/) contains all assessment instruments (https://osf.io/nhm2v/) and the full COVID\u2010Dynamic data dictionary (https://osf.io/z8k2t/). The component specific to the current manuscript (https://osf.io/hy3aq/) contains a project\u2010specific dataset, data dictionary, analysis code, and output. \n\nThis article has earned an Open Materials badge for making publicly available the components of the research methodology needed to reproduce the reported procedure and analysis. All materials are available at https://osf.io/9vgzj/.\n\nPublished - JTS-9999-0.pdf
Supplemental Material - JTS-9999-0-s001.docx
", "abstract": "COVID-19 pandemic presents an unheralded opportunity to better understand trajectories of posttraumatic stress disorder (PTSD) symptoms across a prolonged period of social disruption and stress. We tracked PTSD symptoms among trauma-exposed individuals in the United States and sought to identify population-based variability in PTSD symptom trajectories and understand what, if any, early pandemic experiences predicted membership in one trajectory versus others. As part of a longitudinal study of U.S. residents during the pandemic, participants who reported at least one potentially traumatic experience in their lifetime (N = 1,206) at Wave 1 (April 2020) were included in the current study. PTSD symptoms were assessed using the PCL-5 at four time points extending to July 2021. Latent growth mixture modeling was used to identify heterogeneous symptom trajectories. Trajectory membership was regressed on experiences from the early stage of the pandemic as measured using the Epidemic-Pandemic Impacts Inventory in a model that controlled for variables with documented associations to PTSD trajectories, including age, sex, income, and trauma history. Four trajectories were identified, categorized as resilient (73.0%), recurring (13.3%), recovering (8.3%), and chronic (5.5%). Emotional and physical health problems and positive changes associated with the early phase of the pandemic were each significant predictors of trajectory membership over and above all other variables in the model. Predictors primarily differentiated the resilient trajectory from each of the other three trajectories. Distinct PTSD symptom trajectories during the COVID-19 pandemic suggest a need for targeted efforts to help individuals at most risk for ongoing distress.", "date": "2023-02", "date_type": "published", "publication": "Journal of Traumatic Stress", "volume": "36", "number": "1", "publisher": "Wiley", "pagerange": "180-192", "id_number": "CaltechAUTHORS:20230113-708423000.15", "issn": "0894-9867", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230113-708423000.15", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50MH094258" }, { "agency": "Tianqiao and Chrissy Chen Institute for Neuroscience" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "Yale Law School" }, { "agency": "Rutgers University" }, { "agency": "John Templeton Foundation" }, { "agency": "Kay Family Foundation" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "corp_creators": { "items": [ "COVID-Dynamic Team" ] }, "doi": "10.1002/jts.22899", "pmcid": "PMC9880687", "primary_object": { "basename": "JTS-9999-0.pdf", "url": "https://authors.library.caltech.edu/records/tvebq-q9m96/files/JTS-9999-0.pdf" }, "related_objects": [ { "basename": "JTS-9999-0-s001.docx", "url": "https://authors.library.caltech.edu/records/tvebq-q9m96/files/JTS-9999-0-s001.docx" } ], "pub_year": "2023", "author_list": "L\u00f3pez-Castro, Teresa; Papini, Santiago; et al." }, { "id": "https://authors.library.caltech.edu/records/0mjqz-64458", "eprint_id": 118971, "eprint_status": "archive", "datestamp": "2023-08-22 18:35:42", "lastmod": "2025-11-22 04:04:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Carter-Alyssa-M", "name": { "family": "Carter", "given": "Alyssa M." }, "orcid": "0000-0002-2776-9421" }, { "id": "Winnett-Alexander-Viloria", "name": { "family": "Winnett", "given": "Alexander Viloria" }, "orcid": "0000-0002-7338-5605" }, { "id": "Romano-Anne-E", "name": { "family": "Romano", "given": "Anna E." }, "orcid": "0000-0002-7148-0668" }, { "id": "Akana-Reid", "name": { "family": "Akana", "given": "Reid" }, "orcid": "0000-0003-4422-587X" }, { "id": "Shelby-Natasha", "name": { "family": "Shelby", "given": "Natasha" }, "orcid": "0000-0001-9097-3663" }, { "id": "Ismagilov-R-F", "name": { "family": "Ismagilov", "given": "Rustem F." }, "orcid": "0000-0002-3680-4399" } ] }, "title": "Laboratory Evaluation Links Some False-Positive COVID-19 Antigen Test Results Observed in a Field Study to a Specific Lot of Test Strips", "ispublished": "pub", "full_text_status": "public", "keywords": "Infectious Diseases; Oncology", "note": "\u00a9 The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. \n\nWe thank the study participants for making this work possible. We thank Study Coordinators Saharai Caldera for suggesting the laboratory evaluation and both Saharai and Hannah Davich for removing lot 152000 from circulation in the study. We thank Taikun Yamada, John Raymond B. Reyna, Paolo Piatti and Yap Ching Chew for performing and verifying the validity of RT-qPCR results as previously reported. Finally, we thank all the case investigators and contact tracers at the Pasadena Public Health Department and Caltech Student Wellness Services for their efforts in study recruitment and their work in the pandemic response. \n\nThis work was supported by the Ronald and Maxine Linde Center for New Initiatives at the California Institute of Technology and the Jacobs Institute for Molecular Engineering for Medicine at the California Institute of Technology. A UCLA DGSOM Geffen Fellowship to AVW. \n\nData Availability: The data underlying the results presented in the study are available at CaltechDATA at: https://doi.org/10.22002/fmz6a-0x036.\n\nAlyssa M. Carter and Alexander Viloria Winnett contributed equally to this manuscript.\n\nPublished - ofac701.pdf
Supplemental Material - ofac701_supplementary_data.pdf
", "abstract": "During a household-transmission field study using COVID-19 antigen rapid diagnostic tests (Ag-RDT), a common test strip lot was identified among three participants with false-positive results. In blinded laboratory evaluation, this lot, exhibited a significantly higher false-positive rate than other lots. Because a positive Ag-RDT result often prompts action, reducing lot-specific false positives can maintain confidence and actionability of true-positive Ag-RDT results.", "date": "2023-01-30", "date_type": "published", "publication": "Open Forum Infectious Diseases", "volume": "10", "number": "1", "publisher": "Oxford University Press", "pagerange": "Art. No. ofac701", "id_number": "CaltechAUTHORS:20230130-263514000.2", "issn": "2328-8957", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230130-263514000.2", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ronald and Maxine Linde Center for New Initiatives" }, { "agency": "Jacobs Institute for Molecular Engineering for Medicine" }, { "agency": "UCLA" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Jacobs-Institute-for-Molecular-Engineering-for-Medicine" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/ofid/ofac701", "pmcid": "PMC9887260", "primary_object": { "basename": "ofac701.pdf", "url": "https://authors.library.caltech.edu/records/0mjqz-64458/files/ofac701.pdf" }, "related_objects": [ { "basename": "ofac701_supplementary_data.pdf", "url": "https://authors.library.caltech.edu/records/0mjqz-64458/files/ofac701_supplementary_data.pdf" } ], "pub_year": "2023", "author_list": "Carter, Alyssa M.; Winnett, Alexander Viloria; et al." }, { "id": "https://authors.library.caltech.edu/records/34q7b-h0a48", "eprint_id": 122524, "eprint_status": "archive", "datestamp": "2023-08-22 18:49:37", "lastmod": "2025-11-22 03:47:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Periyakoil-Divya", "name": { "family": "Periyakoil", "given": "Divya" }, "orcid": "0000-0001-7479-8332" }, { "id": "Periyakoil-Preethi", "name": { "family": "Periyakoil", "given": "Preethi" }, "orcid": "0000-0002-1536-8743" }, { "id": "Tee-Cherica-A", "name": { "family": "Tee", "given": "Cherica A." }, "orcid": "0000-0002-0766-0189" }, { "id": "Spanos-Costas-J", "name": { "family": "Spanos", "given": "Costas J." } }, { "id": "Diener-West-Marie", "name": { "family": "Diener-West", "given": "Marie" }, "orcid": "0000-0002-3082-1323" }, { "id": "Tee-Michael", "name": { "family": "Tee", "given": "Michael" }, "orcid": "0000-0003-0113-8290" }, { "id": "Prata-Ndola", "name": { "family": "Prata", "given": "Ndola" }, "orcid": "0000-0002-5913-0737" } ] }, "title": "Are There Differences between the Stress Responses of Philippine Men and Women to the COVID-19 Pandemic?", "ispublished": "pub", "full_text_status": "public", "keywords": "Health, Toxicology and Mutagenesis; Public Health, Environmental and Occupational Health", "note": "\u00a9 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).\n\nDivya Periyakoil completed this work while a Master of Public Health Student and Bloomberg American Health Initiative Fellow at the Johns Hopkins Bloomberg School of Public Health in Baltimore, MD. \n\nThis research is partially funded by the University of California, Berkeley Regents' and Chancellor's Research Grant to Divya Periyakoil. \n\nAuthor Contributions: Conceptualization, D.P. and N.P.; methodology, D.P. and N.P.; software, D.P.; validation, D.P. and N.P.; formal analysis, D.P., N.P., and M.D.-W.; investigation, D.P. and N.P.; resources, N.P. and C.J.S.; data curation, D.P., N.P., M.T., C.A.T.; writing\u2014original draft preparation, D.P. and P.P.; writing\u2014review and editing, D.P., P.P., N.P., M.T., C.A.T., M.D.-W.; visualization, D.P. and N.P.; supervision, N.P. and C.J.S.; project administration, N.P.; funding acquisition, D.P. and N.P. All authors have read and agreed to the published version of the manuscript. \n\nInstitutional Review Board Statement: This study was approved by the Research Ethics Board of the University of the Philippines Manila (UPMREB 2020-198-01). \n\nInformed Consent Statement: Informed consent was obtained from all subjects involved in the study. \n\nData Availability Statement: Restrictions apply to the availability of these data. Data was obtained from the University of the Philippines, Manila and are available at the discretion of the data curators. \n\nThe authors declare no conflict of interest.\n\nPublished - ijerph-20-02326-v2.pdf
", "abstract": "The SARS-CoV-2 pandemic has had a deleterious impact on human health since its beginning in 2019. The purpose of this study was to examine the psychosocial impact of the COVID-19 pandemic in the Philippines and determine if there were differential impacts on women compared to men. A web-based survey was conducted in the Luzon Islands of the Philippines, during the pandemic quarantine. A total of 1879 participants completed online surveys between 28 March\u201312 April 2020. A bivariate analysis of both men and women for each psychological measure (stress, anxiety, depression, and impact of COVID-19) was conducted. Multivariable logistic regression models were built for each measure, dichotomized as high or low, separately for men and women. Younger age (p < 0.001), being married (p < 0.001), and being a parent (p < 0.004) were associated with women's poor mental health. Marriage and large household size are protective factors for men (p < 0.002 and p < 0.0012, respectively), but marriage may be a risk factor for women (p < 0.001). Overall, women were disproportionately negatively impacted by the pandemic compared to men.", "date": "2023-01-28", "date_type": "published", "publication": "International Journal of Environmental Research and Public Health", "volume": "20", "number": "3", "publisher": "MDPI", "pagerange": "Art. No. 2326", "id_number": "CaltechAUTHORS:20230725-706050000.31", "issn": "1660-4601", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230725-706050000.31", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of California, Berkeley" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.3390/ijerph20032326", "pmcid": "PMC9915070", "primary_object": { "basename": "ijerph-20-02326-v2.pdf", "url": "https://authors.library.caltech.edu/records/34q7b-h0a48/files/ijerph-20-02326-v2.pdf" }, "pub_year": "2023", "author_list": "Periyakoil, Divya; Periyakoil, Preethi; et al." }, { "id": "https://authors.library.caltech.edu/records/57cxq-6fa54", "eprint_id": 122358, "eprint_status": "archive", "datestamp": "2023-09-28 12:12:22", "lastmod": "2025-11-22 02:12:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Huang-Kuan-Ying-A", "name": { "family": "Huang", "given": "Kuan-Ying A." }, "orcid": "0000-0001-6891-6945" }, { "id": "Chen-Xiaorui", "name": { "family": "Chen", "given": "Xiaorui" }, "orcid": "0000-0002-4492-0883" }, { "id": "Mohapatra-Arpita", "name": { "family": "Mohapatra", "given": "Arpita" }, "orcid": "0000-0003-3468-6912" }, { "id": "Nguyen-Hong-Thuy-Vy", "name": { "family": "Nguyen", "given": "Hong Thuy Vy" }, "orcid": "0000-0001-7577-3452" }, { "id": "Schimanski-Lisa", "name": { "family": "Schimanski", "given": "Lisa" } }, { "id": "Tan-Tiong-Kit", "name": { "family": "Tan", "given": "Tiong Kit" }, "orcid": "0000-0001-8746-8308" }, { "id": "Rijal-Pramila", "name": { "family": "Rijal", "given": "Pramila" }, "orcid": "0000-0002-9214-9851" }, { "id": "Vester-Susan-K", "name": { "family": "Vester", "given": "Susan K." }, "orcid": "0000-0002-4210-118X" }, { "id": "Hills-Rory-A", "name": { "family": "Hills", "given": "Rory A." }, "orcid": "0000-0002-5698-9538" }, { "id": "Howarth-Mark", "name": { "family": "Howarth", "given": "Mark" }, "orcid": "0000-0001-8870-7147" }, { "id": "Keeffe-Jennifer-R", "name": { "family": "Keeffe", "given": "Jennifer R." }, "orcid": "0000-0002-5317-6398" }, { "id": "Cohen-Alexander-A", "name": { "family": "Cohen", "given": "Alexander A." }, "orcid": "0000-0002-2818-656X" }, { "id": "Kakutani-Leesa-M", "name": { "family": "Kakutani", "given": "Leesa M." }, "orcid": "0000-0003-3822-7449" }, { "id": "Wu-Yi-Min", "name": { "family": "Wu", "given": "Yi-Min" }, "orcid": "0000-0001-9745-6298" }, { "id": "Shahed-Al-Mahmud-Md", "name": { "family": "Shahed-Al-Mahmud", "given": "Md" }, "orcid": "0000-0002-4285-7016" }, { "id": "Chou-Yu-Chi", "name": { "family": "Chou", "given": "Yu-Chi" }, "orcid": "0000-0002-0783-1339" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Townsend-Alain-R", "name": { "family": "Townsend", "given": "Alain R." }, "orcid": "0000-0002-3702-0107" }, { "id": "Ma-Che", "name": { "family": "Ma", "given": "Che" }, "orcid": "0000-0002-4741-2307" } ] }, "title": "Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2", "ispublished": "pub", "full_text_status": "public", "keywords": "General Physics and Astronomy; General Biochemistry, Genetics and Molecular Biology; General Chemistry; Multidisciplinary", "note": "\u00a9 The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nWe acknowledge the BD FACSAria cell sorter service provided by the Core Instrument Center of Chang Gung University, Taiwan. We thank National RNAi Core Facility at Academia Sinica, Taiwan for pseudovirus neutralization assays. We thank the technical support provided by the National Synchrotron Radiation Research Center (NSRRC), Taiwan. We thank the Academia Sinica Biological Electron Microscopy Core Facility for negative stain EM and Academia Sinica Cryo-EM Facility (ASCEM) for cryo-EM support. We appreciate the advice from Dr. Shu-Chuan Jao for biolayer interferometry. The mutant BtKY72 was a kind gift from Alexandra Walls and David Veesler, University of Washington. This work was supported by the National Science and Technology Council of Taiwan (MOST 110-2628-B-182-009, MOST 110-2628-B-182-013, NTSC 111-2628-B-002-052) to K.-Y.A.H. The research was funded by Genomics Research Center, Summit Project (AS-SUMMIT-109) and the Translational Medical Research Program (AS-KPQ-109-BioMed), Academia Sinica, and Taiwan Bio-Development Foundation, to C.M. S.K.V. and M.H. were funded by the Biotechnology and Biological Sciences Research Council (BBSRC grant BB/T004983/1). P.J.B. was funded by Bill and Melinda Gates Foundation INV-034638, Caltech Merkin Institute, and George Mason University Fast Grant. R.A.H. was funded by the Rhodes Trust. M.H. also thanks the University of Oxford COVID-19 Research Response Fund and its donors (reference 0009517). The EM Facilities were funded by Academia Sinica Core Facility and Innovative Instrument Projects (AS-CFII-108-110 and AS-CFII-108-119) and Taiwan Protein Project (AS-KPQ-109-TPP2). This research was funded in whole or in part by BBSRC grant BB/T004983/1. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. \n\nData availability: The data associated with this study are available within the article, its supplementary information and Source Data file. Source data are provided with this paper. The coordinates and structure factors of the SARS-CoV-2 RBD/FP-12A, RBD/IS-9A and RBD/IY-2A crystallographic complexes generated in this study have been deposited in the PDB (Protein Data Bank) under accession codes 8HHF, 8HHG and 8HHH, respectively. Cryo-EM volumes and structure models of the SARS-CoV-2 Delta Spike/FP-12A, Delta Spike/IS-9A and BA.1 Spike/IY-2A generated in this study have been deposited in the EMDB (Electron Microscopy Data Bank) under accession codes EMD 34806, EMD 34807, and EMD 34808, and in the PDB under accession codes 8HHX, 8HHY and 8HHZ, respectively. Source data are provided with this paper. \n\nThese authors contributed equally: Kuan-Ying A. Huang, Xiaorui Chen. \n\nContributions: K.-Y.A.H. conceived and designed the study. K.-Y.A.H. isolated and characterized antibodies. L.S., T.K.T., P.R., and A.R.T. performed binding experiments and analyzed data. C.M. and X.C. supervised the structural study of antibodies. Y.C.C. performed SARS-CoV-2 variant neutralization experiments. S.K.V., R.A.H., and M.H. performed sarbecovirus RBD binding experiments and analyzed data. J.R.K., A.A.C., L.M.K., and P.J.B. performed sarbecovirus neutralization experiments and analyzed data. A.M. and H.T.V.N. determined crystal structures. A.M., X.C., Y.-M.W., and M.S-A.-M. performed cryo-EM grid preparation, data processing and structure refinement. K.-Y.A.H. and X.C. analyzed data and prepared figures and tables. K.-Y.A.H. and X.C. wrote the first draft of the manuscript. All authors read and approved the manuscript.\n\nThe authors declare no competing interests.\n\nPublished - s41467-023-35949-8.pdf
Supplemental Material - s41467-023-35949-8MOESM1-ESM.pdf
Supplemental Material - s41467-023-35949-8MOESM3-ESM.xlsx
", "abstract": "Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the \"down\" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.", "date": "2023-01-19", "date_type": "published", "publication": "Nature Communications", "volume": "14", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 311", "id_number": "CaltechAUTHORS:20230719-853635200.8", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230719-853635200.8", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "MOST 110-2628-B-182-009" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "MOST 110-2628-B-182-013" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "NTSC 111-2628-B-002-052" }, { "agency": "Bio-Development Foundation (Taipei)" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/T004983/1" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-034638" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "George Mason University" }, { "agency": "Rhodes Trust" }, { "agency": "University of Oxford", "grant_number": "0009517" }, { "agency": "Academia Sinica", "grant_number": "AS-CFII-108-110" }, { "agency": "Academia Sinica", "grant_number": "AS-CFII-108-119" }, { "agency": "Taiwan Protein Project", "grant_number": "AS-KPQ-109-TPP2" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/T004983/1" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-023-35949-8", "pmcid": "PMC9852238", "primary_object": { "basename": "s41467-023-35949-8.pdf", "url": "https://authors.library.caltech.edu/records/57cxq-6fa54/files/s41467-023-35949-8.pdf" }, "related_objects": [ { "basename": "s41467-023-35949-8MOESM1-ESM.pdf", "url": "https://authors.library.caltech.edu/records/57cxq-6fa54/files/s41467-023-35949-8MOESM1-ESM.pdf" }, { "basename": "s41467-023-35949-8MOESM3-ESM.xlsx", "url": "https://authors.library.caltech.edu/records/57cxq-6fa54/files/s41467-023-35949-8MOESM3-ESM.xlsx" } ], "pub_year": "2023", "author_list": "Huang, Kuan-Ying A.; Chen, Xiaorui; et al." }, { "id": "https://authors.library.caltech.edu/records/rhktp-a6270", "eprint_id": 117475, "eprint_status": "archive", "datestamp": "2023-08-22 18:33:26", "lastmod": "2023-10-24 22:32:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dommer-Abigail", "name": { "family": "Dommer", "given": "Abigail" }, "orcid": "0000-0003-4847-4136" }, { "id": "Casalino-Lorenzo", "name": { "family": "Casalino", "given": "Lorenzo" }, "orcid": "0000-0003-3581-1148" }, { "id": "Kearns-Fiona", "name": { "family": "Kearns", "given": "Fiona" }, "orcid": "0000-0002-5469-9035" }, { "name": { "family": "Rosenfeld", "given": "Mia" }, "orcid": "0000-0002-8961-8231" }, { "name": { "family": "Wauer", "given": "Nicholas" }, "orcid": "0000-0002-1230-9166" }, { "name": { "family": "Ahn", "given": "Surl-Hee" }, "orcid": "0000-0002-3422-805X" }, { "name": { "family": "Russo", "given": "John" }, "orcid": "0000-0002-2813-6554" }, { "name": { "family": "Oliveira", "given": "Sofia" }, "orcid": "0000-0001-8753-4950" }, { "name": { "family": "Morris", "given": "Clare" }, "orcid": "0000-0002-4314-5387" }, { "name": { "family": "Bogetti", "given": "Anthony" }, "orcid": "0000-0003-0610-2879" }, { "name": { "family": "Trifan", "given": "Anda" }, "orcid": "0000-0003-4808-9502" }, { "name": { "family": "Brace", "given": "Alexander" }, "orcid": "0000-0001-9873-9177" }, { "name": { "family": "Sztain", "given": "Terra" }, "orcid": "0000-0002-1327-8541" }, { "name": { "family": "Clyde", "given": "Austin" }, "orcid": "0000-0002-3697-7070" }, { "name": { "family": "Ma", "given": "Heng" }, "orcid": "0000-0002-7667-922X" }, { "name": { "family": "Chennubhotla", "given": "Chakra" }, "orcid": "0000-0002-0024-1627" }, { "name": { "family": "Lee", "given": "Hyungro" }, "orcid": "0000-0002-4221-7094" }, { "name": { "family": "Turilli", "given": "Matteo" }, "orcid": "0000-0003-0527-1435" }, { "name": { "family": "Khalid", "given": "Syma" }, "orcid": "0000-0002-3694-5044" }, { "name": { "family": "Tamayo-Mendoza", "given": "Teresa" } }, { "name": { "family": "Welborn", "given": "Matthew" }, "orcid": "0000-0001-8659-6535" }, { "name": { "family": "Christensen", "given": "Anders S." }, "orcid": "0000-0002-7253-6897" }, { "name": { "family": "Smith", "given": "Daniel G. A." }, "orcid": "0000-0001-8626-0900" }, { "id": "Qiao-Zhuoran", "name": { "family": "Qiao", "given": "Zhuoran" }, "orcid": "0000-0002-5704-7331" }, { "name": { "family": "Sirumalla", "given": "Sai K." } }, { "name": { "family": "O'Connor", "given": "Michael" } }, { "name": { "family": "Manby", "given": "Frederick" }, "orcid": "0000-0001-7611-714X" }, { "id": "Anandkumar-A", "name": { "family": "Anandkumar", "given": "Anima" }, "orcid": "0000-0002-6974-6797" }, { "name": { "family": "Hardy", "given": "David" } }, { "name": { "family": "Phillips", "given": "James" }, "orcid": "0000-0002-2296-3591" }, { "name": { "family": "Stern", "given": "Abraham" } }, { "name": { "family": "Romero", "given": "Josh" } }, { "name": { "family": "Clark", "given": "David" } }, { "name": { "family": "Dorrell", "given": "Mitchell" } }, { "name": { "family": "Maiden", "given": "Tom" } }, { "name": { "family": "Huang", "given": "Lei" } }, { "name": { "family": "McCalpin", "given": "John" }, "orcid": "0000-0002-2535-1355" }, { "name": { "family": "Woods", "given": "Christopher" }, "orcid": "0000-0001-6563-9903" }, { "name": { "family": "Gray", "given": "Alan" } }, { "name": { "family": "Williams", "given": "Matt" }, "orcid": "0000-0003-2198-1058" }, { "name": { "family": "Barker", "given": "Bryan" } }, { "name": { "family": "Rajapaksha", "given": "Harinda" } }, { "name": { "family": "Pitts", "given": "Richard" }, "orcid": "0000-0002-2037-3360" }, { "name": { "family": "Gibbs", "given": "Tom" } }, { "name": { "family": "Stone", "given": "John" }, "orcid": "0000-0001-7215-762X" }, { "name": { "family": "Zuckerman", "given": "Daniel M." }, "orcid": "0000-0001-7662-2031" }, { "name": { "family": "Mulholland", "given": "Adrian J." }, "orcid": "0000-0003-1015-4567" }, { "id": "Miller-T-F-III", "name": { "family": "Miller", "given": "Thomas F., III" }, "orcid": "0000-0002-1882-5380" }, { "name": { "family": "Jha", "given": "Shantenu" }, "orcid": "0000-0002-5040-026X" }, { "name": { "family": "Ramanathan", "given": "Arvind" }, "orcid": "0000-0002-1622-5488" }, { "name": { "family": "Chong", "given": "Lillian" }, "orcid": "0000-0002-0590-483X" }, { "name": { "family": "Amaro", "given": "Rommie E." }, "orcid": "0000-0002-9275-9553" } ] }, "title": "#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol", "ispublished": "pub", "full_text_status": "public", "keywords": "Hardware and Architecture; Theoretical Computer Science; Software", "note": "\u00a9 The Author(s) 2022. This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access page (https://us.sagepub.com/en-us/nam/open-access-at-sage). \n\nWe thank Prof. Kim Prather for inspiring and informative discussions about aerosols and for her commitment to convey the airborne nature of SARS-CoV-2. We thank D. Veesler for sharing the Delta spike NTD coordinates in advance of publication. We thank B. Messer, D. Maxwell, and the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory supported by the DOE under Contract DE-AC05-00OR22725. We thank the Texas Advanced Computing Center Frontera team, especially D. Stanzione and T. Cockerill, and for compute time made available through a Director's Discretionary Allocation (NSF OAC-1818253). We thank the Argonne Leadership Computing Facility supported by the DOE under DE-AC02-06CH11357. We thank the Pittsburgh Supercomputer Center for providing priority queues on Bridges-2 through the XSEDE allocation NSF TG-CHE060063. We thank N. Kern and J. Lee of the CHARMM-GUI support team for help converting topologies between NAMD and GROMACS. We thank J. Copperman, G. Simpson, D. Aristoff, and J. Leung for valuable discussions and support from NIH grant GM115805. NAMD and VMD are funded by NIH P41-GM104601. This work was supported by the NSF Center for Aerosol Impacts on Chemistry of the Environment (CAICE), National Science Foundation Center for Chemical Innovation (NSF CHE-1801971), as well as NIH GM132826, NSF RAPID MCB-2032054, an award from the RCSA Research Corp., a UC San Diego Moore's Cancer Center 2020 SARS-CoV-2 seed grant, to R.E.A. This work was also supported by Oracle Cloud credits and related resources provided by the Oracle for Research program. AJM and ASFO receive funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (PREDACTED Advanced Grant, Grant agreement No.: 101021207). \n\nThe author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by National Science Foundation (CHE- 1801971); National Science Foundation (MCB- 2032054); National Science Foundation (OAC-1818253); National Science Foundation (TG-CHE060063); U.S. Department of Energy (DE-AC02-06CH11357); U.S. Department of Energy (DE-AC05- 00OR22725); National Institutes of Health (P41-GM104601); National Institutes of Health (R01-GM132826). \n\nThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.\n\nPublished - 10943420221128233.pdf
", "abstract": "We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.", "date": "2023-01", "date_type": "published", "publication": "International Journal of High Performance Computing Applications", "volume": "37", "number": "1", "publisher": "SAGE Publications", "pagerange": "28-44", "id_number": "CaltechAUTHORS:20221017-15547800.39", "issn": "1094-3420", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221017-15547800.39", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CHE-1801971" }, { "agency": "NSF", "grant_number": "MCB-2032054" }, { "agency": "NSF", "grant_number": "OAC-1818253" }, { "agency": "NSF", "grant_number": "TG-CHE060063" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-06CH11357" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC05-00OR22725" }, { "agency": "NIH", "grant_number": "P41-GM104601" }, { "agency": "NIH", "grant_number": "R01-GM132826" }, { "agency": "European Research Council (ERC)", "grant_number": "101021207" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1177/10943420221128233", "pmcid": "PMC9527558", "primary_object": { "basename": "10943420221128233.pdf", "url": "https://authors.library.caltech.edu/records/rhktp-a6270/files/10943420221128233.pdf" }, "pub_year": "2023", "author_list": "Dommer, Abigail; Casalino, Lorenzo; et al." }, { "id": "https://authors.library.caltech.edu/records/00s15-xar08", "eprint_id": 117825, "eprint_status": "archive", "datestamp": "2023-10-25 15:58:49", "lastmod": "2025-11-20 22:10:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winnett-Alexander-Viloria", "name": { "family": "Winnett", "given": "Alexander Viloria" }, "orcid": "0000-0002-7338-5605" }, { "id": "Porter-Michael-K", "name": { "family": "Porter", "given": "Michael K." }, "orcid": "0000-0002-0777-7563" }, { "id": "Romano-Anne-E", "name": { "family": "Romano", "given": "Anna E." }, "orcid": "0000-0002-7148-0668" }, { "id": "Savela-Emily-S", "name": { "family": "Savela", "given": "Emily S." }, "orcid": "0000-0001-9614-4276" }, { "id": "Akana-Reid", "name": { "family": "Akana", "given": "Reid" }, "orcid": "0000-0003-4422-587X" }, { "id": "Shelby-Natasha", "name": { "family": "Shelby", "given": "Natasha" }, "orcid": "0000-0001-9097-3663" }, { "id": "Reyes-Jessica-A", "name": { "family": "Reyes", "given": "Jessica A." }, "orcid": "0000-0002-5507-7633" }, { "id": "Schlenker-Noah-W", "name": { "family": "Schlenker", "given": "Noah W." }, "orcid": "0000-0002-8581-4403" }, { "id": "Cooper-Matthew-M", "name": { "family": "Cooper", "given": "Matthew M." }, "orcid": "0000-0002-5868-5159" }, { "id": "Carter-Alyssa-M", "name": { "family": "Carter", "given": "Alyssa M." }, "orcid": "0000-0002-2776-9421" }, { "id": "Ji-Jenny", "name": { "family": "Ji", "given": "Jenny" }, "orcid": "0000-0002-7901-5605" }, { "id": "Barlow-Jacob-T", "name": { "family": "Barlow", "given": "Jacob T." }, "orcid": "0000-0002-1842-4835" }, { "id": "Tognazzini-Colten", "name": { "family": "Tognazzini", "given": "Colten" }, "orcid": "0000-0002-2754-3588" }, { "id": "Feaster-Matthew", "name": { "family": "Feaster", "given": "Matthew" }, "orcid": "0000-0001-9966-2845" }, { "id": "Goh-Ying-Ying", "name": { "family": "Goh", "given": "Ying-Ying" }, "orcid": "0000-0001-5136-7214" }, { "id": "Ismagilov-R-F", "name": { "family": "Ismagilov", "given": "Rustem F." }, "orcid": "0000-0002-3680-4399" } ] }, "title": "Morning SARS-CoV-2 Testing Yields Better Detection of Infection Due to Higher Viral Loads in Saliva and Nasal Swabs upon Waking", "ispublished": "pub", "full_text_status": "public", "keywords": "Infectious Diseases; Cell Biology; Microbiology (medical); Genetics; General Immunology and Microbiology; Ecology; Physiology", "note": "We sincerely thank the study participants for making this work possible. We thank Lauriane Quenee, Grace Fisher-Adams, Junie Hildebrandt, Megan Hyashi, RuthAnne Bevier, Chantal D'Apuzzo, Ralph Adolphs, Victor Rivera, Steve Chapman, Gary Waters, Leonard Edwards, Gaylene Ursua, Cynthia Ramos, and Shannon Yamashita for their assistance and advice on study implementation and/or administration. We thank Jessica Leong, Jessica Slagle, Mika Walton, Angel Navarro, Daniel Brenner, Ojas Pradhan, Si Hyung Jin, and Mary Arrastia for volunteering their time to help with this study. We thank Angie Cheng, Susan Magdaleno, Christian Kis, Monica Herrera, and Zaina Lemeir for technical discussions regarding saliva extraction and detection. We thank Jennifer Fulcher, Debika Bhattacharya, and Matthew Bidwell Goetz for their ideas on potential study populations and early study design. We thank Omai Garner and David Beenhouwer for providing materials for initial nasal swab validation. We thank Martin Hill, Alma Sanchez, Scott Kim, Debbie Noble, Nina Paddock, Whitney Harrison, Emily Holman, Isaac Turner, Vivek Desai, Luke Wade, Tom Mayell, Stu Miller, Jennifer Howes, and Nari Shin for their support with recruitment. We thank Allison Rhines, Karen Heichman, and Dan Wattendorf for valuable discussions and guidance. We thank David Prober for discussions of circadian rhythms and feedback on the manuscript. Finally, we thank all the case investigators and contact tracers at the Pasadena Public Health Department, the City of Long Beach Department of Health & Human Services, and Caltech Student Wellness Services for their efforts in study recruitment and their work in the pandemic response.\n\nR.F.I. is a cofounder, consultant, and a director and has stock ownership of Talis Biomedical Corp.\n\nThis study is based on research funded in part by the Bill & Melinda Gates Foundation (INV-023124). The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation. This work was also funded by the Ronald and Maxine Linde Center for New Initiatives at the California Institute of Technology and the Jacobs Institute for Molecular Engineering for Medicine at the California Institute of Technology. A.V.W. is supported by a UCLA DGSOM Geffen Fellowship, and M.M.C. is supported by a Caltech Graduate Student Fellowship.", "abstract": "Optimizing specimen collection methods to achieve the most reliable SARS-CoV-2 detection for a given diagnostic sensitivity would improve testing and minimize COVID-19 outbreaks. From September 2020 to April 2021, we performed a household-transmission study in which participants self-collected specimens every morning and evening throughout acute SARS-CoV-2 infection. Seventy mildly symptomatic participants collected saliva, and of those, 29 also collected nasal swab specimens. Viral load was quantified in 1,194 saliva and 661 nasal swab specimens using a high-analytical-sensitivity reverse transcription-quantitative PCR (RT-qPCR) assay. Viral loads in both saliva and nasal swab specimens were significantly higher in morning-collected specimens than in evening-collected specimens after symptom onset. This aspect of the biology of SARS-CoV-2 infection has implications for diagnostic testing. We infer that morning collection would have resulted in significantly improved detection and that this advantage would be most pronounced for tests with low to moderate analytical sensitivity. Collecting specimens for COVID-19 testing in the morning offers a simple and low-cost improvement to clinical diagnostic sensitivity of low- to moderate-analytical-sensitivity tests.\n\nImportance: Our findings suggest that collecting saliva and nasal swab specimens in the morning immediately after waking yields higher SARS-CoV-2 viral loads than collection later in the day. The higher viral loads from morning specimen collection are predicted to significantly improve detection of SARS-CoV-2 in symptomatic individuals, particularly when using moderate- to low-analytical-sensitivity COVID-19 diagnostic tests, such as rapid antigen tests.", "date": "2022-12-21", "date_type": "published", "publication": "Microbiology Spectrum", "volume": "10", "number": "6", "publisher": "American Society for Microbiology", "pagerange": "e03873-22", "id_number": "CaltechAUTHORS:20221110-430693700.10", "issn": "2165-0497", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221110-430693700.10", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-023124" }, { "agency": "Ronald and Maxine Linde Center for New Initiatives" }, { "agency": "Jacobs Institute for Molecular Engineering for Medicine" }, { "agency": "UCLA" }, { "agency": "Caltech" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Jacobs-Institute-for-Molecular-Engineering-for-Medicine" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/spectrum.03873-22", "pmcid": "PMC9769854", "primary_object": { "basename": "jhaveri-et-al-2022-morning-sars-cov-2-testing-yields-better-detection-of-infection-due-to-higher-viral-loads-in-saliva.pdf", "url": "https://authors.library.caltech.edu/records/00s15-xar08/files/jhaveri-et-al-2022-morning-sars-cov-2-testing-yields-better-detection-of-infection-due-to-higher-viral-loads-in-saliva.pdf" }, "related_objects": [ { "basename": "spectrum.03873-22-s0001.pdf", "url": "https://authors.library.caltech.edu/records/00s15-xar08/files/spectrum.03873-22-s0001.pdf" } ], "pub_year": "2022", "author_list": "Winnett, Alexander Viloria; Porter, Michael K.; et al." }, { "id": "https://authors.library.caltech.edu/records/hvpcx-02f07", "eprint_id": 118815, "eprint_status": "archive", "datestamp": "2023-10-09 21:20:05", "lastmod": "2025-11-20 22:31:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fan-Chengcheng", "name": { "family": "Fan", "given": "Chengcheng" }, "orcid": "0000-0003-4213-5758" }, { "id": "Cohen-Alexander-A", "name": { "family": "Cohen", "given": "Alexander A." }, "orcid": "0000-0002-2818-656X" }, { "id": "Park-Miso", "name": { "family": "Park", "given": "Miso" }, "orcid": "0000-0001-9914-4351" }, { "id": "Hung-Alfur-Fu-Hsin", "name": { "family": "Hung", "given": "Alfur Fu-Hsin" } }, { "id": "Keeffe-Jennifer-R", "name": { "family": "Keeffe", "given": "Jennifer R." }, "orcid": "0000-0002-5317-6398" }, { "id": "Gnanapragasam-Priyanthi-N-P", "name": { "family": "Gnanapragasam", "given": "Priyanthi N. P." } }, { "id": "Lee-Yu-Erica", "name": { "family": "Lee", "given": "Yu E." }, "orcid": "0000-0001-5989-326X" }, { "id": "Gao-Han", "name": { "family": "Gao", "given": "Han" } }, { "id": "Kakutani-Leesa-M", "name": { "family": "Kakutani", "given": "Leesa M." }, "orcid": "0000-0003-3822-7449" }, { "id": "Wu-Ziyan", "name": { "family": "Wu", "given": "Ziyan" }, "orcid": "0000-0002-6378-2949" }, { "id": "Kleanthous-Harry", "name": { "family": "Kleanthous", "given": "Harry" }, "orcid": "0000-0001-7115-235X" }, { "id": "Malecek-Kathryn-E", "name": { "family": "Malecek", "given": "Kathryn E." } }, { "id": "Williams-John-C", "name": { "family": "Williams", "given": "John C." }, "orcid": "0000-0002-0522-384X" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes", "ispublished": "pub", "full_text_status": "public", "keywords": "Infectious Diseases; Immunology; Immunology and Allergy", "note": "\u00a9 2022 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nWe thank J. Vielmetter, P. Hoffman, A. Rorick, K. Storm, and the Caltech Beckman Institute Protein Expression Center for protein production; D. Veesler for BtKY72 neutralization advice; A. Gonzales for isolation and sequencing of positive B cells; the Antibody Discovery Engine and the Drug Discovery and Structural Biology Shared Facility at City of Hope, Songye Chen, and the Caltech Cryo-EM facility for cryo-EM data collection; Jens Kaiser, staff at Stanford Synchrotron Radiation Lightsource, and the Caltech Molecular Observatory for X-ray data collection support; and the Bjorkman lab members for helpful discussions. Cryo-EM was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by the National Institutes of Health, National Institute of General Medical Sciences (P30GM133894). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. These studies were funded by the National Institutes of Health (NIH) P01-AI138938-S1 (P.J.B.) and City of Hope's Integrated Drug Development Venture supported by the National Cancer Institute of the National Institutes of Health P30 CA033572 (J.C.W.), Bill and Melinda Gates Foundation INV-034638, INV-004949 (P.J.B.), the Caltech Merkin Institute (P.J.B.), and a George Mason University Fast Grant (P.J.B.). \n\nAuthor contributions. C.F., A.A.C., J.R.K., H.K., J.C.W., and P.J.B. conceived the study and analyzed the data. C.F. performed single-particle cryo-EM, X-ray crystallography, interpreted structures, and analyzed antibody sequences. A.A.C. prepared nanoparticles and performed negative stain EM. M.P. and A.F.-H.H. isolated B cells and generated mAb sequences. C.F., Y.E.L., and H.G. prepared and purified proteins. A.A.C., J.R.K., and Z.W. performed ELISAs. P.N.P.G. and L.M.K. performed neutralization assays. J.R.K. and C.F. performed SPR assays. C.F., J.R.K., K.E.M., and P.J.B. wrote the paper with contributions from other authors. \n\nData and code availability. Atomic models and cryo-EM maps generated from cryo-EM studies of the M8a-3\u2013WA1 spike 6P, M8a-6\u2013WA1 spike 6P, M8a-28\u2013WA1 spike 6P, M8a-31\u2013WA1 spike 6P, M8a-31\u2013Omicron BA.1 spike 6P, M8a-34\u2013WA1 spike 6P, HSW-1\u2013WA1 spike 6P, and HSW-2\u2013WA1 spike S1 domain complexes have been deposited at the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) under the following accession codes: PDB: 7UZ4, 7UZ5, 7UZ6, 7UZ7, 7UZ8, 7UZ9, 7UZA, and 7UZB; EMDB: EMD-26878, EMD-26879, EMD-26880, EMD-26881, EMD-26882, EMD-26883, EMD-26884, and EMD-26885. Atomic models generated from crystal structures of M8a-34\u2013RBD and HSW-2\u2013RBD complexes have been deposited at the PDB under accession codes PDB: 7UZC and 7UZD, respectively. Additional information required to analyze the data reported in this paper is available from the lead contact upon request. \n\nThis paper does not report original code. \n\nP.J.B. serves on the scientific advisory boards for the Vir Biotechnology and Vaccine Company. P.J.B. and A.A.C. are inventors on a US patent application filed by the California Institute of Technology that covers the mosaic nanoparticles described in this work. P.J.B. and A.A.C. are inventors on a US patent application filed by the California Institute of Technology that covers the methodology to generate cross-reactive antibodies using mosaic nanoparticles. P.J.B., A.A.C., C.F., and J.C.W. are inventors on a US patent application filed by the California Institute of Technology that covers the mAbs elicited by vaccination with mosaic-8 RBD-mi3 nanoparticles described in this work. P.J.B., A.A.C., and J.R.K. are inventors on a US patent application filed by the California Institute of Technology that covers the methods of isolating cross-reactive antibodies by vaccination with mosaic nanoparticles. \n\nWe support inclusive, diverse, and equitable conduct of research.\n\nPublished - main.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.pdf
", "abstract": "Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.", "date": "2022-12-13", "date_type": "published", "publication": "Immunity", "volume": "55", "number": "12", "publisher": "Cell Press", "pagerange": "2419-2435.e10", "id_number": "CaltechAUTHORS:20230117-369491100.9", "issn": "1074-7613", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230117-369491100.9", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-76SF00515" }, { "agency": "NIH", "grant_number": "P30GM133894" }, { "agency": "NIH", "grant_number": "P01-AI138938-S1" }, { "agency": "NIH", "grant_number": "P30 CA033572" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-034638" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-004949" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "George Mason University" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.immuni.2022.10.019", "pmcid": "PMC9606073", "primary_object": { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/hvpcx-02f07/files/main.pdf" }, "related_objects": [ { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/hvpcx-02f07/files/mmc1.pdf" }, { "basename": "mmc2.pdf", "url": "https://authors.library.caltech.edu/records/hvpcx-02f07/files/mmc2.pdf" } ], "pub_year": "2022", "author_list": "Fan, Chengcheng; Cohen, Alexander A.; et al." }, { "id": "https://authors.library.caltech.edu/records/0tw65-n3m21", "eprint_id": 117477, "eprint_status": "archive", "datestamp": "2023-08-22 18:17:56", "lastmod": "2025-11-20 17:58:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cable-Jennifer", "name": { "family": "Cable", "given": "Jennifer" } }, { "name": { "family": "Fauci", "given": "Anthony" }, "orcid": "0000-0002-7865-7235" }, { "name": { "family": "Dowling", "given": "William E." } }, { "name": { "family": "G\u00fcnther", "given": "Stephan" }, "orcid": "0000-0002-6562-0230" }, { "id": "Bente-Dennis-A", "name": { "family": "Bente", "given": "Dennis A." }, "orcid": "0000-0002-5150-7368" }, { "name": { "family": "Yadav", "given": "Pragya Dhruv" }, "orcid": "0000-0002-0861-7166" }, { "name": { "family": "Madoff", "given": "Lawrence C." }, "orcid": "0000-0003-2589-7777" }, { "name": { "family": "Wang", "given": "Lin-Fa" }, "orcid": "0000-0003-2752-0535" }, { "name": { "family": "Arora", "given": "Rahul K." }, "orcid": "0000-0003-3526-6338" }, { "name": { "family": "Van Kerkhove", "given": "Maria" }, "orcid": "0000-0002-6135-0018" }, { "name": { "family": "Chu", "given": "May C." }, "orcid": "0000-0002-7896-0496" }, { "name": { "family": "Jaenisch", "given": "Thomas" }, "orcid": "0000-0001-8252-7444" }, { "name": { "family": "Epstein", "given": "Jonathan H." }, "orcid": "0000-0002-1373-9301" }, { "name": { "family": "Frost", "given": "Simon David William" } }, { "name": { "family": "Bausch", "given": "Daniel G." }, "orcid": "0000-0002-7209-6983" }, { "name": { "family": "Hensley", "given": "Lisa E." }, "orcid": "0000-0003-1188-4342" }, { "name": { "family": "Bergeron", "given": "\u00c9ric" }, "orcid": "0000-0003-3398-8628" }, { "name": { "family": "Sitaras", "given": "Ioannis" }, "orcid": "0000-0003-0161-8024" }, { "name": { "family": "Gunn", "given": "Michael D." }, "orcid": "0000-0003-4602-0667" }, { "name": { "family": "Geisbert", "given": "Thomas W." }, "orcid": "0000-0003-0858-1877" }, { "name": { "family": "Mu\u00f1oz-Fontela", "given": "C\u00e9sar" }, "orcid": "0000-0002-7725-2586" }, { "name": { "family": "Krammer", "given": "Florian" }, "orcid": "0000-0003-4121-776X" }, { "name": { "family": "de Wit", "given": "Emmie" }, "orcid": "0000-0002-9763-7758" }, { "name": { "family": "Nordenfelt", "given": "Pontus" }, "orcid": "0000-0002-9481-9951" }, { "name": { "family": "Saphire", "given": "Erica Ollmann" }, "orcid": "0000-0002-1206-7451" }, { "name": { "family": "Gilbert", "given": "Sarah C." } }, { "name": { "family": "Corbett", "given": "Kizzmekia S." }, "orcid": "0000-0002-2641-4688" }, { "name": { "family": "Branco", "given": "Luis M." } }, { "name": { "family": "Baize", "given": "Sylvain" }, "orcid": "0000-0002-3234-7477" }, { "name": { "family": "van Doremalen", "given": "Neeltje" }, "orcid": "0000-0003-4368-6359" }, { "name": { "family": "Krieger", "given": "Marco A." }, "orcid": "0000-0003-0030-3952" }, { "name": { "family": "Costa Clemens", "given": "Sue Ann" }, "orcid": "0000-0001-9576-0878" }, { "name": { "family": "Hesselink", "given": "Renske" } }, { "name": { "family": "Hartman", "given": "Dan" } } ] }, "title": "Lessons from the pandemic: Responding to emerging zoonotic viral diseases \u2014 a Keystone Symposia report", "ispublished": "pub", "full_text_status": "public", "keywords": "History and Philosophy of Science; General Biochemistry, Genetics and Molecular Biology; General Neuroscience", "note": "Funding Information: National Institute of Allergy and Infectious Diseases; Canadian Medical Association; Public Health Agency of Canada; Robert Koch Institute; German Federal Ministry of Health COVID-19 Research and Development; WHO Solidarity Response Fund\n\nR.K.A. and M.V.K. presented work funded by the WHO Solidarity Response Fund and the German Federal Ministry of Health COVID\u201019 Research and Development. R.K.A. would also like to thank the following additional funders of SeroTracker's SARS\u2010CoV\u20102 evidence synthesis efforts: the Public Health Agency of Canada through Canada's COVID\u201019 Immunity Task Force, the Robert Koch Institute, and the Canadian Medical Association Joule Innovation Fund. M.V.K. is employed by the WHO; the authors alone are responsible for the views expressed in this publication and they do not necessarily represent the decisions, policies, or views of WHO. E.d.W. and N.v.D. are supported by the Intramural Research Program of NIAID, NIH.", "abstract": "The COVID\u201019 pandemic caught the world largely unprepared, including scientific and policy communities. On April 10\u201313, 2022, researchers across academia, industry, government, and nonprofit organizations met at the Keystone symposium \"Lessons from the Pandemic: Responding to Emerging Zoonotic Viral Diseases\" to discuss the successes and challenges of the COVID\u201019 pandemic and what lessons can be applied moving forward. Speakers focused on experiences not only from the COVID\u201019 pandemic but also from outbreaks of other pathogens, including the Ebola virus, Lassa virus, and Nipah virus. A general consensus was that investments made during the COVID\u201019 pandemic in infrastructure, collaborations, laboratory and manufacturing capacity, diagnostics, clinical trial networks, and regulatory enhancements \u2014 notably, in low\u2010to\u2010middle income countries \u2014 must be maintained and strengthened to enable quick, concerted responses to future threats, especially to zoonotic pathogens.", "date": "2022-12", "date_type": "published", "publication": "Annals of the New York Academy of Sciences", "volume": "1518", "number": "1", "publisher": "New York Academy of Sciences", "pagerange": "209-225", "id_number": "CaltechAUTHORS:20221017-15547800.42", "issn": "0077-8923", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221017-15547800.42", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute of Allergy and Infectious Diseases" }, { "agency": "Canadian Medical Association" }, { "agency": "Public Health Agency of Canada" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1111/nyas.14898", "pmcid": "PMC9538336", "pub_year": "2022", "author_list": "Cable, Jennifer; Fauci, Anthony; et al." }, { "id": "https://authors.library.caltech.edu/records/nf9sb-7xa18", "eprint_id": 116217, "eprint_status": "archive", "datestamp": "2023-08-22 17:48:52", "lastmod": "2025-11-20 19:41:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Satta-Sandro", "name": { "family": "Satta", "given": "Sandro" } }, { "id": "Shahabipour-Fahimeh", "name": { "family": "Shahabipour", "given": "Fahimeh" } }, { "id": "Gao-Wei", "name": { "family": "Gao", "given": "Wei" }, "orcid": "0000-0002-8503-4562" }, { "id": "Lentz-Steven-R", "name": { "family": "Lentz", "given": "Steven R." } }, { "id": "Perlman-Stanley", "name": { "family": "Perlman", "given": "Stanley" } }, { "id": "Ashammakhi-Nureddin", "name": { "family": "Ashammakhi", "given": "Nureddin" } }, { "id": "Hsiai-Tzung-K", "name": { "family": "Hsiai", "given": "Tzung" }, "orcid": "0000-0003-1734-0792" } ] }, "title": "Engineering viral genomics and nano-liposomes in microfluidic platforms for patient-specific analysis of SARS-CoV-2 variants", "ispublished": "pub", "full_text_status": "public", "keywords": "Organ on-a-chip, microfluidics, viral genomics, mutations, variants of concerns, COVID-19, nano-liposomes; Pharmacology, Toxicology and Pharmaceutics (miscellaneous); Medicine (miscellaneous)", "note": "\u00a9 2022 The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). \n\nReceived: 2022.02.23; Accepted: 2022.04.21; Published: 2022.06.06. \n\nThe authors acknowledge that they have no competing interests. The authors also acknowledge funding sources from National Institutes of Health (1UG3TR003148, R01HL111437, R01HL129727), the American Heart Association (COVID-19 Rapid Response Award 20203858), California Institute for Regenerative Medicine (Grant Number DISC2COVID19-11838), UCLA David Geffen School of Medicine - Oversight COVID-19 Research Committee (OCRC) (Award Number: OCRC #45). The authors also acknowledge that some of the figures have been created or adapted using BioRender.com. \n\nThe authors have declared that no competing interest exists.\n\nPublished - v12p4779.pdf
", "abstract": "New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuing to spread globally, contributing to the persistence of the COVID-19 pandemic. Increasing resources have been focused on developing vaccines and therapeutics that target the Spike glycoprotein of SARS-CoV-2. Recent advances in microfluidics have the potential to recapitulate viral infection in the organ-specific platforms, known as organ-on-a-chip (OoC), in which binding of SARS-CoV-2 Spike protein to the angiotensin-converting enzyme 2 (ACE2) of the host cells occurs. As the COVID-19 pandemic lingers, there remains an unmet need to screen emerging mutations, to predict viral transmissibility and pathogenicity, and to assess the strength of neutralizing antibodies following vaccination or reinfection. Conventional detection of SARS-CoV-2 variants relies on two-dimensional (2-D) cell culture methods, whereas simulating the micro-environment requires three-dimensional (3-D) systems. To this end, analyzing SARS-CoV-2-mediated pathogenicity via microfluidic platforms minimizes the experimental cost, duration, and optimization needed for animal studies, and obviates the ethical concerns associated with the use of primates. In this context, this review highlights the state-of-the-art strategy to engineer the nano-liposomes that can be conjugated with SARS-CoV-2 Spike mutations or genomic sequences in the microfluidic platforms; thereby, allowing for screening the rising SARS-CoV-2 variants and predicting COVID-19-associated coagulation. Furthermore, introducing viral genomics to the patient-specific blood accelerates the discovery of therapeutic targets in the face of evolving viral variants, including B1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), c.37 (Lambda), and B.1.1.529 (Omicron). Thus, engineering nano-liposomes to encapsulate SARS-CoV-2 viral genomic sequences enables rapid detection of SARS-CoV-2 variants in the long COVID-19 era.", "date": "2022-10", "date_type": "published", "publication": "Theranostics", "volume": "12", "number": "10", "publisher": "Ivyspring International Publisher", "pagerange": "4779-4790", "id_number": "CaltechAUTHORS:20220810-254276000", "issn": "1838-7640", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220810-254276000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1UG3TR003148" }, { "agency": "NIH", "grant_number": "R01HL111437" }, { "agency": "NIH", "grant_number": "R01HL129727" }, { "agency": "American Heart Association", "grant_number": "COVID-19 Rapid Response Award 20203858" }, { "agency": "California Institute for Regenerative Medicine (CIRM)", "grant_number": "DISC2COVID19-11838" }, { "agency": "UCLA Oversight COVID-19 Research Committee", "grant_number": "OCRC 45" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.7150/thno.72339", "pmcid": "PMC9254234", "primary_object": { "basename": "v12p4779.pdf", "url": "https://authors.library.caltech.edu/records/nf9sb-7xa18/files/v12p4779.pdf" }, "pub_year": "2022", "author_list": "Satta, Sandro; Shahabipour, Fahimeh; et al." }, { "id": "https://authors.library.caltech.edu/records/fkzdk-46b82", "eprint_id": 118343, "eprint_status": "archive", "datestamp": "2023-08-22 17:37:04", "lastmod": "2025-11-21 02:02:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Karthikeyan-Smruthi", "name": { "family": "Karthikeyan", "given": "Smruthi" }, "orcid": "0000-0001-6226-4536" }, { "name": { "family": "Levy", "given": "Joshua I." }, "orcid": "0000-0001-7573-7793" }, { "name": { "family": "De Hoff", "given": "Peter" } }, { "name": { "family": "Humphrey", "given": "Greg" } }, { "name": { "family": "Birmingham", "given": "Amanda" } }, { "name": { "family": "Jepsen", "given": "Kristen" } }, { "name": { "family": "Farmer", "given": "Sawyer" } }, { "name": { "family": "Tubb", "given": "Helena M." } }, { "name": { "family": "Valles", "given": "Tommy" } }, { "name": { "family": "Tribelhorn", "given": "Caitlin E." } }, { "name": { "family": "Tsai", "given": "Rebecca" } }, { "name": { "family": "Aigner", "given": "Stefan" } }, { "name": { "family": "Sathe", "given": "Shashank" } }, { "name": { "family": "Moshiri", "given": "Niema" } }, { "name": { "family": "Henson", "given": "Benjamin" } }, { "name": { "family": "Mark", "given": "Adam M." } }, { "name": { "family": "Hakim", "given": "Abbas" } }, { "name": { "family": "Baer", "given": "Nathan A." } }, { "name": { "family": "Barber", "given": "Tom" } }, { "name": { "family": "Belda-Ferre", "given": "Pedro" }, "orcid": "0000-0001-6532-1161" }, { "name": { "family": "Chac\u00f3n", "given": "Marisol" } }, { "name": { "family": "Cheung", "given": "Willi" } }, { "name": { "family": "Cresini", "given": "Evelyn S." } }, { "name": { "family": "Eisner", "given": "Emily R." } }, { "name": { "family": "Lastrella", "given": "Alma L." } }, { "name": { "family": "Lawrence", "given": "Elijah S." } }, { "name": { "family": "Marotz", "given": "Clarisse A." } }, { "name": { "family": "Ngo", "given": "Toan T." } }, { "name": { "family": "Ostrander", "given": "Tyler" } }, { "name": { "family": "Plascencia", "given": "Ashley" } }, { "name": { "family": "Salido", "given": "Rodolfo A." } }, { "name": { "family": "Seaver", "given": "Phoebe" } }, { "name": { "family": "Smoot", "given": "Elizabeth W." } }, { "name": { "family": "McDonald", "given": "Daniel" }, "orcid": "0000-0003-0876-9060" }, { "name": { "family": "Neuhard", "given": "Robert M." } }, { "name": { "family": "Scioscia", "given": "Angela L." } }, { "name": { "family": "Satterlund", "given": "Alysson M." } }, { "name": { "family": "Simmons", "given": "Elizabeth H." }, "orcid": "0000-0002-0646-3458" }, { "name": { "family": "Abelman", "given": "Dismas B." } }, { "name": { "family": "Brenner", "given": "David" } }, { "name": { "family": "Bruner", "given": "Judith C." } }, { "name": { "family": "Buckley", "given": "Anne" } }, { "name": { "family": "Ellison", "given": "Michael" } }, { "name": { "family": "Gattas", "given": "Jeffrey" } }, { "name": { "family": "Gonias", "given": "Steven L." } }, { "name": { "family": "Hale", "given": "Matt" } }, { "name": { "family": "Hawkins", "given": "Faith" } }, { "name": { "family": "Ikeda", "given": "Lydia" } }, { "name": { "family": "Jhaveri", "given": "Hemlata" } }, { "name": { "family": "Johnson", "given": "Ted" } }, { "name": { "family": "Kellen", "given": "Vince" } }, { "name": { "family": "Kremer", "given": "Brendan" } }, { "name": { "family": "Matthews", "given": "Gary" } }, { "name": { "family": "McLawhon", "given": "Ronald W." } }, { "name": { "family": "Ouillet", "given": "Pierre" } }, { "name": { "family": "Park", "given": "Daniel" } }, { "name": { "family": "Pradenas", "given": "Allorah" } }, { "name": { "family": "Reed", "given": "Sharon" } }, { "name": { "family": "Riggs", "given": "Lindsay" } }, { "name": { "family": "Sanders", "given": "Alison" } }, { "name": { "family": "Sollenberger", "given": "Bradley" } }, { "name": { "family": "Song", "given": "Angela" } }, { "name": { "family": "White", "given": "Benjamin" } }, { "name": { "family": "Winbush", "given": "Terri" } }, { "name": { "family": "Aceves", "given": "Christine M." } }, { "name": { "family": "Anderson", "given": "Catelyn" } }, { "name": { "family": "Gangavarapu", "given": "Karthik" } }, { "name": { "family": "Hufbauer", "given": "Emory" } }, { "name": { "family": "Kurzban", "given": "Ezra" } }, { "name": { "family": "Lee", "given": "Justin" }, "orcid": "0000-0002-3657-4386" }, { "name": { "family": "Matteson", "given": "Nathaniel L." } }, { "name": { "family": "Parker", "given": "Edyth" } }, { "name": { "family": "Perkins", "given": "Sarah A." }, "orcid": "0000-0002-0557-3102" }, { "name": { "family": "Ramesh", "given": "Karthik S." } }, { "name": { "family": "Robles-Sikisaka", "given": "Refugio" } }, { "name": { "family": "Schwab", "given": "Madison A." }, "orcid": "0000-0003-0748-1858" }, { "name": { "family": "Spencer", "given": "Emily" } }, { "name": { "family": "Wohl", "given": "Shirlee" } }, { "name": { "family": "Nicholson", "given": "Laura" }, "orcid": "0000-0002-1761-0951" }, { "name": { "family": "McHardy", "given": "Ian H." }, "orcid": "0000-0002-2121-5460" }, { "name": { "family": "Dimmock", "given": "David P." }, "orcid": "0000-0001-6690-2523" }, { "name": { "family": "Hobbs", "given": "Charlotte A." } }, { "name": { "family": "Bakhtar", "given": "Omid" } }, { "name": { "family": "Harding", "given": "Aaron" } }, { "name": { "family": "Mendoza", "given": "Art" } }, { "name": { "family": "Bolze", "given": "Alexandre" }, "orcid": "0000-0001-7399-2766" }, { "name": { "family": "Becker", "given": "David" } }, { "name": { "family": "Cirulli", "given": "Elizabeth T." } }, { "name": { "family": "Isaksson", "given": "Magnus" }, "orcid": "0000-0001-6278-0522" }, { "name": { "family": "Schiabor Barrett", "given": "Kelly M." }, "orcid": "0000-0001-6194-787X" }, { "name": { "family": "Washington", "given": "Nicole L." }, "orcid": "0000-0001-8936-9143" }, { "name": { "family": "Malone", "given": "John D." } }, { "name": { "family": "Murphy Schafer", "given": "Ashleigh" }, "orcid": "0000-0002-5131-8399" }, { "name": { "family": "Gurfield", "given": "Nikos" } }, { "name": { "family": "Stous", "given": "Sarah" } }, { "name": { "family": "Fielding-Miller", "given": "Rebecca" }, "orcid": "0000-0002-5099-0589" }, { "name": { "family": "Garfein", "given": "Richard S." } }, { "name": { "family": "Gaines", "given": "Tommi" } }, { "name": { "family": "Anderson", "given": "Cheryl" } }, { "name": { "family": "Martin", "given": "Natasha K." } }, { "name": { "family": "Schooley", "given": "Robert" }, "orcid": "0000-0002-2498-8426" }, { "name": { "family": "Austin", "given": "Brett" } }, { "name": { "family": "MacCannell", "given": "Duncan R." } }, { "name": { "family": "Kingsmore", "given": "Stephen F." } }, { "name": { "family": "Lee", "given": "William" } }, { "name": { "family": "Shah", "given": "Seema" } }, { "name": { "family": "McDonald", "given": "Eric" } }, { "name": { "family": "Yu", "given": "Alexander T." } }, { "name": { "family": "Zeller", "given": "Mark" } }, { "name": { "family": "Fisch", "given": "Kathleen M." } }, { "name": { "family": "Longhurst", "given": "Christopher" }, "orcid": "0000-0003-4908-6856" }, { "name": { "family": "Maysent", "given": "Patty" } }, { "name": { "family": "Pride", "given": "David" } }, { "name": { "family": "Khosla", "given": "Pradeep K." } }, { "name": { "family": "Laurent", "given": "Louise C." } }, { "name": { "family": "Yeo", "given": "Gene W." }, "orcid": "0000-0002-0799-6037" }, { "name": { "family": "Andersen", "given": "Kristian G." }, "orcid": "0000-0001-6431-5982" }, { "name": { "family": "Knight", "given": "Rob" }, "orcid": "0000-0002-0975-9019" } ] }, "title": "Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "We thank L. Asato and the Microbiology Laboratory at the SD Public Utilities Department for providing us with county wastewater samples; UCSD's Return to Learn (RTL) program for funding the campus-wide wastewater surveillance efforts; J. Kayne, R. Cota, J. Ortiz and the Facilities management team at the UCSD; J. Mayer from the Center for Aerosol Impacts on Chemistry of the Environment (CAICE); L. Arnold of the Campus Research Machine Shop (CRMS) for assistance with the installation and operation of the autosamplers; R. Jacobs, S. Knepple and their team at UCSD Logistics for assisting with our daily sampling efforts; B. Pollak and the UCSD Information Technology Services team for assisting with the daily notifications; the Office of Academic Affairs for contact tracing and targeted campus messaging assistance; J. Severson, P. Hochstein, the UCSD HDH team and the UCSD Environmental Health and Safety personnel; J. Gilbert and the Microbiome Sample Processing Core at UCSD for access to qPCR equipment; the CDC SPHERES consortium, SEARCH (San Diego Epidemiology and Research for COVID Health) Alliance and members of the Andersen laboratory for discussion and help with logistics; and the healthcare workers, frontline workers and patients who made the collection of this SARS-CoV-2 dataset possible and all those who made genomic data available for analysis via GISAID. This work has been funded by CDC BAA contracts 75D30121P10258 (Helix) and 75D30120C09795 (to G.W.Y., R.K., L.C.L. and K.G.A.), NIH NIAID 3U19AI135995-03S2 (to K.G.A.), U19AI135995 (to K.G.A.), U01AI151812 (to K.G.A.), NIH NCATS UL1TR002550 (to K.G.A.), the Conrad Prebys Foundation (to K.G.A.), NIH 5T32AI007244-38 (to J.I.L.), NIH Pioneer grant 1DP1AT010885 (to R.K), NSF RAPID 2029069 (to R.K.), San Diego County Health and Human Services Agency (to R.F.-M.) and NIH S10OD026929 (to K.J.). The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the CDC and California Department of Public Health or the California Health and Human Services Agency. Use of trade names is for identification only and does not imply endorsement by the CDC. \n\nThese authors contributed equally: Smruthi Karthikeyan, Joshua I. Levy. \n\nThese authors jointly supervised this work: Kristian G. Andersen, Rob Knight. \n\nData availability. All raw wastewater sequencing data are available via the NCBI Sequence Read Archive under the BioProject ID PRJNA819090. Consensus sequences from clinical and wastewater surveillance are all available on GISAID. Spike-in sequencing data are available via Google cloud (https://console.cloud.google.com/storage/browser/search-reference_data). The UCSD campus dashboard can be accessed at https://returntolearn.ucsd.edu/dashboard/. The county wastewater data from Point Loma are available through the public dashboard at https://searchcovid.info/dashboards/wastewater-surveillance/. The SEARCH genomic surveillance dashboard is available at https://searchcovid.info/dashboards/sequencing-statistics/. \n\nCode availability. Freyja is hosted publicly on GitHub (https://github.com/andersen-lab/Freyja) and is available under a BSD-2-Clause license (https://doi.org/10.5281/zenodo.6585067, all versions). Freyja is accessible as a package via bioconda (https://bioconda.github.io/recipes/freyja/README.html) in container form via dockerhub (https://hub.docker.com/r/andersenlabapps/freyja). COVID-19 Viral Epidemiology Workflow (C-VIEW) is available at https://github.com/ucsd-ccbb/C-VIEW as an open-source, end-to-end workflow for viral epidemiology focused on SARS-CoV-2 lineage assignment and phylogenetics. C-VIEW uses minimap2 (v2.17), samtools(v1.11), iVar(v1.3.1) and pangolin (varying versions). \n\nContributions. R.K. and K.G.A. conceptualized the study. S.K., J.I.L., N.K.M., P.D.H., A. Birmingham, S. Sathe, K.M.F., L.C.L., G.W.Y., K.G.A. and R.K. contributed the methodology. J.I.L., D.M., N.M., K.M.F., A. Birmingham, K.J., B.H., S. Sathe, K.G., N.L.M., K.S.R., C.M.A., E.H. and A.M.M. provided software. S.K. and J.I.L. performed formal analysis. S.K., J.I.L., N.M., S.F., H.M.T., T.V., C.E.T., R.T., N.A.B., T.B., M.C., W.C., E.S.C., E.R.E., A. Hakim, G.H., A.L.L., E.S.L., T.T.N., T.O., A. Plascencia, R.A.S., P.S., P.B.-F., E.W.S., S.A., P.D.H., C.A.M., L.C.L., G.W.Y., Cheryl Anderson, E.K., M.A.S., S.A.P., J.L., E.P., M.Z., E.S., R.F.-M., T.G., R.S.G., K.G.A. and R.K. conducted the investigation. Catelyn Anderson, N.K.M., R.M.N., R.S., E.H.S., A.M. Schafer, S.F.K., D.P.D., C.A.H., A.M., S. Strous, B.A., S. Shah, N.G., J.D.M., E.M., I.H.M., A. Harding, O.B., A.M., A. Bolze, K.M.S.B., E.T.C., N.L.W., W.L., M.I., D. Becker, L.N., S.W., M.Z., R.R.-S., R.F.-M., T.G., R.S.G., D.B.A., D. Brenner, J.C.B., A. Buckley, M.E., J.G., S.L.G., M.H., F.H., L.I., H.J., T.J., V.K., B.K., L.R., C.A.H., G.M., P.M., R.F.-M., P.O., D. Park, A. Pradenas, A.M.S., B.S., A. Song, B.W., T.W., S.R., P.K.K., A.T.Y., D.R.M., F.H., G.M., R.W.M. and C.L. provided resources. S.K., J.I.L., P.D.H., G.H., S.F., H.M.T., C.E.T., R.T., T.V., A. Birmingham, N.M., A.M.M. and K.M.F. curated data. S.K., J.I.L., K.G.A. and R.K. wrote the original draft of the manuscript. All authors reviewed and edited the manuscript. S.K. and J.I.L. performed visualization. R.M.N., N.K.M., R.S., A.L.S., E.H.S., A.M. Satterlund, P.D.H., L.C.L., D. Pride, G.W.Y., K.G.A. and R.K. supervised the study. R.M.N., N.K.M., R.S., A.L.S., E.H.S., A.M. Satterlund, P.D.H., L.C.L., G.W.Y., K.G.A. and R.K. undertook project administration. R.K. and K.G.A. acquired funding. \n\nCompeting interests. A. Bolze, D. Becker, E.T.C., M.I., K.M.S.B., N.L.W. and W.L. are employees of Helix. K.G.A. has received consulting fees for advising on SARS-CoV-2, variants and the COVID-19 pandemic. \n\nNature thanks Timothy Julian and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.", "abstract": "As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1\u20133. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.", "date": "2022-09-01", "date_type": "published", "publication": "Nature", "volume": "609", "number": "7925", "publisher": "Nature Publishing Group", "pagerange": "101-108", "id_number": "CaltechAUTHORS:20221215-539953000.2", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221215-539953000.2", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of California, San Diego" }, { "agency": "Centers for Disease Control and Prevention", "grant_number": "75D30121P10258" }, { "agency": "Centers for Disease Control and Prevention", "grant_number": "75D30120C09795" }, { "agency": "NIH", "grant_number": "3U19AI135995-03S2" }, { "agency": "NIH", "grant_number": "U19AI135995" }, { "agency": "NIH", "grant_number": "U01AI151812" }, { "agency": "NIH", "grant_number": "UL1TR002550" }, { "agency": "Conrad Prebys Foundation" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32AI007244-38" }, { "agency": "NIH", "grant_number": "1DP1AT010885" }, { "agency": "NSF", "grant_number": "AGS-2029069" }, { "agency": "San Diego County" }, { "agency": "NIH", "grant_number": "S10OD026929" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1038/s41586-022-05049-6", "pmcid": "PMC9433318", "pub_year": "2022", "author_list": "Karthikeyan, Smruthi; Levy, Joshua I.; et al." }, { "id": "https://authors.library.caltech.edu/records/w8tyx-7qq38", "eprint_id": 115017, "eprint_status": "archive", "datestamp": "2023-08-22 17:28:39", "lastmod": "2025-11-20 22:17:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ravanfar-Raheleh", "name": { "family": "Ravanfar", "given": "Raheleh" }, "orcid": "0000-0003-2992-0575" }, { "id": "Sheng-Yuling", "name": { "family": "Sheng", "given": "Yuling" } }, { "id": "Shahgholi-Mona", "name": { "family": "Shahgholi", "given": "Mona" }, "orcid": "0000-0002-8879-4305" }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "id": "Jones-Jeff", "name": { "family": "Jones", "given": "Jeff" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Gray-H-B", "name": { "family": "Gray", "given": "Harry B." }, "orcid": "0000-0002-7937-7876" }, { "id": "Winkler-Jay-R", "name": { "family": "Winkler", "given": "Jay R." }, "orcid": "0000-0002-4453-9716" } ] }, "title": "Surface cysteines could protect the SARS-CoV-2 main protease from oxidative damage", "ispublished": "pub", "full_text_status": "public", "keywords": "SARS-CoV-2 main protease; Reactive oxygen species; Cysteine; Inorganic Chemistry; Biochemistry", "note": "\u00a9 2022 Elsevier Inc. \n\nReceived 2 March 2022, Revised 28 April 2022, Accepted 29 May 2022, Available online 2 June 2022. \n\nWe thank Dr. Jennifer Keeffe for assistance with SEC-MALS. Experimental work was performed in the Caltech Mass Spectrometry Laboratory in the Division of Chemistry and Chemical Engineering; and the Beckman Institute Laser Resource Center and Proteome Exploration Laboratory supported by the Arnold and Mabel Beckman Foundation. The work was supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under award number R01DK019038. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.\n\nCRediT authorship contribution statement:\nRaheleh Ravanfar: Investigation, Methodology, Writing \u2013 original draft, Writing \u2013 review & editing. Yuling Sheng: Investigation. Mona Shahgholi: Investigation, Methodology, Writing \u2013 review & editing. Brett Lomenick: Investigation, Methodology, Formal analysis, Writing \u2013 review & editing. Jeff Jones: Investigation, Methodology, Formal analysis, Writing \u2013 review & editing. Tsui-Fen Chou: Writing \u2013 review & editing, Methodology. Harry B. Gray: Funding acquisition, Project administration, Writing \u2013 review & editing. Jay R. Winkler: Conceptualization, Funding acquisition, Project administration, Writing \u2013 review & editing.\n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nPublished - 1-s2.0-S0162013422001751-main.pdf
Supplemental Material - 1-s2.0-S0162013422001751-mmc1.docx
", "abstract": "The SARS-CoV-2 main protease (M\u1d56\u02b3\u1d52) is responsible for cleaving twelve nonstructural proteins from the viral polyprotein. M\u1d56\u02b3\u1d52, a cysteine protease, is characterized by a large number of noncatalytic cysteine (Cys) residues, none involved in disulfide bonds. In the absence of a tertiary-structure stabilizing role for these residues, a possible alternative is that they are involved in redox processes. We report experimental work in support of a proposal that surface cysteines on M^(pro) can protect the active-site Cys145 from oxidation by reactive oxygen species (ROS). In investigations of enzyme kinetics, we found that mutating three surface cysteines to serines did not greatly affect activity, which in turn indicates that these cysteines could protect Cys145 from oxidative damage.", "date": "2022-09", "date_type": "published", "publication": "Journal of Inorganic Biochemistry", "volume": "234", "publisher": "Elsevier", "pagerange": "Art. No. 111886", "id_number": "CaltechAUTHORS:20220603-698843600", "issn": "0162-0134", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220603-698843600", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "NIH", "grant_number": "R01DK019038" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.jinorgbio.2022.111886", "pmcid": "PMC9161685", "primary_object": { "basename": "1-s2.0-S0162013422001751-main.pdf", "url": "https://authors.library.caltech.edu/records/w8tyx-7qq38/files/1-s2.0-S0162013422001751-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0162013422001751-mmc1.docx", "url": "https://authors.library.caltech.edu/records/w8tyx-7qq38/files/1-s2.0-S0162013422001751-mmc1.docx" } ], "pub_year": "2022", "author_list": "Ravanfar, Raheleh; Sheng, Yuling; et al." }, { "id": "https://authors.library.caltech.edu/records/djcpp-84e21", "eprint_id": 116720, "eprint_status": "archive", "datestamp": "2023-08-22 17:26:54", "lastmod": "2025-11-20 19:01:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Harrison-Neil-L", "name": { "family": "Harrison", "given": "Neil L." }, "orcid": "0000-0002-8013-7765" }, { "id": "Abbott-Geoffrey-W", "name": { "family": "Abbott", "given": "Geoffrey W." }, "orcid": "0000-0003-4552-496X" }, { "id": "Gentzsch-Martina", "name": { "family": "Gentzsch", "given": "Martina" }, "orcid": "0000-0002-9435-0321" }, { "id": "Aleksandrov-Andrei", "name": { "family": "Aleksandrov", "given": "Andrei" } }, { "id": "Moroni-Anna", "name": { "family": "Moroni", "given": "Anna" }, "orcid": "0000-0002-1860-406X" }, { "id": "Thiel-Gerhard", "name": { "family": "Thiel", "given": "Gerhard" } }, { "id": "Grant-Stephen", "name": { "family": "Grant", "given": "Stephen" }, "orcid": "0000-0003-0923-8886" }, { "id": "Nichols-Colin-G", "name": { "family": "Nichols", "given": "Colin G." } }, { "id": "Lester-H-A", "name": { "family": "Lester", "given": "Henry A." }, "orcid": "0000-0002-5470-5255" }, { "id": "Hartel-Andreas", "name": { "family": "Hartel", "given": "Andreas" } }, { "id": "Shepard-Kenneth-L", "name": { "family": "Shepard", "given": "Kenneth" }, "orcid": "0000-0003-0665-6775" }, { "id": "Garcia-David-Cabrera", "name": { "family": "Garcia", "given": "David Cabrera" }, "orcid": "0000-0001-9609-9102" }, { "id": "Yazawa-Masayuki", "name": { "family": "Yazawa", "given": "Masayuki" } } ] }, "title": "How many SARS-CoV-2 \"viroporins\" are really ion channels?", "ispublished": "pub", "full_text_status": "public", "keywords": "General Agricultural and Biological Sciences; General Biochemistry, Genetics and Molecular Biology; Medicine (miscellaneous)", "abstract": "The SARS-CoV-2 virus uses a small number of viral proteins to enter host cells and disrupt their activity, including the spike (S), membrane (M), and envelope (E) proteins, as well as a number of accessory proteins of unknown function (Orf3a, Orf8, Orf10, etc.), some of which may function to alter ion flux across membranes. Toft-Bertelsen et al.1 recently reported that the drug amantadine may interact with virally encoded ion channels and proposed that inhibitors of these \"viroporins\" might have therapeutic use in COVID-19. We concur with the idea that the E protein of SARS-CoV-2 can form an ion channel and that amantadine inhibits this channel, but we suggest below that a number of additional specific criteria need to be met in order for SARS-CoV-2 accessory proteins (Orf3a, Orf8, Orf10) to be accepted as having ion channel activity, and that further work will be necessary. This field represents a neglected area of overlap between biophysics and virology that continues to be understudied and underfunded and\nclearly merits greater attention from the relevant funding agencies.", "date": "2022-08-25", "date_type": "published", "publication": "Communications Biology", "volume": "5", "number": "1", "publisher": "Nature Publishing Group", "id_number": "CaltechAUTHORS:20220906-252586000", "issn": "2399-3642", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220906-252586000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM130377" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s42003-022-03669-2", "pub_year": "2022", "author_list": "Harrison, Neil L.; Abbott, Geoffrey W.; et al." }, { "id": "https://authors.library.caltech.edu/records/b0jag-6ds25", "eprint_id": 114269, "eprint_status": "archive", "datestamp": "2023-08-22 17:11:44", "lastmod": "2025-11-21 03:00:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bia\u0142obrzeska-Wioleta", "name": { "family": "Bia\u0142obrzeska", "given": "Wioleta" }, "orcid": "0000-0001-7662-1880" }, { "id": "Ficek-Mateusz", "name": { "family": "Ficek", "given": "Mateusz" }, "orcid": "0000-0003-2334-9697" }, { "id": "Dec-Bart\u0142omiej", "name": { "family": "Dec", "given": "Bart\u0142omiej" }, "orcid": "0000-0001-5103-2000" }, { "id": "Osella-Silvio", "name": { "family": "Osella", "given": "Silvio" }, "orcid": "0000-0001-8541-1914" }, { "id": "Trzaskowski-Batosz", "name": { "family": "Trzaskowski", "given": "Bartosz" }, "orcid": "0000-0003-2385-1476" }, { "id": "Jaramillo-Botero-Andres", "name": { "family": "Jaramillo-Botero", "given": "Andres" }, "orcid": "0000-0003-2844-0756" }, { "id": "Pierpaoli-Mattia", "name": { "family": "Pierpaoli", "given": "Mattia" }, "orcid": "0000-0002-7508-1824" }, { "id": "Rycewicz-Micha\u0142", "name": { "family": "Rycewicz", "given": "Micha\u0142" }, "orcid": "0000-0002-1186-6657" }, { "id": "Dashkevich-Yanina", "name": { "family": "Dashkevich", "given": "Yanina" } }, { "id": "\u0141\u0119ga-Tomasz", "name": { "family": "\u0141\u0119ga", "given": "Tomasz" } }, { "id": "Malinowska-Natalia", "name": { "family": "Malinowska", "given": "Natalia" }, "orcid": "0000-0001-9146-9565" }, { "id": "Cebula-Zofia", "name": { "family": "Cebula", "given": "Zofia" }, "orcid": "0000-0002-4506-6498" }, { "id": "Bigus-Daniel", "name": { "family": "Bigus", "given": "Daniel" }, "orcid": "0000-0001-8477-3761" }, { "id": "Firganek-Daniel", "name": { "family": "Firganek", "given": "Daniel" }, "orcid": "0000-0002-8870-2714" }, { "id": "Bi\u0119ga-Ewelina", "name": { "family": "Bi\u0119ga", "given": "Ewelina" }, "orcid": "0000-0002-2216-5493" }, { "id": "Dzi\u0105bowska-Karolina", "name": { "family": "Dzi\u0105bowska", "given": "Karolina" }, "orcid": "0000-0002-0226-3635" }, { "id": "Brodowski-Mateusz", "name": { "family": "Brodowski", "given": "Mateusz" }, "orcid": "0000-0001-5439-4701" }, { "id": "Kowalski-Marcin", "name": { "family": "Kowalski", "given": "Marcin" } }, { "id": "Panasiuk-Miroslawa", "name": { "family": "Panasiuk", "given": "Miros\u0142awa" }, "orcid": "0000-0001-7470-7306" }, { "id": "Gromadzka-beata", "name": { "family": "Gromadzka", "given": "Beata" }, "orcid": "0000-0002-3525-2158" }, { "id": "\u017bo\u0142\u0119dowska-Sabina", "name": { "family": "\u017bo\u0142\u0119dowska", "given": "Sabina" }, "orcid": "0000-0001-6218-8342" }, { "id": "Nidzworski-Dawid", "name": { "family": "Nidzworski", "given": "Dawid" }, "orcid": "0000-0003-0533-0837" }, { "id": "Pyr\u0107-Krzysztof", "name": { "family": "Pyr\u0107", "given": "Krzysztof" }, "orcid": "0000-0002-3867-7688" }, { "id": "Goddard-W-A-III", "name": { "family": "Goddard", "given": "William A., III" }, "orcid": "0000-0003-0097-5716" }, { "id": "Bogdanowicz-Robert", "name": { "family": "Bogdanowicz", "given": "Robert" }, "orcid": "0000-0002-7543-2620" } ] }, "title": "Performance of electrochemical immunoassays for clinical diagnostics of SARS-CoV-2 based on selective nucleocapsid N protein detection: Boron-doped diamond, gold and glassy carbon evaluation", "ispublished": "pub", "full_text_status": "public", "keywords": "Electrochemistry; Biomedical Engineering; General Medicine; Biophysics; Biotechnology", "note": "\u00a9 2022 Elsevier. \n\nReceived 22 October 2021, Revised 17 March 2022, Accepted 24 March 2022, Available online 8 April 2022. \n\nWe thank SkyWayBiolab for providing upper respiratory tract inactivated viruses that served as negative controls in our experiments and for the technological input needed for antibody production. \n\nThe authors gratefully acknowledge financial support from the National Science Centre (NCN) under Grant \"Express Call \u2013 Research on COVID-19\" No. 2020/01/0/ST7/00104. The DS funds of the Faculty of Electronics, Telecommunications and Informatics of the Gda\u0144sk University of Technology are also acknowledged. Molecular Dynamics simulations have been performed in part at the Interdisciplinary Centre for Mathematical and Computational Modelling of the University of Warsaw (grants g86-1058 and g87-1079). \n\nAuthor contributions: W.B., R.B., B.G., D.N. and K.P. conceived and designed the work. T.\u0141, Y.D., B.G. and M.P. produced the recombinant protein and polyclonal antibody. M.F., M. R., Z.C., E.B. and W.B. prepared electrodes. M.B., M.K., W.B., D.B., and K.D. modified electrodes. M.B., M.K., N.M., D.F. and W.B. optimized the assays and performed analysis. W.B.; B.G., M. Pi., and R.B. wrote the manuscript with corrections from all authors. Theoretical and computational validation models were conceived and prepared by B.D, W.A.G., A.J.B., B.T and S.O. R.B , D.N. and S.\u017b. were responsible for project administration and funding acquisition. All the authors analyzed the data, discussed the results, and reviewed the manuscript. \n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nSupplemental Material - 1-s2.0-S0956566322002627-mmc1.docx
", "abstract": "The 21st century has already brought us a plethora of new threats related to viruses that emerge in humans after zoonotic transmission or drastically change their geographic distribution or prevalence. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first spotted at the end of 2019 to rapidly spread in southwest Asia and later cause a global pandemic, which paralyzes the world since then. We have designed novel immunosensors targeting conserved protein sequences of the N protein of SARS-CoV-2 based on lab-produced and purified anti-SARS-CoV-2 nucleocapsid antibodies that are densely grafted onto various surfaces (diamond/gold/glassy carbon). Titration of antibodies shows very strong reactions up to 1:72 900 dilution. Next, we showed the mechanism of interactions of our immunoassay with nucleocapsid N protein revealing molecular recognition by impedimetric measurements supported by hybrid modeling results with both density functional theory and molecular dynamics methods. Biosensors allowed for a fast (in less than 10 min) detection of SARS-CoV-2 virus with a limit of detection from 0.227 ng/ml through 0.334 ng/ml to 0.362 ng/ml for glassy carbon, boron-doped diamond, and gold surfaces, respectively. For all tested surfaces, we obtained a wide linear range of concentrations from 4.4 ng/ml to 4.4 pg/ml. Furthermore, our sensor leads to a highly specific response to SARS-CoV-2 clinical samples versus other upper respiratory tract viruses such as influenza, respiratory syncytial virus, or Epstein-Barr virus. All clinical samples were tested simultaneously on biosensors and real-time polymerase chain reactions.", "date": "2022-08-01", "date_type": "published", "publication": "Biosensors and Bioelectronics", "volume": "209", "publisher": "Elsevier", "pagerange": "Art. 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"eprint_status": "archive", "datestamp": "2023-08-20 08:18:59", "lastmod": "2023-10-23 15:12:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cramer-Estee-Y", "name": { "family": "Cramer", "given": "Estee Y." }, "orcid": "0000-0003-1373-3177" }, { "id": "Huang-Yuxin", "name": { "family": "Huang", "given": "Yuxin" } }, { "id": "Wang-Yijin", "name": { "family": "Wang", "given": "Yijin" } }, { "id": "Ray-Evan-L", "name": { "family": "Ray", "given": "Evan L." } }, { "id": "Cornell-Matthew", "name": { "family": "Cornell", "given": "Matthew" } }, { "id": "Bracher-Johannes", "name": { "family": "Bracher", "given": "Johannes" }, "orcid": "0000-0002-3777-1410" }, { "id": "Brennen-Andrea", "name": { "family": "Brennen", "given": "Andrea" } }, { "id": "Castro-Rivadeneira-Alvaro-J", "name": { "family": "Castro Rivadeneira", "given": "Alvaro J." } }, { "id": "Gerding-Aaron", "name": { "family": "Gerding", "given": "Aaron" } }, { "id": "House-Katie", "name": { 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"given": "Nicholas G." }, "orcid": "0000-0003-3503-9899" }, { "id": "Abu-Mostafa-Y-S", "name": { "family": "Abu-Mostafa", "given": "Yaser S." } }, { "id": "Bathwal-Rahil", "name": { "family": "Bathwal", "given": "Rahil" } }, { "id": "Chang-Nicholas-A", "name": { "family": "Chang", "given": "Nicholas A." } }, { "id": "Chitta-Pavan", "name": { "family": "Chitta", "given": "Pavan" } }, { "id": "Erickson-Anne", "name": { "family": "Erickson", "given": "Anne" } }, { "id": "Goel-Sumit", "name": { "family": "Goel", "given": "Sumit" }, "orcid": "0000-0003-3266-9035" }, { "id": "Gowda-Jethin", "name": { "family": "Gowda", "given": "Jethin" } }, { "id": "Jin-Qixuan", "name": { "family": "Jin", "given": "Qixuan" } }, { "id": "Jo-HyeongChan", "name": { "family": "Jo", "given": "HyeongChan" } }, { "id": "Kim-Juhyun", "name": { "family": "Kim", "given": "Juhyun" } }, { "id": "Kulkarni-Pranav-D", "name": { "family": "Kulkarni", "given": "Pranav" }, "orcid": "0000-0002-1461-0948" }, { "id": "Lushtak-Samuel-M", "name": { "family": "Lushtak", "given": "Samuel M." } }, { "id": "Mann-Ethan", "name": { "family": "Mann", "given": "Ethan" } }, { "id": "Popken-Max", "name": { "family": "Popken", "given": "Max" } }, { "id": "Soohoo-Connor", "name": { "family": "Soohoo", "given": "Connor" } }, { "id": "Tirumala-Kushal", "name": { "family": "Tirumala", "given": "Kushal" } }, { "id": "Tseng-Albert", "name": { "family": "Tseng", "given": "Albert" } }, { "id": "Varadarajan-Vignesh", "name": { "family": "Varadarajan", "given": "Vignesh" } }, { "id": "Vytheeswaran-Jagath", "name": { "family": "Vytheeswaran", "given": "Jagath" }, "orcid": "0000-0002-5250-7714" }, { "id": "Wang-Christopher", "name": { "family": "Wang", "given": "Christopher" } }, { "id": "Yeluri-Akshay", "name": { "family": "Yeluri", "given": "Akshay" }, "orcid": "0000-0001-8654-1673" }, { "id": "Yurk-Dominic", "name": { "family": "Yurk", "given": "Dominic" }, "orcid": "0000-0002-2276-4189" }, { "id": "Zhang-Michael", "name": { "family": "Zhang", "given": "Michael" } }, { "id": "Zlokapa-Alexander-M", "name": { "family": "Zlokapa", "given": "Alexander" }, "orcid": "0000-0002-4153-8646" } ] }, "title": "The United States COVID-19 Forecast Hub dataset", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 17 January 2022; Accepted 29 June 2022; Published 01 August 2022. \n\nThis work has been supported in part by the US Centers for Disease Control and Prevention (1U01IP001122) and the National Institutes of General Medical Sciences (R35GM119582). The content is solely the responsibility of the authors and does not necessarily represent the official views of the CDC, FDA, NIGMS or the National Institutes of Health. Johannes Bracher was supported by the Helmholtz Foundation via the SIMCARD Information & Data Science Pilot Project. For teams that reported receiving funding for their work, we report the sources and disclosures below. AIpert-pwllnod: Natural Sciences and Engineering Research Council of Canada. Caltech-CS156: Gary Clinard Innovation Fund. CEID-Walk: University of Georgia. CMU-TimeSeries: CDC Center of Excellence, gifts from Google and Facebook. Covid19Sim: National Science Foundation awards 2035360 and 2035361, Gordon and Betty Moore Foundation, and Rockefeller Foundation to support the work of the Society for Medical Decision Making COVID-19 Decision Modeling Initiative. COVIDhub: This work has been supported by the US Centers for Disease Control and Prevention (1U01IP001122) and the National Institutes of General Medical Sciences (R35GM119582). The content is solely the responsibility of the authors and does not necessarily represent the official views of the CDC, NIGMS or the National Institutes of Health. Johannes Bracher was supported by the Helmholtz Foundation via the SIMCARD Information & Data Science Pilot Project. Tilmann Gneiting gratefully acknowledges support by the Klaus Tschira Foundation. CUBoulder, CUB-PopCouncil: The Population Council, and the University of Colorado Population Center (CUPC) funded by Eunice Kennedy Shriver National Institute of Child Health & Human Development of the National Institutes of Health (P2CHD066613). CU-select: NSF DMS-2027369 and a gift from the Morris-Singer Foundation. DDS-NBDS: NSF III-1812699. epiforecasts-ensemble1: Wellcome Trust (210758/Z/18/Z). FDANIHASU: supported by the Intramural Research Program of the NIH/NIDDK. GT_CHHS-COVID19: William W. George Endowment, Virginia C. and Joseph C. Mello Endowment, NSF DGE-1650044, NSF MRI 1828187, research cyberinfrastructure resources and services provided by the Partnership for an Advanced Computing Environment (PACE) at Georgia Tech, and the following benefactors at Georgia Tech: Andrea Laliberte, Joseph C. Mello, Richard \"Rick\" E. & Charlene Zalesky, and Claudia & Paul Raines, CDC MInD-Healthcare U01CK000531-Supplement. GT-DeepCOVID: This work was supported in part by the NSF (Expeditions CCF-1918770, CAREER IIS-2028586, RAPID IIS-2027862, Medium IIS-1955883, Medium IIS-2106961, CCF-2115126), CDC MInD program, ORNL, faculty research award from Facebook and funds/computing resources from Georgia Tech. BA was supported by CDC-MIND U01CK000594 and start-up funds from University of Iowa. IHME: This work was supported by the Bill & Melinda Gates Foundation, as well as funding from the state of Washington and the National Science Foundation (award nocoviddata. FAIN: 2031096). Imperial-ensemble1: SB acknowledges funding from the Wellcome Trust (219415). Institute of Business Forecasting: IBF. IowaStateLW-STEM: NSF DMS-1916204, Iowa State University Plant Sciences Institute Scholars Program, NSF CCF-1934884, Laurence H. Baker Center for Bioinformatics and Biological Statistics. IUPUI CIS: NSF. JHU_CSSE-DECOM: JHU CSSE: National Science Foundation (NSF) RAPID \"Real-time Forecasting of COVID-19 risk in the USA\". 2021-2022. Award ID: 2108526. National Science Foundation (NSF) RAPID \"Development of an interactive web-based dashboard to track COVID-19 in real-time\". 2020. Award ID: 2028604. JHU_IDD-CovidSP: State of California, US Dept of Health and Human Services, US Dept of Homeland Security, Johns Hopkins Health System, Office of the Dean at Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University Modeling and Policy Hub, Centers for Disease Control and Prevention. (5U01CK000538-03), University of Utah Immunology, Inflammation, & Infectious Disease Initiative (26798 Seed Grant). JHU_UNC_GAS-StatMechPool: NIH NIGMS: R01GM140564. JHUAPL-Bucky: US Dept of Health and Human Services. KITmetricslab-select_ensemble: Daniel Wolffram was supported by the Klaus Tschira Foundation as well as the Helmholtz Association under the joint research school \"HIDSS4Health \u2013 Helmholtz Information and Data Science School for Health\". Moreover, his work was funded by the German Federal Ministry of Education and Research (BMBF) and the Baden-W\u00fcrttemberg Ministry of Science as part of the Excellence Strategy of the German Federal and State Governments. LANL-GrowthRate: LANL LDRD 20200700ER. LosAlamos_NAU-CModel_SDVaxVar: NIH/NIGMS grant R01GM111510; LANL-Directed Research and Development Program, Defense Threat Reduction Agency; Laboratory-Directed Research and Development Program project 20220268ER. LU-compUncertLab: UMass Amherst Center of Excellence for Influenza, Institute for Data Intelligent Systems and Computation. MIT-Cassandra: MIT Quest for Intelligence. MOBS-GLEAM_COVID: COVID Supplement CDC-HHS-6U01IP001137-01; CA NU38OT000297 from the Council of State and Territorial Epidemiologists (CSTE). NCSU-COVSIM: Cooperative Agreement NU38OT000297 from the CSTE and the CDC. NotreDame-FRED: NSF RAPID DEB 2027718. NotreDame-mobility: NSF RAPID DEB 2027718. PSI-DRAFT: NSF RAPID Grant # 2031536. QJHong-Encounter: NSF DMR-2001411 and DMR-1835939. SDSC_ISG-TrendModel: The development of the dashboard was partly funded by the Fondation Priv\u00e9e des H\u00f4pitaux Universitaires de Gen\u00e8ve. UA-EpiCovDA: NSF RAPID Grant # 2028401. UChicagoCHATTOPADHYAY-UnIT: Defense Advanced Research Projects Agency (DARPA) #HR00111890043/P00004 (I. Chattopadhyay, University of Chicago). UCSB-ACTS: NSF RAPID IIS 2029626. UCSD_NEU-DeepGLEAM: Google Faculty Award, W31P4Q-21-C-0014. UMass-MechBayes: NIGMS #R35GM119582, NSF #1749854, NIGMS #R35GM119582. UMich-RidgeTfReg: This project is funded by the University of Michigan Physics Department and the University of Michigan Office of Research. USC-SikJalpha: This material is based upon work supported by the National Science. Foundation RAPID under Grant No. 2135784 with support from Centers for Disease Control and Prevention (CDC). UVA-Ensemble: National Institutes of Health (NIH) Grant 1R01GM109718, NSF BIG DATA Grant IIS-1633028, NSF Grant No.: OAC-1916805, NSF Expeditions in Computing Grant CCF-1918656, CCF-1917819, NSF RAPID CNS-2028004, NSF RAPID OAC-2027541, US Centers for Disease Control and Prevention 75D30119C05935, a grant from Google, University of Virginia Strategic Investment Fund award number SIF160, Defense Threat Reduction Agency (DTRA) under Contract No. HDTRA1-19-D-0007, and Virginia Dept of Health Grant VDH-21-501-0141. Wadnwani_AI-BayesOpt: This study is made possible by the generous support of the American People through the United States Agency for International Development (USAID). The work described in this article was implemented under the TRACETB Project, managed by WIAI under the terms of Cooperative Agreement Number 72038620CA00006. The contents of this manuscript are the sole responsibility of the authors and do not necessarily reflect the views of USAID or the United States Government. WalmartLabsML-LogForecasting: Team acknowledges Walmart to support this study. \n\nData availability: The datasets generated and/or analyzed during the current study are available in the reichlab/covid19-forecast-hub GitHub repository, https://github.com/reichlab/covid19-forecast-hub. A permanent DOI for the GitHub repository for the Forecast Hub is available as https://doi.org/10.5281/zenodo.520821010 Forecast data are also available through our Zoltar forecast repository at https://zoltardata.com/project/44. \n\nCode availability: All code for forecast data validation and storage associated with the current submission is available in the Forecast Hub GitHub repository, https://github.com/reichlab/covid19-forecast-hub-validations. Ensemble models are built with code in the covidEnsembles R package, https://github.com/reichlab/covidEnsembles. The code for forecast analysis is at https://doi.org/10.5281/zenodo.520794012 (covidHubUtils R package) and https://doi.org/10.5281/zenodo.52082247 (covidData R package). Any updates will also be published on Zenodo. \n\nThese authors contributed equally: Estee Y. Cramer, Yuxin Huang, Yijin Wang. \n\nCompeting interests: AV, MC, and APP report grants from Metabiota Inc outside the submitted work.\n\nPublished - s41597-022-01517-w.pdf
Submitted - 2021.11.04.21265886v1.full.pdf
", "abstract": "Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages.", "date": "2022-08-01", "date_type": "published", "publication": "Scientific Data", "volume": "9", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 462", "id_number": "CaltechAUTHORS:20211105-194210514", "issn": "2052-4463", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211105-194210514", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Centers for Disease Control and Prevention (CDC)", "grant_number": "1U01IP001122" }, { "agency": "NIH", "grant_number": "R35GM119582" }, { "agency": "Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF)" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "Gary Clinard Innovation Fund" }, { "agency": "University of Georgia" }, { "agency": "Google" }, { "agency": "Facebook" }, { "agency": "NSF", "grant_number": "DEB-2035360" }, { "agency": "NSF", "grant_number": "DEB-2035361" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Rockefeller Foundation" }, { "agency": "Klaus Tschira Foundation" }, { "agency": "NIH", "grant_number": "P2CHD066613" }, { "agency": "NSF", "grant_number": "DMS-2027369" }, { "agency": "Morris-Singer Foundation" }, { "agency": "NSF", "grant_number": "III-1812699" }, { "agency": "Wellcome Trust", "grant_number": "210758/Z/18/Z" }, { "agency": "William W. 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Mello Endowment" }, { "agency": "NSF", "grant_number": "DGE-1650044" }, { "agency": "NSF", "grant_number": "MRI-1828187" }, { "agency": "Centers for Disease Control and Prevention (CDC)", "grant_number": "U01CK000531" }, { "agency": "NSF", "grant_number": "CCF-1918770" }, { "agency": "NSF", "grant_number": "IIS-2028586" }, { "agency": "NSF", "grant_number": "IIS-2027862" }, { "agency": "NSF", "grant_number": "IIS-1955883" }, { "agency": "NSF", "grant_number": "IIS-2106961" }, { "agency": "NSF", "grant_number": "CCF-2115126" }, { "agency": "Oak Ridge National Laboratory" }, { "agency": "Centers for Disease Control and Prevention (CDC)", "grant_number": "U01CK000594" }, { "agency": "University of Iowa" }, { "agency": "Bill and Melinda Gates Foundation" }, { "agency": "State of Washington" }, { "agency": "NSF", "grant_number": "DEB-2031096" }, { "agency": "Wellcome Trust", "grant_number": "219415" }, { "agency": "NSF", "grant_number": "DMS-1916204" }, { "agency": "Iowa State University" }, { "agency": "NSF", "grant_number": "CCF-1934884" }, { "agency": "NSF", "grant_number": "DEB-2108526" }, { "agency": "NSF", "grant_number": "CMMI-2028604" }, { "agency": "State of California" }, { "agency": "Department of Health and Human Services" }, { "agency": "Department of Homeland Security" }, { "agency": "Johns Hopkins University", "grant_number": "5U01CK000538-03" }, { "agency": "University of Utah", "grant_number": "26798" }, { "agency": "NIH", "grant_number": "R01GM140564" }, { "agency": "Klaus Tschira Foundation" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)" }, { "agency": "Baden-W\u00fcrttemberg Ministry of Science" }, { "agency": "Laboratory Directed Research & Development (LDRD)", "grant_number": "20200700ER" }, { "agency": "NIH", "grant_number": "R01GM111510" }, { "agency": "Laboratory Directed Research & Development (LDRD)", "grant_number": "20220268ER" }, { "agency": "University of Massachusetts" }, { "agency": "Centers for Disease Control and Prevention (CDC)", "grant_number": "6U01IP001137-01" }, { "agency": "Council of State and Territorial Epidemiologists (CSTE)", "grant_number": "NU38OT000297" }, { "agency": "NSF", "grant_number": "DEB-2027718" }, { "agency": "NSF", "grant_number": "DEB-2031536" }, { "agency": "NSF", "grant_number": "DMR-2001411" }, { "agency": "NSF", "grant_number": "DMR-1835939" }, { "agency": "Fondation Priv\u00e9e des H\u00f4pitaux Universitaires de Gen\u00e8ve" }, { "agency": "NSF", "grant_number": "DMS-2028401" }, { "agency": "Defense Threat Reduction Agency (DTRA)", "grant_number": "HR00111890043/P00004" }, { "agency": "NSF", "grant_number": "IIS-2029626" }, { "agency": "Google Faculty Research Award", "grant_number": "W31P4Q-21-C-0014" }, { "agency": "NIH", "grant_number": "R35GM119582" }, { "agency": "NSF", "grant_number": "IIS-1749854" }, { "agency": "NIH", "grant_number": "R35GM119582" }, { "agency": "University of Michigan" }, { "agency": "NSF", "grant_number": "DEB-2135784" }, { "agency": "NIH", "grant_number": "1R01GM109718" }, { "agency": "NSF", "grant_number": "IIS-1633028" }, { "agency": "NSF", "grant_number": "OAC-1916805" }, { "agency": "NSF", "grant_number": "CCF-1918656" }, { "agency": "NSF", "grant_number": "CCF-1917819" }, { "agency": "NSF", "grant_number": "CNS-2028004" }, { "agency": "NSF", "grant_number": "OAC-2027541" }, { "agency": "Centers for Disease Control and Prevention (CDC)", "grant_number": "75D30119C05935" }, { "agency": "University of Virginia", "grant_number": "SIF160" }, { "agency": "Defense Threat Reduction Agency (DTRA)", "grant_number": "HDTRA1-19-D-0007" }, { "agency": "Virginia Department of Health", "grant_number": "VDH-21-501-0141" }, { "agency": "United States Agency for International Development (USAID)" }, { "agency": "Wadhwani AI", "grant_number": "72038620CA00006" }, { "agency": "Walmart" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "corp_creators": { "items": [ "US COVID-19 Forecast Hub Consortium" ] }, "doi": "10.1038/s41597-022-01517-w", "pmcid": "PMC8236414", "primary_object": { "basename": "2021.11.04.21265886v1.full.pdf", "url": "https://authors.library.caltech.edu/records/ys28f-z5094/files/2021.11.04.21265886v1.full.pdf" }, "related_objects": [ { "basename": "s41597-022-01517-w.pdf", "url": "https://authors.library.caltech.edu/records/ys28f-z5094/files/s41597-022-01517-w.pdf" } ], "pub_year": "2022", "author_list": "Cramer, Estee Y.; Huang, Yuxin; et al." }, { "id": "https://authors.library.caltech.edu/records/4xm8c-sh061", "eprint_id": 114086, "eprint_status": "archive", "datestamp": "2023-08-20 08:02:37", "lastmod": "2025-11-20 18:30:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schneider-T", "name": { "family": "Schneider", "given": "Tapio" }, "orcid": "0000-0001-5687-2287" }, { "id": "Dunbar-Oliver-R-A", "name": { "family": "Dunbar", "given": "Oliver R. A." }, "orcid": "0000-0001-7374-0382" }, { "id": "Wu-Jinlong", "name": { "family": "Wu", "given": "Jinlong" }, "orcid": "0000-0001-7438-4228" }, { "id": "B\u00f6ttcher-Lucas", "name": { "family": "B\u00f6ttcher", "given": "Lucas" }, "orcid": "0000-0003-1700-1897" }, { "id": "Burov-Dmitry", "name": { "family": "Burov", "given": "Dmitry" }, "orcid": "0000-0002-5060-6794" }, { "id": "Garbuno-I\u00f1igo-Alfredo", "name": { "family": "Garbuno-I\u00f1igo", "given": "Alfredo" }, "orcid": "0000-0003-3279-619X" }, { "id": "Wagner-Gregory-L", "name": { "family": "Wagner", "given": "Gregory L." }, "orcid": "0000-0001-5317-2445" }, { "id": "Pei-Sen", "name": { "family": "Pei", "given": "Sen" }, "orcid": "0000-0002-7072-2995" }, { "id": "Daraio-C", "name": { "family": "Daraio", "given": "Chiara" }, "orcid": "0000-0001-5296-4440" }, { "id": "Ferrari-Raffaele", "name": { "family": "Ferrari", "given": "Raffaele" }, "orcid": "0000-0003-1895-4294" }, { "id": "Shaman-Jeffrey", "name": { "family": "Shaman", "given": "Jeffrey" }, "orcid": "0000-0002-7216-7809" } ] }, "title": "Epidemic management and control through risk-dependent individual contact interventions", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2022 Schneider et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: September 25, 2021; Accepted: May 5, 2022; Published: June 23, 2022. \n\nWe thank Tobias Bischoff, Mason Porter, and Andrew Stuart for helpful discussions. \n\nThis research was supported by Eric and Wendy Schmidt and Schmidt Futures (T.S., O.R.A. D., J.W., D.B.); Swiss National Science Foundation (P2EZP2_191888), National Institutes of Health (R01HL146552), and Army Research Office (W911NF-18-1-0345) (L.B.); National Science Foundation (DMS-2027369), National Institute of Allergy and Infectious Diseases (R01AI163023) (S. P., J.S.), and the Morris-Singer Foundation (J.S.). \n\nThe funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nData Availability Statement: All code written in support of this publication is publicly available at https://github.com/tapios/risk-networks. \n\nAuthor Contributions: Conceptualization: Tapio Schneider, Chiara Daraio. Formal analysis: Tapio Schneider, Oliver R. A. Dunbar, Jinlong Wu, Lucas B\u00f6ttcher, Sen Pei, Jeffrey Shaman. Funding acquisition: Tapio Schneider, Lucas B\u00f6ttcher, Jeffrey Shaman. Investigation: Oliver R. A. Dunbar, Jinlong Wu, Dmitry Burov, Alfredo Garbuno-Inigo. Methodology: Tapio Schneider, Oliver R. A. Dunbar, Jinlong Wu, Lucas B\u00f6ttcher, Alfredo Garbuno-Inigo, Sen Pei, Jeffrey Shaman. Project administration: Tapio Schneider. Software: Oliver R. A. Dunbar, Jinlong Wu, Lucas B\u00f6ttcher, Dmitry Burov, Gregory L. Wagner. Supervision: Tapio Schneider. Visualization: Oliver R. A. Dunbar, Jinlong Wu, Lucas B\u00f6ttcher, Alfredo Garbuno-Inigo. Writing \u2013 original draft: Tapio Schneider, Oliver R. A. Dunbar, Lucas B\u00f6ttcher, Jeffrey Shaman. Writing \u2013 review & editing: Tapio Schneider, Oliver R. A. Dunbar, Jinlong Wu, Lucas B\u00f6ttcher, Alfredo Garbuno-Inigo, Chiara Daraio, Raffaele Ferrari, Jeffrey Shaman. \n\nCompeting interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: J.S. and Columbia University disclose partial ownership of SK Analytics. J.S. discloses consulting for BNI. The California Institute of Technology has filed a patent application covering the epidemic management and control methods described in this paper. All other authors declare no competing interests.\n\nPublished - pcbi.1010171.pdf
Submitted - 2109.10970.pdf
Supplemental Material - Figs_S1-S18.zip
", "abstract": "Testing, contact tracing, and isolation (TTI) is an epidemic management and control approach that is difficult to implement at scale because it relies on manual tracing of contacts. Exposure notification apps have been developed to digitally scale up TTI by harnessing contact data obtained from mobile devices; however, exposure notification apps provide users only with limited binary information when they have been directly exposed to a known infection source. Here we demonstrate a scalable improvement to TTI and exposure notification apps that uses data assimilation (DA) on a contact network. Network DA exploits diverse sources of health data together with the proximity data from mobile devices that exposure notification apps rely upon. It provides users with continuously assessed individual risks of exposure and infection, which can form the basis for targeting individual contact interventions. Simulations of the early COVID-19 epidemic in New York City are used to establish proof-of-concept. In the simulations, network DA identifies up to a factor 2 more infections than contact tracing when both harness the same contact data and diagnostic test data. This remains true even when only a relatively small fraction of the population uses network DA. When a sufficiently large fraction of the population (\u2273 75%) uses network DA and complies with individual contact interventions, targeting contact interventions with network DA reduces deaths by up to a factor 4 relative to TTI. Network DA can be implemented by expanding the computational backend of existing exposure notification apps, thus greatly enhancing their capabilities. Implemented at scale, it has the potential to precisely and effectively control future epidemics while minimizing economic disruption.", "date": "2022-06-23", "date_type": "published", "publication": "PLoS Computational Biology", "volume": "18", "number": "6", "publisher": "Public Library of Science", "pagerange": "Art. No. e1010171", "id_number": "CaltechAUTHORS:20220325-220336231", "issn": "1553-734X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220325-220336231", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Schmidt Futures Program" }, { "agency": "Swiss National Science Foundation (SNSF)", "grant_number": "P2EZP2_191888" }, { "agency": "NIH", "grant_number": "R01HL146552" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-18-1-0345" }, { "agency": "NSF", "grant_number": "DMS-2027369" }, { "agency": "NIH", "grant_number": "R01AI163023" }, { "agency": "Andrew and Corey Morris-Singer Foundation" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1371/journal.pcbi.1010171", "pmcid": "PMC9223336", "primary_object": { "basename": "2109.10970.pdf", "url": "https://authors.library.caltech.edu/records/4xm8c-sh061/files/2109.10970.pdf" }, "related_objects": [ { "basename": "Figs_S1-S18.zip", "url": "https://authors.library.caltech.edu/records/4xm8c-sh061/files/Figs_S1-S18.zip" }, { "basename": "pcbi.1010171.pdf", "url": "https://authors.library.caltech.edu/records/4xm8c-sh061/files/pcbi.1010171.pdf" } ], "pub_year": "2022", "author_list": "Schneider, Tapio; Dunbar, Oliver R. A.; et al." }, { "id": "https://authors.library.caltech.edu/records/cwedr-ptb50", "eprint_id": 115031, "eprint_status": "archive", "datestamp": "2023-12-04 17:31:47", "lastmod": "2025-11-21 04:10:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Morales-Maryann", "name": { "family": "Morales", "given": "Maryann" }, "orcid": "0000-0002-1778-8901" }, { "id": "Ravanfar-Raheleh", "name": { "family": "Ravanfar", "given": "Raheleh" }, "orcid": "0000-0003-2992-0575" }, { "id": "Oyala-Paul-H", "name": { "family": "Oyala", "given": "Paul H." }, "orcid": "0000-0002-8761-4667" }, { "id": "Gray-H-B", "name": { "family": "Gray", "given": "Harry B." }, "orcid": "0000-0002-7937-7876" }, { "id": "Winkler-J-R", "name": { "family": "Winkler", "given": "Jay R." }, "orcid": "0000-0002-4453-9716" } ] }, "title": "Copper(II) Binding to the Intrinsically Disordered C-Terminal Peptide of SARS-CoV-2 Virulence Factor Nsp1", "ispublished": "pub", "full_text_status": "public", "keywords": "Chemical structure, Electron paramagnetic resonance spectroscopy, Fluorescence, Peptides and proteins, SARS-CoV-2; Inorganic Chemistry; Physical and Theoretical Chemistry", "note": "\u00a9 2022 American Chemical Society. This article is made available via the ACS COVID-19 subset for unrestricted RESEARCH re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. \n\nReceived: April 19, 2022; Published: June 6, 2022. \n\nThe work was supported by the Arnold and Mabel Beckman Foundation and by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under Award R01DK019038. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. \n\nThe authors declare no competing financial interest.\n\nPublished - acs.inorgchem.2c01329.pdf
Supplemental Material - ic2c01329_si_001.pdf
", "abstract": "The first encoded SARS-CoV-2 protein (Nsp1) binds to the human 40S ribosome and blocks synthesis of host proteins, thereby inhibiting critical elements of the innate immune response. The final 33 residues of the natively unstructured Nsp1 C-terminus adopt a helix-turn-helix geometry upon binding to the ribosome. We have characterized the fluctuating conformations of this peptide using circular dichroism spectroscopy along with measurements of tryptophan fluorescence and energy transfer. Tryptophan fluorescence decay kinetics reveal that copper(II) binds to the peptide at micromolar concentrations, and electron paramagnetic resonance spectroscopy indicates that the metal ion coordinates to the lone histidine residue.", "date": "2022-06-20", "date_type": "published", "publication": "Inorganic Chemistry", "volume": "61", "number": "24", "publisher": "American Chemical Society", "pagerange": "8992-8996", "id_number": "CaltechAUTHORS:20220606-736150000", "issn": "0020-1669", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220606-736150000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "NIH", "grant_number": "DK019038" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1021/acs.inorgchem.2c01329", "pmcid": "PMC9195567", "primary_object": { "basename": "ic2c01329_si_001.pdf", "url": "https://authors.library.caltech.edu/records/cwedr-ptb50/files/ic2c01329_si_001.pdf" }, "related_objects": [ { "basename": "acs.inorgchem.2c01329.pdf", "url": "https://authors.library.caltech.edu/records/cwedr-ptb50/files/acs.inorgchem.2c01329.pdf" }, { "basename": "nihms-1922634.pdf", "url": "https://authors.library.caltech.edu/records/cwedr-ptb50/files/nihms-1922634.pdf" } ], "pub_year": "2022", "author_list": "Morales, Maryann; Ravanfar, Raheleh; et al." }, { "id": "https://authors.library.caltech.edu/records/dg3cp-nqj89", "eprint_id": 115242, "eprint_status": "archive", "datestamp": "2023-08-22 16:03:37", "lastmod": "2025-11-20 22:18:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Luo-Qi", "name": { "family": "Luo", "given": "Qi" } }, { "id": "Weightman-Ryan", "name": { "family": "Weightman", "given": "Ryan" } }, { "id": "McQuade-Sean-T", "name": { "family": "McQuade", "given": "Sean T." } }, { "id": "D\u00edaz-Mateo", "name": { "family": "D\u00edaz", "given": "Mateo" } }, { "id": "Tr\u00e9lat-Emmanuel", "name": { "family": "Tr\u00e9lat", "given": "Emmanuel" } }, { "id": "Barbour-William", "name": { "family": "Barbour", "given": "William" } }, { "id": "Work-Dan", "name": { "family": "Work", "given": "Dan" } }, { "id": "Samaranayake-Samitha", "name": { "family": "Samaranayake", "given": "Samitha" } }, { "id": "Piccoli-Benedetto", "name": { "family": "Piccoli", "given": "Benedetto" } } ] }, "title": "Optimization of vaccination for COVID-19 in the midst of a pandemic", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19, SARS-CoV-2, SEIR compartmental models, vaccine, optimal control; Applied Mathematics; Computer Science Applications; General Engineering; Statistics and Probability", "note": "\u00a9 2022 American Institute of Mathematical Sciences. \n\nThe authors acknowledge the support of the NSF CMMI project # 2033580 \"Managing pandemic by managing mobility\". R.W., S.T.M. and B.P. acknowledge the support of the Joseph and\nLoretta Lopez Chair endowment.\n\nSubmitted - 2203.09502.pdf
Supplemental Material - 034e5a88-63b3-4957-8e63-cbdb3f76920a.xls
Supplemental Material - 393ec09c-e307-4681-b7a1-287a9e52fc7f.xls
Supplemental Material - 5564b0f2-8e2b-47d6-a3e7-b445e0a6ec94.xls
", "abstract": "During the Covid-19 pandemic a key role is played by vaccination to combat the virus. There are many possible policies for prioritizing vaccines, and different criteria for optimization: minimize death, time to herd immunity, functioning of the health system. Using an age-structured population compartmental finite-dimensional optimal control model, our results suggest that the eldest to youngest vaccination policy is optimal to minimize deaths. Our model includes the possible infection of vaccinated populations. We apply our model to real-life data from the US Census for New Jersey and Florida, which have a significantly different population structure. We also provide various estimates of the number of lives saved by optimizing the vaccine schedule and compared to no vaccination.", "date": "2022-06", "date_type": "published", "publication": "Networks and Heterogeneous Media", "volume": "17", "number": "3", "publisher": "American Institute of Mathematical Sciences", "pagerange": "443-466", "id_number": "CaltechAUTHORS:20220622-933053900", "issn": "1556-1801", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220622-933053900", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CMMI-2033580" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.3934/nhm.2022016", "primary_object": { "basename": "034e5a88-63b3-4957-8e63-cbdb3f76920a.xls", "url": "https://authors.library.caltech.edu/records/dg3cp-nqj89/files/034e5a88-63b3-4957-8e63-cbdb3f76920a.xls" }, "related_objects": [ { "basename": "2203.09502.pdf", "url": "https://authors.library.caltech.edu/records/dg3cp-nqj89/files/2203.09502.pdf" }, { "basename": "393ec09c-e307-4681-b7a1-287a9e52fc7f.xls", "url": "https://authors.library.caltech.edu/records/dg3cp-nqj89/files/393ec09c-e307-4681-b7a1-287a9e52fc7f.xls" }, { "basename": "5564b0f2-8e2b-47d6-a3e7-b445e0a6ec94.xls", "url": "https://authors.library.caltech.edu/records/dg3cp-nqj89/files/5564b0f2-8e2b-47d6-a3e7-b445e0a6ec94.xls" } ], "pub_year": "2022", "author_list": "Luo, Qi; Weightman, Ryan; et al." }, { "id": "https://authors.library.caltech.edu/records/4615m-h0a79", "eprint_id": 113631, "eprint_status": "archive", "datestamp": "2023-08-22 15:49:24", "lastmod": "2025-11-20 22:15:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hjorleifsson-Kristjan-E", "name": { "family": "Hjorleifsson", "given": "Kristjan E." }, "orcid": "0000-0002-7851-1818" }, { "name": { "family": "Rognvaldsson", "given": "Solvi" } }, { "name": { "family": "Jonsson", "given": "Hakon" } }, { "name": { "family": "Agustsdottir", "given": "Arna B." } }, { "name": { "family": "Andresdottir", "given": "Margret" } }, { "name": { "family": "Birgisdottir", "given": "Kolbrun" } }, { "name": { "family": "Eiriksson", "given": "Ogmundur" } }, { "name": { "family": "Eythorsson", "given": "Elias S." } }, { "name": { "family": "Fridriksdottir", "given": "Run" } }, { "name": { "family": "Georgsson", "given": "Gudmundur" } }, { "name": { "family": "Gudmundsson", "given": "Kjartan R." } }, { "name": { "family": "Gylfason", "given": "Arnaldur" } }, { "name": { "family": "Haraldsdottir", "given": "Gudbjorg" } }, { "name": { "family": "Jensson", "given": "Brynjar O." } }, { "name": { "family": "Jonasdottir", "given": "Adalbjorg" } }, { "name": { "family": "Jonasdottir", "given": "Aslaug" } }, { "name": { "family": "Josefsdottir", "given": "Kamilla S." } }, { "name": { "family": "Kristinsdottir", "given": "Nina" } }, { "name": { "family": "Kristjansdottir", "given": "Borghildur" } }, { "name": { "family": "Kristjansson", "given": "Thordur" } }, { "name": { "family": "Magnusdottir", "given": "Droplaug N." } }, { "name": { "family": "Palsson", "given": "Runolfur" } }, { "name": { "family": "le Roux", "given": "Louise" } }, { "name": { "family": "Sigurbergsdottir", "given": "Gudrun M." } }, { "name": { "family": "Sigurdsson", "given": "Asgeir" } }, { "name": { "family": "Sigurdsson", "given": "Martin I." } }, { "name": { "family": "Sveinbjornsson", "given": "Gardar" } }, { "name": { "family": "Thorarensen", "given": "Emil Aron" } }, { "name": { "family": "Thorbjornsson", "given": "Bjarni" } }, { "name": { "family": "Thordardottir", "given": "Marianna" } }, { "name": { "family": "Helgason", "given": "Agnar" } }, { "name": { "family": "Holm", "given": "Hilma" } }, { "name": { "family": "Jonsdottir", "given": "Ingileif" } }, { "name": { "family": "Jonsson", "given": "Frosti" } }, { "name": { "family": "Magnusson", "given": "Olafur T." } }, { "name": { "family": "Masson", "given": "Gisli" } }, { "name": { "family": "Norddahl", "given": "Gudmundur L." } }, { "name": { "family": "Saemundsdottir", "given": "Jona" } }, { "name": { "family": "Sulem", "given": "Patrick" } }, { "name": { "family": "Thorsteinsdottir", "given": "Unnur" } }, { "name": { "family": "Gudbjartsson", "given": "Daniel F." } }, { "name": { "family": "Melsted", "given": "Pall" } }, { "name": { "family": "Stefansson", "given": "Kari" } } ] }, "title": "Reconstruction of a large-scale outbreak of SARS-CoV-2 infection in Iceland informs vaccination strategies", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; Outbreak reconstruction; SARS-CoV-2; Transmission tree; Vaccination strategy; Infectious Diseases; Microbiology (medical); General Medicine", "note": "\u00a9 2022 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.\n\nReceived 29 June 2021, Revised 19 January 2022, Accepted 5 February 2022, Available online 17 February 2022.\n\nAuthor contributions:\nK.E.H. and S.R. contributed equally to this article. KEH, SR, PM, and KS designed the study and interpreted the results. ABA, MA, KB, GH, AdJ, AsJ, NK, BK, DNM, LLR, GMS, AS, FJ, OTM, GLN, and JS planned and performed the laboratory work. ESE, RP, MIS, and MT performed the data collection. KEH, SR, HJ, ESE, RF, GG, KRG, AG, BOJ, KSJ, TK, RP, MIS, GS, EAT, BT, MT, AH, HH, IJ, GM, PS, UT, and PM performed the data curation. KEH, SR, HJ, OE, DFG, and PM performed the statistical and bioinformatics analyses. KEH, SR, PM, and KS drafted the manuscript. All authors contributed to the final version of the paper.\n\nEthics statement:\nThis study was approved by the National Bioethics Committee of Iceland (approval no. VSN-20-070) after review by the Icelandic Data Protection Authority. Consent was not required from the participants in the study.\n\nTransparency declaration:\nAll authors declare no conflicts of interest. No external funding.\n\nPublished - main.pdf
Supplemental Material - 1-s2.0-S1198743X22000854-mmc1.docx
", "abstract": "Objectives: The spread of SARS-CoV-2 is dependent on several factors, both biological and behavioural. The effectiveness of nonpharmaceutical interventions can be attributed largely to changes in human behaviour, but quantifying this effect remains challenging. Reconstructing the transmission tree of the third wave of SARS-CoV-2 infections in Iceland using contact tracing and viral sequence data from 2522 cases enables us to directly compare the infectiousness of distinct groups of persons. \nMethods: The transmission tree enables us to model the effect that a given population prevalence of vaccination would have had on the third wave had one of three different vaccination strategies been implemented before that time. This allows us to compare the effectiveness of the strategies in terms of minimizing the number of cases, deaths, critical cases, and severe cases. \n\nResults: We found that people diagnosed outside of quarantine (\u0212 = 1.31) were 89% more infectious than those diagnosed while in quarantine (\u0212 = 0.70) and that infectiousness decreased as a function of time spent in quarantine before diagnosis, with people diagnosed outside of quarantine being 144% more infectious than those diagnosed after \u22653 days in quarantine (\u0212 = 0.54). People of working age, 16 to 66 years (\u0212 = 1.08), were 46% more infectious than those outside of that age range (\u0212 = 0.74). \n\nDiscussion: We found that vaccinating the population in order of ascending age or uniformly at random would have prevented more infections per vaccination than vaccinating in order of descending age, without significantly affecting the expected number of deaths, critical cases, or severe cases.", "date": "2022-06", "date_type": "published", "publication": "Clinical Microbiology and Infection", "volume": "28", "number": "6", "publisher": "Elsevier", "pagerange": "852-858", "id_number": "CaltechAUTHORS:20220228-862133400", "issn": "1198-743X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220228-862133400", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.cmi.2022.02.012", "pmcid": "PMC8849849", "primary_object": { "basename": "1-s2.0-S1198743X22000854-mmc1.docx", "url": "https://authors.library.caltech.edu/records/4615m-h0a79/files/1-s2.0-S1198743X22000854-mmc1.docx" }, "related_objects": [ { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/4615m-h0a79/files/main.pdf" } ], "pub_year": "2022", "author_list": "Hjorleifsson, Kristjan E.; Rognvaldsson, Solvi; et al." }, { "id": "https://authors.library.caltech.edu/records/31kck-3rm15", "eprint_id": 116434, "eprint_status": "archive", "datestamp": "2023-09-19 22:39:49", "lastmod": "2025-11-20 20:07:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jo-HyeongChan", "name": { "family": "Jo", "given": "HyeongChan" } }, { "id": "Kim-Juhyun", "name": { "family": "Kim", "given": "Juhyun" } }, { "id": "Huang-Tzu-Chen", "name": { "family": "Huang", "given": "Tzu-Chen" } }, { "id": "Ni-Yu-Li", "name": { "family": "Ni", "given": "Yu-Li" } } ] }, "title": "condLSTM-Q: A novel deep learning model for predicting COVID-19 mortality in fine geographical scale", "ispublished": "pub", "full_text_status": "public", "keywords": "Applied Mathematics; Computer Science Applications; Biochemistry, Genetics and Molecular Biology (miscellaneous); Modeling and Simulation", "note": "The authors thank Prof Yaser Abu-Mostafa, and the Teaching Assistants of CS156 in Caltech for organizing the COVID19 prediction initiative and for providing the data pipeline for parsing data sources. We thank Isaac Yen-Hao Chu, M.D. for reading the manuscript. Yu-Li Ni was supported by Taipei Veterans General Hospital Yang-Ming University Excellent Physician Scientists Cultivation Program (No.103-Y-A-003).\n\n\u00a9 2022 The Author (s). Published by Higher Education Press. This article is licensed by the CC By under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
", "abstract": "Background: Modern machine learning-based models have not been harnessed to their total capacity for disease trend predictions prior to the COVID-19 pandemic. This work is the first use of the conditional RNN model in predicting disease trends that we know of during development that complemented classical epidemiological approaches.\n\nMethods: We developed the long short-term memory networks with quantile output (condLSTM-Q) model for making quantile predictions on COVID-19 death tolls.\n\nResults: We verified that the condLSTM-Q was accurately predicting fine-scale, county-level daily deaths with a two-week window. The model's performance was robust and comparable to, if not slightly better than well-known, publicly available models. This provides unique opportunities for investigating trends within the states and interactions between counties along state borders. In addition, by analyzing the importance of the categorical data, one could learn which features are risk factors that affect the death trend and provide handles for officials to ameliorate the risks.\n\nConclusion: The condLSTM-Q model performed robustly, provided fine-scale, county-level predictions of daily deaths with a two-week window. Given the scalability and generalizability of neural network models, this model could incorporate additional data sources with ease and could be further developed to generate other valuable predictions such as new cases or hospitalizations intuitively.", "date": "2022-06", "date_type": "published", "publication": "Quantitative Biology", "volume": "10", "number": "2", "publisher": "Engineering Sciences Press", "pagerange": "125-138", "id_number": "CaltechAUTHORS:20220823-628672500.759", "issn": "2095-4689", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220823-628672500.759", "funders": { "items": [ { "agency": "Taipei Veterans General Hospital / National Yang-Ming University", "grant_number": "103-Y-A-003" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.15302/J-QB-021-0276", "primary_object": { "basename": "condLSTM-Q_ A novel deep learning model for predicting COVID-19 mortality in fine geographical scale.pdf", "url": "https://authors.library.caltech.edu/records/31kck-3rm15/files/condLSTM-Q_ A novel deep learning model for predicting COVID-19 mortality in fine geographical scale.pdf" }, "pub_year": "2022", "author_list": "Jo, HyeongChan; Kim, Juhyun; et al." }, { "id": "https://authors.library.caltech.edu/records/9sgp0-wf083", "eprint_id": 110280, "eprint_status": "archive", "datestamp": "2023-08-20 07:37:27", "lastmod": "2025-11-21 00:58:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jacobs-Jana-L", "name": { "family": "Jacobs", "given": "Jana L." }, "orcid": "0000-0002-0322-585X" }, { "name": { "family": "Bain", "given": "William" }, "orcid": "0000-0001-8506-0552" }, { "name": { "family": "Naqvi", "given": "Asma" } }, { "name": { "family": "Staines", "given": "Brittany" } }, { "name": { "family": "Castanha", "given": "Priscila M. S." } }, { "name": { "family": "Yang", "given": "Haopu" }, "orcid": "0000-0001-6858-1778" }, { "name": { "family": "Boltz", "given": "Valerie F." }, "orcid": "0000-0001-8872-5599" }, { "name": { "family": "Barratt-Boyes", "given": "Simon" }, "orcid": "0000-0002-8869-4945" }, { "name": { "family": "Marques", "given": "Ernesto T. A." }, "orcid": "0000-0003-3826-9358" }, { "name": { "family": "Mitchell", "given": "Stephanie L." } }, { "name": { "family": "Meth\u00e9", "given": "Barbara" }, "orcid": "0000-0001-8711-1448" }, { "name": { "family": "Olonisakin", "given": "Tolani F." }, "orcid": "0000-0002-8342-3409" }, { "name": { "family": "Haidar", "given": "Ghady" }, "orcid": "0000-0003-0634-8211" }, { "name": { "family": "Burke", "given": "Thomas W." }, "orcid": "0000-0003-0592-5822" }, { "name": { "family": "Petzold", "given": "Elizabeth" }, "orcid": "0000-0001-8207-4406" }, { "name": { "family": "Denny", "given": "Thomas" }, "orcid": "0000-0002-7364-8276" }, { "name": { "family": "Woods", "given": "Chris W." } }, { "id": "McVerry-Bryan-J", "name": { "family": "McVerry", "given": "Bryan J." }, "orcid": "0000-0002-1175-4874" }, { "name": { "family": "Lee", "given": "Janet S." }, "orcid": "0000-0002-6812-6043" }, { "name": { "family": "Watkins", "given": "Simon C." }, "orcid": "0000-0003-4092-1552" }, { "id": "St-Croix-Claudette-M", "name": { "family": "St. Croix", "given": "Claudette M." }, "orcid": "0000-0003-0794-4939" }, { "name": { "family": "Morris", "given": "Alison" }, "orcid": "0000-0002-7290-6536" }, { "name": { "family": "Kearney", "given": "Mary F." }, "orcid": "0000-0003-3839-6576" }, { "id": "Ladinsky-Mark-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Kitsios", "given": "Georgios D." } }, { "name": { "family": "Mellors", "given": "John W." }, "orcid": "0000-0002-3737-9742" } ] }, "title": "Severe Acute Respiratory Syndrome Coronavirus 2 Viremia Is Associated With Coronavirus Disease 2019 Severity and Predicts Clinical Outcome", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nReceived: 14 June 2021; Editorial decision: 02 August 2021; Published: 10 August 2021; Corrected and typeset: 20 September 2021. \n\nWe thank the patients and patient families who have enrolled in our research studies at the University of Pittsburgh. We also thank the physicians, nurses, respiratory therapists, and other staff at the University of Pittsburgh Medical Center Presbyterian and Shadyside Hospital units for assistance with coordination of patient enrollment and collection of patient samples. We thank Heather Michael, Michelle Busch, Caitlin Schaefer, and Cathy Kessinger for assistance with patient enrollment and processing research samples. We also thank Lorraine Pollini for her careful review of the manuscript. \n\nDisclaimer. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services; the National Center for Advancing Translational Sciences; the National Heart, Lung, and Blood Institute (NHLBI); or the National Institutes of Health (NIH) nor does mention of trade names, commercial products, or organizations imply endorsement by the US government. \n\nThis work was supported in part by pilot coronavirus disease 2019 (COVID-19) awards received from the University of Pittsburgh Clinical and Translational Science Institute, the National Center for Advancing Translational Sciences, and the NIH (UL1TR001436 to G. D. K. and E. T. A. M.); a George Mason Fast grant (to P. J. B.); NIH/ NHLBI (P01HL114453 to B. J. M. and J. S. L.); NIH/National Institute of Allergy and Infectious Diseases (NIAID; U01AI066569 and UM1AI104681 to C. W. W., T. W. B., and E. P.); the US Defense Advanced Projects Agency (N66001-09-C-2082 and HR0011-17-2-0069 to C. W. W., T. W. B., and E. P.); the Virology Quality Assurance (75N93019C00015 to T. D.); in whole or in part by federal funds from the National Cancer Institute, NIH (under contract 75N91019D00024, task order 75N91020F00003 to J. W. M.), and intramural funds from the National Cancer Institute (to M. F. K.); NIH/NHLBI (agreement 1OT2HL156812-01 to W. B.); the US Department of Veterans Affairs Biomedical Laboratory R&D Career Development Award (IK2 BX004886 to WB.); and the University of Pittsburgh Vascular Medicine Institute, the Hemophilia Center of Western Pennsylvania, and the Institute for Transfusion Medicine (to W. B). \n\nPotential conflicts of interest. H. Y. reports a scholarship to pursue study in the United States from the China Scholarship Council outside the submitted work. G. H. reports grants from NIH and Karius and personal fees for reviewing a legal case from Meyers, Rodbell & Rosenbaum, PA, outside the submitted work. T. W. B. reports grants from NIH/NIAID and Defense Advanced Research Projects Agency (DARPA) during the conduct of the study and equity options for consulting work from Predigen, Inc, outside the submitted work. J. S. L. discloses a paid consultantship with Janssen R&D unrelated to this work and discloses clinical adjudication of severity outcomes in the ENSEMBLE study of COVID-19 vaccine. C. W. W. reports personal fees from Duke University and Durham VA Health Care System for employment; grants from DARPA, NIH/Antibacterial Resistance Leadership Group (ARLG), equity/founder from Predigen, Inc, Sanofi, and NIH/Vaccine and Treatment Evaluation Unit (VTEU); personal fees from bioMerieux for consulting; personal fees from Roche Molecular Sciences for advisory board participation; personal fees for consulting from Biofire, Giner, Biomeme, FHI Clinical, and Arena; personal fees from Janssen for Data and Safety Monitoring Board (DSMB); and personal fees from Regeneron for advisory board participation outside the submitted work. B. J. M. reports grants from NIH/NHLBI, the Translational Breast Cancer Research Consortium, and the UPMC Learning While Doing Program during the conduct of the study; grants from Bayer Pharmaceuticals, Inc; and personal consultation fees from Boehringer Ingelheim, Inc, outside the submitted work. G. K. reports research funding from Karius, Inc. J. W. M. reports grants to the University of Pittsburgh from NIH, USAID, Gilead Sciences, Inc, and Janssen Pharmaceuticals; serves or has served as a consultant for Gilead Sciences, Inc; has served as a scientific advisory board member for Merck, Accelevir Diagnostics, and Xi'an Yufan Biotechnologies; owns share options in Co-Crystal Pharmaceuticals, Inc, and Infectious Diseases Connect; is a part-time employee and shareholder of Abound Bio, Inc; and is employed by the University of Pittsburgh. His holdings and roles in Co-Crystal Pharmaceuticals, Infectious Diseases Connect, and Abound Bio are unrelated to the current work. All remaining authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.\n\nSupplemental Material - ciab686_suppl_supplementary_figure_s1.jpeg
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Supplemental Material - ciab686_suppl_supplementary_video_s3.mp4
", "abstract": "Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA (vRNA) is detected in the bloodstream of some patients with coronavirus disease 2019 (COVID-19), but it is not clear whether this RNAemia reflects viremia (ie, virus particles) and how it relates to host immune responses and outcomes. \n\nMethods: SARS-CoV-2 vRNA was quantified in plasma samples from observational cohorts of 51 COVID-19 patients including 9 outpatients, 19 hospitalized (non\u2013intensive care unit [ICU]), and 23 ICU patients. vRNA levels were compared with cross-sectional indices of COVID-19 severity and prospective clinical outcomes. We used multiple imaging methods to visualize virions in plasma. \n\nResults: SARS-CoV-2 vRNA was detected in plasma of 100%, 52.6%, and 11.1% of ICU, non-ICU, and outpatients, respectively. Virions were detected in plasma pellets using electron tomography and immunostaining. Plasma vRNA levels were significantly higher in ICU\u2005>\u2005non-ICU\u2005>\u2005outpatients (P\u2005<\u2005.0001); for inpatients, plasma vRNA levels were strongly associated with higher World Health Organization (WHO) score at admission (P\u2005=\u2005.01), maximum WHO score (P\u2005=\u2005.002), and discharge disposition (P\u2005=\u2005.004). A plasma vRNA level >6000 copies/mL was strongly associated with mortality (hazard ratio, 10.7). Levels of vRNA were significantly associated with several inflammatory biomarkers (P\u2005<\u2005.01) but not with plasma neutralizing antibody titers (P\u2005=\u2005.8). \n\nConclusions: Visualization of virus particles in plasma indicates that SARS-CoV-2 RNAemia is due, at least in part, to viremia. The levels of SARS-CoV-2 RNAemia correlate strongly with disease severity, patient outcome, and specific inflammatory biomarkers but not with neutralizing antibody titers.", "date": "2022-05-01", "date_type": "published", "publication": "Clinical Infectious Diseases", "volume": "74", "number": "9", "publisher": "Oxford University Press", "pagerange": "1525-1533", "id_number": "CaltechAUTHORS:20210816-230140809", "issn": "1058-4838", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210816-230140809", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Pittsburgh" }, { "agency": "National Center for Advancing Translational Sciences" }, { "agency": "NIH", "grant_number": "UL1TR001436" }, { "agency": "George Mason University" }, { "agency": "NIH", "grant_number": "P01HL114453" }, { "agency": "NIH", "grant_number": "U01AI066569" }, { "agency": "NIH", "grant_number": "UM1AI104681" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "N66001-09-C-2082" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "HR0011-17-2-0069" }, { "agency": "NIH", "grant_number": "75N93019C00015" }, { "agency": "National Cancer Institute" }, { "agency": "NIH", "grant_number": "75N91019D00024" }, { "agency": "NIH", "grant_number": "75N91020F00003" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "1OT2HL156812-01" }, { "agency": "Department of Veterans Affairs", "grant_number": "IK2 BX004886" }, { "agency": "Hemophilia Center of Western Pennsylvania" }, { "agency": "Institute for Transfusion Medicine" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/cid/ciab686", "pmcid": "PMC9070832", "primary_object": { "basename": "ciab686_suppl_supplementary_table_s2.ppt", "url": "https://authors.library.caltech.edu/records/9sgp0-wf083/files/ciab686_suppl_supplementary_table_s2.ppt" }, "related_objects": [ { "basename": "ciab686_suppl_supplementary_video_s1.mp4", "url": "https://authors.library.caltech.edu/records/9sgp0-wf083/files/ciab686_suppl_supplementary_video_s1.mp4" }, { "basename": "ciab686_suppl_supplementary_video_s2.mp4", "url": "https://authors.library.caltech.edu/records/9sgp0-wf083/files/ciab686_suppl_supplementary_video_s2.mp4" }, { "basename": "ciab686_suppl_supplementary_video_s3.mp4", "url": "https://authors.library.caltech.edu/records/9sgp0-wf083/files/ciab686_suppl_supplementary_video_s3.mp4" }, { "basename": "ciab686_suppl_supplementary_figure_s1.jpeg", "url": "https://authors.library.caltech.edu/records/9sgp0-wf083/files/ciab686_suppl_supplementary_figure_s1.jpeg" }, { "basename": "ciab686_suppl_supplementary_figure_s2.jpeg", "url": "https://authors.library.caltech.edu/records/9sgp0-wf083/files/ciab686_suppl_supplementary_figure_s2.jpeg" }, { "basename": "ciab686_suppl_supplementary_figure_s3.jpeg", "url": "https://authors.library.caltech.edu/records/9sgp0-wf083/files/ciab686_suppl_supplementary_figure_s3.jpeg" }, { "basename": "ciab686_suppl_supplementary_table_s1.ppt", "url": "https://authors.library.caltech.edu/records/9sgp0-wf083/files/ciab686_suppl_supplementary_table_s1.ppt" } ], "pub_year": "2022", "author_list": "Jacobs, Jana L.; Bain, William; et al." }, { "id": "https://authors.library.caltech.edu/records/qr9fj-3x817", "eprint_id": 113226, "eprint_status": "archive", "datestamp": "2023-08-22 15:20:06", "lastmod": "2025-11-20 22:02:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cable-Jennifer", "name": { "family": "Cable", "given": "Jennifer" } }, { "name": { "family": "Rappuoli", "given": "Rino" }, "orcid": "0000-0002-8827-254X" }, { "name": { "family": "Klemm", "given": "Elizabeth J." }, "orcid": "0000-0002-2175-3752" }, { "name": { "family": "Kang", "given": "Gagandeep" }, "orcid": "0000-0002-3656-564X" }, { "name": { "family": "Mutreja", "given": "Ankur" }, "orcid": "0000-0002-1118-8075" }, { "name": { "family": "Wright", "given": "Gavin J." }, "orcid": "0000-0003-0537-0863" }, { "name": { "family": "Pizza", "given": "Mariagrazia" }, "orcid": "0000-0002-7800-1404" }, { "name": { "family": "Ajay Castro", "given": "Sowmya" }, "orcid": "0000-0001-9831-2907" }, { "name": { "family": "Hoffmann", "given": "Joseph P." }, "orcid": "0000-0001-8300-7782" }, { "name": { "family": "Alter", "given": "Galit" }, "orcid": "0000-0003-1570-9445" }, { "name": { "family": "Carfi", "given": "Andrea" }, "orcid": "0000-0001-5508-3809" }, { "name": { "family": "Pollard", "given": "Andrew J." } }, { "name": { "family": "Krammer", "given": "Florian" }, "orcid": "0000-0003-4121-776X" }, { "name": { "family": "Gupta", "given": "Ravindra K." }, "orcid": "0000-0001-9751-1808" }, { "name": { "family": "Wagner", "given": "Caroline E." }, "orcid": "0000-0001-5193-2797" }, { "name": { "family": "Machado", "given": "Viviane" } }, { "name": { "family": "Modjarrad", "given": "Kayvon" }, "orcid": "0000-0002-6514-5572" }, { "name": { "family": "Corey", "given": "Lawrence" }, "orcid": "0000-0002-2179-2436" }, { "name": { "family": "Gilbert", "given": "Peter B." }, "orcid": "0000-0002-2662-9427" }, { "name": { "family": "Dougan", "given": "Gordon" } }, { "name": { "family": "Lurie", "given": "Nicole" }, "orcid": "0000-0003-0022-965X" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Chiu", "given": "Christopher" } }, { "name": { "family": "Nemes", "given": "Elisa" }, "orcid": "0000-0003-1662-4961" }, { "name": { "family": "Gordon", "given": "Stephen B." }, "orcid": "0000-0001-6576-1116" }, { "name": { "family": "Steer", "given": "Andrew C." }, "orcid": "0000-0001-7346-0196" }, { "name": { "family": "Rudel", "given": "Thomas" }, "orcid": "0000-0003-4740-6991" }, { "name": { "family": "Blish", "given": "Catherine A." }, "orcid": "0000-0001-6946-7627" }, { "name": { "family": "Sandberg", "given": "John Tyler" }, "orcid": "0000-0001-6747-6933" }, { "name": { "family": "Brennan", "given": "Kiva" }, "orcid": "0000-0003-4960-7076" }, { "name": { "family": "Klugman", "given": "Keith P." }, "orcid": "0000-0001-6637-728X" }, { "name": { "family": "Stuart", "given": "Lynda M." }, "orcid": "0000-0001-7606-7883" }, { "name": { "family": "Madhi", "given": "Shabir A." }, "orcid": "0000-0002-7629-0636" }, { "name": { "family": "Karp", "given": "Christopher L." }, "orcid": "0000-0002-0832-2659" } ] }, "title": "Innovative vaccine approaches\u2014a Keystone Symposia report", "ispublished": "pub", "full_text_status": "public", "keywords": "correlates of protection; COVID-19; human challenge studies; influenza; pneumococcal disease; streptococcus; vaccines; vaccine equity; History and Philosophy of Science; General Biochemistry, Genetics and Molecular Biology; General Neuroscience", "note": "\u00a9 2022 New York Academy of Sciences. \n\nIssue Online: 16 May 2022; Version of Record online: 14 January 2022; Manuscript accepted: 03 December 2021; Manuscript received: 03 December 2021. \n\nThe authors declare no competing interests.\n\nPublished - Annals_NY_Academy_of_Science_-_2022_-_Cable_-_Innovative_vaccine_approaches_a_Keystone_Symposia_report.pdf
", "abstract": "The rapid development of COVID-19 vaccines was the result of decades of research to establish flexible vaccine platforms and understand pathogens with pandemic potential, as well as several novel changes to the vaccine discovery and development processes that partnered industry and governments. And while vaccines offer the potential to drastically improve global health, low-and-middle-income countries around the world often experience reduced access to vaccines and reduced vaccine efficacy. Addressing these issues will require novel vaccine approaches and platforms, deeper insight how vaccines mediate protection, and innovative trial designs and models. On June 28\u201330, 2021, experts in vaccine research, development, manufacturing, and deployment met virtually for the Keystone eSymposium \"Innovative Vaccine Approaches\" to discuss advances in vaccine research and development.", "date": "2022-05", "date_type": "published", "publication": "Annals of the New York Academy of Sciences", "volume": "1511", "number": "1", "publisher": "New York Academy of Sciences", "pagerange": "59-86", "id_number": "CaltechAUTHORS:20220202-543652000", "issn": "0077-8923", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220202-543652000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1111/nyas.14739", "primary_object": { "basename": "Annals_NY_Academy_of_Science_-_2022_-_Cable_-_Innovative_vaccine_approaches_a_Keystone_Symposia_report.pdf", "url": "https://authors.library.caltech.edu/records/qr9fj-3x817/files/Annals_NY_Academy_of_Science_-_2022_-_Cable_-_Innovative_vaccine_approaches_a_Keystone_Symposia_report.pdf" }, "pub_year": "2022", "author_list": "Cable, Jennifer; Rappuoli, Rino; et al." }, { "id": "https://authors.library.caltech.edu/records/g5zsj-a6f53", "eprint_id": 113946, "eprint_status": "archive", "datestamp": "2023-08-22 15:21:12", "lastmod": "2025-11-21 00:28:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Debnath-Ramit", "name": { "family": "Debnath", "given": "Ramit" }, "orcid": "0000-0003-0727-5683" }, { "id": "Bardhan-Ronita", "name": { "family": "Bardhan", "given": "Ronita" }, "orcid": "0000-0001-5336-4084" }, { "id": "Misra-Ashwin", "name": { "family": "Misra", "given": "Ashwin" }, "orcid": "0000-0003-0554-9409" }, { "id": "Hong-Tianzhen", "name": { "family": "Hong", "given": "Tianzhen" }, "orcid": "0000-0003-1886-9137" }, { "id": "Rozite-Vida", "name": { "family": "Rozite", "given": "Vida" } }, { "id": "Ramage-Michael-H", "name": { "family": "Ramage", "given": "Michael H." } } ] }, "title": "Lockdown impacts on residential electricity demand in India: A data-driven and non-intrusive load monitoring study using Gaussian mixture models", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; Work-from-home; NILM; Machine learning; Mixture models; India; Management, Monitoring, Policy and Law; General Energy", "note": "\u00a9 2022 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nReceived 15 November 2021, Revised 23 February 2022, Accepted 25 February 2022, Available online 17 March 2022, Version of Record 17 March 2022. \n\nThis study is supported by Bill and Melinda Gates Foundation through the Gates Cambridge Scholarship awarded to RD under the grant number OPP1144 and Churchill College Sustainability Fellowship. RD would like to thank Caltech for hosting him as a visiting faculty associate in Computational Social Science for 2021\u201322. In addition, RB and RD received funding from the Isaac Newton Trust through the Energy Transition Small Grant \u2013 2020. RD and MH would also like to thank the Laudes Foundation for supporting this study through the 'Growing the Future' project at the University of Cambridge. RB would further like to thank the UK Space Agency for funding her work. \n\nAll opinions, findings and conclusions are that of the authors and do not necessarily reflect the views of the funding organisation and authors' affiliated institutions. \n\nCRediT authorship contribution statement. Ramit Debnath: Conceptualization, Methodology, Validation, Formal analysis, Investigation, Resources, Data curation, Writing \u2013 original draft, Writing \u2013 review & editing, Visualization, Supervision, Funding acquisition. Ronita Bardhan: Conceptualization, Methodology, Validation, Formal analysis, Writing \u2013 review & editing, Visualization, Supervision, Funding acquisition. Ashwin Misra: Data curation. Tianzhen Hong: Writing \u2013 review & editing. Vida Rozite: Writing \u2013 review & editing. Michael H. Ramage: Writing \u2013 review & editing, Funding acquisition. \n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\n", "abstract": "This study evaluates the effect of complete nationwide lockdown in 2020 on residential electricity demand across 13 Indian cities and the role of digitalisation using a public smart meter dataset. We undertake a data-driven approach to explore the energy impacts of work-from-home norms across five dwelling typologies. Our methodology includes climate correction, dimensionality reduction and machine learning-based clustering using Gaussian Mixture Models of daily load curves. Results show that during the lockdown, maximum daily peak demand increased by 150\u2013200% as compared to 2018 and 2019 levels for one room-units (RM1), one bedroom-units (BR1) and two bedroom-units (BR2) which are typical for low- and middle-income families. While the upper-middle- and higher-income dwelling units (i.e., three (3BR) and more-than-three bedroom-units (M3BR)) saw night-time demand rise by almost 44% in 2020, as compared to 2018 and 2019 levels. Our results also showed that new peak demand emerged for the lockdown period for RM1, BR1 and BR2 dwelling typologies. We found that the lack of supporting socioeconomic and climatic data can restrict a comprehensive analysis of demand shocks using similar public datasets, which informed policy implications for India's digitalisation. We further emphasised improving the data quality and reliability for effective data-centric policymaking.", "date": "2022-05", "date_type": "published", "publication": "Energy Policy", "volume": "164", "publisher": "Elsevier", "pagerange": "Art. No. 112886", "id_number": "CaltechAUTHORS:20220317-376372000", "issn": "0301-4215", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220317-376372000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Bill and Melinda Gates Foundation", "grant_number": "OPP1144" }, { "agency": "Churchill College" }, { "agency": "Isaac Newton Trust" }, { "agency": "Laudes Foundation" }, { "agency": "United Kingdom Space Agency (UKSA)" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.enpol.2022.112886", "pmcid": "PMC9022708", "primary_object": { "basename": "Lockdown_impacts_on_residential_electricity_demand_in_India__A_data-driven_and_non-intrusive_load_monitoring_study_using_Gaussian_mixture_models_-_PMC.pdf", "url": "https://authors.library.caltech.edu/records/g5zsj-a6f53/files/Lockdown_impacts_on_residential_electricity_demand_in_India__A_data-driven_and_non-intrusive_load_monitoring_study_using_Gaussian_mixture_models_-_PMC.pdf" }, "pub_year": "2022", "author_list": "Debnath, Ramit; Bardhan, Ronita; et al." }, { "id": "https://authors.library.caltech.edu/records/drvwk-k1b90", "eprint_id": 118351, "eprint_status": "archive", "datestamp": "2023-08-22 14:59:49", "lastmod": "2025-11-20 23:51:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Knyazev-Sergey", "name": { "family": "Knyazev", "given": "Sergey" }, "orcid": "0000-0003-0385-1831" }, { "name": { "family": "Chhugani", "given": "Karishma" }, "orcid": "0000-0001-8764-9352" }, { "name": { "family": "Sarwal", "given": "Varuni" }, "orcid": "0000-0001-7563-9835" }, { "name": { "family": "Ayyala", "given": "Ram" }, "orcid": "0000-0001-7275-271X" }, { "name": { "family": "Singh", "given": "Harman" }, "orcid": "0000-0002-3970-6276" }, { "id": "Karthikeyan-Smruthi", "name": { "family": "Karthikeyan", "given": "Smruthi" }, "orcid": "0000-0001-6226-4536" }, { "name": { "family": "Deshpande", "given": "Dhrithi" }, "orcid": "0000-0003-3794-7364" }, { "name": { "family": "Icer Baykal", "given": "Pelin" }, "orcid": "0000-0002-9542-5292" }, { "name": { "family": "Comarova", "given": "Zoia" } }, { "name": { "family": "Lu", "given": "Angela" } }, { "name": { "family": "Porozov", "given": "Yuri" }, "orcid": "0000-0002-5450-3135" }, { "name": { "family": "Vasylyeva", "given": "Tetyana I." }, "orcid": "0000-0002-9736-7022" }, { "name": { "family": "Wertheim", "given": "Joel O." }, "orcid": "0000-0003-4882-5856" }, { "name": { "family": "Tierney", "given": "Braden T." } }, { "name": { "family": "Chiu", "given": "Charles Y." }, "orcid": "0000-0003-2915-2094" }, { "name": { "family": "Sun", "given": "Ren" } }, { "name": { "family": "Wu", "given": "Aiping" } }, { "name": { "family": "Abedalthagafi", "given": "Malak S." }, "orcid": "0000-0003-1786-3366" }, { "name": { "family": "Pak", "given": "Victoria M." } }, { "name": { "family": "Nagaraj", "given": "Shivashankar H." } }, { "name": { "family": "Smith", "given": "Adam L." } }, { "name": { "family": "Skums", "given": "Pavel" }, "orcid": "0000-0003-4007-5624" }, { "name": { "family": "Pasaniuc", "given": "Bogdan" } }, { "name": { "family": "Komissarov", "given": "Andrey" } }, { "name": { "family": "Mason", "given": "Christopher E." }, "orcid": "0000-0002-1850-1642" }, { "name": { "family": "Bortz", "given": "Eric" }, "orcid": "0000-0002-1376-0012" }, { "name": { "family": "Lemey", "given": "Philippe" }, "orcid": "0000-0003-2826-5353" }, { "name": { "family": "Kondrashov", "given": "Fyodor" } }, { "name": { "family": "Beerenwinkel", "given": "Niko" }, "orcid": "0000-0002-0573-6119" }, { "name": { "family": "Lam", "given": "Tommy Tsan-Yuk" }, "orcid": "0000-0002-9769-1527" }, { "name": { "family": "Wu", "given": "Nicholas C." }, "orcid": "0000-0002-9078-6697" }, { "name": { "family": "Zelikovsky", "given": "Alex" }, "orcid": "0000-0003-4424-4691" }, { "name": { "family": "Knight", "given": "Rob" }, "orcid": "0000-0002-0975-9019" }, { "name": { "family": "Crandall", "given": "Keith A." }, "orcid": "0000-0002-0836-3389" }, { "name": { "family": "Mangul", "given": "Serghei" }, "orcid": "0000-0003-4770-3443" } ] }, "title": "Unlocking capacities of genomics for the COVID-19 response and future pandemics", "ispublished": "pub", "full_text_status": "public", "keywords": "Cell Biology; Molecular Biology; Biochemistry; Biotechnology", "note": "Our paper is dedicated to all freedom-loving people around the world, and to the people of Ukraine who fight for our freedom. We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions. We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially supported by National Science Foundation grants 2041984. T.L. is supported by the NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund (R7021-20), Innovation and Technology Commission's InnoHK funding (D24H) and Health and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828. M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W. was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S. acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly supported by Molecular Basis of Disease at Georgia State University and NIH awards R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread. J.O.W. was supported by NIH\u2013National Institute of Allergy and Infectious Diseases (NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V. is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers \"Digital biodesign and personalized healthcare\" N\u25e6075-15-2020-926. E.B. was supported by a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395) and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the California Department of Public Health, the Innovative Genomics Institute (IGI) at the University of California, Berkeley, and University of California, San Francisco, NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project 206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C. acknowledges support from the US NSF award EEID-IOS-2109688. F.K.'s work was supported by an ERC Consolidator grant to F.K. (771209\u2013CharFL). \n\nThese authors contributed equally: Sergey Knyazev, Karishma Chhugani. \n\nContributions. S.M. conceived of the idea presented and supervised the project. S.M., S. Knyazev and K.C. led the project. S.M., S. Knyazev, K.C., S. Karthikeyan, D.D., P.I.B., Z.C., A.L., Y.P., T.I.V., J.O.W., B.T.T., C.Y.C., R.S., A.W., M.S.A., V.M.P., S.H.N, A.L.S., P.S., A.K., B.P., C.E.M., E.B., F.K., N.C.W., N.B., P.L., S.K.N., T.T.-Y.L., A.Z., R.K. and K.A.C. contributed to the writing of the manuscript. V.S. produced figures in the main text. V.S. and H.S. produced supplementary figures. H.S. and R.A. created supplementary tables. All authors discussed the text and commented on the manuscript. All authors read and approved the final manuscript. These authors contributed equally: Sergey Knyazev and Karishma Chhugani (joint first co-authors). These authors contributed equally: Varuni Sarwal, Ram Ayyala and Harman Singh (joint second co-authors). \n\nThe authors declare no competing interests.", "abstract": "During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.", "date": "2022-04", "date_type": "published", "publication": "Nature Methods", "volume": "19", "number": "4", "publisher": "Nature Publishing Group", "pagerange": "374-380", "id_number": "CaltechAUTHORS:20221215-540336000.14", "issn": "1548-7091", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221215-540336000.14", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "DBI-2041984" }, { "agency": "National Natural Science Foundation of China", "grant_number": "31922087" }, { "agency": "Research Grants Council of Hong Kong", "grant_number": "C7144-20GF" }, { "agency": "Research Grants Council of Hong Kong", "grant_number": "R7021-20" }, { "agency": "Innovation and Technology Commission (Hong Kong)", "grant_number": "D24H" }, { "agency": "Health and Medical Research Fund (China)", "grant_number": "COVID190223" }, { "agency": "NIH", "grant_number": "1R01EB025022" }, { "agency": "NSF", "grant_number": "CCF-2047828" }, { "agency": "King Abdulaziz City for Science and Technology (KACST)" }, { "agency": "Saudi Human Genome Project" }, { "agency": "NIH", "grant_number": "R00 AI139445" }, { "agency": "NIH", "grant_number": "DP2 AT011966" }, { "agency": "NIH", "grant_number": "R01 AI167910" }, { "agency": "NSF", "grant_number": "CBET-2029025" }, { "agency": "NIH", "grant_number": "1R01EB025022-01" }, { "agency": "NIH", "grant_number": "1R21CA241044-01A1" }, { "agency": "Georgia State University" }, { "agency": "NIH", "grant_number": "R01 HG009120" }, { "agency": "NIH", "grant_number": "R01 MH115676" }, { "agency": "NIH", "grant_number": "R01 AI153827" }, { "agency": "NIH", "grant_number": "U01 HG011715" }, { "agency": "Chinese Academy of Medical Sciences", "grant_number": "2021-I2M-1-061" }, { "agency": "NSF", "grant_number": "DBI-2038509" }, { "agency": "Centers for Disease Control and Prevention", "grant_number": "30055281" }, { "agency": "NIH", "grant_number": "R01 AI135992" }, { "agency": "Branco Weiss Fellowship" }, { "agency": "Ministry of Science and Higher Education of the Russian Federation", "grant_number": "N\u25e6075-15-2020-926" }, { "agency": "NIH", "grant_number": "P20GM103395" }, { "agency": "NIH", "grant_number": "75N93019R00028" }, { "agency": "Testing for America" }, { "agency": "OpenCovidScreen Foundation" }, { "agency": "Igor Tulchinsky" }, { "agency": "WorldQuant Foundation" }, { "agency": "Pershing Square Foundation" }, { "agency": "Citadel Foundation" }, { "agency": "NIH", "grant_number": "R01AI125416" }, { "agency": "NIH", "grant_number": "R01AI151059" }, { "agency": "NIH", "grant_number": "R21AI129851" }, { "agency": "NIH", "grant_number": "U01DA053941" }, { "agency": "Alfred P. Sloan Foundation", "grant_number": "G-2015-13964" }, { "agency": "Centers for Disease Control and Prevention", "grant_number": "6NU50CK000539" }, { "agency": "California Department of Public Health" }, { "agency": "University of California, Berkeley" }, { "agency": "University of California, San Francisco" }, { "agency": "NIH", "grant_number": "R33AI12945" }, { "agency": "Centers for Disease Control and Prevention", "grant_number": "75D30121C10991" }, { "agency": "Russian Foundation for Basic Research", "grant_number": "20-515-80017" }, { "agency": "European Research Council (ERC)", "grant_number": "725422" }, { "agency": "Wellcome Trust", "grant_number": "206298/Z/17/Z" }, { "agency": "NIH", "grant_number": "R01 AI153044" }, { "agency": "NIH", "grant_number": "U19 AI135995" }, { "agency": "NSF", "grant_number": "DEB-2109688" }, { "agency": "European Research Council (ERC)", "grant_number": "771209" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1038/s41592-022-01444-z", "pmcid": "PMC9467803", "pub_year": "2022", "author_list": "Knyazev, Sergey; Chhugani, Karishma; et al." }, { "id": "https://authors.library.caltech.edu/records/jy800-3zf83", "eprint_id": 114207, "eprint_status": "archive", "datestamp": "2023-08-22 14:06:45", "lastmod": "2025-11-20 22:09:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kadakia-Shevali", "name": { "family": "Kadakia", "given": "Shevali" }, "orcid": "0000-0002-6322-8956" }, { "id": "Stratton-Catherine", "name": { "family": "Stratton", "given": "Catherine" }, "orcid": "0000-0002-1841-4565" }, { "id": "Wu-Yinfei", "name": { "family": "Wu", "given": "Yinfei" }, "orcid": "0000-0002-9486-1279" }, { "id": "Feliciano-Josemari", "name": { "family": "Feliciano", "given": "Josemari" }, "orcid": "0000-0002-2107-0687" }, { "id": "Tuakli-Wosornu-Yetsa-A", "name": { "family": "Tuakli-Wosornu", "given": "Yetsa A." }, "orcid": "0000-0001-5557-6953" } ] }, "title": "The Accessibility of YouTube Fitness Videos for Individuals Who Are Disabled Before and During the COVID-19 Pandemic: Preliminary Application of a Text Analytics Approach", "ispublished": "pub", "full_text_status": "public", "keywords": "persons with disabilities; disability; exercise; physical activity; digital health; YouTube; accessibility; fitness; COVID-19; text analysis; social media; video; Computer Science Applications; Health Informatics; Medicine (miscellaneous)", "note": "\u00a9 2022 Shevali Kadakia, Catherine Stratton, Yinfei Wu, Josemari Feliciano, Yetsa A Tuakli-Wosornu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work, first published in JMIR Formative Research, is properly cited. The complete bibliographic information, a link to the original publication on https://formative.jmir.org, as well as this copyright and license information must be included. \n\nEdited by A Mavragani; submitted 09.10.21; peer-reviewed by R Shimkhada, L Herrmann; comments to author 23.11.21; revised version received 31.12.21; accepted 14.01.22; published 15.02.22. \n\nConflicts of Interest: None declared.\n\nPublished - PDF.pdf
", "abstract": "Background: People with disabilities face barriers to in-person physical activity (PA), including a lack of adaptive equipment and knowledgeable instructors. Given this and the increased need for digital resources due to widespread COVID-19 lockdowns, it is necessary to assess the accessibility of digital fitness resources for people with disabilities. To investigate whether YouTube fitness content creators have made videos accessible to people with disabilities would be informative about access to PA during COVID-19 and could also provide insight into the feasibility of individuals who are disabled relying on YouTube for PA in a post\u2013COVID-19 world. \n\nObjective: This study aims to ascertain if disability-friendly PA videos on YouTube are accessible through searching general fitness terms and whether a change in the availability of accessible fitness resources for people with disabilities occurred on YouTube between before and during the COVID-19 pandemic on \"Hospital/Medical Institutions,\" \"Individual(s),\" and \"Other(s)\" channels. Secondary aims are to investigate if different categories of YouTube channels produce more accessible fitness content and highlight any disparities in disability-friendly PA content on YouTube. \n\nMethods: A cross-sectional text analysis of exercise-related YouTube videos was conducted. The authors used Python (version 3.0) to access the YouTube database via its data application programming interface. Terms pertaining to PA that were searched on YouTube were at-home exercise, exercise at home, exercise no equipment, home exercise, home-based exercise, no equipment workout, and workout no equipment. Various elements (eg, view count and content generation) of the videos published between January 1 and June 30, 2019 (n=700), were compared to the elements of videos published between January 1 and June 30, 2020 (n=700). To capture a broad idea of disability-friendly videos on YouTube, videos were labeled \"accessible\" if they were found in the first 100 video results and if their title, description, or tags contained the following terms: para, paralympic, adaptive, adapted, disabled, disability, differently abled, disability-friendly, wheelchair accessible, and inclusive. Each video and channel were categorized as \"Hospitals/Medical Institutions,\" \"Individuals,\" or \"Other(s).\" \n\nResults: The analysis revealed a statistically significant increase in viewership of fitness content on YouTube (P=.001) and in fitness content generated by Hospitals/Medical Institutions (P=.004). Accessible terms applicable to people with disabilities had minimal appearances in 2019 (21 videos) and 2020 (19 videos). None of the top viewed fitness videos that populated on YouTube from 2019 or 2020 were accessible. \n\nConclusions: The proportion of accessible disability-friendly videos remains diminutive relative to the prevalence of disability in the general population, revealing that disability-friendly videos are seldom findable on YouTube. Thus, the need for disability-friendly fitness content to be easily searched and found remains urgent if access to digital fitness resources is to improve.", "date": "2022-02-22", "date_type": "published", "publication": "JMIR Formative Research", "volume": "6", "number": "2", "publisher": "JMIR Publications Inc.", "pagerange": "Art. No. e34176", "id_number": "CaltechAUTHORS:20220411-77938600", "issn": "2561-326X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220411-77938600", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.2196/34176", "pmcid": "PMC8849230", "primary_object": { "basename": "PDF.pdf", "url": "https://authors.library.caltech.edu/records/jy800-3zf83/files/PDF.pdf" }, "pub_year": "2022", "author_list": "Kadakia, Shevali; Stratton, Catherine; et al." }, { "id": "https://authors.library.caltech.edu/records/mz8bn-8ne72", "eprint_id": 110909, "eprint_status": "archive", "datestamp": "2023-10-04 22:00:08", "lastmod": "2025-11-20 22:08:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tanaka-Shiho", "name": { "family": "Tanaka", "given": "Shiho" }, "orcid": "0000-0002-2562-9660" }, { "id": "Olson-C-Anders", "name": { "family": "Olson", "given": "C. Anders" } }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "id": "Higashide-Wendy", "name": { "family": "Higashide", "given": "Wendy" } }, { "id": "Gonzales-Marcos", "name": { "family": "Gonzales", "given": "Marcos" } }, { "id": "Taft-Justin", "name": { "family": "Taft", "given": "Justin" }, "orcid": "0000-0002-9998-0429" }, { "id": "Richardson-Ashley", "name": { "family": "Richardson", "given": "Ashley" } }, { "id": "Martin-Fernandez-Marta", "name": { "family": "Martin-Fernandez", "given": "Marta" }, "orcid": "0000-0003-2714-8120" }, { "id": "Bogunovic-Dusan", "name": { "family": "Bogunovic", "given": "Dusan" }, "orcid": "0000-0002-9277-3232" }, { "id": "Gnanapragasam-Priyanthi-N-P", "name": { "family": "Gnanapragasam", "given": "Priyanthi N. P." } }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Spilman-Patricia-R", "name": { "family": "Spilman", "given": "Patricia" } }, { "id": "Niazi-Kayvan", "name": { "family": "Niazi", "given": "Kayvan" } }, { "id": "Rabizadeh-Shahrooz", "name": { "family": "Rabizadeh", "given": "Shahrooz" }, "orcid": "0000-0002-8609-7645" }, { "id": "Soon-Shiong-Patrick", "name": { "family": "Soon-Shiong", "given": "Patrick" }, "orcid": "0000-0002-4682-8298" } ] }, "title": "Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2022 The author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).\n\nReceived 17 September 2021, Revised 6 December 2021, Accepted 14 January 2022, Available online 20 January 2022, Version of Record 8 February 2022.\n\nWe thank J. Vielmetter, P. Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance and K. Huey-Tubman for assistance with soluble spike purification. Electron microscopy was performed in the Caltech Cryo-EM Center with assistance from S. Chen and A. Malyutin. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support the Molecular Observatory. We thank J. Kaiser, director of the Molecular Observatory at Caltech, and beamline staff C. Smith and S. Russi at SSRL for data collection assistance. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the US Department of Energy Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by the National Institutes of Health, National Institute of General Medical Sciences (P30GM133894). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. This work was supported by NIH (P01-AI138938-S1 to P.J.B.), the Caltech Merkin Institute for Translational Research (P.J.B.), and a George Mason University Fast Grant (P.J.B.). C.O.B was supported by the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Postdoctoral Enrichment Program from the Burroughs Wellcome Fund. This work was also supported by ImmunityBio, Inc.\n\nAuthor contributions:\nExperimental designs, C.A.O., S.T., C.O.B., K.N., S.R., and P.S.-S.; mRNA library display, C.A.O.; cloning, C.A.O. and W.H.; protein expression and purification, C.A.O., S.T., and M.G.; kinetic analysis, ACE2 blocking assay, epitope binning, and convalescent plasma blocking assay, S.T.; developability assays M.G. and S.T.; cryo-EM and X-ray crystallography, C.O.B. and P.J.B.; Vero E6 live virus neutralization assay, J.T., A.R., M.M.-F., and D.B.; pseudovirus neutralization assay, P.G.; manuscript preparation, S.T., C.O.B., C.A.O., and P.S.\n\nDeclaration of interests:\nC.A.O., S.T., W.H., K.N., and P.S.-S. are inventors for an international patent application with this work (US 11,015,188 B2). M.G. and P.S. are employees of ImmunityBio, Inc., and S.R. was a former employee and is a current shareholder of ImmunityBio, Inc.\n\nPublished - 1-s20-S221112472200064X-main.pdf
Submitted - 20210914-460356v1full.pdf
Supplemental Material - 1-s20-S221112472200064X-mmc1.pdf
", "abstract": "The increasing prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identify a set of antibodies against SARS-CoV-2 spike (S) proteins and characterize the structures of nAbs that recognize epitopes in the S1 subunit of the S glycoprotein. These structural studies reveal distinct binding modes for several antibodies, including the targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interact with angiotensin-converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. Further, we engineer a potent ACE2-blocking nAb to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is an approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.", "date": "2022-02-08", "date_type": "published", "publication": "Cell Reports", "volume": "38", "number": "6", "publisher": "Cell Press", "pagerange": "Art. No. 110348", "id_number": "CaltechAUTHORS:20210915-214123136", "issn": "2211-1247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210915-214123136", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-76SF00515" }, { "agency": "NIH", "grant_number": "P30GM133894" }, { "agency": "NIH", "grant_number": "P01-AI138938-S1" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "George Mason University" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "ImmunityBio, Inc." } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.celrep.2022.110348", "pmcid": "PMC8769934", "primary_object": { "basename": "1-s20-S221112472200064X-main.pdf", "url": "https://authors.library.caltech.edu/records/mz8bn-8ne72/files/1-s20-S221112472200064X-main.pdf" }, "related_objects": [ { "basename": "1-s20-S221112472200064X-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/mz8bn-8ne72/files/1-s20-S221112472200064X-mmc1.pdf" }, { "basename": "20210914-460356v1full.pdf", "url": "https://authors.library.caltech.edu/records/mz8bn-8ne72/files/20210914-460356v1full.pdf" } ], "pub_year": "2022", "author_list": "Tanaka, Shiho; Olson, C. Anders; et al." }, { "id": "https://authors.library.caltech.edu/records/3evkm-adv60", "eprint_id": 113129, "eprint_status": "archive", "datestamp": "2023-08-22 13:50:23", "lastmod": "2025-11-21 00:09:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pushpawela-Buddhi", "name": { "family": "Pushpawela", "given": "Buddhi" }, "orcid": "0000-0002-3633-4104" }, { "id": "Amanatidis-Stavros", "name": { "family": "Amanatidis", "given": "Stavros" }, "orcid": "0000-0002-4924-8424" }, { "id": "Huang-Yuanlong", "name": { "family": "Huang", "given": "Yuanlong" }, "orcid": "0000-0002-6726-8904" }, { "id": "Flagan-R-C", "name": { "family": "Flagan", "given": "Richard C." }, "orcid": "0000-0001-5690-770X" } ] }, "title": "Variability of the penetration of particles through facemasks", "ispublished": "pub", "full_text_status": "public", "keywords": "Pollution; General Materials Science; Environmental Chemistry", "note": "\u00a9 2021 American Association for Aerosol Research. \n\nReceived 30 Jun 2021, Accepted 21 Oct 2021, Accepted author version posted online: 30 Nov 2021, Published online: 16 Dec 2021. \n\nThe authors acknowledge Professor Niles Pierce and Caltech book store for supplying some samples. The authors also like to thank Ryan Ward and Benjamin Laccetti for useful discussions. \n\nThe research was supported by the Jacobs Institute for Molecular Engineering for Medicine, California Institute of Technology, Pasadena, CA. \n\nAuthor contributions: RCF planned and designed the experiments. BP, SA and YH prepared the experimental setup. BP carried out the measurements, analyzed the data, and generated the figures. BP and RCF wrote and edited the manuscript. All authors reviewed the manuscript. \n\nNo potential conflict of interest was reported by the authors.\n\nSupplemental Material - uast_a_2003291_sm4019.docx
", "abstract": "COVID-19 is transmitted, at least in part, by airborne particles emitted by infected individuals. Wearing masks is one of the key actions that are required to prevent spreading COVID-19. To understand the variability in the performance, we evaluated the material performance of the whole mask, as manufactured, in terms of the penetration of particles, comfort and the quality factor of multiple copies of 29 different types. All masks were mounted to prevent leakage around the edges so the mask material and manufacture was tested, but the effects of the fit were not considered. The results of this study thus represent the upper bound of the performance of facemasks since leakage around the edges due to poor fit often overwhelms filtration through the mask material. The tests were performed at a steady flow rate of 30\u2009L/min; mean values of the performance parameters were calculated for two different sizes; 0.12\u2009\u00b5m and 0.3\u2009\u00b5m. Of the masks tested, for 0.12\u2009\u00b5m particles, N95 face filtering respirators consistently had the lowest peak penetration 1.7\u2009\u00b1\u20090.5%, while KN95 masks allowed 3.7\u2009\u00b1\u20092.6% penetration. In contrast, penetration through pleated procedure masks was 14.7\u2009\u00b1\u200916.9% due to one outlier - with that outlier removed, penetration decreased to 7.1\u2009\u00b1\u20094.3%; cloth masks allowed 26.4\u2009\u00b1\u20099.3% penetration. Tests on multiple copies of different masks demonstrated consistent performance of N95s, but considerably greater variability within the other classes of masks tested, leading to uncertainty in the degree of protection that they would provide.", "date": "2022-02-01", "date_type": "published", "publication": "Aerosol Science and Technology", "volume": "56", "number": "2", "publisher": "American Association for Aerosol Research", "pagerange": "186-203", "id_number": "CaltechAUTHORS:20220127-913884200", "issn": "0278-6826", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220127-913884200", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Jacobs Institute for Molecular Engineering for Medicine" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Jacobs-Institute-for-Molecular-Engineering-for-Medicine" } ] }, "doi": "10.1080/02786826.2021.2003291", "primary_object": { "basename": "uast_a_2003291_sm4019.docx", "url": "https://authors.library.caltech.edu/records/3evkm-adv60/files/uast_a_2003291_sm4019.docx" }, "pub_year": "2022", "author_list": "Pushpawela, Buddhi; Amanatidis, Stavros; et al." }, { "id": "https://authors.library.caltech.edu/records/r8qh8-y4065", "eprint_id": 108641, "eprint_status": "archive", "datestamp": "2023-08-20 06:53:20", "lastmod": "2025-11-21 01:44:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Savela-Emily-S", "name": { "family": "Savela", "given": "Emily S." }, "orcid": "0000-0001-9614-4276" }, { "id": "Winnett-Alexander-Viloria", "name": { "family": "Winnett", "given": "Alexander Viloria" }, "orcid": "0000-0002-7338-5605" }, { "id": "Romano-Anna-E", "name": { "family": "Romano", "given": "Anna E." }, "orcid": "0000-0003-1871-1727" }, { "id": "Porter-Michael-K", "name": { "family": "Porter", "given": "Michael K." }, "orcid": "0000-0002-0777-7563" }, { "id": "Shelby-Natasha", "name": { "family": "Shelby", "given": "Natasha" }, "orcid": "0000-0001-9097-3663" }, { "id": "Akana-Reid", "name": { "family": "Akana", "given": "Reid" }, "orcid": "0000-0003-4422-587X" }, { "id": "Ji-Jenny", "name": { "family": "Ji", "given": "Jenny" }, "orcid": "0000-0002-7901-5605" }, { "id": "Cooper-Matthew-M", "name": { "family": "Cooper", "given": "Matthew M." }, "orcid": "0000-0002-5868-5159" }, { "id": "Schlenker-Noah-W", "name": { "family": "Schlenker", "given": "Noah W." }, "orcid": "0000-0002-8581-4403" }, { "id": "Reyes-Jessica-A", "name": { "family": "Reyes", "given": "Jessica A." }, "orcid": "0000-0002-5507-7633" }, { "id": "Carter-Alyssa-M", "name": { "family": "Carter", "given": "Alyssa M." }, "orcid": "0000-0002-2776-9421" }, { "id": "Barlow-Jacob-T", "name": { "family": "Barlow", "given": "Jacob T." }, "orcid": "0000-0002-1842-4835" }, { "id": "Tognazzini-Colten", "name": { "family": "Tognazzini", "given": "Colten" } }, { "id": "Feaster-Matthew", "name": { "family": "Feaster", "given": "Matthew" }, "orcid": "0000-0001-9966-2845" }, { "id": "Goh-Ying-Ying", "name": { "family": "Goh", "given": "Ying-Ying" }, "orcid": "0000-0001-5136-7214" }, { "id": "Ismagilov-R-F", "name": { "family": "Ismagilov", "given": "Rustem F." }, "orcid": "0000-0002-3680-4399" } ] }, "title": "Quantitative SARS-CoV-2 Viral-Load Curves in Paired Saliva Samples and Nasal Swabs Inform Appropriate Respiratory Sampling Site and Analytical Test Sensitivity Required for Earliest Viral Detection", "ispublished": "pub", "full_text_status": "public", "keywords": "RT-qPCR, COVID-19, case-ascertained, diagnostics, household study,\nlongitudinal sampling, nasal swab, presymptomatic, saliva, surveillance, transmission", "note": "\u00a9 2022 Savela et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived 24 August 2021; Returned for modification 21 September 2021; Accepted 10 December 2021; Accepted manuscript posted online 15 December 2021; Published 16 February 2022. \n\nWe thank Lauriane Quenee, Junie Hildebrandt, Grace Fisher-Adams, RuthAnne Bevier, Chantal D'Apuzzo, Ralph Adolphs, Victor Rivera, Steve Chapman, Gary Waters, Leonard Edwards, Gaylene Ursua, Cynthia Ramos, and Shannon Yamashita for their assistance and advice on study implementation and/or administration. We thank Jessica Leong, Jessica Slagle, Mika Walton, Angel Navarro, Daniel Brenner, and Ojas Pradhan for volunteering their time to help with this study, Si Hyung Jin for helping with a literature review, and Mary Arrastia for providing biosafety support. We thank Maira Phelps, Lienna Chan, Lucy Li, Dan Lu, and Amy Kistler at the Chan Zuckerberg Biohub for performing SARS-CoV-2 sequencing. We thank Angie Cheng, Susan Magdaleno, Christian Kis, Monica Herrera, and Zaina Lemeir for technical discussions regarding saliva extraction and ddPCR detection. We thank Jennifer Fulcher, Debika Bhattacharya, and Matthew Bidwell Goetz for their ideas on potential study populations and early study design. We thank Omai Garner and David Beenhouwer for providing materials for initial nasal-swab validation. We thank Martin Hill, Alma Sanchez, Scott Kim, Debbie Noble, Nina Paddock, Whitney Harrison, Emily Holman, Isaac Turner, Vivek Desai, Luke Wade, Tom Mayell, Stu Miller, and Jennifer Howes for their support with recruitment. We thank Allison Rhines, Karen Heichman, and Dan Wattendorf for valuable discussions. Finally, we thank all the case investigators and contact tracers at the Pasadena Public Health Department and the City of Long Beach Department of Health & Human Services for their efforts in study recruitment and their work in the pandemic response. \n\nR.F.I. is a cofounder, consultant, and a director and has stock ownership of Talis Biomedical Corp. In addition, R.F.I. is an inventor on a series of patents licensed by the University of Chicago to Bio-Rad Laboratories, Inc., in the context of ddPCR. \n\nThis study is based on research funded in part by the Bill & Melinda Gates Foundation (INV-023124). The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation. This work was also funded by the Ronald and Maxine Linde Center for New Initiatives at the California Institute of Technology and the Jacobs Institute for Molecular Engineering for Medicine at the California Institute of Technology. A.V.W. is supported by a National Institutes of Health NIGMS predoctoral training grant (GM008042) and a UCLA DGSOM Geffen fellowship; M.M.C. is supported by a Caltech graduate student fellowship, and M.K.P. and J.T.B. are each partially supported by a National Institutes of Health Biotechnology Leadership Predoctoral Training Program (BLP) fellowship from Caltech's Donna and Benjamin M. Rosen Bioengineering Center (T32GM112592).\n\nPublished - jcm.01785-21.pdf
Submitted - 2021.04.02.21254771v2.full.pdf
Supplemental Material - jcm.01785-21-s0001.pdf
", "abstract": "Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and presymptomatic transmission, curb the spread of variants, and maximize treatment efficacy. Low-analytical-sensitivity nasal-swab testing is commonly used for surveillance and symptomatic testing, but the ability of these tests to detect the earliest stages of infection has not been established. In this study, conducted between September 2020 and June 2021 in the greater Los Angeles County, California, area, initially SARS-CoV-2-negative household contacts of individuals diagnosed with COVID-19 prospectively self-collected paired anterior-nares nasal-swab and saliva samples twice daily for viral-load quantification by high-sensitivity reverse-transcription quantitative PCR (RT-qPCR) and digital-RT-PCR assays. We captured viral-load profiles from the incidence of infection for seven individuals and compared diagnostic sensitivities between respiratory sites. Among unvaccinated persons, testing saliva with a high-analytical-sensitivity assay detected infection up to 4.5\u2009days before viral loads in nasal swabs reached concentrations detectable by low-analytical-sensitivity nasal-swab tests. For most participants, nasal swabs reached higher peak viral loads than saliva but were undetectable or at lower loads during the first few days of infection. High-analytical-sensitivity saliva testing was most reliable for earliest detection. Our study illustrates the value of acquiring early (within hours after a negative high-sensitivity test) viral-load profiles to guide the appropriate analytical sensitivity and respiratory site for detecting earliest infections. Such data are challenging to acquire but critical to designing optimal testing strategies with emerging variants in the current pandemic and to respond to future viral pandemics.", "date": "2022-02", "date_type": "published", "publication": "Journal of Clinical Microbiology", "volume": "60", "number": "2", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e01785-21", "id_number": "CaltechAUTHORS:20210407-080559241", "issn": "0095-1137", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210407-080559241", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-023124" }, { "agency": "Ronald and Maxine Linde Center for New Initiatives" }, { "agency": "Jacobs Institute for Molecular Engineering for Medicine" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM008042" }, { "agency": "UCLA" }, { "agency": "Caltech" }, { "agency": "Donna and Benjamin M. Rosen Bioengineering Center" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM112592" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Rosen-Bioengineering-Center" }, { "id": "Jacobs-Institute-for-Molecular-Engineering-for-Medicine" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/JCM.01785-21", "pmcid": "PMC8849374", "primary_object": { "basename": "2021.04.02.21254771v2.full.pdf", "url": "https://authors.library.caltech.edu/records/r8qh8-y4065/files/2021.04.02.21254771v2.full.pdf" }, "related_objects": [ { "basename": "jcm.01785-21.pdf", "url": "https://authors.library.caltech.edu/records/r8qh8-y4065/files/jcm.01785-21.pdf" }, { "basename": "jcm.01785-21-s0001.pdf", "url": "https://authors.library.caltech.edu/records/r8qh8-y4065/files/jcm.01785-21-s0001.pdf" } ], "pub_year": "2022", "author_list": "Savela, Emily S.; Winnett, Alexander Viloria; et al." }, { "id": "https://authors.library.caltech.edu/records/z1xg5-jwm73", "eprint_id": 112649, "eprint_status": "archive", "datestamp": "2023-09-15 07:20:57", "lastmod": "2025-11-21 02:05:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhu-Yanzhe", "name": { "family": "Zhu", "given": "Yanzhe" }, "orcid": "0000-0002-2260-1830" }, { "id": "Wu-Xunyi", "name": { "family": "Wu", "given": "Xunyi" }, "orcid": "0000-0001-9710-6896" }, { "id": "Gu-Alan-Yalun", "name": { "family": "Gu", "given": "Alan Y." }, "orcid": "0000-0001-8095-3634" }, { "id": "Dobelle-L\u00e9opold", "name": { "family": "Dobelle", "given": "L\u00e9opold" } }, { "id": "Cid-Cl\u00e9ment-A", "name": { "family": "Cid", "given": "Cl\u00e9ment A." }, "orcid": "0000-0002-7293-035X" }, { "id": "Li-Jing-ENVENG", "name": { "family": "Li", "given": "Jing" }, "orcid": "0000-0003-0639-9422" }, { "id": "Hoffmann-M-R", "name": { "family": "Hoffmann", "given": "Michael R." }, "orcid": "0000-0001-6495-1946" } ] }, "title": "Membrane-Based In-Gel Loop-Mediated Isothermal Amplification (mgLAMP) System for SARS-CoV-2 Quantification in Environmental Waters", "ispublished": "pub", "full_text_status": "public", "keywords": "SARS-CoV-2, RT-LAMP, hydrogel, membrane, environmental quantification of SARS-CoV-2 in milliliters of environmental water samples; Environmental Chemistry; General Chemistry", "note": "\u00a9 2021 American Chemical Society. This article is made available via the ACS COVID-19 subset for unrestricted RESEARCH re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. \n\nReceived: July 10, 2021; Revised: November 17, 2021; Accepted: November 17, 2021; Published: December 30, 2021. \n\nThe authors thank Caltech Biological Imaging Facility for use of the confocal microscope and Dr. Yuxing Yao for assistance with DLS measurements. This work was supported in whole by the Bill & Melinda Gates Foundation OPP1192379, INV-018569, and INV-030223. \n\nAuthor Contributions: The manuscript was written through contributions of all authors. M.R.H., J.L., and C.A.C. acquired funding for this study. M.R.H. and J.L. conceived the concept of this study. J.L. and Y.Z. designed the study. J.L., Y.Z., X.W., L.D., and A.G. performed the experiments. J.L., Y.Z., and A.G. analyzed the data. Y.Z., J.L., and A.G. wrote the manuscript. M.R.H., L.D., and C.A.C. edited the manuscript. All authors approved the manuscript. \n\nThe authors declare no competing financial interest. \n\nData and materials availability: The manuscript and the Supporting Information contain all the data needed to evaluate the conclusions in the paper. Correspondence and requests for materials should be addressed to J.L. and M.R.H.\n\nPublished - acs.est.1c04623.pdf
Supplemental Material - es1c04623_si_001.pdf
", "abstract": "Since the COVID-19 pandemic is expected to become endemic, quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambient waters is critical for environmental surveillance and for early detection of outbreaks. Herein, we report the development of a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system that is designed for the rapid point-of-use quantification of SARS-CoV-2 particles in environmental waters. The mgLAMP system integrates the viral concentration, in-assay viral lysis, and on-membrane hydrogel-based RT-LAMP quantification using enhanced fluorescence detection with a target-specific probe. With a sample-to-result time of less than 1 h, mgLAMP successfully detected SARS-CoV-2 below 0.96 copies/mL in Milli-Q water. In surface water, the lowest detected SARS-CoV-2 concentration was 93 copies/mL for mgLAMP, while the reverse transcription quantitative polymerase chain reaction (RT-qPCR) with optimal pretreatment was inhibited at 930 copies/mL. A 3D-printed portable device is designed to integrate heated incubation and fluorescence illumination for the simultaneous analysis of nine mgLAMP assays. Smartphone-based imaging and machine learning-based image processing are used for the interpretation of results. In this report, we demonstrate that mgLAMP is a promising method for large-scale environmental surveillance of SARS-CoV-2 without the need for specialized equipment, highly trained personnel, and labor-intensive procedures.", "date": "2022-01-18", "date_type": "published", "publication": "Environmental Science and Technology", "volume": "56", "number": "2", "publisher": "American Chemical Society", "pagerange": "862-873", "id_number": "CaltechAUTHORS:20220103-231324400", "issn": "0013-936X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220103-231324400", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Bill and Melinda Gates Foundation", "grant_number": "OPP1192379" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-018569" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-030223" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1021/acs.est.1c04623", "pmcid": "PMC8751019", "primary_object": { "basename": "acs.est.1c04623.pdf", "url": "https://authors.library.caltech.edu/records/z1xg5-jwm73/files/acs.est.1c04623.pdf" }, "related_objects": [ { "basename": "es1c04623_si_001.pdf", "url": "https://authors.library.caltech.edu/records/z1xg5-jwm73/files/es1c04623_si_001.pdf" } ], "pub_year": "2022", "author_list": "Zhu, Yanzhe; Wu, Xunyi; et al." }, { "id": "https://authors.library.caltech.edu/records/dgkdq-9f077", "eprint_id": 112568, "eprint_status": "archive", "datestamp": "2023-10-09 15:34:35", "lastmod": "2025-11-21 02:01:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Vanshylla-Kanika", "name": { "family": "Vanshylla", "given": "Kanika" }, "orcid": "0000-0003-4552-9170" }, { "id": "Fan-Chengcheng", "name": { "family": "Fan", "given": "Chengcheng" }, "orcid": "0000-0003-4213-5758" }, { "id": "Wunsch-Marie", "name": { "family": "Wunsch", "given": "Marie" } }, { "id": "Poopalasingam-Nareshkumar", "name": { "family": "Poopalasingam", "given": "Nareshkumar" }, "orcid": "0000-0002-4981-6209" }, { "id": "Meijers-Matthijs", "name": { "family": "Meijers", "given": "Matthijs" }, "orcid": "0000-0002-1876-8064" }, { "id": "Kreer-Christoph", "name": { "family": "Kreer", "given": "Christoph" }, "orcid": "0000-0002-9140-9850" }, { "id": "Kleipass-Franziska", "name": { "family": "Kleipass", "given": "Franziska" } }, { "id": "Ruchnewitz-Denis", "name": { "family": "Ruchnewitz", "given": "Denis" }, "orcid": "0000-0001-5740-6958" }, { "id": "Ercanoglu-Meryem-S", "name": { "family": "Ercanoglu", "given": "Meryem S." } }, { "id": "Gruell-Henning", "name": { "family": "Gruell", "given": "Henning" }, "orcid": "0000-0002-0725-7138" }, { "id": "M\u00fcnn-Friederike", "name": { "family": "M\u00fcnn", "given": "Friederike" } }, { "id": "Pohl-Kai", "name": { "family": "Pohl", "given": "Kai" } }, { "id": "Janicki-Hanna", "name": { "family": "Janicki", "given": "Hanna" } }, { "id": "Nolden-Tobias", "name": { "family": "Nolden", "given": "Tobias" }, "orcid": "0000-0002-8996-5612" }, { "id": "Bartl-Simone", "name": { "family": "Bartl", "given": "Simone" } }, { "id": "Stein-Saskia-Catherina", "name": { "family": "Stein", "given": "Saskia C." } }, { "id": "Augustin-Max", "name": { "family": "Augustin", "given": "Max" }, "orcid": "0000-0002-2300-9337" }, { "id": "Dewald-Felix", "name": { "family": "Dewald", "given": "Felix" } }, { "id": "Gieselmann-Lutz", "name": { "family": "Gieselmann", "given": "Lutz" } }, { "id": "Schommers-Philipp", "name": { "family": "Schommers", "given": "Philipp" }, "orcid": "0000-0003-3375-6800" }, { "id": "Schulz-Thomas-F", "name": { "family": "Schulz", "given": "Thomas F." } }, { "id": "Sander-Leif-Erik", "name": { "family": "Sander", "given": "Leif Erik" } }, { "id": "Koch-Manuel", "name": { "family": "Koch", "given": "Manuel" }, "orcid": "0000-0002-2962-7814" }, { "id": "\u0141uksza-Marta", "name": { "family": "\u0141uksza", "given": "Marta" } }, { "id": "L\u00e4ssig-Michael", "name": { "family": "L\u00e4ssig", "given": "Michael" }, "orcid": "0000-0002-3575-6719" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Klein-Florian", "name": { "family": "Klein", "given": "Florian" } } ] }, "title": "Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; SARS-CoV-2; broadly neutralizing antibodies; cryo-EM; variants of concern; emerging variants; ultrapotent monoclonal antibodies; Virology; Microbiology; Parasitology", "note": "\u00a9 2021 Elsevier Inc. \n\nReceived 28 September 2021, Revised 8 November 2021, Accepted 10 December 2021, Available online 18 December 2021. \n\nWe would like to thank all members of the Klein lab for helpful discussions; Clara Lehmann for critical review of this manuscript and facilitating our work with the COVID-19 outpatient unit; Petra Meyer, Nicole Riet, and Ricarda Stumpf for technical assistance; Daniela Weiland, Nadine Henn, and Susanne Salomon for project and laboratory management; Knut Elbers for support with SARS-CoV-2 spike escape variants; Ching-Lin Hsieh and Jason S. McLellan for the SARS-CoV-2 HexaPro spike construct; Michael Korenkov and the team at Boehringer Ingelheim for antibody plasmids and antibodies; Pauline Hoffman, Dr. Jost Vielmetter, and the Caltech Beckman Institute Protein Expression Center for protein expression and purification; and Dr. Songye Chen for maintaining the electron microscope. Cryo-EM was performed in the Beckman Institute Resource Center for Transmission Electron Microscope at Caltech. This work was funded by grants to M.K. (DFG FOR2722); to P.J.B. by National Institutes of Health (1P01AI138938-S1); to M. Laessig by German Research Foundation (DFG) (CRC1310); to L.E.S. from COVIM \"NaFoUniMedCovid19\" (FKZ: 01KX2021); to F. Klein from the German Center for Infection Research (DZIF), the DFG (CRC1279 and CRC1310), European Research Council (ERC) (ERC-StG639961), and COVIM \"NaFoUniMedCovid19\" (FKZ: 01KX2021). \n\nData and code availability: All data has been included in main figures or supplementary information. \n\nSARS-CoV-2 antibody sequences are available at GenBank with accession numbers OL741060 - OL741311. The atomic coordinate and 3D EM reconstruction for SARS-CoV-2 S 6P in complex with R40-1G8 Fab has been deposited in the Protein Data Bank (PDB) with PDB ID 7SC1 and the Electron Microscopy Data Bank (EMDB) with EMDB 25008, respectively. \n\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. \n\nAuthor contributions: Conceptualization, F. Klein and K.V.; methodology, F. Klein, K.V., M.M., C.K., D.R., and C.F.; formal analysis, K.V., C.F., M.M., C.K., M.W., N.P., F.M., K.P., and H.G.; investigation, K.V., C.F., M.W., N.P., C.K., F. Kleipass, H.J., M.S.E., D.R., H.G., T.N., S.B., M.K., F.M., and K.P.; phylogenetic analysis, M.M.; sequence analysis, C.K.; resources, S.C.S., M.A., F.D., L.G., P.S., and M. Luksza; writing \u2013 original draft, K.V. and F. Klein; writing \u2013 reviewing and editing, C.F., M.M., H.G., N.P., C.K., and M.K.; supervision; F. Klein, P.J.B., M. Laessig, T.F.S., and L.E.S.; funding acquisition, F. Klein, L.E.S., M.K., M. Laessig, and P.J.B. \n\nDeclaration of interests: F. Klein, K.V., and H.G. are listed as inventors on a patent application that covers aspects of this work. F.K., C.K., and H.G. are listed as inventors on a patent application regarding neutralizing antibodies against SARS-related coronaviruses. All other authors declare no competing interests.\n\nPublished - 1-s20-S1931312821005813-main.pdf
Supplemental Material - 1-s20-S1931312821005813-main-acc.pdf
Supplemental Material - 1-s20-S1931312821005813-mmc1.pdf
", "abstract": "A fraction of COVID-19 convalescent individuals mount a potent antibody response to SARS-CoV-2 with cross-reactivity to SARS-CoV-1. To uncover their humoral response in detail, we performed single B cell analysis from 10 SARS-CoV-2 elite neutralizers. We isolated and analyzed 126 monoclonal antibodies, many of which were sarbecovirus cross-reactive, with some displaying merbecovirus- and embecovirus-reactivity. Several isolated broadly neutralizing antibodies were effective against B.1.1.7, B.1.351, B.1.429, B.1.617, and B.1.617.2 variants and 19 prominent potential escape sites. Furthermore, assembly of 716,806 SARS-CoV-2 sequences predicted emerging escape variants, which were also effectively neutralized. One of these broadly neutralizing potent antibodies, R40-1G8, is a IGHV3-53 RBD-class-1 antibody. Remarkably, cryo-EM analysis revealed that R40-1G8 has a flexible binding mode, targeting both \"up\" and \"down\" conformations of the RBD. Given the threat of emerging SARS-CoV-2 variants, we demonstrate that elite neutralizers are a valuable source for isolating ultrapotent antibody candidates to prevent and treat SARS-CoV-2 infection.", "date": "2022-01-12", "date_type": "published", "publication": "Cell Host and Microbe", "volume": "30", "number": "1", "publisher": "Cell Press", "pagerange": "69-82", "id_number": "CaltechAUTHORS:20211220-495801000", "issn": "1931-3128", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211220-495801000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "FOR2722" }, { "agency": "NIH", "grant_number": "1P01AI138938-S1" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "CRC1310" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)", "grant_number": "01KX2021" }, { "agency": "German Center for Infection Research (DZIF)" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "CRC1279" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "CRC1310" }, { "agency": "European Research Council (ERC)", "grant_number": "639961" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.chom.2021.12.010", "pmcid": "PMC8683262", "primary_object": { "basename": "1-s20-S1931312821005813-main-acc.pdf", "url": "https://authors.library.caltech.edu/records/dgkdq-9f077/files/1-s20-S1931312821005813-main-acc.pdf" }, "related_objects": [ { "basename": "1-s20-S1931312821005813-main.pdf", "url": "https://authors.library.caltech.edu/records/dgkdq-9f077/files/1-s20-S1931312821005813-main.pdf" }, { "basename": "1-s20-S1931312821005813-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/dgkdq-9f077/files/1-s20-S1931312821005813-mmc1.pdf" } ], "pub_year": "2022", "author_list": "Vanshylla, Kanika; Fan, Chengcheng; et al." }, { "id": "https://authors.library.caltech.edu/records/2hr4x-ny239", "eprint_id": 112326, "eprint_status": "archive", "datestamp": "2023-08-20 06:27:42", "lastmod": "2025-11-21 02:28:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gu-Alan-Y", "name": { "family": "Gu", "given": "Alan Y." }, "orcid": "0000-0001-8095-3634" }, { "id": "Zhu-Yanzhe", "name": { "family": "Zhu", "given": "Yanzhe" }, "orcid": "0000-0002-2260-1830" }, { "id": "Li-Jing-ENVENG", "name": { "family": "Li", "given": "Jing" }, "orcid": "0000-0003-0639-9422" }, { "id": "Hoffmann-M-R", "name": { "family": "Hoffmann", "given": "Michael R." }, "orcid": "0000-0001-6495-1946" } ] }, "title": "Speech-generated aerosol settling times and viral viability can improve COVID-19 transmission prediction", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 The Author(s). Published by the Royal Society of Chemistry. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. \n\nSubmitted 19 Feb 2021. Accepted 25 Nov 2021. First published 08 Dec 2021. \n\nThis work is supported by the Bill & Melinda Gates Foundation Investment Grant INV-018569. The authors thank Paul Dabisch at National Biodefense Analysis and Countermeasures Center for sharing his insights on SARS-CoV-2 viability. The authors would like to acknowledge Richard Flagan for helpful discussions.\n\nPublished - d1ea00013f.pdf
Supplemental Material - d1ea00013f1.pdf__ga=2.177883685.1627782830.1639070284-494341399.1632163545
", "abstract": "Droplets during human speech are found to remain suspended in the air for minutes, while studies suggest that the SARS-CoV-2 virus is infectious in experimentally produced aerosols for more than one hour. However, the absence of a large-scale association between regional outbreaks and weather-influenced virus-laden speech-generated aerosol characteristics such as settling time and viral viability makes it challenging for policy making on appropriate infection control measures. Here we investigate the correlation between the time series of daily infections and of settling times of virus-containing particles produced by speaking. Characteristic droplet settling times determined by the Stokes\u2013Cunningham equation as influenced by daily weather conditions were estimated based on local meteorological data. Daily infection data were calibrated from local reported cases based on established infection timeframes. Linear regression, vector autoregression, simple recurrent neural network, and long short-term memory models predict transmission rates within one-sigma intervals using the settling times and viral viability over 5 days before the day of prediction. Corroborating with previous health science studies, from the perspective of meteorology-modulated transmission, our results strengthen that airborne aerosol transmission is an important pathway for the spread of SARS-CoV-2. Furthermore, historical weather data can improve the prediction accuracy of infection spreading rates.", "date": "2022-01-01", "date_type": "published", "publication": "Environmental Science: Atmospheres", "volume": "2", "number": "1", "publisher": "Royal Society of Chemistry", "pagerange": "34-45", "id_number": "CaltechAUTHORS:20211209-456403000", "issn": "2634-3606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211209-456403000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-018569" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1039/d1ea00013f", "primary_object": { "basename": "d1ea00013f.pdf", "url": "https://authors.library.caltech.edu/records/2hr4x-ny239/files/d1ea00013f.pdf" }, "pub_year": "2022", "author_list": "Gu, Alan Y.; Zhu, Yanzhe; et al." }, { "id": "https://authors.library.caltech.edu/records/x0qdq-9tb57", "eprint_id": 110200, "eprint_status": "archive", "datestamp": "2023-08-22 13:00:12", "lastmod": "2026-02-03 23:38:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "McNeill-V-Faye", "name": { "family": "McNeill", "given": "V. Faye" }, "orcid": "0000-0003-0379-6916" }, { "id": "Corsi-Richard", "name": { "family": "Corsi", "given": "Richard" }, "orcid": "0000-0002-1291-3566" }, { "id": "Huffman-J-Alex", "name": { "family": "Huffman", "given": "J. Alex" }, "orcid": "0000-0002-5363-9516" }, { "id": "King-Cathleen", "name": { "family": "King", "given": "Cathleen" }, "orcid": "0000-0003-3147-4834" }, { "id": "Klein-Robert", "name": { "family": "Klein", "given": "Robert" } }, { "id": "Lamore-Michael", "name": { "family": "Lamore", "given": "Michael" } }, { "id": "Maeng-Do-Young", "name": { "family": "Maeng", "given": "Do Young" }, "orcid": "0000-0001-8371-5404" }, { "id": "Miller-Shelly-L", "name": { "family": "Miller", "given": "Shelly L." }, "orcid": "0000-0002-1967-7551" }, { "id": "Ng-Nga-Lee", "name": { "family": "Ng", "given": "Nga Lee" }, "orcid": "0000-0001-8460-4765" }, { "id": "Olsiewski-Paula", "name": { "family": "Olsiewski", "given": "Paula" }, "orcid": "0000-0001-7014-6126" }, { "id": "Godri-Pollitt-Krystal-J", "name": { "family": "Godri Pollitt", "given": "Krystal J." }, "orcid": "0000-0001-7332-2228" }, { "id": "Segalman-Rachel-A", "name": { "family": "Segalman", "given": "Rachel" }, "orcid": "0000-0002-4292-5103" }, { "id": "Sessions-A-L", "name": { "family": "Sessions", "given": "Alex" }, "orcid": "0000-0001-6120-2763" }, { "id": "Squires-Todd", "name": { "family": "Squires", "given": "Todd" }, "orcid": "0000-0001-6609-9275" }, { "id": "Westgate-Sabrina", "name": { "family": "Westgate", "given": "Sabrina" }, "orcid": "0000-0001-7272-2465" } ] }, "title": "Room-level ventilation in schools and universities", "ispublished": "pub", "full_text_status": "public", "keywords": "Ventilation; HVAC; Indoor air; Schools; Sensors", "note": "\u00a9 2022 The Authors. Published by Elsevier Ltd.\nThis is an open access article under the CC BY-NC-ND license \n(http://creativecommons.org/licenses/by-nc-nd/4.0/).\n\nReceived 10 August 2021, Revised 13 January 2022, Accepted 16 January 2022, Available online 26 January 2022.\n\nThe authors thank Prof. Bill Nazaroff and Prof. Atila Novoselac for helpful discussions. VFM and DYM acknowledge Columbia University School of Engineering and Applied Sciences and the Alfred P. Sloan Foundation Chemistry of Indoor Environments program for financial support, and Columbia Facilities. TMS and RAS gratefully acknowledge the Santa Barbara Unified School District and Goleta Union School District for their cooperation and help with measurements. ALS acknowledges Caltech and the Divisions of Geological & Planetary Sciences and Chemistry and Chemical Engineering for financial support, Caltech Facilities for testing and data collection, and Nathan Dalleska, John Crounse, and Paul Wennberg for contributions to method development and deployment. SW and NLN acknowledge support from Georgia Tech COVID-19 Rapid Response fund, and helpful discussions with Philip Johnston, Richard Chew, and Gregory Spiro from Georgia Tech Facilities. JAH acknowledges the University of Denver COVID-19 Response team, Department of Facilities Management, Lamont School of Music, and Planning, and Office of the Provost for funding and support. CK, RK, ML, and KJGP acknowledge the support of Julie Paquette, Anthony Kosior, and JP Fernandez with method development and deployment. PJO acknowledges support from the Johns Hopkins Center for Health Security and the Open Philanthropy Project.\n\nAuthor contributions:\nVFM, JAH, DYM, NLN, KJGP, RS, AS, TS, and SW designed experiments, analyzed and interpreted data. JAH, DYM, NLN, KJGP, RS, AS, TS, and SW collected data. All authors participated in writing the manuscript and the development of Table 1.\n\nDeclaration of competing interest:\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nPublished - 1-s2.0-S2590162122000065-main.pdf
Submitted - room-level-ventilation-in-schools-and-universities.pdf
Supplemental Material - 1-s2.0-S2590162122000065-mmc1.pdf
", "abstract": "Ventilation is of primary concern for maintaining healthy indoor air quality and reducing the spread of airborne infectious disease, including COVID-19. In addition to building-level guidelines, increased attention is being placed on room-level ventilation. However, for many universities and schools, ventilation data on a room-by-room basis are not available for classrooms and other key spaces. We present an overview of approaches for measuring ventilation along with their advantages and disadvantages. We also present data from recent case studies for a variety of institutions across the United States, with various building ages, types, locations, and climates, highlighting their commonalities and differences, and examples of the use of this data to support decision making.", "date": "2022-01", "date_type": "published", "publication": "Atmospheric Environment: X", "volume": "13", "publisher": "Elsevier", "pagerange": "Art. No. 100152", "id_number": "CaltechAUTHORS:20210811-170707088", "issn": "2590-1621", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210811-170707088", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Columbia University" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Caltech Division of Geological and Planetary Sciences" }, { "agency": "Caltech Division of Chemistry and Chemical Engineering" }, { "agency": "Georgia Tech" }, { "agency": "University of Denver" }, { "agency": "Johns Hopkins University" }, { "agency": "Open Philanthropy" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1016/j.aeaoa.2022.100152", "pmcid": "PMC8789458", "primary_object": { "basename": "1-s2.0-S2590162122000065-main.pdf", "url": "https://authors.library.caltech.edu/records/x0qdq-9tb57/files/1-s2.0-S2590162122000065-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2590162122000065-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/x0qdq-9tb57/files/1-s2.0-S2590162122000065-mmc1.pdf" }, { "basename": "room-level-ventilation-in-schools-and-universities.pdf", "url": "https://authors.library.caltech.edu/records/x0qdq-9tb57/files/room-level-ventilation-in-schools-and-universities.pdf" } ], "pub_year": "2022", "author_list": "McNeill, V. Faye; Corsi, Richard; et al." }, { "id": "https://authors.library.caltech.edu/records/5nssr-tkn65", "eprint_id": 112193, "eprint_status": "archive", "datestamp": "2023-08-22 13:02:14", "lastmod": "2023-10-23 17:51:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cao-Jian", "name": { "family": "Cao", "given": "Jian" }, "orcid": "0000-0001-9266-1970" }, { "id": "Ramirez-Christina-M", "name": { "family": "Ramirez", "given": "Christina" }, "orcid": "0000-0002-8435-0416" }, { "id": "Alvarez-R-M", "name": { "family": "Alvarez", "given": "R. Michael" }, "orcid": "0000-0002-8113-4451" } ] }, "title": "The politics of vaccine hesitancy in the United States", "ispublished": "pub", "full_text_status": "public", "keywords": "politics; United States; vaccine hesitancy", "note": "\u00a9 2021 by the Southwestern Social Science Association. \n\nIssue Online: 24 March 2022; Version of Record online: 24 December 2021; Manuscript accepted: 29 November 2021; Manuscript revised: 12 November 2021; Manuscript received: 10 August 2021. \n\nResearch Funding: John Randolph and Dora Haynes Foundation. Grant Number: 1377575.\n\nSubmitted - 2021.12.01.21267160v1.full.pdf
Supplemental Material - ssqu13106-sup-0001-suppmat.pdf
", "abstract": "Objective: Why are Americans COVID-19 vaccine hesitant? We test social science hypotheses for vaccine hesitancy, focusing on partisanship, trust in institutions, and social-demographic characteristics of registered voters. \n\nMethods: We use survey data from a representative sample of American registered voters collected in November 2020 to study vaccine hesitancy, and the reasons for vaccine hesitancy, at a point in time before the vaccine was available and hence show underlying responses based on beliefs and not on clinical trial data. We use multivariate logistic regression models to test hypotheses on vaccine hesitancy. \n\nResults: We find that consistently similar groups of people tend to be vaccine hesitant. Specifically, black voters, those between the ages of 45 and 64, female voters, voters without college degrees, voters not worried about the spread of COVID-19, and voters who are concerned about government and the CDC's handling of the COVID-19 pandemic, were vaccine hesitant. We also provide intriguing results showing the nuanced reasons that the vaccine hesitant provide. \n\nConclusions: Our analysis allows us to establish important baseline information from a social science perspective on vaccine hesitancy at a crucial time, right before COVID-19 vaccines were beginning to be made available to adult Americans. What emerges from our analysis is a nuanced perspective on vaccine hesitancy in the United States, from this important point in the history of the COVID-19 pandemic.", "date": "2022-01", "date_type": "published", "publication": "Social Science Quarterly", "volume": "103", "number": "1", "publisher": "Wiley", "pagerange": "42-54", "id_number": "CaltechAUTHORS:20211203-174950438", "issn": "0038-4941", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211203-174950438", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "John Randolph Haynes and Dora Haynes Foundation", "grant_number": "1377575" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1111/ssqu.13106", "primary_object": { "basename": "2021.12.01.21267160v1.full.pdf", "url": "https://authors.library.caltech.edu/records/5nssr-tkn65/files/2021.12.01.21267160v1.full.pdf" }, "related_objects": [ { "basename": "ssqu13106-sup-0001-suppmat.pdf", "url": "https://authors.library.caltech.edu/records/5nssr-tkn65/files/ssqu13106-sup-0001-suppmat.pdf" } ], "pub_year": "2022", "author_list": "Cao, Jian; Ramirez, Christina; et al." }, { "id": "https://authors.library.caltech.edu/records/3nnxh-bh852", "eprint_id": 112358, "eprint_status": "archive", "datestamp": "2023-08-22 12:56:04", "lastmod": "2026-03-30 16:05:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nesterenko-Pavlo-A", "name": { "family": "Nesterenko", "given": "Pavlo A." }, "orcid": "0000-0001-9841-8170" }, { "id": "McLaughlin-Jami", "name": { "family": "McLaughlin", "given": "Jami" } }, { "id": "Tsai-Brandon-L", "name": { "family": "Tsai", "given": "Brandon L." }, "orcid": "0000-0002-7372-3504" }, { "id": "Burton-Sojo-Giselle", "name": { "family": "Burton Sojo", "given": "Giselle" } }, { "id": "Cheng-Donghui", "name": { "family": "Cheng", "given": "Donghui" } }, { "id": "Zhao-Daniel", "name": { "family": "Zhao", "given": "Daniel" }, "orcid": "0000-0001-7779-5452" }, { "id": "Mao-Zhiyuan", "name": { "family": "Mao", "given": "Zhiyuan" }, "orcid": "0000-0002-5536-4691" }, { "id": "Bangayan-Nathanael-J", "name": { "family": "Bangayan", "given": "Nathanael J." } }, { "id": "Obusan-Matthew-B", "name": { "family": "Obusan", "given": "Matthew B." }, "orcid": "0000-0002-9579-2308" }, { "id": "Su-Yapeng", "name": { "family": "Su", "given": "Yapeng" }, "orcid": "0000-0002-6305-8467" }, { "id": "Ng-Rachel-H", "name": { "family": "Ng", "given": "Rachel H." }, "orcid": "0000-0003-3692-8524" }, { "id": "Chour-William", "name": { "family": "Chour", "given": "William" }, "orcid": "0000-0003-1817-0123" }, { "id": "Xie-Jingyi", "name": { "family": "Xie", "given": "Jingyi" } }, { "id": "Li-Yan-Ruide", "name": { "family": "Li", "given": "Yan-Ruide" } }, { "id": "Lee-Derek", "name": { "family": "Lee", "given": "Derek" } }, { "id": "Noguchi-Miyako", "name": { "family": "Noguchi", "given": "Miyako" }, "orcid": "0000-0003-0909-7358" }, { "id": "Carmona-Camille", "name": { "family": "Carmona", "given": "Camille" }, "orcid": "0000-0001-7040-5773" }, { "id": "Phillips-John-W", "name": { "family": "Phillips", "given": "John W." } }, { "id": "Kim-Jocelyn-T", "name": { "family": "Kim", "given": "Jocelyn T." }, "orcid": "0000-0001-8723-8190" }, { "id": "Yang-Lili", "name": { "family": "Yang", "given": "Lili" } }, { "id": "Heath-J-R", "name": { "family": "Heath", "given": "James R." }, "orcid": "0000-0001-5356-4385" }, { "id": "Boutros-Paul-C", "name": { "family": "Boutros", "given": "Paul C." }, "orcid": "0000-0003-0553-7520" }, { "id": "Witte-Owen-N", "name": { "family": "Witte", "given": "Owen N." }, "orcid": "0000-0003-4461-4533" } ] }, "title": "HLA-A\u221702:01 restricted T cell receptors against the highly conserved SARS-CoV-2 polymerase cross-react with human coronaviruses", "ispublished": "pub", "full_text_status": "public", "keywords": "T cells; SARS-CoV-2; antigen; specific; CD8; TCR; single-cell; COVID-19; immune response; cell therapy; General Biochemistry, Genetics and Molecular Biology", "note": "\u00a9 2021 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nReceived 11 August 2021, Revised 15 October 2021, Accepted 2 December 2021, Available online 10 December 2021. \n\nWe thank Michael T. Bethune for providing advice throughout this project, as well as providing the Jurkat-CD8 cells while at the laboratory of David Baltimore (Caltech). The NFAT reporter was a gift from Christopher S. Seet (UCLA) and the laboratory of David Baltimore (Caltech). We thank Caius Radu and Ting-Ting Wu (UCLA) for critical reading of the manuscript. The UCLA Technology Center for Genomics and Bioinformatics constructed single-cell human TCR libraries and performed TCR sequencing. \n\nFunding: National Cancer Institute grants U01 CA233074 (O.N.W.) and U24 CA248265 (P.C.B.); Parker Institute for Cancer Immunotherapy grant (O.N.W. and J.R.H.); UCLA Broad Stem Cell Research Center (O.N.W.); USHHS Ruth L. Kirschstein Institutional National Research Service Award T32 CA009056 (P.A.N.); Broad Stem Cell Research Center (BSCRC) predoctoral fellowship (Z.M.); The Jeff and Liesl Wilke Foundation (J.R.H.); The Washington State Andy Hill CARE Fund (J.R.H.); The Biomedical Advanced Research and Development Authority HHSO10201600031C (J.R.H.); UCLA W. M. Keck Foundation COVID-19 Research Award Program (O.N.W.). \n\nData and code availability: Reactive TCR alpha/beta nucleotide sequences are provided in this paper. \n\nWe have not created any original code. \n\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. \n\nAuthor contributions: Conceptualization, P.A.N. and O.N.W.; supervision, P.A.N., O.N.W., J.M., J.T.K., J.R.H., P.C.B., and J.W.P.; methodology, M.T.B., P.A.N., P.C.B., J.R.H., W.C., Y.S., L.Y., Z.M., N.J.B., Y.L., D.L., and J.T.K.; investigation, G.B.S., J.M., P.A.N., J.X., R.N., B.L.T., D.C., C.C., and M.N.; funding acquisition, J.W.P., P.C.B., and O.N.W.; software, M.B.O., B.L.T., R.N., and D.Z.; resources, J.X., W.C., and Y.L.; visualization, M.B.O., P.A.N., B.L.T., D.Z., and R.N.; project administration, P.A.N., J.M., and O.N.W.; writing \u2013 original draft, review & editing, P.A.N., O.N.W., and J.W.P. \n\nDeclaration of interests: O.N.W., J.M., and P.A.N. are inventors of a patent application in progress that will be filed prior to manuscript publication. J.R.H. is a board member of PACT Pharma and Isoplexis. O.N.W. currently has consulting, equity, and/or board relationships with Trethera Corporation, Kronos Biosciences, Sofie Biosciences, Breakthrough Properties, Vida Ventures, Nammi Therapeutics, Two River, Iconovir, Appia BioSciences, Neogene Therapeutics, and Allogene Therapeutics. None of these companies contributed to or directed any of the research reported in this article.\n\nPublished - 1-s2.0-S2211124721016673-main.pdf
Supplemental Material - 1-s2.0-S2211124721016673-mmc1.pdf
Supplemental Material - 1-s2.0-S2211124721016673-mmc2.xlsx
Supplemental Material - 1-s2.0-S2211124721016673-mmc3.xlsx
Supplemental Material - 1-s2.0-S2211124721016673-mmc4.csv
Supplemental Material - 1-s2.0-S2211124721016673-mmc5.csv
", "abstract": "Cross-reactivity and direct killing of target cells remain underexplored for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-specific CD8\u207a T cells. Isolation of T cell receptors (TCRs) and overexpression in allogeneic cells allows for extensive T cell reactivity profiling. We identify SARS-CoV-2 RNA-dependent RNA polymerase (RdRp/NSP12) as highly conserved, likely due to its critical role in the virus life cycle. We perform single-cell TCR\u03b1\u03b2 sequencing in human leukocyte antigen (HLA)-A\u221702:01-restricted, RdRp-specific T cells from SARS-CoV-2-unexposed individuals. Human T cells expressing these TCR\u03b1\u03b2 constructs kill target cell lines engineered to express full-length RdRp. Three TCR constructs recognize homologous epitopes from common cold coronaviruses, indicating CD8\u207a T cells can recognize evolutionarily diverse coronaviruses. Analysis of individual TCR clones may help define vaccine epitopes that can induce long-term immunity against SARS-CoV-2 and other coronaviruses.", "date": "2021-12-28", "date_type": "published", "publication": "Cell Reports", "volume": "37", "number": "13", "publisher": "Cell Press", "pagerange": "Art. No. 110167", "id_number": "CaltechAUTHORS:20211210-240628000", "issn": "2211-1247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211210-240628000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U01 CA233074" }, { "agency": "NIH", "grant_number": "U24 CA248265" }, { "agency": "Parker Institute for Cancer Immunotherapy" }, { "agency": "Broad Stem Cell Research Center" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 CA009056" }, { "agency": "Jeff and Liesl Wilke Foundation" }, { "agency": "Washington State Andy Hill CARE Fund" }, { "agency": "Biomedical Advanced Research and Development Authority", "grant_number": "HHSO10201600031C" }, { "agency": "W. M. Keck Foundation" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.celrep.2021.110167", "pmcid": "PMC8660260", "primary_object": { "basename": "1-s2.0-S2211124721016673-mmc5.csv", "url": "https://authors.library.caltech.edu/records/3nnxh-bh852/files/1-s2.0-S2211124721016673-mmc5.csv" }, "related_objects": [ { "basename": "1-s2.0-S2211124721016673-main.pdf", "url": "https://authors.library.caltech.edu/records/3nnxh-bh852/files/1-s2.0-S2211124721016673-main.pdf" }, { "basename": "1-s2.0-S2211124721016673-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/3nnxh-bh852/files/1-s2.0-S2211124721016673-mmc1.pdf" }, { "basename": "1-s2.0-S2211124721016673-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/3nnxh-bh852/files/1-s2.0-S2211124721016673-mmc2.xlsx" }, { "basename": "1-s2.0-S2211124721016673-mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/3nnxh-bh852/files/1-s2.0-S2211124721016673-mmc3.xlsx" }, { "basename": "1-s2.0-S2211124721016673-mmc4.csv", "url": "https://authors.library.caltech.edu/records/3nnxh-bh852/files/1-s2.0-S2211124721016673-mmc4.csv" } ], "pub_year": "2021", "author_list": "Nesterenko, Pavlo A.; McLaughlin, Jami; et al." }, { "id": "https://authors.library.caltech.edu/records/qppb3-4q284", "eprint_id": 108275, "eprint_status": "archive", "datestamp": "2023-08-22 12:25:28", "lastmod": "2026-03-28 23:49:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Linardi-Sera", "name": { "family": "Linardi", "given": "Sera" }, "orcid": "0000-0002-8085-1555" }, { "id": "Camerer-C-F", "name": { "family": "Camerer", "given": "Colin" }, "orcid": "0000-0003-4049-1871" } ] }, "title": "Worker-firm relational contracts in the time of shutdowns: experimental evidence", "ispublished": "pub", "full_text_status": "public", "keywords": "Relational contracts; Gift exchange; Labor markets; Unemployment; Shocks; Layoffs; Recession; Repeated game", "note": "\u00a9 2021 Economic Science Association. \n\nReceived 04 August 2020; Revised 06 December 2020; Accepted 22 December 2020; Published 15 February 2021. \n\nThe authors would like to thank the following individuals for their excellent research assistance: Erin Carbone, Xiaohong Wang, Jinyong Jeong, Taisuke Imai, Devdeepta Bose. We thank the referees, editors, and participants at seminars for their very useful feedback. We acknowledge the financial support from Behavioral and Neuroeconomics Discovery Fund (via MacArthur Foundation) and grant administration assistance of Tiffany Kim and Alisha Cunniff.\n\nSupplemental Material - 10683_2020_9697_MOESM1_ESM.docx
", "abstract": "Exogeneous disruptions in labor demand have become more frequent in recent times. The COVID-19 pandemic has resulted in millions of workers being repeatedly laid off and rehired according to local public health conditions. This may be bad news for market efficiency. Typical employment relations\u2014which resemble non-enforceable (implicit) contracts\u2014rely on reciprocity (Brown et al. in Econometrica 72:747\u2013780, 2004), and hence could be harmed when workers' efforts no longer guarantee reemployment in the next period. In this paper we extend the BFF paradigm to include a per-period probability (0%, 10%, 50%) of publicly observable \"shutdown\", where a specific firm cannot contract with any workers for several periods. A Perfect Bayesian Equilibrium exists in which these shutdowns destabilize relationships, but do not harm efficiency. Our experiment shows that, remarkably, market efficiency can be maintained even with very frequent stochastic shutdowns. However, the dynamic of relational contracts changes from one where a worker finds stable employment to one where she juggles multiple employers, laying the burden of maintaining productivity upon workers and worsening worker-side inequality.", "date": "2021-12", "date_type": "published", "publication": "Experimental Economics", "volume": "24", "number": "4", "publisher": "Springer", "pagerange": "1267-1293", "id_number": "CaltechAUTHORS:20210302-145031108", "issn": "1386-4157", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210302-145031108", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Behavioral and Neuroeconomics Discovery Fund" }, { "agency": "John D. and Catherine T. MacArthur Foundation" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1007/s10683-020-09697-1", "pmcid": "PMC7883973", "primary_object": { "basename": "10683_2020_9697_MOESM1_ESM.docx", "url": "https://authors.library.caltech.edu/records/qppb3-4q284/files/10683_2020_9697_MOESM1_ESM.docx" }, "pub_year": "2021", "author_list": "Linardi, Sera and Camerer, Colin" }, { "id": "https://authors.library.caltech.edu/records/8fsjr-j4288", "eprint_id": 114351, "eprint_status": "archive", "datestamp": "2023-08-20 06:09:09", "lastmod": "2023-12-22 23:31:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher" }, "orcid": "0000-0003-2754-5951" }, { "id": "Scheid-Johannes-F", "name": { "family": "Scheid", "given": "Johannes F." } }, { "id": "Eraslan-Basak", "name": { "family": "Eraslan", "given": "Basak" }, "orcid": "0000-0003-3698-8279" }, { "id": "Hudak-Andrew", "name": { "family": "Hudak", "given": "Andrew" }, "orcid": "0000-0002-0241-2290" }, { "id": "Muecksch-Frauke", "name": { "family": "Muecksch", "given": "Frauke" }, "orcid": "0000-0002-0132-5101" }, { "id": "Weisblum-Yiska", "name": { "family": "Weisblum", "given": "Yiska" }, "orcid": "0000-0002-9249-1745" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Xavier-Ramnik-J", "name": { "family": "Xavier", "given": "Ramnik J." }, "orcid": "0000-0002-5630-5167" } ] }, "title": "Structural insights into antibody-mediated neutralization of SARS-CoV-2", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 The Author(s) 2021. Published by Oxford University Press. \nThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nPublished: 27 January 2022.", "abstract": "In less than a year, researchers have uncovered structure\u2013function details for many of the proteins encoded by SARS-CoV-2. We report structures that reveal how monoclonal neutralizing antibodies bind spike to prevent infection. One such monoclonal antibody, BG10\u201319, targets a highly-conserved, proteoglycan epitope on the SARS-CoV-2 RBD, which sits outside of mutated residue positions found in all circulating variants of concern (i.e. alpha, beta, gamma, delta, kappa, and lambda). In addition, BG10\u201319 bridges adjacent RBDs and locks the spike trimer in a completely closed conformation to potently neutralize SARSCoV-2 and heterologous SARS-like coronaviruses. Thus, BG10\u201319 is a candidate antibody therapeutic to combat continuing\nSARS-CoV-2 antigenic drift and represents an attractive epitope for pan-sarbecovirus vaccine design.", "date": "2021-12", "date_type": "published", "publication": "Glycobiology", "volume": "31", "number": "12", "publisher": "Oxford University Press", "pagerange": "1696-1697", "id_number": "CaltechAUTHORS:20220415-214637408", "issn": "0959-6658", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220415-214637408", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/glycob/cwab121", "pub_year": "2021", "author_list": "Barnes, Christopher; Scheid, Johannes F.; et al." }, { "id": "https://authors.library.caltech.edu/records/pgn6d-0zt10", "eprint_id": 112043, "eprint_status": "archive", "datestamp": "2023-09-22 22:45:17", "lastmod": "2026-03-28 22:29:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lovenduski-Nicole-S", "name": { "family": "Lovenduski", "given": "Nicole S." }, "orcid": "0000-0001-5893-1009" }, { "id": "Chatterjee-Abhishek", "name": { "family": "Chatterjee", "given": "Abhishek" }, "orcid": "0000-0002-3680-0160" }, { "id": "Swart-Neil-C", "name": { "family": "Swart", "given": "Neil C." }, "orcid": "0000-0002-8200-6187" }, { "id": "Fyfe-John-C", "name": { "family": "Fyfe", "given": "John C." }, "orcid": "0000-0003-2524-0652" }, { "id": "Keeling-Ralph-F", "name": { "family": "Keeling", "given": "Ralph F." }, "orcid": "0000-0002-9749-2253" }, { "id": "Schimel-David-S", "name": { "family": "Schimel", "given": "David" }, "orcid": "0000-0003-3473-8065" } ] }, "title": "On the Detection of COVID\u2010Driven Changes in Atmospheric Carbon Dioxide", "ispublished": "pub", "full_text_status": "public", "keywords": "carbon dioxide; COVID; large ensemble; ocean carbon sink; land carbon sink; carbon climate feedbacks; General Earth and Planetary Sciences; Geophysics", "note": "\u00a9 2021. American Geophysical Union. \n\nIssue Online: 19 November 2021; Version of Record online: 19 November 2021; Accepted manuscript online: 11 November 2021; Manuscript accepted: 07 November 2021; Manuscript revised: 25 October 2021; Manuscript received: 26 July 2021. \n\nThis work had its inception at the \"COVID-19: Identifying Unique Opportunities for Earth System Science\" virtual workshop funded by the W.M. Keck Institute for Space Studies. This research was supported by the National Science Foundation (OCE-1752724 and OCE-1948664). A.C. was supported by funding from the NASA Grant/Cooperative Agreement 80NSSC20K0006. We acknowledge the CCCma staff who contributed to producing these simulations. \n\nData Availability Statement: The data from the CanESM5 simulations used in this study are published through the Government of Canada Open Data Portal, and can be accessed at http://crd-data-donnees-rdc.ec.gc.ca/CCCMA/publications/COVID19/. The \u03c7CO\u2082 flask data are from the Scripps CO2 program, and can be accessed at https://scrippsco2.ucsd.edu/data/atmospheric_co2/sampling_stations.html.\n\nPublished - 2021GL095396.pdf
Supplemental Material - 2021gl095396-sup-0001-supporting_information_si-s01.pdf
", "abstract": "We assess the detectability of COVID-like emissions reductions in global atmospheric CO\u2082 concentrations using a suite of large ensembles conducted with an Earth system model. We find a unique fingerprint of COVID in the simulated growth rate of CO\u2082 sampled at the locations of surface measurement sites. Negative anomalies in growth rates persist from January 2020 through December 2021, reaching a maximum in February 2021. However, this fingerprint is not formally detectable unless we force the model with unrealistically large emissions reductions (2 or 4 times the observed reductions). Internal variability and carbon-concentration feedbacks obscure the detectability of short-term emission reductions in atmospheric CO\u2082. COVID-driven changes in the simulated, column-averaged dry air mole fractions of CO\u2082 are eclipsed by large internal variability. Carbon-concentration feedbacks begin to operate almost immediately after the emissions reduction; these feedbacks reduce the emissions-driven signal in the atmosphere carbon reservoir and further confound signal detection.", "date": "2021-11-28", "date_type": "published", "publication": "Geophysical Research Letters", "volume": "48", "number": "22", "publisher": "American Geophysical Union", "pagerange": "Art. No. e2021GL095396", "id_number": "CaltechAUTHORS:20211124-174243639", "issn": "0094-8276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211124-174243639", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Keck Institute for Space Studies (KISS)" }, { "agency": "NSF", "grant_number": "OCE\u20101752724" }, { "agency": "NSF", "grant_number": "OCE\u20101948664" }, { "agency": "NASA", "grant_number": "80NSSC20K0006" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Keck-Institute-for-Space-Studies" } ] }, "doi": "10.1029/2021gl095396", "primary_object": { "basename": "2021GL095396.pdf", "url": "https://authors.library.caltech.edu/records/pgn6d-0zt10/files/2021GL095396.pdf" }, "related_objects": [ { "basename": "2021gl095396-sup-0001-supporting_information_si-s01.pdf", "url": "https://authors.library.caltech.edu/records/pgn6d-0zt10/files/2021gl095396-sup-0001-supporting_information_si-s01.pdf" } ], "pub_year": "2021", "author_list": "Lovenduski, Nicole S.; Chatterjee, Abhishek; et al." }, { "id": "https://authors.library.caltech.edu/records/45v87-k5065", "eprint_id": 111721, "eprint_status": "archive", "datestamp": "2023-08-20 06:02:53", "lastmod": "2026-03-30 16:51:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Brogan-Daniel-J", "name": { "family": "Brogan", "given": "Daniel J." }, "orcid": "0000-0001-6582-8966" }, { "id": "Chaverra-Rodriguez-Duverney", "name": { "family": "Chaverra-Rodriguez", "given": "Duverney" } }, { "id": "Lin-Calvin-P", "name": { "family": "Lin", "given": "Calvin P." } }, { "id": "Smidler-Andrea-L", "name": { "family": "Smidler", "given": "Andrea L." }, "orcid": "0000-0002-3281-1161" }, { "id": "Yang-Ting", "name": { "family": "Yang", "given": "Ting" }, "orcid": "0000-0003-2301-2525" }, { "id": "Alcantara-Lenissa-M", "name": { "family": "Alcantara", "given": "Lenissa M." } }, { "id": "Antoshechkin-Igor-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Liu-Junru", "name": { "family": "Liu", "given": "Junru" }, "orcid": "0000-0002-6198-8150" }, { "id": "Raban-Robyn-R", "name": { "family": "Raban", "given": "Robyn R." }, "orcid": "0000-0002-5648-6770" }, { "id": "Belda-Ferre-Pedro", "name": { "family": "Belda-Ferre", "given": "Pedro" }, "orcid": "0000-0001-6532-1161" }, { "id": "Knight-Rob", "name": { "family": "Knight", "given": "Rob" }, "orcid": "0000-0002-0975-9019" }, { "id": "Komives-Elizabeth-A", "name": { "family": "Komives", "given": "Elizabeth A." }, "orcid": "0000-0001-5264-3866" }, { "id": "Akbari-Omar-S", "name": { "family": "Akbari", "given": "Omar S." }, "orcid": "0000-0002-6853-9884" } ] }, "title": "Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19, CRISPR, Cas13d, nucleic acid diagnostic, isothermal", "note": "\u00a9 2021 American Chemical Society. This article is made available via the ACS COVID-19 subset for unrestricted RESEARCH re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. \n\nReceived: May 26, 2021; Accepted: October 14, 2021; Published: October 29, 2021. \n\nWe thank the SEARCH (San Diego Epidemiology and Research for COVID-19 Health) Alliance for providing clinical samples. This work was supported in part by UCSD Seed Funds for Emergent COVID-19 Related Research, a Directors New Innovator award from NIH/NIAID (DP2 AI152071-01), NIH/NIAID R21 (1R21AI149161), and a DARPA Safe Genes Program Grant (HR0011-17-2-0047) awarded to O.S.A., and a Director's Pioneer Award from NCCIH (DP1 AT010885) to R.K., and the Molecular Biophysics Training Grant from NIH (T32 GM00832) to C.P.L., and the UCSD Return to Learn program via the EXCITE (EXpedited COVID-19 IdenTification Environment) lab. The views, opinions, and/or findings expressed should not be interpreted as representing the official views or policies of the Department of Defense or the U.S. Government. C.P.L. was supported by the Molecular Biophysics Training Grant, NIH Grant T32 GM00832. \n\nAuthor Contributions: D.J.B., D.C.-R., and C.P.L. are equal first author contributions. \n\nA.L.S. and T.Y. are equal second author contributions. O.S.A. conceptualized the study. D.J.B., D.C.-R., C.P.L., J.L., L.M.A., T.Y., I.A., and P.B.-F., performed, designed, and analyzed various molecular, bioinformatic, and protein biochemistry. A.L.S., R.R.R., R.K., and E.A.K. contributed to analyzing and designing experiments. All authors contributed to writing, analyzing the data, and approving the final manuscript. \n\nThe authors declare the following competing financial interest(s): O.S.A. has a patent pending on this technology. All other authors declare no significant competing financial, professional, or personal interests that might have influenced the performance or presentation of the work described. \n\nBioinformatic scripts can be found in File S1. A limited quantity of CasRx enzyme will be made available upon request.\n\nPublished - acssensors.1c01088.pdf
Supplemental Material - se1c01088_si_001.xlsx
Supplemental Material - se1c01088_si_002.txt
Supplemental Material - se1c01088_si_003.mov
Supplemental Material - se1c01088_si_004.pdf
", "abstract": "The development of an extensive toolkit for potential point-of-care diagnostics that is expeditiously adaptable to new emerging pathogens is of critical public health importance. Recently, a number of novel CRISPR-based diagnostics have been developed to detect SARS-CoV-2. Herein, we outline the development of an alternative CRISPR nucleic acid diagnostic utilizing a Cas13d ribonuclease derived from Ruminococcus flavefaciens XPD3002 (CasRx) to detect SARS-CoV-2, an approach we term SENSR (sensitive enzymatic nucleic acid sequence reporter) that can detect attomolar concentrations of SARS-CoV-2. We demonstrate 100% sensitivity in patient-derived samples by lateral flow and fluorescence readout with a detection limit of 45 copy/\u03bcL. This technology expands the available nucleic acid diagnostic toolkit, which can be adapted to combat future pandemics.", "date": "2021-11-26", "date_type": "published", "publication": "ACS Sensors", "volume": "6", "number": "11", "publisher": "American Chemical Society", "pagerange": "3957-3966", "id_number": "CaltechAUTHORS:20211102-222421621", "issn": "2379-3694", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211102-222421621", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of California, San Diego" }, { "agency": "NIH", "grant_number": "DP2 AI152071-01" }, { "agency": "NIH", "grant_number": "1R21AI149161" }, { "agency": "Defense Advanced Research Project Agency (DARPA)", "grant_number": "HR0011-17-2-0047" }, { "agency": "NIH", "grant_number": "DP1 AT010885" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM00832" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1021/acssensors.1c01088", "pmcid": "PMC8577378", "primary_object": { "basename": "acssensors.1c01088.pdf", "url": "https://authors.library.caltech.edu/records/45v87-k5065/files/acssensors.1c01088.pdf" }, "related_objects": [ { "basename": "se1c01088_si_001.xlsx", "url": "https://authors.library.caltech.edu/records/45v87-k5065/files/se1c01088_si_001.xlsx" }, { "basename": "se1c01088_si_002.txt", "url": "https://authors.library.caltech.edu/records/45v87-k5065/files/se1c01088_si_002.txt" }, { "basename": "se1c01088_si_003.mov", "url": "https://authors.library.caltech.edu/records/45v87-k5065/files/se1c01088_si_003.mov" }, { "basename": "se1c01088_si_004.pdf", "url": "https://authors.library.caltech.edu/records/45v87-k5065/files/se1c01088_si_004.pdf" } ], "pub_year": "2021", "author_list": "Brogan, Daniel J.; Chaverra-Rodriguez, Duverney; et al." }, { "id": "https://authors.library.caltech.edu/records/5n0s7-76p22", "eprint_id": 111955, "eprint_status": "archive", "datestamp": "2023-08-20 06:00:13", "lastmod": "2026-03-30 07:27:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Van-Rooy-Paul", "name": { "family": "Van Rooy", "given": "Paul" }, "orcid": "0000-0003-1193-0994" }, { "id": "Tasnia-Afsara", "name": { "family": "Tasnia", "given": "Afsara" }, "orcid": "0000-0002-3048-5083" }, { "id": "Barletta-Barbara", "name": { "family": "Barletta", "given": "Barbara" }, "orcid": "0000-0003-3046-014X" }, { "id": "Buenconsejo-Reina-S", "name": { "family": "Buenconsejo", "given": "Reina" }, "orcid": "0000-0002-0162-905X" }, { "id": "Crounse-John-D", "name": { "family": "Crounse", "given": "John D." }, "orcid": "0000-0001-5443-729X" }, { "id": "Kenseth-Christopher-M", "name": { "family": "Kenseth", "given": "Christopher M." }, "orcid": "0000-0003-3188-2336" }, { "id": "Meinardi-Simone", "name": { "family": "Meinardi", "given": "Simone" }, "orcid": "0000-0003-4828-9889" }, { "id": "Murphy-Sara", "name": { "family": "Murphy", "given": "Sara" } }, { "id": "Parker-Harrison", "name": { "family": "Parker", "given": "Harrison" }, "orcid": "0000-0002-0041-2764" }, { "id": "Schulze-Benjamin-C", "name": { "family": "Schulze", "given": "Benjamin" }, "orcid": "0000-0002-6405-8872" }, { "id": "Seinfeld-J-H", "name": { "family": "Seinfeld", "given": "John H." }, "orcid": "0000-0003-1344-4068" }, { "id": "Wennberg-P-O", "name": { "family": "Wennberg", "given": "Paul O." }, "orcid": "0000-0002-6126-3854" }, { "id": "Blake-Donald-R", "name": { "family": "Blake", "given": "Donald R." }, "orcid": "0000-0002-8283-5014" }, { "id": "Barsanti-Kelley-C", "name": { "family": "Barsanti", "given": "Kelley C." }, "orcid": "0000-0002-6065-8643" } ] }, "title": "Observations of Volatile Organic Compounds in the Los Angeles Basin during COVID-19", "ispublished": "pub", "full_text_status": "public", "keywords": "VOCs, urban air quality, COVID-19, mobile source emissions, off-road emissions, VCPs", "note": "\u00a9 2021 American Chemical Society. \n\nReceived: July 9, 2021; Revised: September 27, 2021; Accepted: October 9, 2021; Published: October 28, 2021. \n\nThe authors would like to sincerely thank Joost de Gouw for conversations during the campaign period in which he shared his knowledge of the composition and chemistry in the LA Basin. The authors would also like to thank Joost de Gouw and Carsten Warneke for the quality data collected during the CalNex-2010 campaign and subsequent analysis of that data, which were foundational to this study. \n\nPVR, AT, KCB acknowledge funding support from NSF RAPID award #2030049. BB, SM, and DRB acknowledge funding support from NSF RAPID award #2030112. \n\nAuthor Contributions: The study was conceived by KCB, JHS, DRB, and POW. All authors contributed to data collection, analysis, and/or interpretation. The manuscript was written largely by PVR and KCB, with contributions from AT, BB, JDC, HP, PS, and POW. The manuscript was edited through contributions of all authors. All authors have given approval to the final version of the manuscript. \n\nThe authors declare no competing financial interest.\n\nSupplemental Material - sp1c00248_si_001.xlsx
Supplemental Material - sp1c00248_si_002.pdf
", "abstract": "Volatile organic compounds (VOCs) were measured in the Los Angeles (LA) Basin from mid-April to mid-July 2020 during the COVID-19 pandemic, as a part of the Los Angeles Air Quality Campaign (LAAQC). VOCs were quantified in over 450 samples using one- and two-dimensional gas chromatography with different detectors; mixing ratios were determined for 150 compounds associated with on- and off-road mobile, volatile chemical product, and biogenic sources. During the sampling period, traffic counts increased from \u223c55% to \u223c80% of pre-COVID levels. While the average afternoon combustion-derived VOCs and carbon monoxide (CO) mixing ratios did not change significantly between April\u2013May and June\u2013July, there was a shift in the distribution to higher mixing ratios in June\u2013July, particularly for VOCs associated with gasoline evaporation. Compared to observations made in the last major air quality campaign in the LA Basin (CalNex-2010), emission ratios for 40 compounds relative to acetylene (VOC/acetylene) have remained similar, while emission ratios relative to CO (VOC/CO) have dropped to \u223c60% of their 2010 values. This divergence in trends suggests that whereas mobile sources are still the dominant source of the combustion-derived VOCs measured in the LA Basin, there has been a shift in the mobile source sectors, with a growing contribution from sources that have lower CO/acetylene emission ratios, including off-road equipment and vehicles. In addition to the observed shift in source sector contributions, estimated OH exposure was 70\u2013120% higher than in 2010.", "date": "2021-11-18", "date_type": "published", "publication": "ACS Earth and Space Chemistry", "volume": "5", "number": "11", "publisher": "American Chemical Society", "pagerange": "3045-3055", "id_number": "CaltechAUTHORS:20211118-233559021", "issn": "2472-3452", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211118-233559021", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "AGS-2030049" }, { "agency": "NSF", "grant_number": "AGS-2030112" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1021/acsearthspacechem.1c00248", "primary_object": { "basename": "sp1c00248_si_001.xlsx", "url": "https://authors.library.caltech.edu/records/5n0s7-76p22/files/sp1c00248_si_001.xlsx" }, "related_objects": [ { "basename": "sp1c00248_si_002.pdf", "url": "https://authors.library.caltech.edu/records/5n0s7-76p22/files/sp1c00248_si_002.pdf" } ], "pub_year": "2021", "author_list": "Van Rooy, Paul; Tasnia, Afsara; et al." }, { "id": "https://authors.library.caltech.edu/records/92btd-ccb84", "eprint_id": 109806, "eprint_status": "archive", "datestamp": "2023-08-20 05:59:24", "lastmod": "2026-03-28 23:19:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jiang-Yonghou", "name": { "family": "Jiang", "given": "Yonghou" } }, { "id": "Duffy-Fergal", "name": { "family": "Duffy", "given": "Fergal" }, "orcid": "0000-0002-4675-0937" }, { "id": "Hadlock-Jennifer", "name": { "family": "Hadlock", "given": "Jennifer" }, "orcid": "0000-0001-6103-7606" }, { "id": "Raappana-Andrew", "name": { "family": "Raappana", "given": "Andrew" }, "orcid": "0000-0001-5248-4172" }, { "id": "Styrchak-Sheila", "name": { "family": "Styrchak", "given": "Sheila" } }, { "id": "Beck-Ingrid", "name": { "family": "Beck", "given": "Ingrid" }, "orcid": "0000-0001-7438-3209" }, { "id": "Mast-Fred-D", "name": { "family": "Mast", "given": "Fred D." }, "orcid": "0000-0002-2177-6647" }, { "id": "Miller-Leslie-R", "name": { "family": "Miller", "given": "Leslie R." } }, { "id": "Chour-William", "name": { "family": "Chour", "given": "William" }, "orcid": "0000-0003-1817-0123" }, { "id": "Houck-John", "name": { "family": "Houck", "given": "John" } }, { "id": "Armistead-Blair", "name": { "family": "Armistead", "given": "Blair" }, "orcid": "0000-0001-9902-3955" }, { "id": "Duvvuri-Venkata-R", "name": { "family": "Duvvuri", "given": "Venkata R." }, "orcid": "0000-0001-7356-338X" }, { "id": "Yeung-Winnie", "name": { "family": "Yeung", "given": "Winnie" }, "orcid": "0000-0001-8083-7449" }, { "id": "Haglund-Micaela", "name": { "family": "Haglund", "given": "Micaela" } }, { "id": "Wallner-Jackson", "name": { "family": "Wallner", "given": "Jackson" } }, { "id": "Wallick-Julie-A", "name": { "family": "Wallick", "given": "Julie A." }, "orcid": "0000-0002-4568-4704" }, { "id": "Hardy-Samantha", "name": { "family": "Hardy", "given": "Samantha" } }, { "id": "Oldroyd-Alyssa", "name": { "family": "Oldroyd", "given": "Alyssa" } }, { "id": "Ko-Daisy", "name": { "family": "Ko", "given": "Daisy" } }, { "id": "Gervassi-Ana-L", "name": { "family": "Gervassi", "given": "Ana" }, "orcid": "0000-0003-0321-5632" }, { "id": "Murray-Kim-M", "name": { "family": "Murray", "given": "Kim M." } }, { "id": "Kaplan-Henry", "name": { "family": "Kaplan", "given": "Henry" }, "orcid": "0000-0001-9866-5200" }, { "id": "Aitchison-John-D", "name": { "family": "Aitchison", "given": "John D." }, "orcid": "0000-0002-9153-6497" }, { "id": "Heath-J-R", "name": { "family": "Heath", "given": "James R." }, "orcid": "0000-0001-5356-4385" }, { "id": "Sather-D-Noah", "name": { "family": "Sather", "given": "D. Noah" }, "orcid": "0000-0002-9128-172X" }, { "id": "Goldman-Jason-D", "name": { "family": "Goldman", "given": "Jason D." }, "orcid": "0000-0002-3825-6832" }, { "id": "Frenkel-Lisa", "name": { "family": "Frenkel", "given": "Lisa" }, "orcid": "0000-0001-9566-8959" }, { "id": "Harrington-Whitney-E", "name": { "family": "Harrington", "given": "Whitney E." }, "orcid": "0000-0002-0121-978X" } ] }, "title": "Angiotensin II receptor I auto-antibodies following SARS-CoV-2 infection", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Jiang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: June 11, 2021; Accepted: October 28, 2021; Published: November 17, 2021. \n\nThis work was supported by Seattle Children's Research Institute [to LF, WEH, NS, and JDA]; the National Institute of Allergy and Infectious Diseases [K08 AI135072 to WEH]; the Burroughs Wellcome Fund [CAMS 1017213 to WEH]; the Biomedical Advanced Research and Development Authority [HHSO10201600031C to JRH]; and the Swedish Medical Center Foundation [to JDG]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\nAuthor Contributions: Conceptualization: Ana Gervassi, Henry Kaplan, John D. Aitchison, James R. Heath, Jason D. Goldman, Lisa Frenkel, Whitney E. Harrington. Data curation: Yonghou Jiang, Jennifer Hadlock, Ingrid Beck, Fred D. Mast, Leslie R. Miller, John Houck, Blair Armistead, Venkata R. Duvvuri, Winnie Yeung, Micaela Haglund, Julie A. Wallick, Kim M. Murray, Jason D. Goldman, Lisa Frenkel, Whitney E. Harrington. Formal analysis: Yonghou Jiang, Fergal Duffy, Whitney E. Harrington. Funding acquisition: James R. Heath, Jason D. Goldman, Whitney E. Harrington. Investigation: Yonghou Jiang, Fergal Duffy, Andrew Raappana, Sheila Styrchak, Ingrid Beck, Fred D. Mast, Leslie R. Miller, William Chour, Jackson Wallner, Samantha Hardy, Alyssa Oldroyd, Daisy Ko, John D. Aitchison, D. Noah Sather, Whitney E. Harrington. Methodology: Yonghou Jiang, Andrew Raappana, Sheila Styrchak, Ingrid Beck, William Chour, Venkata R. Duvvuri, Ana Gervassi, Henry Kaplan, D. Noah Sather, Lisa Frenkel, Whitney E. Harrington. Project administration: Jennifer Hadlock, Fred D. Mast, John Houck, Winnie Yeung, Micaela Haglund, Jackson Wallner, Julie A. Wallick, Kim M. Murray, Jason D. Goldman, Lisa Frenkel,\nWhitney E. Harrington. Resources: Lisa Frenkel. Supervision: John D. Aitchison, James R. Heath, D. Noah Sather, Jason D. Goldman, Whitney E. Harrington. Validation: Whitney E. Harrington. Visualization: Yonghou Jiang, Fergal Duffy, Blair Armistead. Writing \u2013 original draft: Yonghou Jiang, Fergal Duffy, Jason D. Goldman, Lisa Frenkel, Whitney E. Harrington. Writing \u2013 review & editing: Jason D. Goldman, Lisa Frenkel, Whitney E. Harrington. \n\nCompeting interests: J.D.G. declared research support from Gilead, Lilly, and Regeneron, and Monogram Biosciences and served on advisory board for Gilead. The other authors declare no conflicts of interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials. \n\nData Availability: All relevant data are within the manuscript and its Supporting Information files.\n\nPublished - journal.pone.0259902.pdf
Submitted - 2021.06.30.21259796v1.full.pdf
Supplemental Material - journal.pone.0259902.s001.docx
Supplemental Material - journal.pone.0259902.s002.xlsx
Supplemental Material - journal.pone.0259902.s003.xlsx
", "abstract": "Background: Coronavirus disease 2019 (COVID-19) is associated with endothelial activation and coagulopathy, which may be related to pre-existing or infection-induced pro-thrombotic autoantibodies such as those targeting angiotensin II type I receptor (AT1R-Ab). \n\nMethods: We compared prevalence and levels of AT1R-Ab in COVID-19 cases with mild or severe disease to age and sex matched negative controls utilizing multivariate logistic and quantile regression adjusted for comorbidities including hypertension, diabetes, and heart disease. \n\nResults: There were trends toward increased prevalence (50% vs. 33%, p = 0.1) and level of AT1R-Ab (median 9.8 vs. 6.1 U/mL, p = 0.06) in all cases versus controls. When considered by COVID-19 disease severity, there was a trend toward increased prevalence of AT1R-Ab (55% vs. 31%, p = 0.07), as well as significantly higher AT1R-Ab levels (median 10.7 vs. 5.9 U/mL, p = 0.03) amongst individuals with mild COVID-19 versus matched controls. In contrast, the prevalence (42% vs. 37%, p = 0.9) and level (both medians 6.7 U/mL, p = 0.9) of AT1R-Ab amongst those with severe COVID-19 did not differ from matched controls. \n\nConclusions: These findings support an association between COVID-19 and AT1R-Ab, emphasizing that vascular pathology may be present in individuals with mild COVID-19 as well as those with severe disease.", "date": "2021-11-17", "date_type": "published", "publication": "PLoS ONE", "volume": "16", "number": "11", "publisher": "Public Library of Science", "pagerange": "Art. No. e0259902", "id_number": "CaltechAUTHORS:20210714-152527909", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210714-152527909", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Seattle Childrens Research Institute" }, { "agency": "NIH", "grant_number": "K08 AI135072" }, { "agency": "Burroughs Wellcome Fund", "grant_number": "CAMS 1017213" }, { "agency": "Biomedical Advanced Research and Development Authority", "grant_number": "HHSO10201600031C" }, { "agency": "Swedish Medical Center Foundation" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1371/journal.pone.0259902", "pmcid": "PMC8598062", "primary_object": { "basename": "2021.06.30.21259796v1.full.pdf", "url": "https://authors.library.caltech.edu/records/92btd-ccb84/files/2021.06.30.21259796v1.full.pdf" }, "related_objects": [ { "basename": "journal.pone.0259902.pdf", "url": "https://authors.library.caltech.edu/records/92btd-ccb84/files/journal.pone.0259902.pdf" }, { "basename": "journal.pone.0259902.s001.docx", "url": "https://authors.library.caltech.edu/records/92btd-ccb84/files/journal.pone.0259902.s001.docx" }, { "basename": "journal.pone.0259902.s002.xlsx", "url": "https://authors.library.caltech.edu/records/92btd-ccb84/files/journal.pone.0259902.s002.xlsx" }, { "basename": "journal.pone.0259902.s003.xlsx", "url": "https://authors.library.caltech.edu/records/92btd-ccb84/files/journal.pone.0259902.s003.xlsx" } ], "pub_year": "2021", "author_list": "Jiang, Yonghou; Duffy, Fergal; et al." }, { "id": "https://authors.library.caltech.edu/records/9rwbg-mx492", "eprint_id": 111843, "eprint_status": "archive", "datestamp": "2023-09-15 07:11:31", "lastmod": "2023-10-23 21:33:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Laughner-Joshua-L", "name": { "family": "Laughner", "given": "Joshua L." }, "orcid": "0000-0002-8599-4555" }, { "id": "Neu-Jessica-L", "name": { "family": "Neu", "given": "Jessica L." } }, { "id": "Schimel-David-S", "name": { "family": "Schimel", "given": "David" }, "orcid": "0000-0003-3473-8065" }, { "id": "Wennberg-P-O", "name": { "family": "Wennberg", "given": "Paul O." }, "orcid": "0000-0002-6126-3854" }, { "id": "Barsanti-Kelley", "name": { "family": "Barsanti", "given": "Kelley" }, "orcid": "0000-0002-6065-8643" }, { "id": "Bowman-Kevin-W", "name": { "family": "Bowman", "given": "Kevin W." }, "orcid": "0000-0002-8659-1117" }, { "id": "Chatterjee-Abhishek", "name": { "family": "Chatterjee", "given": "Abhishek" }, "orcid": "0000-0002-3680-0160" }, { "id": "Croes-Bart-E", "name": { "family": "Croes", "given": "Bart E." }, "orcid": "0000-0002-9351-0434" }, { "id": "Fitzmaurice-Helen-L", "name": { "family": "Fitzmaurice", "given": "Helen L." }, "orcid": "0000-0002-1631-5491" }, { "id": "Henze-Daven-K", "name": { "family": "Henze", "given": "Daven K." }, "orcid": "0000-0001-6431-4963" }, { "id": "Kim-Jinsol", "name": { "family": "Kim", "given": "Jinsol" } }, { "id": "Kort-Eric-A", "name": { "family": "Kort", "given": "Eric A." }, "orcid": "0000-0003-4940-7541" }, { "id": "Liu-Zhu", "name": { "family": "Liu", "given": "Zhu" }, "orcid": "0000-0002-8968-7050" }, { "id": "Miyazaki-Kazuyuki", "name": { "family": "Miyazaki", "given": "Kazuyuki" }, "orcid": "0000-0002-1466-4655" }, { "id": "Turner-Alexander-J", "name": { "family": "Turner", "given": "Alexander J." }, "orcid": "0000-0003-1406-7372" }, { "id": "Anenberg-Susan", "name": { "family": "Anenberg", "given": "Susan" }, "orcid": "0000-0002-9668-603X" }, { "id": "Avise-Jeremy", "name": { "family": "Avise", "given": "Jeremy" } }, { "id": "Cao-Hansen", "name": { "family": "Cao", "given": "Hansen" }, "orcid": "0000-0003-2713-0430" }, { "id": "Crisp-David", "name": { "family": "Crisp", "given": "David" }, "orcid": "0000-0002-4573-9998" }, { "id": "de-Gouw-Joost-A", "name": { "family": "de Gouw", "given": "Joost" }, "orcid": "0000-0002-0385-1826" }, { "id": "Eldering-Annmarie", "name": { "family": "Eldering", "given": "Annmarie" }, "orcid": "0000-0003-1080-9922" }, { "id": "Fyfe-John-C", "name": { "family": "Fyfe", "given": "John C." }, "orcid": "0000-0003-2524-0652" }, { "id": "Goldberg-Daniel-L", "name": { "family": "Goldberg", "given": "Daniel L." }, "orcid": "0000-0003-0784-3986" }, { "id": "Gurney-Kevin-R", "name": { "family": "Gurney", "given": "Kevin R." }, "orcid": "0000-0001-9218-7164" }, { "id": "Hasheminassab-Sina", "name": { "family": "Hasheminassab", "given": "Sina" } }, { "id": "Hopkins-Francesca", "name": { "family": "Hopkins", "given": "Francesca" }, "orcid": "0000-0002-6110-7675" }, { "id": "Ivey-Cesunica-E", "name": { "family": "Ivey", "given": "Cesunica E." }, "orcid": "0000-0002-4740-2627" }, { "id": "Jones-Dylan-B-A", "name": { "family": "Jones", "given": "Dylan B. A." } }, { "id": "Liu-Junjie", "name": { "family": "Liu", "given": "Junjie" }, "orcid": "0000-0002-7184-6594" }, { "id": "Lovenduski-Nicole-S", "name": { "family": "Lovenduski", "given": "Nicole S." }, "orcid": "0000-0001-5893-1009" }, { "id": "Martin-Randall-V", "name": { "family": "Martin", "given": "Randall V." }, "orcid": "0000-0003-2632-8402" }, { "id": "McKinley-Galen-A", "name": { "family": "McKinley", "given": "Galen A." }, "orcid": "0000-0002-4072-9221" }, { "id": "Ott-Lesley", "name": { "family": "Ott", "given": "Lesley" }, "orcid": "0000-0002-0035-9625" }, { "id": "Poulter-Benjamin", "name": { "family": "Poulter", "given": "Benjamin" }, "orcid": "0000-0002-9493-8600" }, { "id": "Ru-Muye", "name": { "family": "Ru", "given": "Muye" }, "orcid": "0000-0003-3252-1030" }, { "id": "Sander-Stanley-P", "name": { "family": "Sander", "given": "Stanley P." }, "orcid": "0000-0003-1424-3620" }, { "id": "Swart-Neil", "name": { "family": "Swart", "given": "Neil" }, "orcid": "0000-0002-8200-6187" }, { "id": "Yung-Y-L", "name": { "family": "Yung", "given": "Yuk L." }, "orcid": "0000-0002-4263-2562" }, { "id": "Zeng-Zhao-Cheng", "name": { "family": "Zeng", "given": "Zhao-Cheng" }, "orcid": "0000-0002-0008-6508" } ] }, "title": "Societal shifts due to COVID-19 reveal large-scale complexities and feedbacks between atmospheric chemistry and climate change", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; air quality; greenhouse gases; earth system; mitigation", "note": "\u00a9 2021 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND). \n\nEdited by Akkihebbal R. Ravishankara, Colorado State University, Fort Collins, CO, and approved September 29, 2021 (received for review June 10, 2021). \n\nWe thank the Keck Institute for Space Studies for organizing and supporting the study \"COVID-19: Identifying Unique Opportunities for Earth System Science\" that led to the writing of this manuscript. We also acknowledge the use of data from the Port of Oakland and Port of LA website, Apple mobility data, and US EIA electricity-use data. We also thank Charles Carter for his artwork in Fig. 1. We thank the TCCON science team for their effort in providing data. Support for operation of the Park Falls TCCON site is provided by NASA. The Lauder TCCON programme is funded by NIWA (National Institute of Water & Atmospheric Research Ltd.) through Aotearoa New Zealand's Ministry of Business, Innovation and Employment's Strategic Science Investment Fund. The views expressed in this manuscript are solely those of the authors and do not necessarily reflect those of the South Coast Air Quality Management District. A portion of this research was carried out at the Jet Propulsion Laboratory (JPL), California Institute of Technology, under a contract with NASA. This work was supported by NASA Grant NNX17AE15G (to J.L.L. and P.O.W.), NASA Carbon Monitoring System Grant 80NSSC20K0006 (to A.C.), NASA Grant 80NSSC18K0689 (to D.K.H. and H.C.), NASA Aura Science Team Program 19-AURAST19-0044 (to K.M. and K.W.B.), NASA Grant 80NSSC20K1122 (to D.L.G. and S.A.), NASA Grant 80NSSC21K0508 (to R.V.M.), NSF RAPID Grant 2030049 (to K.B.), NSF Grants OCE-1752724 and OCE-1948664 (to N.S.L.), and NSF Grant OCE-1948624 (to G.A.M.). A.J.T. was supported as a Miller Fellow with the Miller Institute for Basic Research in Science at the University of California Berkeley. K.R.G. was supported by Northern Arizona University startup funds. C.E.I. was supported by the University of California Institute of Transportation Studies. S.P.S. and Z.-C.Z. were supported by the California Air Resources Board, NASA Science Mission Directorate/Earth Science Division, and JPL Earth Science and Technology Directorate. Y.L.Y. was supported in part by JPL OCO-2 Grant JPL.1613918 (to the California Institute of Technology). J.L. was supported by the NASA OCO science team program. \n\nData Availability: GEOS-Chem Model Output data have been deposited in Zenodo (https://zenodo.org/record/4849416) (71). Publicly available datasets are listed along with data generated from this study and stored in public-facing repositories in SI Appendix, Table S1. Emissions data for Figs. 3 and 9 are given in SI Appendix, Table S2. Data for the OPE values in Fig. 7 are given in SI Appendix, Table S4. Emissions and OPE data are also included as Datasets S1 and S2. In addition, previously published data (1, 2, 13, 25, 29\u201331, 35, 72\u201384) were used for this work. \n\nAuthor contributions: J.L.L., K.B., K.W.B., A.C., B.E.C., H.L.F., D.K.H., J.K., E.A.K., Z.L., K.M., A.J.T., S.A., J.A., H.C., D.C., J.d.G., A.E., J.C.F., D.L.G., K.R.G., S.H., F.H., C.E.I., D.B.A.J., J.L., N.S.L., R.V.M., G.A.M., L.O., B.P., M.R., S.P.S., N.S., Y.L.Y., and Z.-C.Z. performed research; J.L.N., D.S., and P.O.W. designed research; J.L.L., J.L.N., D.S., P.O.W., K.B., K.W.B., A.C., B.E.C., H.L.F., D.K.H., J.K., E.A.K., Z.L., K.M., A.J.T., S.A., J.A., H.C., D.C., J.d.G., A.E., J.C.F., D.L.G., K.R.G., S.H., F.H., C.E.I., D.B.A.J., J.L., N.S.L., R.V.M., G.A.M., L.O., B.P., M.R., S.P.S., N.S., Y.L.Y., and Z.-C.Z. analyzed data; J.L.L., J.L.N., D.S., and P.O.W. wrote the paper; and K.B., K.W.B., A.C., B.E.C., H.L.F., D.K.H., J.K., E.A.K., Z.L., K.M., A.J.T., S.A., J.A., H.C., D.C., J.d.G., A.E., J.C.F., D.L.G., K.R.G., S.H., F.H., C.E.I., D.B.A.J., J.L., N.S.L., R.V.M., G.A.M., L.O., B.P., M.R., S.P.S., N.S., Y.L.Y., and Z.-C.Z. edited and approved the manuscript draft. \n\nThe authors declare no competing interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2109481118/-/DCSupplemental.\n\nPublished - e2109481118.full.pdf
Supplemental Material - pnas.2109481118.sapp.pdf
Supplemental Material - pnas.2109481118.sd01.docx
Supplemental Material - pnas.2109481118.sd01.xlsx
Supplemental Material - pnas.2109481118.sd02.xlsx
", "abstract": "The COVID-19 global pandemic and associated government lockdowns dramatically altered human activity, providing a window into how changes in individual behavior, enacted en masse, impact atmospheric composition. The resulting reductions in anthropogenic activity represent an unprecedented event that yields a glimpse into a future where emissions to the atmosphere are reduced. Furthermore, the abrupt reduction in emissions during the lockdown periods led to clearly observable changes in atmospheric composition, which provide direct insight into feedbacks between the Earth system and human activity. While air pollutants and greenhouse gases share many common anthropogenic sources, there is a sharp difference in the response of their atmospheric concentrations to COVID-19 emissions changes, due in large part to their different lifetimes. Here, we discuss several key takeaways from modeling and observational studies. First, despite dramatic declines in mobility and associated vehicular emissions, the atmospheric growth rates of greenhouse gases were not slowed, in part due to decreased ocean uptake of CO\u2082 and a likely increase in CH\u2084 lifetime from reduced NO_x emissions. Second, the response of O\u2083 to decreased NO_x emissions showed significant spatial and temporal variability, due to differing chemical regimes around the world. Finally, the overall response of atmospheric composition to emissions changes is heavily modulated by factors including carbon-cycle feedbacks to CH\u2084 and CO\u2082, background pollutant levels, the timing and location of emissions changes, and climate feedbacks on air quality, such as wildfires and the ozone climate penalty.", "date": "2021-11-16", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences", "volume": "118", "number": "46", "publisher": "National Academy of Sciences", "pagerange": "Art. No. e2109481118", "id_number": "CaltechAUTHORS:20211111-200602979", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211111-200602979", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NASA/JPL/Caltech" }, { "agency": "NASA", "grant_number": "NNX17AE15G" }, { "agency": "NASA", "grant_number": "80NSSC20K0006" }, { "agency": "NASA", "grant_number": "80NSSC18K0689" }, { "agency": "NASA", "grant_number": "19-AURAST19-0044" }, { "agency": "NASA", "grant_number": "80NSSC20K1122" }, { "agency": "NASA", "grant_number": "80NSSC21K0508" }, { "agency": "NSF", "grant_number": "2030049" }, { "agency": "NSF", "grant_number": "OCE-1752724" }, { "agency": "NSF", "grant_number": "OCE-1948664" }, { "agency": "NSF", "grant_number": "OCE-1948624" }, { "agency": "Miller Institute for Basic Research in Science" }, { "agency": "Northern Arizona University" }, { "agency": "University of California" }, { "agency": "California Air Resources Board" }, { "agency": "JPL", "grant_number": "JPL.1613918" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Keck-Institute-for-Space-Studies" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1073/pnas.2109481118", "pmcid": "PMC8609622", "primary_object": { "basename": "e2109481118.full.pdf", "url": "https://authors.library.caltech.edu/records/9rwbg-mx492/files/e2109481118.full.pdf" }, "related_objects": [ { "basename": "pnas.2109481118.sapp.pdf", "url": "https://authors.library.caltech.edu/records/9rwbg-mx492/files/pnas.2109481118.sapp.pdf" }, { "basename": "pnas.2109481118.sd01.docx", "url": "https://authors.library.caltech.edu/records/9rwbg-mx492/files/pnas.2109481118.sd01.docx" }, { "basename": "pnas.2109481118.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/9rwbg-mx492/files/pnas.2109481118.sd01.xlsx" }, { "basename": "pnas.2109481118.sd02.xlsx", "url": "https://authors.library.caltech.edu/records/9rwbg-mx492/files/pnas.2109481118.sd02.xlsx" } ], "pub_year": "2021", "author_list": "Laughner, Joshua L.; Neu, Jessica L.; et al." }, { "id": "https://authors.library.caltech.edu/records/d6q6k-9t527", "eprint_id": 111317, "eprint_status": "archive", "datestamp": "2023-10-04 22:02:30", "lastmod": "2026-03-30 08:32:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Brune-Karl-D", "name": { "family": "Brune", "given": "Karl D." }, "orcid": "0000-0003-2796-972X" }, { "id": "Liekni\u0146a-Ilva", "name": { "family": "Liekni\u0146a", "given": "Ilva" } }, { "id": "Sutov-Grigorij", "name": { "family": "Sutov", "given": "Grigorij" } }, { "id": "Morris-Alexander-R", "name": { "family": "Morris", "given": "Alexander R." } }, { "id": "Jovicevic-Dejana", "name": { "family": "Jovicevic", "given": "Dejana" } }, { "id": "Kalni\u0146\u0161-Gints", "name": { "family": "Kalni\u0146\u0161", "given": "Gints" }, "orcid": "0000-0002-9593-6308" }, { "id": "Kaz\u0101ks-Andris", "name": { "family": "Kaz\u0101ks", "given": "Andris" } }, { "id": "Kluga-Rihards", "name": { "family": "Kluga", "given": "Rihards" }, "orcid": "0000-0003-1308-9019" }, { "id": "Kastaljana-Sab\u012bne", "name": { "family": "Kastaljana", "given": "Sabine" }, "orcid": "0000-0002-7700-4371" }, { "id": "Zajakina-Anna", "name": { "family": "Zajakina", "given": "Anna" }, "orcid": "0000-0002-4753-1103" }, { "id": "Jansons-Juris", "name": { "family": "Jansons", "given": "Juris" }, "orcid": "0000-0003-0845-4392" }, { "id": "Skrasti\u0146a-Dace", "name": { "family": "Skrasti\u0146a", "given": "Dace" }, "orcid": "0000-0001-5836-6441" }, { "id": "Spunde-Kar\u012bna", "name": { "family": "Spunde", "given": "Kar\u012bna" } }, { "id": "Cohen-Alexander-A", "name": { "family": "Cohen", "given": "Alexander A." }, "orcid": "0000-0002-2818-656X" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Morris-Howard-R", "name": { "family": "Morris", "given": "Howard R." } }, { "id": "Suna-Edgars", "name": { "family": "Suna", "given": "Edgars" }, "orcid": "0000-0002-3078-0576" }, { "id": "T\u0101rs-Kaspars", "name": { "family": "T\u0101rs", "given": "Kaspars" }, "orcid": "0000-0001-8421-9023" } ] }, "title": "N-Terminal Modification of Gly-His-Tagged Proteins with Azidogluconolactone", "ispublished": "pub", "full_text_status": "public", "keywords": "click chemistry; immunology; nanoparticles; protein modifications; site-specific conjugation", "note": "\u00a9 2021 Wiley-VCH. \n\nIssue Online: 16 November 2021; Version of Record online: 06 October 2021; Accepted manuscript online: 14 September 2021; Manuscript revised: 13 September 2021; Manuscript received: 30 July 2021. \n\nThis research was funded by the Latvian Council of Science (VPP-COVID-2020/1-0014), The Lithuanian Agency for Science, Innovation and Technology (MITA, 01.2.1-MITA-T-852-01-0109), the Merkin Institute for Translational Medicine at The California Institute of Technology, BioPharmaSpec Ltd and Genie Biotech Ltd. \n\nA.R.M., G.S., and K.D.B. are named inventors on Genie Biotech patent applications for azidogluconoylation. All other authors declare no conflict of interest.\n\nAccepted Version - cbic202100381.pdf
Supplemental Material - cbic202100381-sup-0001-misc_information.pdf
", "abstract": "Site-specific protein modifications are vital for biopharmaceutical drug development. Gluconoylation is a non-enzymatic, post-translational modification of N-terminal HisTags. We report high-yield, site-selective in\u2005vitro \u03b1-aminoacylation of peptides, glycoproteins, antibodies, and virus-like particles (VLPs) with azidogluconolactone at pH\u20057.5 in 1\u2005h. Conjugates slowly hydrolyse, but diol-masking with borate esters inhibits reversibility. In an example, we multimerise azidogluconoylated SARS-CoV-2 receptor-binding domain (RBD) onto VLPs via click-chemistry, to give a COVID-19 vaccine. Compared to yeast antigen, HEK-derived RBD was immunologically superior, likely due to observed differences in glycosylation. We show the benefits of ordered over randomly oriented multimeric antigen display, by demonstrating single-shot seroconversion and best virus-neutralizing antibodies. Azidogluconoylation is simple, fast and robust chemistry, and should accelerate research and development.", "date": "2021-11-16", "date_type": "published", "publication": "ChemBioChem", "volume": "22", "number": "22", "publisher": "Wiley", "pagerange": "3199-3207", "id_number": "CaltechAUTHORS:20211008-224615060", "issn": "1439-4227", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211008-224615060", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Latvian Council of Science", "grant_number": "VPP-COVID-2020/1-0014" }, { "agency": "Lithuanian Agency for Science, Innovation and Technology", "grant_number": "01.2.1-MITA-T-852-01-0109" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "BioPharmaSpec Ltd." }, { "agency": "Genie Biotech Ltd." } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1002/cbic.202100381", "primary_object": { "basename": "cbic202100381-sup-0001-misc_information.pdf", "url": "https://authors.library.caltech.edu/records/d6q6k-9t527/files/cbic202100381-sup-0001-misc_information.pdf" }, "pub_year": "2021", "author_list": "Brune, Karl D.; Liekni\u0146a, Ilva; et al." }, { "id": "https://authors.library.caltech.edu/records/cw5xt-hys06", "eprint_id": 106550, "eprint_status": "archive", "datestamp": "2023-11-15 16:48:47", "lastmod": "2026-03-30 15:28:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Moln\u00e1r-Tam\u00e1s-G", "name": { "family": "Moln\u00e1r", "given": "Tam\u00e1s G." }, "orcid": "0000-0002-9379-7121" }, { "id": "Singletary-Andrew-W", "name": { "family": "Singletary", "given": "Andrew W." }, "orcid": "0000-0001-6635-4256" }, { "id": "Orosz-G\u00e1bor", "name": { "family": "Orosz", "given": "G\u00e1bor" }, "orcid": "0000-0002-9000-3736" }, { "id": "Ames-A-D", "name": { "family": "Ames", "given": "Aaron D." }, "orcid": "0000-0003-0848-3177" } ] }, "title": "Safety-Critical Control of Compartmental Epidemiological Models with Measurement Delays", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19, epidemiology, safety-critical control, time delay", "note": "This work was supported in part by the National Science Foundation, CPS Award 1932091. Recommended by Senior Editor S. Tarbouriech. The authors would like to thank Franca Hoffmann and G\u00e1bor St\u00e9p\u00e1n for the valuable discussions on this topic.
\n\nSubmitted - 2009.10262.pdf
\n\n\u00a9 IEEE 2020. This article is free to access and download, along with rights for full text and data mining, re-use and analysis.
", "abstract": "We introduce a methodology to guarantee safety against the spread of infectious diseases by viewing epidemiological models as control systems and human interventions (such as quarantining or social distancing) as control input. We consider a generalized compartmental model that represents the form of the most popular epidemiological models and we design safety-critical controllers that formally guarantee safe evolution with respect to keeping certain populations of interest under prescribed safe limits. Furthermore, we discuss how measurement delays originated from incubation period and testing delays affect safety and how delays can be compensated via predictor feedback. We demonstrate our results by synthesizing active intervention policies that bound the number of infections, hospitalizations and deaths for epidemiological models capturing the spread of COVID-19 in the USA.", "date": "2021-11", "date_type": "published", "publication": "IEEE Control Systems Letters", "volume": "5", "number": "5", "publisher": "IEEE", "pagerange": "1537-1542", "id_number": "CaltechAUTHORS:20201109-140935453", "issn": "2475-1456", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201109-140935453", "funders": { "items": [ { "agency": "NSF", "grant_number": "CNS-1932091" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1109/LCSYS.2020.3040948", "pmcid": "PMC8545040", "primary_object": { "basename": "lcsys-molnar-3040948.pdf", "url": "https://authors.library.caltech.edu/records/cw5xt-hys06/files/lcsys-molnar-3040948.pdf" }, "related_objects": [ { "basename": "2009.10262.pdf", "url": "https://authors.library.caltech.edu/records/cw5xt-hys06/files/2009.10262.pdf" } ], "pub_year": "2021", "author_list": "Moln\u00e1r, Tam\u00e1s G.; Singletary, Andrew W.; et al." }, { "id": "https://authors.library.caltech.edu/records/6ez4q-hx548", "eprint_id": 114693, "eprint_status": "archive", "datestamp": "2023-08-20 05:51:57", "lastmod": "2023-12-22 23:31:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ji-Jenny", "name": { "family": "Ji", "given": "Jenny" }, "orcid": "0000-0002-7901-5605" }, { "id": "Winnett-Alexander", "name": { "family": "Winnett", "given": "Alexander" }, "orcid": "0000-0002-7338-5605" }, { "id": "Shelby-Natasha", "name": { "family": "Shelby", "given": "Natasha" }, "orcid": "0000-0001-9097-3663" }, { "id": "Reyes-Jessica-A", "name": { "family": "Reyes", "given": "Jessica A." }, "orcid": "0000-0002-5507-7633" }, { "id": "Akana-Reid", "name": { "family": "Akana", "given": "Reid" }, "orcid": "0000-0003-4422-587X" }, { "id": "Schlenker-Noah-W", "name": { "family": "Schlenker", "given": "Noah W." }, "orcid": "0000-0002-8581-4403" }, { "id": "Savela-Emily-S", "name": { "family": "Savela", "given": "Emily S." }, "orcid": "0000-0001-9614-4276" }, { "id": "Romano-Anna-E", "name": { "family": "Romano", "given": "Anna" }, "orcid": "0000-0003-1871-1727" }, { "id": "Porter-Michael-K", "name": { "family": "Porter", "given": "Michael K." }, "orcid": "0000-0002-0777-7563" }, { "id": "Carter-Alyssa-M", "name": { "family": "Carter", "given": "Alyssa M." }, "orcid": "0000-0002-2776-9421" }, { "id": "Cooper-Matthew-M", "name": { "family": "Cooper", "given": "Matthew M." }, "orcid": "0000-0002-5868-5159" }, { "id": "Barlow-Jacob-T", "name": { "family": "Barlow", "given": "Jacob T." }, "orcid": "0000-0002-1842-4835" }, { "id": "Tognazzini-Colten", "name": { "family": "Tognazzini", "given": "Colten" } }, { "id": "Feaster-Matthew", "name": { "family": "Feaster", "given": "Matthew" }, "orcid": "0000-0001-9966-2845" }, { "id": "Goh-Ying-Ying", "name": { "family": "Goh", "given": "Ying-Ying" }, "orcid": "0000-0001-5136-7214" }, { "id": "Ismagilov-R-F", "name": { "family": "Ismagilov", "given": "Rustem F." }, "orcid": "0000-0002-3680-4399" } ] }, "title": "Modulating Factors of Household Transmission of SARS\u2011CoV\u20112 in a Community-Based Study", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 American Society of Tropical Medicine and Hygiene. \n\nMeeting abstract 0975.", "abstract": "[no abstract]", "date": "2021-11", "date_type": "published", "publication": "American Journal of Tropical Medicine and Hygiene", "volume": "105", "number": "5", "publisher": "American Society of Tropical Medicine and Hygiene", "pagerange": "313", "id_number": "CaltechAUTHORS:20220512-142847077", "issn": "0002-9637", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220512-142847077", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.4269/ajtmh.abstract2021", "pub_year": "2021", "author_list": "Ji, Jenny; Winnett, Alexander; et al." }, { "id": "https://authors.library.caltech.edu/records/566p9-bva47", "eprint_id": 107593, "eprint_status": "archive", "datestamp": "2023-08-20 05:45:56", "lastmod": "2026-03-29 18:11:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sottile-Peter-D", "name": { "family": "Sottile", "given": "Peter D." }, "orcid": "0000-0002-1071-730X" }, { "id": "Albers-David-J", "name": { "family": "Albers", "given": "David" }, "orcid": "0000-0002-5369-526X" }, { "id": "DeWitt-Peter-E", "name": { "family": "DeWitt", "given": "Peter E." }, "orcid": "0000-0002-6391-0795" }, { "id": "Russell-Seth", "name": { "family": "Russell", "given": "Seth" }, "orcid": "0000-0002-2436-1367" }, { "id": "Stroh-J-N", "name": { "family": "Stroh", "given": "J. N." }, "orcid": "0000-0003-4844-1983" }, { "id": "Kao-David-P", "name": { "family": "Kao", "given": "David P." } }, { "id": "Adrian-Bonnie", "name": { "family": "Adrian", "given": "Bonnie" } }, { "id": "Levine-Matthew-E", "name": { "family": "Levine", "given": "Matthew E." }, "orcid": "0000-0002-5627-3169" }, { "id": "Mooney-Ryan", "name": { "family": "Mooney", "given": "Ryan" }, "orcid": "0000-0002-5401-0891" }, { "id": "Larchick-Lenny", "name": { "family": "Larchick", "given": "Lenny" } }, { "id": "Kutner-Jean-S", "name": { "family": "Kutner", "given": "Jean S." } }, { "id": "Wynia-Matthew-K", "name": { "family": "Wynia", "given": "Matthew K." }, "orcid": "0000-0003-3307-069X" }, { "id": "Glasheen-Jeffrey-J", "name": { "family": "Glasheen", "given": "Jeffrey J." } }, { "id": "Bennett-Tellen-D", "name": { "family": "Bennett", "given": "Tellen D." }, "orcid": "0000-0003-1483-4236" } ] }, "title": "Real-time electronic health record mortality prediction during the COVID-19 pandemic: a prospective cohort study", "ispublished": "pub", "full_text_status": "public", "keywords": "crisis triage, mortality prediction, COVID-19, decision support systems, clinical, machine learning", "note": "\u00a9 The Author(s) 2021. Published by Oxford University Press on behalf of the American Medical Informatics Association. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nReceived 23 February 2021; Revised 19 April 2021; Editorial Decision 4 May 2021; Accepted 6 May 2021. Published: 02 September 2021. \n\nWe would like to acknowledge Sarah Davis, Michelle Edelmann, and Michael Kahn at Health Data Compass. \n\nPS is supported by NIH K23 HL 145001; DA and ML by NIH R01 LM012734; DK by NIH K08 HL125725; TB by NIH UL1 TR002535 and NIH UL1 TR002535 - 03S2. \n\nAuthor Contributions: TDB had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. PDS, DA, PED, SR, JS, and TDB contributed substantially to the study design, data acquisition, data analysis and interpretation, and the writing of the manuscript. DPK, BA, RM, and LL contributed substantially to data acquisition, verifying data integrity, and the writing of the manuscript. MEK contributed substantially to study design and the writing of the manuscript. DA, MEL, and PDS conceptualized and initially designed the statistical modeling framework. JSK, MKW, and JJG contributed substantially to the study design, data acquisition, and the writing of the manuscript. \n\nConflict of Interest Statement: None declared.\n\nSubmitted - 2021.01.14.21249793v1.full.pdf
Supplemental Material - ocab100_supplementary_data.docx
", "abstract": "Objective: To rapidly develop, validate, and implement a novel real-time mortality score for the COVID-19 pandemic that improves upon sequential organ failure assessment (SOFA) for decision support for a Crisis Standards of Care team. \n\nMaterials and Methods: We developed, verified, and deployed a stacked generalization model to predict mortality using data available in the electronic health record (EHR) by combining 5 previously validated scores and additional novel variables reported to be associated with COVID-19-specific mortality. We verified the model with prospectively collected data from 12 hospitals in Colorado between March 2020 and July 2020. We compared the area under the receiver operator curve (AUROC) for the new model to the SOFA score and the Charlson Comorbidity Index. \n\nResults: The prospective cohort included 27 296 encounters, of which 1358 (5.0%) were positive for SARS-CoV-2, 4494 (16.5%) required intensive care unit care, 1480 (5.4%) required mechanical ventilation, and 717 (2.6%) ended in death. The Charlson Comorbidity Index and SOFA scores predicted mortality with an AUROC of 0.72 and 0.90, respectively. Our novel score predicted mortality with AUROC 0.94. In the subset of patients with COVID-19, the stacked model predicted mortality with AUROC 0.90, whereas SOFA had AUROC of 0.85. \n\nDiscussion: Stacked regression allows a flexible, updatable, live-implementable, ethically defensible predictive analytics tool for decision support that begins with validated models and includes only novel information that improves prediction. \n\nConclusion: We developed and validated an accurate in-hospital mortality prediction score in a live EHR for automatic and continuous calculation using a novel model that improved upon SOFA.", "date": "2021-11", "date_type": "published", "publication": "Journal of the American Medical Informatics Association", "volume": "28", "number": "11", "publisher": "Oxford University Press", "pagerange": "2354-2365", "id_number": "CaltechAUTHORS:20210120-124914573", "issn": "1067-5027", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210120-124914573", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "K23 HL145001" }, { "agency": "NIH", "grant_number": "R01 LM012734" }, { "agency": "NIH", "grant_number": "K08 HL125725" }, { "agency": "NIH", "grant_number": "UL1 TR002535" }, { "agency": "NIH", "grant_number": "UL1 TR002535-03S2" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1093/jamia/ocab100", "primary_object": { "basename": "2021.01.14.21249793v1.full.pdf", "url": "https://authors.library.caltech.edu/records/566p9-bva47/files/2021.01.14.21249793v1.full.pdf" }, "related_objects": [ { "basename": "ocab100_supplementary_data.docx", "url": "https://authors.library.caltech.edu/records/566p9-bva47/files/ocab100_supplementary_data.docx" } ], "pub_year": "2021", "author_list": "Sottile, Peter D.; Albers, David; et al." }, { "id": "https://authors.library.caltech.edu/records/jt523-xd767", "eprint_id": 111925, "eprint_status": "archive", "datestamp": "2023-10-05 22:28:57", "lastmod": "2026-03-30 06:14:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Ruiz-Lopez-Nallely-M", "name": { "family": "Ruiz-Lopez", "given": "Nallely M." } }, { "id": "Houerbi-Nadia", "name": { "family": "Houerbi", "given": "Nadia" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Impacts of p97 on Proteome Changes in Human Cells during Coronaviral Replication", "ispublished": "pub", "full_text_status": "public", "keywords": "coronavirus; p97; ATPase; proteomics; inhibitor", "note": "\u00a9 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived: 15 September 2021; Accepted: 25 October 2021; Published: 29 October 2021. \n\nThis research was funded by the National Institute of Neurological Disorders and Stroke, grant number R01NS102279, and the Merkin Institute for Translational Research at Caltech. \n\nSupplementary Materials: The following are available online at https://www.mdpi.com/article/10.3390/cells10112953/s1, Figure S1: Full blot images of results shown in Figure 1B; Figure S2: Cell viability of HCoV-infected H1299 cells in the presence of CB-5083; Figure S3: Full blot images of results shown in Figure 2B; Figure S4: Cell viability of HCoV-infected H1299 cells in the stage-limited inhibition assay; Figure S5: Full blot images of results shown in Figure 3B; Figure S6: Knockdown of p97 expression in H1299 cells; Figure S7: Cell viability of H1299 cells with inducible control shRNA (Ctrl shRNA) or p97 shRNA after HCoV infection; Figure S8: Full blot images of results shown in Figure 4B; Figure S9: Overlapping host responses in cells after HCoV-229E, HCoV-OC43, or SARS-CoV-2 infection; Figure S10: Proteins enriched in \"Cellular responses to stress\"; Figure S11: Proteins enriched \"Host interactions of HIV factors\"; Figure S12: Proteins enriched \"Mitotic anaphases\"; Table S1: TagMan probes list; Table S2: Proteomics of H1299 cells with control shRNA and p97 shRNA after HCoV-229E infection; Table S3: Proteomics of H1299 cells with control shRNA and p97 shRNA after HCoV-OC43 infection; Table S4: Reactome pathway enrichment analysis; Table S5: Multi-list Reactome pathway enrichment analysis. \n\nAuthor Contributions: T.-F.C. conceived and supervised the project. K.-W.C. designed and performed experiments. S.L. and F.W. assisted in sample preparation for proteomics. N.M.R.-L. provided technique support for RNA extraction and real-time PCR. S.L., F.W. and N.H. assisted in proteomics data analysis and provided suggestions. K.-W.C. wrote the manuscript with support from T.-F.C., N.M.R.-L. and N.H. edited the manuscript. All authors have read and agreed to the published version of the manuscript. \n\nInstitutional Review Board Statement: Not applicable. \n\nInformed Consent Statement: Not applicable. \n\nData Availability Statement: All relevant data generated during this study are included in the article and the supplementary information. The mass spectrometry raw data are deposited to the ProteomeXchance Consortium (https://www.ebi.ac.uk/pride/ (accessed on 21 October 2021)) via the PRIDE repository with the dataset identifier PXD026216 and 10.6019/PXD026216). Additional raw data generated during the current study and relevant information are available from the corresponding authors upon request. \n\nThe authors declare no conflict of interest.\n\nPublished - cells-10-02953-v2.pdf
Supplemental Material - cells-10-02953-s001.zip
", "abstract": "Human coronavirus (HCoV) similar to other viruses rely on host cell machinery for both replication and to spread. The p97/VCP ATPase is associated with diverse pathways that may favor HCoV replication. In this study, we assessed the role of p97 and associated host responses in human lung cell line H1299 after HCoV-229E or HCoV-OC43 infection. Inhibition of p97 function by small molecule inhibitors shows antiviral activity, particularly at early stages of the virus life cycle, during virus uncoating and viral RNA replication. Importantly, p97 activity inhibition protects human cells against HCoV-induced cytopathic effects. The p97 knockdown also inhibits viral production in infected cells. Unbiased quantitative proteomics analyses reveal that HCoV-OC43 infection resulted in proteome changes enriched in cellular senescence and DNA repair during virus replication. Further analysis of protein changes between infected cells with control and p97 shRNA identifies cell cycle pathways for both HCoV-229E and HCoV-OC43 infection. Together, our data indicate a role for the essential host protein p97 in supporting HCoV replication, suggesting that p97 is a therapeutic target to treat HCoV infection.", "date": "2021-10-29", "date_type": "published", "publication": "Cells", "volume": "10", "number": "11", "publisher": "MDPI", "pagerange": "Art. No. 2953", "id_number": "CaltechAUTHORS:20211117-180505059", "issn": "2073-4409", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211117-180505059", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01NS102279" }, { "agency": "Caltech Merkin Institute for Translational Research" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.3390/cells10112953", "pmcid": "PMC8616207", "primary_object": { "basename": "cells-10-02953-s001.zip", "url": "https://authors.library.caltech.edu/records/jt523-xd767/files/cells-10-02953-s001.zip" }, "related_objects": [ { "basename": "cells-10-02953-v2.pdf", "url": "https://authors.library.caltech.edu/records/jt523-xd767/files/cells-10-02953-v2.pdf" } ], "pub_year": "2021", "author_list": "Cheng, Kai-Wen; Li, Shan; et al." }, { "id": "https://authors.library.caltech.edu/records/vemqv-kzm85", "eprint_id": 104601, "eprint_status": "archive", "datestamp": "2023-08-22 11:40:33", "lastmod": "2026-03-29 15:40:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jain-Siddharth", "name": { "family": "Jain", "given": "Siddharth" }, "orcid": "0000-0002-9164-6119" }, { "id": "Xiao-Xiongye", "name": { "family": "Xiao", "given": "Xiongye" } }, { "id": "Bogdan-Paul", "name": { "family": "Bogdan", "given": "Paul" }, "orcid": "0000-0003-2118-0816" }, { "id": "Bruck-J", "name": { "family": "Bruck", "given": "Jehoshua" }, "orcid": "0000-0001-8474-0812" } ] }, "title": "Generator based approach to analyze mutations in genomic datasets", "ispublished": "pub", "full_text_status": "public", "keywords": "Computational biology and bioinformatics; Mathematics and computing", "note": "\u00a9 The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 11 May 2021; Accepted 13 October 2021; Published 26 October 2021. \n\nS.J. was supported by the Center for Evolutionary Science at Caltech. P.B. and X.X. gratefully acknowledge the support by the National Science Foundation Career award under Grant number CPS/CNS-1453860, the NSF awards under Grant numbers CCF-1837131, MCB-1936775, CNS-1932620, CMMI-1936624, the U.S. Army Research Office (ARO) under Grant No. W911NF-17-1-0076, the Okawa Foundation research award, the Defense Advanced Research Projects Agency (DARPA) Young Faculty Award and DARPA Director Award under Grant No. N66001-17-1-4044, a 2021 USC Stevens Center Technology Advancement Grant (TAG) award, an Intel faculty award and a Northrop Grumman grant. The views, opinions, and/or findings contained in this article are those of the authors and should not be interpreted as representing the official views or policies, either expressed or implied by the Defense Advanced Research Projects Agency, the Department of Defense or the National Science Foundation. \n\nData availability: The SARS-CoV-2 datasets analyzed in the current study are provided in GISAID (https://gisaid.org). The implementation of the method, acknowledgement files for the SARS-CoV-2 samples used and the necessary details to generate figures in the paper are provided at https://github.com/joshuaxiao98/Generator-based-approach-to-analyze-mutations-in-genomic-datasets. The acknowledgement files for the SARS-CoV-2 samples are also provided in the supplementary material. \n\nThese authors contributed equally: Siddharth Jain and Xiongye Xiao. \n\nAuthor Contributions: S.J. and X.X wrote the manuscript and code for the implementation of the proposed method and data analysis. All authors discussed the results and commented on the manuscript. P.B. and J.B. originated and directed the study. \n\nThe authors declare no competing interests.\n\nPublished - s41598-021-00609-8.pdf
Submitted - 2020.07.26.222117v1.full.pdf
Supplemental Material - 41598_2021_609_MOESM1_ESM.pdf
", "abstract": "In contrast to the conventional approach of directly comparing genomic sequences using sequence alignment tools, we propose a computational approach that performs comparisons between sequence generators. These sequence generators are learned via a data-driven approach that empirically computes the state machine generating the genomic sequence of interest. As the state machine based generator of the sequence is independent of the sequence length, it provides us with an efficient method to compute the statistical distance between large sets of genomic sequences. Moreover, our technique provides a fast and efficient method to cluster large datasets of genomic sequences, characterize their temporal and spatial evolution in a continuous manner, get insights into the locality sensitive information about the sequences without any need for alignment. Furthermore, we show that the technique can be used to detect local regions with mutation activity, which can then be applied to aid alignment techniques for the fast discovery of mutations. To demonstrate the efficacy of our technique on real genomic data, we cluster different strains of SARS-CoV-2 viral sequences, characterize their evolution and identify regions of the viral sequence with mutations.", "date": "2021-10-26", "date_type": "published", "publication": "Scientific Reports", "volume": "11", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 21084", "id_number": "CaltechAUTHORS:20200728-093329251", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200728-093329251", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CNS-1453860" }, { "agency": "NSF", "grant_number": "CCF-1837131" }, { "agency": "NSF", "grant_number": "MCB-1936775" }, { "agency": "NSF", "grant_number": "CNS-1932620" }, { "agency": "NSF", "grant_number": "CMMI-1936624" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-17-1-0076" }, { "agency": "Okawa Foundation" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "N66001-17-1-4044" }, { "agency": "University of Southern California" }, { "agency": "Intel" }, { "agency": "Northrop Grumman Corporation" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1038/s41598-021-00609-8", "pmcid": "PMC8548350", "primary_object": { "basename": "s41598-021-00609-8.pdf", "url": "https://authors.library.caltech.edu/records/vemqv-kzm85/files/s41598-021-00609-8.pdf" }, "related_objects": [ { "basename": "2020.07.26.222117v1.full.pdf", "url": "https://authors.library.caltech.edu/records/vemqv-kzm85/files/2020.07.26.222117v1.full.pdf" }, { "basename": "41598_2021_609_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/vemqv-kzm85/files/41598_2021_609_MOESM1_ESM.pdf" } ], "pub_year": "2021", "author_list": "Jain, Siddharth; Xiao, Xiongye; et al." }, { "id": "https://authors.library.caltech.edu/records/5ynf8-smx60", "eprint_id": 111578, "eprint_status": "archive", "datestamp": "2023-10-05 22:26:21", "lastmod": "2026-03-30 05:45:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Abernathy-Morgan-E", "name": { "family": "Abernathy", "given": "Morgan E." }, "orcid": "0000-0001-9959-7713" }, { "id": "Dam-Kim-Marie-A", "name": { "family": "Dam", "given": "Kim-Marie A." }, "orcid": "0000-0002-1416-4757" }, { "id": "Esswein-Shannon-R", "name": { "family": "Esswein", "given": "Shannon R." }, "orcid": "0000-0002-5142-0190" }, { "id": "Jette-Claudia-A", "name": { "family": "Jette", "given": "Claudia A." }, "orcid": "0000-0002-5085-8027" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "How Antibodies Recognize Pathogenic Viruses: Structural Correlates of Antibody Neutralization of HIV-1, SARS-CoV-2, and Zika", "ispublished": "pub", "full_text_status": "public", "keywords": "antibody; cryo-electron microscopy; HIV-1; SARS-CoV-2; structural biology; virus; X-ray\ncrystallography; Zika", "note": "\u00a9 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived: 16 September 2021; Accepted: 12 October 2021; Published: 19 October 2021. \n\nWe would like to thank members of the Bjorkman laboratory for helpful discussions; the Caltech Merkin Institute for Translational Research for resources that enable our work; the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy for support in cryo-EM projects; the Gordon and Betty Moore and Beckman Foundations for gifts to support the Molecular Observatory at Caltech, which provides aid for protein crystallization; and the Stanford Synchrotron Radiation Lightsource (SSRL), which provides data collection capabilities for X-ray crystallography. Finally, we are grateful for Rosalind Franklin's contributions to structural biology and for her brazen career as a female scientist that continues to embolden researchers, especially women. \n\nThis research was supported by the National Institute of Allergy and Infectious Diseases (NIAID) Grant HIVRAD P01 AI100148, a George Mason University Fast Grant GMU.SARSCOV2, an NSF GRFP (to M.E.A.), a NIH National Research Service Award Fellowship F30AI147579 (S.R.E.), NIH National Institute of General Medical Sciences Training Grant T32-GM008042 (to S.R.E.) through the University of California, Los Angeles\u2013California Institute of Technology Medical Scientist Training Program, and the National Institutes of Health (NIH) Grant AI138938. This work was supported, in whole or in part, by the Bill & Melinda Gates Foundation (grant INV-002143). Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. \n\nAuthor Contributions: M.E.A., K.-M.A.D., S.R.E., and C.A.J. wrote and edited this review article with critical reading and editing by P.J.B. All authors have read and agreed to the published version of the manuscript. \n\nThe authors declare no conflict of interest for this work. \n\nInstitutional Review Board Statement: Not applicable. \n\nInformed Consent Statement: Not applicable.\n\nPublished - viruses-13-02106-v2.pdf
", "abstract": "The H1N1 pandemic of 2009-2010, MERS epidemic of 2012, Ebola epidemics of 2013-2016 and 2018-2020, Zika epidemic of 2015-2016, and COVID-19 pandemic of 2019-2021, are recent examples in the long history of epidemics that demonstrate the enormous global impact of viral infection. The rapid development of safe and effective vaccines and therapeutics has proven vital to reducing morbidity and mortality from newly emerging viruses. Structural biology methods can be used to determine how antibodies elicited during infection or vaccination target viral proteins and identify viral epitopes that correlate with potent neutralization. Here we review how structural and molecular biology approaches have contributed to our understanding of antibody recognition of pathogenic viruses, specifically HIV-1, SARS-CoV-2, and Zika. Determining structural correlates of neutralization of viruses has guided the design of vaccines, monoclonal antibodies, and small molecule inhibitors in response to the global threat of viral epidemics.", "date": "2021-10-19", "date_type": "published", "publication": "Viruses", "volume": "13", "number": "10", "publisher": "MDPI", "pagerange": "Art. No. 2106", "id_number": "CaltechAUTHORS:20211021-175154754", "issn": "1999-4915", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211021-175154754", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01 AI100148" }, { "agency": "George Mason University", "grant_number": "GMU.SARSCOV2" }, { "agency": "NSF Graduate Research Fellowship" }, { "agency": "NIH", "grant_number": "F30AI147579" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32-GM008042" }, { "agency": "UCLA-Caltech Medical Scientist Training Program" }, { "agency": "NIH", "grant_number": "AI138938" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-002143" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.3390/v13102106", "pmcid": "PMC8537525", "primary_object": { "basename": "viruses-13-02106-v2.pdf", "url": "https://authors.library.caltech.edu/records/5ynf8-smx60/files/viruses-13-02106-v2.pdf" }, "pub_year": "2021", "author_list": "Abernathy, Morgan E.; Dam, Kim-Marie A.; et al." }, { "id": "https://authors.library.caltech.edu/records/2pb5j-m1z64", "eprint_id": 111355, "eprint_status": "archive", "datestamp": "2023-10-05 15:53:15", "lastmod": "2026-03-30 05:27:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shahrestani-Shane", "name": { "family": "Shahrestani", "given": "Shane" }, "orcid": "0000-0001-7561-4590" }, { "id": "Chou-Tzu-Chieh", "name": { "family": "Chou", "given": "Tzu-Chieh" }, "orcid": "0000-0002-6074-8286" }, { "id": "Shang-Kuang-Ming", "name": { "family": "Shang", "given": "Kuang-Ming" } }, { "id": "Zada-Gabriel", "name": { "family": "Zada", "given": "Gabriel" }, "orcid": "0000-0001-5821-902X" }, { "id": "Borok-Zea", "name": { "family": "Borok", "given": "Zea" }, "orcid": "0000-0001-8673-8177" }, { "id": "Rao-Adupa-P", "name": { "family": "Rao", "given": "Adupa P." }, "orcid": "0000-0002-0220-7131" }, { "id": "Tai-Yu-Chong", "name": { "family": "Tai", "given": "Yu-Chong" }, "orcid": "0000-0001-8529-106X" } ] }, "title": "A wearable eddy current based pulmonary function sensor for continuous non-contact point-of-care monitoring during the COVID-19 pandemic", "ispublished": "pub", "full_text_status": "public", "keywords": "Biomedical engineering; Respiratory distress syndrome; Translational research", "note": "\u00a9 The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 29 December 2020; Accepted 29 September 2021; Published 11 October 2021. \n\nParts of Figures 1, 2, and 6, and Supplementary Figures 1, 2, and 3 were created using Biorender.com. \n\nThis study was funded by the Merkin COVID-19 Challenge Grant. Institutional Review Board approval was obtained prior to data collection. All patient identifiers have been removed, and measures were taken to keep data de-identified and ensure privacy throughout the course of the study. There are no conflicts of interest in this study. \n\nAuthor Contributions: S.S. designed experiments, conducted analysis, wrote manuscript, revised manuscript. T.C., G.Z., Z.B., and A.P.R. helped with IRB approval and edited the manuscript. K.M.S. helped with revisions. Y.T. designed experiments, guided direction of research, and edited the manuscript. \n\nThe authors declare no competing interests.\n\nPublished - s41598-021-99682-2.pdf
Supplemental Material - 41598_2021_99682_MOESM1_ESM.docx
", "abstract": "Pulmonary function testing (PFT) allows for quantitative analysis of lung function. However, as a result of the coronavirus disease 2019 (COVID-19) pandemic, a majority of international medical societies have postponed PFTs in an effort to mitigate disease transmission, complicating the continuity of care in high-risk patients diagnosed with COVID-19 or preexisting lung pathologies. Here, we describe the development of a non-contact wearable pulmonary sensor for pulmonary waveform analysis, pulmonary volume quantification, and crude thoracic imaging using the eddy current (EC) phenomenon. Statistical regression analysis is performed to confirm the predictive validity of the sensor, and all data are continuously and digitally stored with a sampling rate of 6,660 samples/second. Wearable pulmonary function sensors may facilitate rapid point-of-care monitoring for high-risk individuals, especially during the COVID-19 pandemic, and easily interface with patient hospital records or telehealth services.", "date": "2021-10-11", "date_type": "published", "publication": "Scientific Reports", "volume": "11", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 20144", "id_number": "CaltechAUTHORS:20211011-193517859", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211011-193517859", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Merkin Institute for Translational Research" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" } ] }, "doi": "10.1038/s41598-021-99682-2", "pmcid": "PMC8505507", "primary_object": { "basename": "41598_2021_99682_MOESM1_ESM.docx", "url": "https://authors.library.caltech.edu/records/2pb5j-m1z64/files/41598_2021_99682_MOESM1_ESM.docx" }, "related_objects": [ { "basename": "s41598-021-99682-2.pdf", "url": "https://authors.library.caltech.edu/records/2pb5j-m1z64/files/s41598-021-99682-2.pdf" } ], "pub_year": "2021", "author_list": "Shahrestani, Shane; Chou, Tzu-Chieh; et al." }, { "id": "https://authors.library.caltech.edu/records/sghah-29349", "eprint_id": 112041, "eprint_status": "archive", "datestamp": "2023-08-22 11:33:12", "lastmod": "2026-03-28 20:57:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Perdomo-Sammy-A", "name": { "family": "Perdomo", "given": "Sammy A." }, "orcid": "0000-0001-5802-2702" }, { "id": "Ortega-Viviana", "name": { "family": "Ortega", "given": "Viviana" }, "orcid": "0000-0001-7927-6082" }, { "id": "Jaramillo-Botero-Andres", "name": { "family": "Jaramillo-Botero", "given": "Andres" }, "orcid": "0000-0003-2844-0756" }, { "id": "Mancilla-Nelson", "name": { "family": "Mancilla", "given": "Nelson" }, "orcid": "0000-0003-3295-5939" }, { "id": "Mosquera-DeLaCruz-Jos\u00e9-Hernando", "name": { "family": "Mosquera-DeLaCruz", "given": "Jos\u00e9 Hernando" }, "orcid": "0000-0002-9324-1692" }, { "id": "Valencia-Drochss-Pettry", "name": { "family": "Valencia", "given": "Drochss Pettry" }, "orcid": "0000-0002-9364-8134" }, { "id": "Quimbaya-Mauricio", "name": { "family": "Quimbaya", "given": "Mauricio" }, "orcid": "0000-0003-2631-270X" }, { "id": "Contreras-Juan-David", "name": { "family": "Contreras", "given": "Juan David" }, "orcid": "0000-0002-0409-4337" }, { "id": "Velez-Gabriel-Esteban", "name": { "family": "Velez", "given": "Gabriel Esteban" }, "orcid": "0000-0001-8063-0747" }, { "id": "Loaiza-Oscar-A", "name": { "family": "Loaiza", "given": "Oscar A." }, "orcid": "0000-0002-6289-9248" }, { "id": "G\u00f3mez-Adriana", "name": { "family": "G\u00f3mez", "given": "Adriana" }, "orcid": "0000-0002-3106-1397" }, { "id": "de-la-Roche-Jhonattan", "name": { "family": "de la Roche", "given": "Jhonattan" }, "orcid": "0000-0003-3131-3096" } ] }, "title": "SenSARS: A Low-Cost Portable Electrochemical System for Ultra-Sensitive, Near Real-Time, Diagnostics of SARS-CoV-2 Infections", "ispublished": "pub", "full_text_status": "public", "keywords": "Biosensors, electrochemical biosensors, electrochemical\nimpedance spectroscopy (EIS), SARS-CoV-2; Electrical and Electronic Engineering; Instrumentation", "note": "\u00a9 IEEE 2021. This article is free to access and download, along with rights for full text and data mining, re-use and analysis. \n\nManuscript received June 4, 2021; revised September 13, 2021; accepted September 24, 2021. Date of publication October 8, 2021; date of current version October 21, 2021. \n\nThis work was supported by the Colombian\nMinistry of Science, Innovation, and Technology, through the Mincienciat\u00f3n health emergency under Award 360-2020. The Associate Editor coordinating the review process was Dr. Alessandra Galli. \n\nThe authors thank Dr. Maria Adelaida Gomez (CIDEIM), Dr. Olga Lucia Agudelo, and Dr. Fernando Rosso (Fundaci\u00f3n Valle del Lili) for their instrumental contributions within a broader collaboration on the development and clinical testing of SenSARS, Lina Hermida, Leidi Rojas, Diego L\u00f3pez, Paola Mejia, Bleider Arizala, and Christopher Valencia from the Universidad Javeriana, and M\u00f3nica Castiblanco, Dr. Luis Hernando Nieto, Luisa Fernanda Cabezas, Dr. Arturo Luna, and Dr. Mabel Torres from the Colombian Ministry of Science, Innovation and Technology for their support.\n\nSupplemental Material - SenSARS_A_Low-Cost_Portable_Electrochemical_System_for_Ultra-Sensitive_Near_Real-Time_Diagnostics_of_SARS-CoV-2_Infections.pdf
", "abstract": "A critical path to solving the SARS-CoV-2 pandemic, without further socioeconomic impact, is to stop its spread. For this to happen, pre- or asymptomatic individuals infected with the virus need to be detected and isolated opportunely. Unfortunately, there are no current ubiquitous (i.e., ultra-sensitive, cheap, and widely available) rapid testing tools capable of early detection of SARS-CoV-2 infections. In this article, we introduce an accurate, portable, and low-cost medical device and bio-nanosensing electrode dubbed SenSARS and its experimental validation. SenSARS' device measures the electrochemical impedance spectra of a disposable bio-modified screen-printed carbon-based working electrode (SPCE) to the changes in the concentration of SARS-CoV-2 antigen molecules (\"S\" spike proteins) contained within a sub-microliter fluid sample deposited on its surface. SenSARS offers real-time diagnostics and viral load tracking capabilities. Positive and negative control tests were performed in phosphate-buffered saline (PBS) at different concentrations (between 1 and 50 fg/mL) of SARS-CoV-2(S), Epstein\u2013Barr virus (EBV) glycoprotein gp350, and Influenza H1N1 M1 recombinant viral proteins. We demonstrate that SenSARS is easy to use, with a portable and lightweight (< 200 g) instrument and disposable test electrodes (< U.S. $5), capable of fast diagnosis (~10 min), with high analytical sensitivity (low limits of detection, LOD = 1.065 fg/mL, and quantitation, LOQ = 3.6 fg/mL) and selectivity to SARS-CoV-2(S) antigens, even in the presence of structural proteins from the other pathogens tested. SenSARS provides a potential path to pervasive rapid diagnostics of SARS-CoV-2 in clinical, point-of-care, and home-care settings, and to breaking the transmission chain of this virus. Medical device compliance testing of SenSARS to EIC-60601 technical standards is underway.", "date": "2021-10-08", "date_type": "published", "publication": "IEEE Transactions on Instrumentation and Measurement", "volume": "70", "publisher": "IEEE", "pagerange": "Art. No. 4007710-10", "id_number": "CaltechAUTHORS:20211124-171711818", "issn": "0018-9456", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211124-171711818", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ministerio de Ciencia Tecnolog\u00eda e Innovaci\u00f3n", "grant_number": "360-2020" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1109/tim.2021.3119147", "pmcid": "PMC8843068", "primary_object": { "basename": "SenSARS_A_Low-Cost_Portable_Electrochemical_System_for_Ultra-Sensitive_Near_Real-Time_Diagnostics_of_SARS-CoV-2_Infections.pdf", "url": "https://authors.library.caltech.edu/records/sghah-29349/files/SenSARS_A_Low-Cost_Portable_Electrochemical_System_for_Ultra-Sensitive_Near_Real-Time_Diagnostics_of_SARS-CoV-2_Infections.pdf" }, "pub_year": "2021", "author_list": "Perdomo, Sammy A.; Ortega, Viviana; et al." }, { "id": "https://authors.library.caltech.edu/records/wrps6-3ze95", "eprint_id": 108864, "eprint_status": "archive", "datestamp": "2023-10-03 22:42:39", "lastmod": "2026-03-30 08:39:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jette-Claudia-A", "name": { "family": "Jette", "given": "Claudia A." }, "orcid": "0000-0002-5085-8027" }, { "id": "Cohen-Alexander-A", "name": { "family": "Cohen", "given": "Alexander A." }, "orcid": "0000-0002-2818-656X" }, { "id": "Gnanapragasam-Priyanthi-N-P", "name": { "family": "Gnanapragasam", "given": "Priyanthi N. P." } }, { "id": "Muecksch-Frauke", "name": { "family": "Muecksch", "given": "Frauke" } }, { "id": "Lee-Yu-E", "name": { "family": "Lee", "given": "Yu E." }, "orcid": "0000-0001-5989-326X" }, { "id": "Huey-Tubman-Kathryn-E", "name": { "family": "Huey-Tubman", "given": "Kathryn E." }, "orcid": "0000-0002-4683-8138" }, { "id": "Schmidt-Fabian", "name": { "family": "Schmidt", "given": "Fabian" } }, { "id": "Hatziioannou-Theodora", "name": { "family": "Hatziioannou", "given": "Theodora" }, "orcid": "0000-0002-7889-0766" }, { "id": "Bieniasz-Paul-D", "name": { "family": "Bieniasz", "given": "Paul D." }, "orcid": "0000-0002-2368-3719" }, { "id": "Nussenzweig-Michel-C", "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" }, { "id": "West-Anthony-P-Jr", "name": { "family": "West", "given": "Anthony P., Jr." }, "orcid": "0000-0003-4213-5184" }, { "id": "Keeffe-Jennifer-R", "name": { "family": "Keeffe", "given": "Jennifer R." }, "orcid": "0000-0002-5317-6398" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" } ] }, "title": "Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies", "ispublished": "pub", "full_text_status": "public", "keywords": "cryo-EM; coronavirus; neutralizing antibody; receptor-binding domain; sarbecovirus; SARS-CoV-2; Spike trimer: structural biology; virology: X-ray crystallography", "note": "\u00a9 2021 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nReceived 28 April 2021, Revised 5 August 2021, Accepted 1 September 2021, Available online 8 September 2021. \n\nWe thank J. Vielmetter, P. Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance and K. Dam for assistance with soluble ACE2 purification. Electron microscopy was performed in the Caltech Cryo-EM Center with assistance from S. Chen and A. Malyutin. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support the Molecular Observatory. We thank J. Kaiser, Director of the Molecular Observatory at Caltech, and beamline staff C. Smith and S. Russi at SSRL for data collection assistance. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by the National Institutes of Health (NIH), National Institute of General Medical Sciences (NIGMS) (P30GM133894). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. This work was supported by the NIH (P01-AI138938-S1 to P.J.B. and M.C.N.; R01AI078788 to T.H.; and R01AI640511 to P.D.B.), the Caltech Merkin Institute for Translational Research (P.J.B.), and a George Mason University Fast Grant (to P.J.B.). F.M. is supported by the Bulgari Women & Science Fellowship in COVID-19 Research. C.O.B was supported by the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Postdoctoral Enrichment Program from the Burroughs Wellcome Fund. M.C.N. is a Howard Hughes Medical Institute (HHMI) investigator. \n\nAuthor contributions: C.A.J., A.A.C., P.J.B., and C.O.B. conceived and designed experiments. Proteins were produced and characterized by A.A.C., K.E.H.-T., C.O.B., and C.A.J. Binding and neutralization studies were done by A.A.C. and F.M. with assistance from P.N.P.G., Y.E.L., and F.S. SPR binding competition experiments were done by C.A.J. with assistance from J.R.K. Structural studies were performed by C.A.J. with assistance from C.O.B. Structure analysis was done by C.A.J. with assistance from C.O.B. and A.A.C. Sequence analysis was done by A.P.W. The paper was written by C.A.J., P.J.B., and C.O.B. with assistance from A.A.C., T.H., M.C.N., P.D.B., and other authors. \n\nDeclaration of interests: The Rockefeller University has filed provisional patent applications in connection with this work on which M.C.N. (US patent 63/021,387) is listed as an inventor. \n\nData and code availability: Atomic models of C118 Fab complexed with SARS-CoV RBD and C022 Fab complexed with SARS-CoV-2 RBD have been deposited in the Protein Data Bank (PDB) (https://www.rcsb.org/) under accession codes 7RKS and 7RKU, respectively. The atomic model and cryo-EM maps generated for the C118 Fab\u2013SARS-CoV-2 S complex have been deposited at the PDB (https://www.rcsb.org/) and the Electron Microscopy Databank (EMDB) (http://www.emdataresource.org/) under accession codes 7RKV (state 1 coordinates), EMD-24504 (state 1) and EMD-24505 (state 2). All models and maps are publicly available as of the date of publication. \n\nThis paper does not report original code. \n\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.\n\nPublished - 1-s20-S2211124721012146-mainext.pdf
Accepted Version - 1-s2.0-S2211124721012146-main.pdf
Submitted - 202104-23-441195v1-full.pdf
Supplemental Material - 1-s20-S2211124721012146-mmc1.pdf
", "abstract": "Many anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) neutralizing antibodies target the angiotensin-converting enzyme 2 (ACE2) binding site on viral spike receptor-binding domains (RBDs). Potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly emergent zoonotic sarbecoviruses and variants, but they usually show only weak neutralization potencies. Here, we characterize two class 4 anti-RBD antibodies derived from coronavirus disease 2019 (COVID-19) donors that exhibit breadth and potent neutralization of zoonotic coronaviruses and SARS-CoV-2 variants. C118-RBD and C022-RBD structures reveal orientations that extend from the cryptic epitope to occlude ACE2 binding and CDRH3-RBD main-chain H-bond interactions that extend an RBD \u03b2 sheet, thus reducing sensitivity to RBD side-chain changes. A C118-spike trimer structure reveals rotated RBDs that allow access to the cryptic epitope and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.", "date": "2021-09-28", "date_type": "published", "publication": "Cell Reports", "volume": "36", "number": "13", "publisher": "Cell Press", "pagerange": "Art. No. 109760", "id_number": "CaltechAUTHORS:20210429-094548605", "issn": "2211-1247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210429-094548605", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-76SF00515" }, { "agency": "NIH", "grant_number": "P30GM133894" }, { "agency": "NIH", "grant_number": "P01-AI138938-S1" }, { "agency": "NIH", "grant_number": "R01AI078788" }, { "agency": "NIH", "grant_number": "R01AI640511" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "George Mason University" }, { "agency": "Bulgari Women & Science Fellowship in COVID-19 Research" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Caltech Beckman Institute" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.celrep.2021.109760", "pmcid": "PMC8423902", "primary_object": { "basename": "202104-23-441195v1-full.pdf", "url": "https://authors.library.caltech.edu/records/wrps6-3ze95/files/202104-23-441195v1-full.pdf" }, "related_objects": [ { "basename": "1-s20-S2211124721012146-mainext.pdf", "url": "https://authors.library.caltech.edu/records/wrps6-3ze95/files/1-s20-S2211124721012146-mainext.pdf" }, { "basename": "1-s2.0-S2211124721012146-main.pdf", "url": "https://authors.library.caltech.edu/records/wrps6-3ze95/files/1-s2.0-S2211124721012146-main.pdf" }, { "basename": "1-s20-S2211124721012146-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/wrps6-3ze95/files/1-s20-S2211124721012146-mmc1.pdf" } ], "pub_year": "2021", "author_list": "Jette, Claudia A.; Cohen, Alexander A.; et al." }, { "id": "https://authors.library.caltech.edu/records/shvfy-73c70", "eprint_id": 108524, "eprint_status": "archive", "datestamp": "2023-08-22 11:13:56", "lastmod": "2026-03-30 05:53:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ullah-Irfan", "name": { "family": "Ullah", "given": "Irfan" }, "orcid": "0000-0002-7760-8693" }, { "name": { "family": "Pr\u00e9vost", "given": "J\u00e9r\u00e9mie" } }, { "id": "Ladinsky-Mark-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "name": { "family": "Stone", "given": "Helen" }, "orcid": "0000-0002-3344-5079" }, { "name": { "family": "Lu", "given": "Maolin" }, "orcid": "0000-0002-8099-6447" }, { "name": { "family": "Anand", "given": "Sai Priya" }, "orcid": "0000-0001-9821-8259" }, { "name": { "family": "Beaudoin-Bussi\u00e8res", "given": "Guillaume" }, "orcid": "0000-0002-8092-4101" }, { "name": { "family": "Symmes", "given": "Kelly" }, "orcid": "0000-0002-4442-8442" }, { "name": { "family": "Benlarbi", "given": "Mehdi" }, "orcid": "0000-0001-9966-3784" }, { "name": { "family": "Ding", "given": "Shilei" } }, { "name": { "family": "Gasser", "given": "Romain" }, "orcid": "0000-0002-8565-1106" }, { "name": { "family": "Fink", "given": "Corby" } }, { "name": { "family": "Chen", "given": "Yaozong" }, "orcid": "0000-0001-5380-2339" }, { "name": { "family": "Tauzin", "given": "Alexandra" }, "orcid": "0000-0001-9153-3600" }, { "name": { "family": "Goyette", "given": "Guillaume" }, "orcid": "0000-0003-3277-568X" }, { "name": { "family": "Bourassa", "given": "Catherine" }, "orcid": "0000-0003-1805-8860" }, { "name": { "family": "Medjahed", "given": "Halima" } }, { "name": { "family": "Mack", "given": "Matthias" }, "orcid": "0000-0002-3157-7262" }, { "name": { "family": "Chung", "given": "Kunho" }, "orcid": "0000-0003-1504-317X" }, { "name": { "family": "Wilen", "given": "Craig B." }, "orcid": "0000-0003-2495-9403" }, { "name": { "family": "Dekaban", "given": "Gregory A." }, "orcid": "0000-0002-3087-4660" }, { "name": { "family": "Dikeakos", "given": "Jimmy D." }, "orcid": "0000-0001-8141-5395" }, { "name": { "family": "Bruce", "given": "Emily A." }, "orcid": "0000-0001-8391-370X" }, { "name": { "family": "Kaufmann", "given": "Daniel E." }, "orcid": "0000-0003-4467-136X" }, { "name": { "family": "Stamatatos", "given": "Leonidas" }, "orcid": "0000-0002-1106-7097" }, { "name": { "family": "McGuire", "given": "Andrew T." }, "orcid": "0000-0003-1841-6859" }, { "name": { "family": "Richard", "given": "Jonathan" }, "orcid": "0000-0002-9015-9589" }, { "name": { "family": "Pazgier", "given": "Marzena" }, "orcid": "0000-0003-0594-5057" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Mothes", "given": "Walther" }, "orcid": "0000-0002-3367-7240" }, { "name": { "family": "Finzi", "given": "Andr\u00e9s" }, "orcid": "0000-0002-4992-5288" }, { "name": { "family": "Kumar", "given": "Priti" }, "orcid": "0000-0002-6901-5601" }, { "name": { "family": "Uchil", "given": "Pradeep D." }, "orcid": "0000-0002-7236-858X" } ] }, "title": "Live imaging of SARS-CoV-2 infection in mice reveals that neutralizing antibodies require Fc function for optimal efficacy", "ispublished": "pub", "full_text_status": "public", "keywords": "SARS-CoV-2; COVID-19; nanoluciferase; bioluminescence imaging; neutralizing antibodies; human ACE2 transgenic mice; monocytes; natural killer cells; pathogenesis; Fc effector functions", "note": "\u00a9 2021 Elsevier Inc. \n\nReceived 23 March 2021, Revised 27 June 2021, Accepted 11 August 2021, Available online 18 August 2021. \n\nThis work was supported by NIH grant R01AI163395 to W.M.; George Mason University Fast Grants to M.S.L. and P.J.B.; P20GM125498 (awarded to UVM Translational Global Infectious Disease Research Center) to E.A.B.; le Minist\u00e8re de l'\u00c9conomie et de l'Innovation du Qu\u00e9bec, Programme de soutien aux organismes de recherche et d'innovation, Foundation du CHUM, Canadian Institutes of Health Research (CIHR) foundation grant 352417 and Rapid Research Funding Opportunity FRN440388 to J.D.D. and G.A.D.; Canada Research Chair on Retroviral Entry no. RCHS0235 950-232424 to A.F.; Canada's COVID-19 Immunity Task Force (CITF) and Canada Foundation for Innovation (CFI) 41027 to A.F. and D.E.K. and 36287 to J.D.D. and G.A.D.; FRQS Merit Research Scholarship to D.E.K.; CIHR fellowships to J.P., S.P.A., and G.B.-B.; MITACS Acc\u00e9l\u00e9ration postdoctoral fellowship to R.G.; Fred Hutch COVID-19 Research Fund to L.S. and A.T.M. The views expressed in this presentation are those of the authors and do not reflect the official policy or position of the Uniformed Services University, US Army, the Department of Defense, or the US Government. \n\nAuthor contributions: Conceptualization, P.D.U., P.K., A.F., W.M., I.U., and J.P.; methodology, P.D.U., I.U., J.P., M.S.L., E.A.B., M.L.,W.M., A.F., and P.K.; investigation, I.U., P.D.U., J.P., H.S., K.S., K.C., L.S., A.T.M., S.P.A., G.B.-B., M.B., S.D., R.G., C.F., Y.C., A.T., G.G., C.B., H.M., G.A.D., J.D.D., D.E.K., J.R., and M.P.; writing \u2013 original draft, P.D.U.; writing \u2013 review & editing, P.D.U., P.K., A.F., W.M., I.U., J.P., L.S., and A.T.M.; funding acquisition, A.F., L.S., A.T.M., P.J.B.; resources, A.F., P.J.B., C.B.W., and M.M.; supervision, P.D.U., W.M., P.K., A.F., and P.J.B. \n\nThe authors declare no competing interests. \n\nData and code availability: All the data that support the findings of this study are available from the lead contact upon request. Additional supplemental items that include raw data for generating all graphs shown in figures and videos are available at Mendeley Data, V3, https://doi.org/10.17632/2wwzg4pb8n.3. \n\nThis paper does not report original code. \n\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.\n\nPublished - 1-s2.0-S1074761321003472-main.pdf
Submitted - 2021.03.22.436337v2.full.pdf
Supplemental Material - 1-s2.0-S1074761321003472-mmc1.pdf
", "abstract": "Neutralizing antibodies (NAbs) are effective in treating COVID-19, but the mechanism of immune protection is not fully understood. Here, we applied live bioluminescence imaging (BLI) to monitor the real-time effects of NAb treatment during prophylaxis and therapy of K18-hACE2 mice intranasally infected with SARS-CoV-2-nanoluciferase. Real-time imaging revealed that the virus spread sequentially from the nasal cavity to the lungs in mice and thereafter systemically to various organs including the brain, culminating in death. Highly potent NAbs from a COVID-19 convalescent subject prevented, and also effectively resolved, established infection when administered within three days. In addition to direct neutralization, depletion studies indicated that Fc effector interactions of NAbs with monocytes, neutrophils, and natural killer cells were required to effectively dampen inflammatory responses and limit immunopathology. Our study highlights that both Fab and Fc effector functions of NAbs are essential for optimal in vivo efficacy against SARS-CoV-2.", "date": "2021-09-14", "date_type": "published", "publication": "Immunity", "volume": "54", "number": "9", "publisher": "Cell Press", "pagerange": "2143-2158", "id_number": "CaltechAUTHORS:20210323-080814224", "issn": "1074-7613", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210323-080814224", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01AI163395" }, { "agency": "George Mason University" }, { "agency": "NIH", "grant_number": "P20GM125498" }, { "agency": "le Minist\u00e8re de l'\u00c9conomie et de l'Innovation du Qu\u00e9bec" }, { "agency": "Programme de soutien aux organismes de recherche et d'innovation" }, { "agency": "Foundation du CHUM" }, { "agency": "Canadian Institutes of Health Research (CIHR)", "grant_number": "352417" }, { "agency": "Rapid Research Funding Opportunity", "grant_number": "FRN440388" }, { "agency": "Canada Research Chairs Program", "grant_number": "RCHS0235 950-232424" }, { "agency": "Canada COVID-19 Immunity Task Force" }, { "agency": "Canada Foundation for Innovation", "grant_number": "41027" }, { "agency": "Canada Foundation for Innovation", "grant_number": "36287" }, { "agency": "Fonds de recherche du Qu\u00e9bec \u2013 Sant\u00e9 (FRQS)" }, { "agency": "MITACS Acc\u00e9l\u00e9ration Postdoctoral Fellowship" }, { "agency": "Fred Hutch COVID-19 Research Fund" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.immuni.2021.08.015", "pmcid": "PMC8372518", "primary_object": { "basename": "1-s2.0-S1074761321003472-main.pdf", "url": "https://authors.library.caltech.edu/records/shvfy-73c70/files/1-s2.0-S1074761321003472-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S1074761321003472-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/shvfy-73c70/files/1-s2.0-S1074761321003472-mmc1.pdf" }, { "basename": "2021.03.22.436337v2.full.pdf", "url": "https://authors.library.caltech.edu/records/shvfy-73c70/files/2021.03.22.436337v2.full.pdf" } ], "pub_year": "2021", "author_list": "Ullah, Irfan; Pr\u00e9vost, J\u00e9r\u00e9mie; et al." }, { "id": "https://authors.library.caltech.edu/records/w38bs-4dq57", "eprint_id": 110056, "eprint_status": "archive", "datestamp": "2023-08-22 11:01:22", "lastmod": "2026-03-29 15:33:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Agranov-M", "name": { "family": "Agranov", "given": "Marina" }, "orcid": "0000-0002-0642-7975" }, { "id": "Elliott-Matt", "name": { "family": "Elliott", "given": "Matt" } }, { "id": "Ortoleva-Pietro", "name": { "family": "Ortoleva", "given": "Pietro" } } ] }, "title": "The importance of Social Norms against Strategic Effects: The case of Covid-19 vaccine uptake", "ispublished": "pub", "full_text_status": "public", "keywords": "Free-riding; Social norms; Experiment; Vaccine", "note": "\u00a9 2021 Elsevier B.V. \n\nReceived 20 April 2021, Revised 26 June 2021, Accepted 29 June 2021, Available online 2 July 2021. \n\nThis project has received funding from the Keynes Fund, and from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement number #757229) (Elliott). We thank J\u00f6rg Kalbfuss for excellent research assistance.\n\nPublished - 1-s2.0-S0165176521002561-main.pdf
Supplemental Material - 1-s2.0-S0165176521002561-mmc1.pdf
", "abstract": "We study how individual decisions are affected by those of other members of the society. We use the vaccine against COVID-19 as a case study and empirically estimate the magnitude of three key forces: Herding, Social Norms, and Free-riding. We find that Free-riding is dominated by the other two forces, and that Social Norms are a key driver of behavior. There is, however, substantial heterogeneity and systematic differences between people by demographics and their political preferences.", "date": "2021-09", "date_type": "published", "publication": "Economics Letters", "volume": "206", "publisher": "Elsevier", "pagerange": "Art. No. 109979", "id_number": "CaltechAUTHORS:20210728-211627192", "issn": "0165-1765", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210728-211627192", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Keynes Fund" }, { "agency": "European Research Council (ERC)", "grant_number": "757229" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.econlet.2021.109979", "pmcid": "PMC8252706", "primary_object": { "basename": "1-s2.0-S0165176521002561-main.pdf", "url": "https://authors.library.caltech.edu/records/w38bs-4dq57/files/1-s2.0-S0165176521002561-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0165176521002561-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/w38bs-4dq57/files/1-s2.0-S0165176521002561-mmc1.pdf" } ], "pub_year": "2021", "author_list": "Agranov, Marina; Elliott, Matt; et al." }, { "id": "https://authors.library.caltech.edu/records/gj3yk-ng036", "eprint_id": 110223, "eprint_status": "archive", "datestamp": "2023-08-22 10:50:34", "lastmod": "2026-03-30 16:14:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Xin", "name": { "family": "Wang", "given": "Xin" }, "orcid": "0000-0002-6180-0058" }, { "id": "Zhan-Zhongwen", "name": { "family": "Zhan", "given": "Zhongwen" }, "orcid": "0000-0002-5586-2607" }, { "id": "Williams-Ethan-F", "name": { "family": "Williams", "given": "Ethan F." }, "orcid": "0000-0002-7917-4104" }, { "id": "Gonz\u00e1lez-Herr\u00e1ez-Miguel", "name": { "family": "Gonz\u00e1lez Herr\u00e1ez", "given": "Miguel" }, "orcid": "0000-0003-2555-2971" }, { "id": "Martins-Hugo-Fidalgo", "name": { "family": "Martins", "given": "Hugo Fidalgo" }, "orcid": "0000-0003-3927-8125" }, { "id": "Karrenbach-Martin", "name": { "family": "Karrenbach", "given": "Martin" }, "orcid": "0000-0003-2190-8598" } ] }, "title": "Ground vibrations recorded by fiber-optic cables reveal traffic response to COVID-19 lockdown measures in Pasadena, California", "ispublished": "pub", "full_text_status": "public", "keywords": "Environmental impact; Environmental studies; Seismology", "note": "\u00a9 The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 12 April 2021; Accepted 23 July 2021; Published 11 August 2021. \n\nWe thank the City of Pasadena for contributing its fiber optic cables to our research. The DAS instruments used in this study were provided by the OptaSense, University of Alcala, and Aragon Photonics. We thank Lisa LaFlame, Victor Yartsev, Steve Cole, and Vlad Bogdanov for their assistance in acquiring the data used in this study. We are grateful for numerous discussions with people in the Department of Transportation, Pasadena. We are also grateful to the editor, reviewer Yunyue Elita Li, and two anonymous reviewers for their suggestions and comments, which help improve the quality of this paper. This work is supported by NSF CAREER award #1848166; the Young Elite Scientists Sponsorship Program by CAST (grant 2020QNRC001); the Key Research Program of the Institute of Geology & Geophysics, CAS (grant IGGCAS-201904); the Spanish MICINN (RTI2018-097957-B-C31, RTI2018-097957-B-C33); the European Research Council (OCEAN-DAS: ERC-2019-POC-875302). The work of HFM was supported by MINECO (\"Juan de la Cierva\" postdoc contract IJCI-2017-33856). \n\nData availability: The obtained traffic data (in MATLAB format, a MATLAB script is also provided to load and plot the data) in this study can be downloaded from CaltechDATA achieve at https://doi.org/10.22002/D1.2022. \n\nCode availability: The codes used in this study are available from Dr. Xin Wang (wangxin@mail.iggcas.ac.cn) upon reasonable request. \n\nAuthor Contributions: X.W. and Z.Z. conceived the main ideas, led the project, and wrote the initial draft of the paper. X.W., Z.Z., E.F.W., M.G.H., H.F.M. and M.K. discussed the results and contributed to the writing of the final paper. \n\nThe authors declare no competing interests. \n\nPeer review information: Communications Earth & Environment Materials thanks Yunyue Elita Li, Siyuan Yuan and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editors: Clare Davis.\n\nPublished - s43247-021-00234-3.pdf
Supplemental Material - 43247_2021_234_MOESM1_ESM.pdf
", "abstract": "The COVID-19 lockdown has unprecedently affected the dynamics of our society. As traffic flow is a good proxy for societal activity, traffic monitoring becomes a useful tool to assess the lockdown's impacts. Here we turned two strands of unused telecommunication fibers in Pasadena, California into a seismic array of ~5,000 sensors and detected ground vibrations caused by moving vehicles along the streets above the cable. We monitor the number of vehicles and their mean speed between December 2019 and August 2020 in high spatial and temporal resolution, and then analyze the traffic patterns change due to the COVID-19 lockdown. Our results show a city-wide decline in traffic volume and an increase in speed due to the lockdown, although the level of impact varies substantially by streets. This study demonstrates the feasibility of using telecommunication fiber optic cables in traffic monitoring, which has implications for public health, economy, and transportation safety.", "date": "2021-08-11", "date_type": "published", "publication": "Communications Earth & Environment", "volume": "2", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 160", "id_number": "CaltechAUTHORS:20210812-141727237", "issn": "2662-4435", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210812-141727237", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "EAR-1848166" }, { "agency": "China Association for Science and Technology", "grant_number": "2020QNRC001" }, { "agency": "Chinese Academy of Sciences", "grant_number": "IGGCAS-201904" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)", "grant_number": "RTI2018-097957-B-C31" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)", "grant_number": "RTI2018-097957-B-C33" }, { "agency": "European Research Council (ERC)", "grant_number": "875302" }, { "agency": "Ministerio de Econom\u00eda, Industria y Competitividad (MINECO)", "grant_number": "IJCI-2017-33856" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Seismological-Laboratory" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1038/s43247-021-00234-3", "primary_object": { "basename": "s43247-021-00234-3.pdf", "url": "https://authors.library.caltech.edu/records/gj3yk-ng036/files/s43247-021-00234-3.pdf" }, "related_objects": [ { "basename": "43247_2021_234_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/gj3yk-ng036/files/43247_2021_234_MOESM1_ESM.pdf" } ], "pub_year": "2021", "author_list": "Wang, Xin; Zhan, Zhongwen; et al." }, { "id": "https://authors.library.caltech.edu/records/pgr4a-53p46", "eprint_id": 110113, "eprint_status": "archive", "datestamp": "2023-08-22 10:48:52", "lastmod": "2026-03-30 16:41:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Muecksch-Frauke", "name": { "family": "Muecksch", "given": "Frauke" }, "orcid": "0000-0002-0132-5101" }, { "name": { "family": "Weisblum", "given": "Yiska" }, "orcid": "0000-0002-9249-1745" }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "name": { "family": "Schmidt", "given": "Fabian" } }, { "name": { "family": "Schaefer-Babajew", "given": "Dennis" }, "orcid": "0000-0002-5380-2950" }, { "name": { "family": "Wang", "given": "Zijun" }, "orcid": "0000-0002-2095-2151" }, { "name": { "family": "C. Lorenzi", "given": "Julio C." }, "orcid": "0000-0003-2492-3961" }, { "id": "Flyak-Andrew-I", "name": { "family": "Flyak", "given": "Andrew I." }, "orcid": "0000-0002-8722-479X" }, { "id": "DeLaitsch-Andrew-T", "name": { "family": "DeLaitsch", "given": "Andrew T." }, "orcid": "0000-0002-3458-3449" }, { "id": "Huey-Tubman-Kathryn-E", "name": { "family": "Huey-Tubman", "given": "Kathryn E." }, "orcid": "0000-0002-4683-8138" }, { "name": { "family": "Hou", "given": "Shurong" }, "orcid": "0000-0001-5143-0797" }, { "name": { "family": "Schiffer", "given": "Celia A." }, "orcid": "0000-0003-2270-6613" }, { "name": { "family": "Gaebler", "given": "Christian" }, "orcid": "0000-0001-7295-8128" }, { "name": { "family": "Da Silva", "given": "Justin" } }, { "name": { "family": "Poston", "given": "Daniel" }, "orcid": "0000-0001-9900-6717" }, { "name": { "family": "Finkin", "given": "Shlomo" }, "orcid": "0000-0003-4474-2658" }, { "name": { "family": "Cho", "given": "Alice" }, "orcid": "0000-0001-6354-6148" }, { "name": { "family": "Cipolla", "given": "Melissa" }, "orcid": "0000-0001-8156-2512" }, { "name": { "family": "Oliveira", "given": "Thiago Y." }, "orcid": "0000-0002-2654-0879" }, { "name": { "family": "Millard", "given": "Katrina G." }, "orcid": "0000-0003-2247-3178" }, { "name": { "family": "Ramos", "given": "Victor" }, "orcid": "0000-0001-8572-1621" }, { "name": { "family": "Gazumyan", "given": "Anna" }, "orcid": "0000-0002-5976-9717" }, { "name": { "family": "Rutkowska", "given": "Magdalena" }, "orcid": "0000-0002-8090-3503" }, { "name": { "family": "Caskey", "given": "Marina" }, "orcid": "0000-0003-1727-8693" }, { "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Hatziioannou", "given": "Theodora" }, "orcid": "0000-0002-7889-0766" }, { "name": { "family": "Bieniasz", "given": "Paul D." }, "orcid": "0000-0002-2368-3719" } ] }, "title": "Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations", "ispublished": "pub", "full_text_status": "public", "keywords": "SARS-CoV-2; antibodies; neutralization", "note": "\u00a9 2021 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). \n\nReceived 15 March 2021, Revised 26 May 2021, Accepted 12 July 2021, Available online 30 July 2021. \n\nWe thank all of the study participants and clinical staff. We thank members of the Bjorkman, Nussenzweig, and Bieniasz laboratories for helpful discussions; and Dr. Jost Vielmetter, Pauline Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance. Electron microscopy was performed in the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy with assistance from Dr. Songye Chen. We thank the Gordon and Betty Moore Foundation and the Beckman Foundation for gifts to Caltech to support the Molecular Observatory (Dr. Jens Kaiser, director), and Drs. Silvia Russi, Aina Cohen, and Clyde Smith and the beamline staff at SSRL for data collection assistance. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-c76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P41GM103393). This work was supported by NIH grants R37-AI64003 (to P.D.B.), R01AI78788 (to T.H.), P01-AI138938-S1 (to P.J.B. and M.C.N.), K99 AI153465 (to A.I.F.), and 2U19AI111825 (to M.C.N.). This work was also supported by a George Mason University Fast Grant (to P.J.B.), NSF grant no. GRFP DGE-1745301 (to A.T.D.), and by the Caltech Merkin Institute for Translational Research (to P.J.B.). C.O.B was supported by the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Postdoctoral Enrichment Program from the Burroughs Wellcome Fund. F.M. was supported by the Bulgari Women & Science Fellowship in COVID-19 Research. C.G. was supported by the Robert S. Wennett Post-Doctoral Fellowship, in part by the National Center for Advancing Translational Sciences (National Institutes of Health Clinical and Translational Science Award program, grant no. UL1 TR001866), and by the Shapiro-Silverberg Fund for the Advancement of Translational Research. M.C.N. and P.D.B. are Howard Hughes Medical Institute investigators. The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS, NIAID, or NIH. \n\nAuthor contributions: F.M., Y.W., C.O.B., F.S., M.C.N., P.J.B., T.H., and P.D.B. conceived the study and analyzed the data. F.S. and J.D.S. generated the Spike plasmids. F.M., D.S.-B., J.C.C.L., and J.D.S. performed neutralization assays with natural SARS-CoV-2 variant and sarbecovirus HIV-1 pseudotypes. Y.W., F.S., and M.R. performed the selection and characterization of escape mutants using VSV/SARS-CoV-2 and HIV-1-pseudotypes. C.O.B. and K.E.H.-T. performed the protein purification and complex assembly. A.I.F. and C.O.B. performed the crystallographic studies and analyzed structures. C.O.B., A.T.D., and A.I.F. performed the cryo-EM studies and analyzed structures. S.H. and C.A.S. generated and performed the analyses of homology models. Z.W. performed the BLI experiments. Z.W., S.F., A.C., T.Y.O., M.C., K.G.M., V.R., and A.G. isolated and characterized monoclonal antibodies. C.G. and M.C. recruited the participants and executed the clinical protocols. F.M., Y.W., C.O.B., F.S., M.C.N., P.J.B., T.H., and P.D.B. wrote the paper, with contributions from the other authors. \n\nDeclaration of interests: The Rockefeller University has filed provisional patent applications in connection with this work on which M.C.N. (US patent 63/021,387) is listed as inventor. P.D.B. has served on an advisory board to Pfizer relating to SARS-CoV-2 vaccines. \n\nData and code availability: Coordinates and maps associated with data reported in this manuscript have been deposited in the Electron Microscopy Data Bank (EMDB: https://www.ebi.ac.uk/pdbe/emdb/) and Protein Data Bank (PDB: www.rcsb.org). The coordinates generated from X-ray crystallographic studies of the C032 Fab, C080 Fab, C098 Fab, C099 Fab, C098-RBD complex, and C099-CR3022-RBD complex have been deposited at the PDB with accession numbers 7N3E, 7N3F, 7N3G, 7N3H, 7N3I, and 7R8L, respectively. The coordinates and cryo-EM maps generated from cryo-EM studies of the C032-S 6P complex, C051-S 6P complex, and C548-S 6P complex have been deposited at the PDB and EMDB with accession numbers PDB: 7R8M, 7R8N, 7R8O and EMDB: 24318, 24319, 24320, respectively. \n\nThis paper does not report original code. \n\nAny additional information required to reanalyze the data reported in this paper is available from the Lead Contact upon request.\n\nPublished - 1-s2.0-S1074761321002946-main.pdf
Supplemental Material - 1-s2.0-S1074761321002946-mmc1.pdf
", "abstract": "Antibodies elicited by infection accumulate somatic mutations in germinal centers that can increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) Spike receptor-binding domain (RBD)-specific antibodies from 5 individuals shortly after infection and later in convalescence to determine the impact of maturation over months. In addition to increased affinity and neutralization potency, antibody evolution changed the mutational pathways for the acquisition of viral resistance and restricted neutralization escape options. For some antibodies, maturation imposed a requirement for multiple substitutions to enable escape. For certain antibodies, affinity maturation enabled the neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.", "date": "2021-08-10", "date_type": "published", "publication": "Immunity", "volume": "54", "number": "8", "publisher": "Cell Press", "pagerange": "1853-1868", "id_number": "CaltechAUTHORS:20210802-161329765", "issn": "1074-7613", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210802-161329765", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-C76SF00515" }, { "agency": "NIH", "grant_number": "P41GM103393" }, { "agency": "NIH", "grant_number": "R37-AI64003" }, { "agency": "NIH", "grant_number": "R01AI78788" }, { "agency": "NIH", "grant_number": "P01-AI138938-S1" }, { "agency": "NIH", "grant_number": "K99 AI153465" }, { "agency": "NIH", "grant_number": "2U19AI111825" }, { "agency": "George Mason University" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Bulgari Women & Science Fellowship in COVID-19 Research" }, { "agency": "Robert S. Wennett Postdoctoral Fellowship" }, { "agency": "NIH", "grant_number": "UL1 TR001866" }, { "agency": "Shapiro-Silverberg Fund for the Advancement of Translational Research" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.immuni.2021.07.008", "pmcid": "PMC8323339", "primary_object": { "basename": "1-s2.0-S1074761321002946-main.pdf", "url": "https://authors.library.caltech.edu/records/pgr4a-53p46/files/1-s2.0-S1074761321002946-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S1074761321002946-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/pgr4a-53p46/files/1-s2.0-S1074761321002946-mmc1.pdf" } ], "pub_year": "2021", "author_list": "Muecksch, Frauke; Weisblum, Yiska; et al." }, { "id": "https://authors.library.caltech.edu/records/gy0ba-gqj31", "eprint_id": 108067, "eprint_status": "archive", "datestamp": "2023-10-03 22:36:36", "lastmod": "2026-03-30 05:53:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "West-Anthony-P-Jr", "name": { "family": "West", "given": "Anthony P., Jr." }, "orcid": "0000-0003-4213-5184" }, { "id": "Wertheim-Joel-O", "name": { "family": "Wertheim", "given": "Joel O." }, "orcid": "0000-0003-4882-5856" }, { "id": "Wang-Jade-C", "name": { "family": "Wang", "given": "Jade C." } }, { "id": "Vasylyeva-Tetyana-I", "name": { "family": "Vasylyeva", "given": "Tetyana I." }, "orcid": "0000-0002-9736-7022" }, { "id": "Havens-Jennifer-L", "name": { "family": "Havens", "given": "Jennifer L." } }, { "id": "Chowdhury-Moinuddin-A", "name": { "family": "Chowdhury", "given": "Moinuddin A." } }, { "id": "Gonzalez-Edimarlyn", "name": { "family": "Gonzalez", "given": "Edimarlyn" } }, { "id": "Fang-Courtney-E", "name": { "family": "Fang", "given": "Courtney E." } }, { "id": "Di-Lonardo-Steve-S", "name": { "family": "Di Lonardo", "given": "Steve S." } }, { "id": "Hughes-Scott-A", "name": { "family": "Hughes", "given": "Scott" }, "orcid": "0000-0001-6211-1388" }, { "id": "Rakeman-Jennifer-L", "name": { "family": "Rakeman", "given": "Jennifer L." }, "orcid": "0000-0002-9464-7723" }, { "id": "Lee-Henry-H", "name": { "family": "Lee", "given": "Henry H." } }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "id": "Gnanapragasam-Priyanthi-N-P", "name": { "family": "Gnanapragasam", "given": "Priyanthi N. P." } }, { "id": "Yang-Zhi", "name": { "family": "Yang", "given": "Zhi" }, "orcid": "0000-0001-8680-3784" }, { "id": "Gaebler-Christian", "name": { "family": "Gaebler", "given": "Christian" }, "orcid": "0000-0001-7295-8128" }, { "id": "Caskey-Marina", "name": { "family": "Caskey", "given": "Marina" }, "orcid": "0000-0003-1727-8693" }, { "id": "Nussenzweig-Michel-C", "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" }, { "id": "Keeffe-Jennifer-R", "name": { "family": "Keeffe", "given": "Jennifer R." }, "orcid": "0000-0002-5317-6398" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York", "ispublished": "pub", "full_text_status": "public", "keywords": "Epidemiology; SARS-CoV-2; Software; Viral infection", "note": "\u00a9 The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 10 June 2021; Accepted 28 July 2021; Published 09 August 2021. \n\nWe thank the Global Initiative on Sharing Avian Influenza Data (GISAID) and the originating and submitting laboratories for sharing the SARS-CoV-2 genome sequences; see Supplementary Data 4 for a list of sequence contributors. We thank Andrew Rambaut and \u00c1ine O'Toole for lineage designation. This work was supported by the Caltech Merkin Institute for Translational Research (P.J.B.). This work was supported, in whole or in part, by the Bill & Melinda Gates Foundation [grant INV-002143 to P.J.B.]. Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. J.O.W. acknowledges funding from the National Institutes of Health (AI135992 and AI136056). T.I.V. is funded by a Branco Weiss Fellowship. M.C.N. is an HHMI Investigator. \n\nData availability: The SARS-CoV-2 genomes generated in this study have been deposited in GenBank under accession codes MZ637509-MZ642234 (see Supplementary Data 1) and GISAID (see Supplementary Data 2 for a list of genomes used in phylogenetic analysis and Supplementary Data 3 for genomes used in geographic distribution analysis). The data analyzed as part of this project were obtained from the GISAID database and through a Data Use Agreement between NYC DOHMH and the University of California San Diego. Sequences analyzed by using the vdb tool were downloaded from GISAID. No personally identifying information were included as part of these analyses. Data for Fig. 5 are provided in Supplementary Tables 2 and 3. \n\nCode availability: The source code for the vdb program is available at the GitHub repository46: https://github.com/variant-database/vdb. \n\nAuthor Contributions: A.P.W., J.O.W., J.L.H., T.I.V., H.H.L., S.H. and J.C.W. analyzed data. J.C.W., M.A.C., E.G. and H.H.L. performed genome sequencing and assembly. J.O.W. curated data. C.G., M. Caskey and M.C.N. provided clinical samples. P.N.P.G. and J.R.K. carried out experiments. A.P.W., C.O.B., Z.Y., S.H., S.S.D., C.E.F., T.I.V, J.L.H. and J.O.W. prepared figures. A.P.W., J.O.W., T.I.V., C.O.B., J.C.W. and S.H. wrote the manuscript with input from all co-authors. A.P.W., P.J.B., J.O.W., J.L.R. and S.H. supervised the study. \n\nCompeting interests: P.J.B. is a co-inventor on a provisional application from the California Institute of Technology for the use of mosaic nanoparticles as coronavirus immunogens. M.C.N., P.J.B. and C.O.B. are co-inventors on provisional applications for several anti-SARS-CoV-2 monoclonal antibodies. J.O.W. has received funding from Gilead Sciences, LLC (completed) and the CDC (ongoing) via grants and contracts to his institution unrelated to this research. All other authors declare no competing interests. \n\nPeer review information: Nature Communications thanks the anonymous reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.\n\nPublished - s41467-021-25168-4.pdf
Submitted - 20210214-431043v3full.pdf
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", "abstract": "Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage.", "date": "2021-08-09", "date_type": "published", "publication": "Nature Communications", "volume": "12", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 4886", "id_number": "CaltechAUTHORS:20210216-123229308", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210216-123229308", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-002143" }, { "agency": "NIH", "grant_number": "AI135992" }, { "agency": "NIH", "grant_number": "AI136056" }, { "agency": "Branco Weiss Fellowship" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-021-25168-4", "pmcid": "PMC8352861", "primary_object": { "basename": "s41467-021-25168-4.pdf", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/s41467-021-25168-4.pdf" }, "related_objects": [ { "basename": "20210214-431043v3full.pdf", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/20210214-431043v3full.pdf" }, { "basename": "41467_2021_25168_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/41467_2021_25168_MOESM1_ESM.pdf" }, { "basename": "41467_2021_25168_MOESM4_ESM.pdf", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/41467_2021_25168_MOESM4_ESM.pdf" }, { "basename": "41467_2021_25168_MOESM5_ESM.txt", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/41467_2021_25168_MOESM5_ESM.txt" }, { "basename": "41467_2021_25168_MOESM7_ESM.txt", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/41467_2021_25168_MOESM7_ESM.txt" }, { "basename": "41467_2021_25168_MOESM8_ESM.zip", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/41467_2021_25168_MOESM8_ESM.zip" }, { "basename": "41467_2021_25168_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/41467_2021_25168_MOESM2_ESM.pdf" }, { "basename": "41467_2021_25168_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/41467_2021_25168_MOESM3_ESM.pdf" }, { "basename": "41467_2021_25168_MOESM6_ESM.txt", "url": "https://authors.library.caltech.edu/records/gy0ba-gqj31/files/41467_2021_25168_MOESM6_ESM.txt" } ], "pub_year": "2021", "author_list": "West, Anthony P., Jr.; Wertheim, Joel O.; et al." }, { "id": "https://authors.library.caltech.edu/records/jp119-47j39", "eprint_id": 103346, "eprint_status": "archive", "datestamp": "2023-08-20 04:35:37", "lastmod": "2026-03-30 13:23:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Booeshaghi-A-Sina", "name": { "family": "Booeshaghi", "given": "A. Sina" }, "orcid": "0000-0002-6442-4502" }, { "id": "Pachter-L", "name": { "family": "Pachter", "given": "Lior" }, "orcid": "0000-0002-9164-6231" } ] }, "title": "Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)*", "ispublished": "pub", "full_text_status": "public", "keywords": "single-cell, log1p, normalization, ACE2", "note": "\u00a9 The Author(s) 2021. Published by Oxford University Press.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 14 October 2020; Revision received: 23 December 2020; Editorial decision: 29 January 2021; Accepted: 01 March 2021; Published: 02 March 2021. \n\nWe thank Charles Herring, Michael Hoffman, Johan Gustafsson,\nHarold Pimentel, Jeffrey Spence, and Valentine Svensson for\nhelpful comments. \n\nA.S.B. and L.P. were partially funded by NIH U19MH114830. \n\nData Availability Statement. Data and code that reproduce the results in this paper are available here: https://github.com/pachterlab/BP_2021_2. \n\nConflict of Interest: none declared.\n\nPublished - btab085.pdf
Submitted - 2020.05.19.100214v3.full.pdf
", "abstract": "Single-cell RNA-seq technologies have been successfully employed over the past decade to generate many high resolution cell atlases. These have proved invaluable in recent efforts aimed at understanding the cell type specificity of host genes involved in SARS-CoV-2 infections. While single-cell atlases are based on well-sampled highly-expressed genes, many of the genes of interest for understanding SARS-CoV-2 can be expressed at very low levels. Common assumptions underlying standard single-cell analyses don't hold when examining low-expressed genes, with the result that standard workflows can produce misleading results.", "date": "2021-08-01", "date_type": "published", "publication": "Bioinformatics", "volume": "37", "number": "15", "publisher": "Oxford University Press", "pagerange": "2223-2224", "id_number": "CaltechAUTHORS:20200520-084505912", "issn": "1367-4803", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200520-084505912", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U19MH114830" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/bioinformatics/btab085", "pmcid": "PMC7989636", "primary_object": { "basename": "2020.05.19.100214v3.full.pdf", "url": "https://authors.library.caltech.edu/records/jp119-47j39/files/2020.05.19.100214v3.full.pdf" }, "related_objects": [ { "basename": "btab085.pdf", "url": "https://authors.library.caltech.edu/records/jp119-47j39/files/btab085.pdf" } ], "pub_year": "2021", "author_list": "Booeshaghi, A. Sina and Pachter, Lior" }, { "id": "https://authors.library.caltech.edu/records/f13q6-k5d26", "eprint_id": 107841, "eprint_status": "archive", "datestamp": "2023-08-20 04:35:48", "lastmod": "2026-03-30 07:01:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hensley-Matthew-K", "name": { "family": "Hensley", "given": "Matthew K." } }, { "name": { "family": "Bain", "given": "William G." }, "orcid": "0000-0001-8506-0552" }, { "name": { "family": "Jacobs", "given": "Jana" }, "orcid": "0000-0002-0322-585X" }, { "name": { "family": "Nambulli", "given": "Sham" }, "orcid": "0000-0002-9781-9703" }, { "name": { "family": "Parikh", "given": "Urvi" }, "orcid": "0000-0002-4016-0629" }, { "name": { "family": "Cillo", "given": "Anthony" }, "orcid": "0000-0002-3213-3129" }, { "name": { "family": "Staines", "given": "Brittany" } }, { "name": { "family": "Heaps", "given": "Amy" }, "orcid": "0000-0003-4410-4007" }, { "name": { "family": "Sobolewski", "given": "Michele D." } }, { "name": { "family": "Rennick", "given": "Linda J." } }, { "name": { "family": "Macatangay", "given": "Bernard J. C." }, "orcid": "0000-0002-0405-0991" }, { "name": { "family": "Klamar-Blain", "given": "Cynthia" } }, { "name": { "family": "Kitsios", "given": "Georgios D." } }, { "name": { "family": "Meth\u00e9", "given": "Barbara" }, "orcid": "0000-0001-8711-1448" }, { "name": { "family": "Somasundaram", "given": "Ashwin" }, "orcid": "0000-0003-3167-406X" }, { "name": { "family": "Bruno", "given": "Tullia C." }, "orcid": "0000-0002-6433-0207" }, { "name": { "family": "Cardello", "given": "Carly" }, "orcid": "0000-0002-2810-7681" }, { "name": { "family": "Shan", "given": "Feng" }, "orcid": "0000-0003-3660-8475" }, { "name": { "family": "Workman", "given": "Creg" }, "orcid": "0000-0002-9964-9509" }, { "name": { "family": "Ray", "given": "Prabir" }, "orcid": "0000-0002-0430-5114" }, { "name": { "family": "Ray", "given": "Anuradha" }, "orcid": "0000-0001-6844-8918" }, { "name": { "family": "Lee", "given": "Janet" }, "orcid": "0000-0002-6812-6043" }, { "name": { "family": "Sethi", "given": "Rahil" } }, { "name": { "family": "Schwarzmann", "given": "William E." } }, { "id": "Ladinsky-Mark-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Vignali", "given": "Dario A." }, "orcid": "0000-0002-2771-5992" }, { "name": { "family": "Duprex", "given": "W. Paul" }, "orcid": "0000-0003-1716-6376" }, { "name": { "family": "Agha", "given": "Mounzer E." }, "orcid": "0000-0002-2275-7544" }, { "name": { "family": "Mellors", "given": "John W." }, "orcid": "0000-0002-3737-9742" }, { "name": { "family": "McCormick", "given": "Kevin D." }, "orcid": "0000-0003-1544-319X" }, { "name": { "family": "Morris", "given": "Alison" }, "orcid": "0000-0002-7290-6536" }, { "name": { "family": "Haidar", "given": "Ghady" }, "orcid": "0000-0003-0634-8211" } ] }, "title": "Intractable Coronavirus Disease 2019 (COVID-19) and Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Replication in a Chimeric Antigen Receptor-Modified T-Cell Therapy Recipient: A Case Study", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19, SARS-CoV-2 immune responses, SARS-CoV-2 RNAemia, SARS-CoV-2 intrahost variation, SARS-CoV-2 infectivity, severe acute respiratory syndrome coronavirus 2", "note": "\u00a9 The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nReceived: 23 November 2020; Editorial decision: 20 January 2021; Published: 28 January 2021; Corrected and typeset: 27 February 2021. \n\nThe authors thank Dr Rima Abdel-Massih, Luann Borowski, Michelle Busch, Dr Jennifer McComb, Dr Bryan McVerry, Heather Michael, Dr Stephanie Mitchell, Asma Naqvi, John Ries, Dr Charles Rinaldo, Caitlin Schaefer, Dr Michael Shurin, Dr Alan Wells, and Dr Sarah Wheeler. \n\nFinancial support. Research reported in this publication was supported by the National Center for Advancing Translational Sciences of the National Institutes of Health (NIH) (award number KL2TR001856 to G. H.); the United States Department of Veterans Affairs Biomedical Laboratory R&D Service (career development award number IK2 BX004886 to W. B.); the NIH (grant number P50 8 P50 AI150464\u201313 to P. J. B.); George Mason University Fast Grants (to P. J. B.); the Center for Vaccine Research/University of Pittsburgh (grant numbers P01HL114453 to P. R. and J. S. L. and R01 HL136143 to J. S. L.); and the University of Pittsburgh Medical Center P01 AI108545, P50 CA097190 & R01s CA203689, DK089125, AI129893, and AI144422 (to D. A. V.). \n\nAuthor contributions. M. K. H. and W. G. B. contributed equally to this work as co-first authors. J. J. and S. N. contributed equally to this work. All authors have seen and approved the manuscript and contributed significantly to this work. \n\nDisclaimer. The content of this work is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. \n\nPotential conflicts of interest. G. H. and G. D. K. have received research funds from Karius, Inc. J. W. M. is a consultant to Gilead Sciences and Merck and owns shares in Co-Crystal Pharmaceuticals, Infectious Disease Connect, and Abound Bio. D. A. V. is a cofounder and stock holder of Novasenta, Tizona, and Potenza; is a stock holder of Oncorus and Werewolf; holds patents and receives royalties from Astellas and BMS; is a scientific advisory board member for Tizona, Werewolf, and F-Star; is a consultant to Astellas, BMS, Almirall, and Incyte; and receives research funding from BMS and Novasenta. All other authors report no potential conflicts of interest. \n\nAll authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.\n\nSupplemental Material - ciab072_suppl_supplementary_material.docx
", "abstract": "A chimeric antigen receptor-modified T-cell therapy recipient developed severe coronavirus disease 2019, intractable RNAemia, and viral replication lasting >2 months. Premortem endotracheal aspirate contained >2 \u00d7 10\u00b9\u2070 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA copies/mL and infectious virus. Deep sequencing revealed multiple sequence variants consistent with intrahost virus evolution. SARS-CoV-2 humoral and cell-mediated immunity were minimal. Prolonged transmission from immunosuppressed patients is possible.", "date": "2021-08-01", "date_type": "published", "publication": "Clinical Infectious Diseases", "volume": "73", "number": "3", "publisher": "Oxford University Press", "pagerange": "e815-e821", "id_number": "CaltechAUTHORS:20210201-145608486", "issn": "1058-4838", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210201-145608486", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "KL2TR001856" }, { "agency": "Department of Veterans Affairs", "grant_number": "IK2 BX004886" }, { "agency": "NIH", "grant_number": "P50 8 P50 AI150464-13" }, { "agency": "George Mason University" }, { "agency": "University of Pittsburgh" }, { "agency": "NIH", "grant_number": "P01HL114453" }, { "agency": "NIH", "grant_number": "R01 HL136143" }, { "agency": "NIH", "grant_number": "P01 AI108545" }, { "agency": "NIH", "grant_number": "P50 CA097190" }, { "agency": "NIH", "grant_number": "R01 CA203689" }, { "agency": "NIH", "grant_number": "R01 DK089125" }, { "agency": "NIH", "grant_number": "R01 AI129893" }, { "agency": "NIH", "grant_number": "R01 AI144422" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/cid/ciab072", "pmcid": "PMC7929077", "primary_object": { "basename": "ciab072_suppl_supplementary_material.docx", "url": "https://authors.library.caltech.edu/records/f13q6-k5d26/files/ciab072_suppl_supplementary_material.docx" }, "pub_year": "2021", "author_list": "Hensley, Matthew K.; Bain, William G.; et al." }, { "id": "https://authors.library.caltech.edu/records/a5wz9-d5x72", "eprint_id": 109033, "eprint_status": "archive", "datestamp": "2023-08-22 10:46:29", "lastmod": "2026-03-29 20:04:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Greenwald-Hannah-D", "name": { "family": "Greenwald", "given": "Hannah D." }, "orcid": "0000-0001-5213-421X" }, { "id": "Kennedy-Lauren-C", "name": { "family": "Kennedy", "given": "Lauren C." }, "orcid": "0000-0002-4451-2361" }, { "id": "Hinkle-Adrian", "name": { "family": "Hinkle", "given": "Adrian" }, "orcid": "0000-0002-2444-0874" }, { "id": "Whitney-Oscar-N", "name": { "family": "Whitney", "given": "Oscar N." }, "orcid": "0000-0002-4858-2615" }, { "id": "Fan-Vinson-B", "name": { "family": "Fan", "given": "Vinson B." }, "orcid": "0000-0002-1688-7780" }, { "id": "Crits-Christoph-Alexander", "name": { "family": "Crits-Christoph", "given": "Alexander" } }, { "id": "Harris-Lovett-Sasha", "name": { "family": "Harris-Lovett", "given": "Sasha" } }, { "id": "Flamholz-Avi-I", "name": { "family": "Flamholz", "given": "Avi I." }, "orcid": "0000-0002-9278-5479" }, { "id": "Al-Shayeb-Basem", "name": { "family": "Al-Shayeb", "given": "Basem" }, "orcid": "0000-0002-3120-3201" }, { "id": "Liao-Lauren-D", "name": { "family": "Liao", "given": "Lauren D." } }, { "id": "Beyers-Matt", "name": { "family": "Beyers", "given": "Matt" } }, { "id": "Brown-Daniel", "name": { "family": "Brown", "given": "Daniel" } }, { "id": "Chakrabarti-Alicia-R", "name": { "family": "Chakrabarti", "given": "Alicia R." } }, { "id": "Dow-Jason", "name": { "family": "Dow", "given": "Jason" } }, { "id": "Frost-Dan", "name": { "family": "Frost", "given": "Dan" } }, { "id": "Koekemoer-Mark", "name": { "family": "Koekemoer", "given": "Mark" } }, { "id": "Lynch-Chris", "name": { "family": "Lynch", "given": "Chris" } }, { "id": "Sarkar-Payal", "name": { "family": "Sarkar", "given": "Payal" } }, { "id": "White-Eileen", "name": { "family": "White", "given": "Eileen" } }, { "id": "Kantor-Rose-S", "name": { "family": "Kantor", "given": "Rose" }, "orcid": "0000-0002-5402-8979" }, { "id": "Nelson-Kara-L", "name": { "family": "Nelson", "given": "Kara L." }, "orcid": "0000-0001-8899-2662" } ] }, "title": "Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; Wastewater-based epidemiology; Pepper mild mottle virus; CrAssphage; Bacteroides; Human 18S rRNA", "note": "\u00a9 2021 The Authors. Published by Elsevier Ltd.\nThis is an open access article under the CC BY-NC-ND license.\n\nReceived 30 April 2021, Revised 30 June 2021, Accepted 25 July 2021, Available online 31 July 2021.\n\nWe thank Matt Metzger, Melissa Thornton, and the whole COVID-WEB team for support. We also thank our wastewater utility partners for facilitating and assisting with wastewater sampling and physicochemical measurements, including from East Bay Municipal Utility District (Florencio Gonzalez, Bill Chan, Gabriela Esparza, Paula Hansen, Kiley Kinnon, Nick Klumpp, Debra Mapp, Christine Pagtakhan, Daniel Siu, Dave Williams, Zach Wu, and Cheryl Yee), Central Contra Costa Sanitary District (Lori Schectel, Mary Lou Esparza, Blake Brown, Amanda Cauble), San Jose-Santa Clara Regional Wastewater Facility (RWF) Operations and Laboratory staff, and Central Marin Sanitation Agency. We are grateful to the wastewater treatment agencies as well as the San Francisco Estuary Institute for providing us with sewershed shape files. We thank the COVID-19 WBE Collaborative (https://www.covid19wbec.org/) community for discussions of methods and approaches. Additionally, we thank Robert Tjian, Sarah Stanley, Erik Van Dis, Thomas Graham, and Mira Chaplin. We gratefully acknowledge funding from The Catena Foundation as well as rapid response grants from the Center for Information Technology Research in the Interest of Society and the Innovative Genomics Institute at UC Berkeley to K.L.N.. H.D.G. and L.C.K were supported by the National Science Foundation (NSF) Graduate Research Fellowship [grant number DGE-1752814]. In addition, H.D.G was supported by the Berkeley Fellowship, and L.C.K. was supported by NSF INTERN through Re-Inventing the Nation's Urban Water Infrastructure [grant number: 28139880-50542-C].\n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nPublished - 1-s2.0-S2589914721000244-main.pdf
Published - main.pdf
Submitted - 2021.05.04.21256418v1.full.pdf
Supplemental Material - 1-s2.0-S2589914721000244-mmc1.pdf
", "abstract": "Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic methods to interpret the true SARS-CoV-2 signal from noise introduced in wastewater samples (e.g., from sewer conditions, sampling and extraction methods, etc.). In this study, raw wastewater was collected weekly from five sewersheds and one residential facility. The concentrations of SARS-CoV-2 in wastewater samples were compared to geocoded COVID-19 clinical testing data. SARS-CoV-2 was reliably detected (95% positivity) in frozen wastewater samples when reported daily new COVID-19 cases were 2.4 or more per 100,000 people. To adjust for variation in sample fecal content, four normalization biomarkers were evaluated: crAssphage, pepper mild mottle virus, Bacteroides ribosomal RNA (rRNA), and human 18S rRNA. Of these, crAssphage displayed the least spatial and temporal variability. Both unnormalized SARS-CoV-2 RNA signal and signal normalized to crAssphage had positive and significant correlation with clinical testing data (Kendall's Tau-b (\u03c4)=0.43 and 0.38, respectively), but no normalization biomarker strengthened the correlation with clinical testing data. Locational dependencies and the date associated with testing data impacted the lead time of wastewater for clinical trends, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical testing data. This study supports that trends in wastewater surveillance data reflect trends in COVID-19 disease occurrence and presents tools that could be applied to make wastewater signal more interpretable and comparable across studies.", "date": "2021-08-01", "date_type": "published", "publication": "Water Research X", "volume": "12", "publisher": "Elsevier", "pagerange": "Art. No. 100111", "id_number": "CaltechAUTHORS:20210510-105354773", "issn": "2589-9147", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210510-105354773", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Catena Foundation" }, { "agency": "University of California, Berkeley" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1752814" }, { "agency": "NSF", "grant_number": "28139880-50542-C" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.wroa.2021.100111", "pmcid": "PMC8325558", "primary_object": { "basename": "1-s2.0-S2589914721000244-main.pdf", "url": "https://authors.library.caltech.edu/records/a5wz9-d5x72/files/1-s2.0-S2589914721000244-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2589914721000244-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/a5wz9-d5x72/files/1-s2.0-S2589914721000244-mmc1.pdf" }, { "basename": "2021.05.04.21256418v1.full.pdf", "url": "https://authors.library.caltech.edu/records/a5wz9-d5x72/files/2021.05.04.21256418v1.full.pdf" }, { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/a5wz9-d5x72/files/main.pdf" } ], "pub_year": "2021", "author_list": "Greenwald, Hannah D.; Kennedy, Lauren C.; et al." }, { "id": "https://authors.library.caltech.edu/records/wkfmb-cea27", "eprint_id": 111134, "eprint_status": "archive", "datestamp": "2023-08-20 04:31:45", "lastmod": "2026-03-30 08:28:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela" }, "orcid": "0000-0002-2277-3990" } ] }, "title": "Neutralizing antibodies against coronaviruses", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 The Author(s), 2021. Published by Cambridge University Press on behalf of the Microscopy Society of America. \n\nPublished online by Cambridge University Press: 30 July 2021.", "abstract": "We are using single-particle cryo-electron microscopy (cryo-EM) to solve structures of infection- and vaccination-induced antibodies complexed with the spike trimer of SARS-CoV-2 in order to elucidate the structural correlates of antibody-based immune protection. Structural comparisons allowed us to classify antibodies against the receptor-binding domain (RBD) of spike trimer into categories: (1) neutralizing antibodies encoded by the VH3-53 gene segment with short CDRH3 loops that block the host receptor ACE2 and bind only to 'up' RBDs; (2) ACE2-blocking neutralizing antibodies that bind both up and 'down' RBDs and can contact adjacent RBDs; (3) neutralizing antibodies that bind outside the ACE2 site and recognize both up and down RBDs; and (4) previously described antibodies that do not block ACE2 and bind only to up RBDs. Class 2 contained four neutralizing antibodies with epitopes that bridged RBDs, including a VH3-53 antibody that used a long CDRH3 with a hydrophobic tip to bridge between adjacent down RBDs, thereby locking the spike into a closed conformation. Epitope and paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 to escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects and suggesting combinations for clinical use, and provide insight into immune responses against SARS-CoV-2. Our structural studies have also guided the development of a potential pan-betacoronavirus vaccine. The vaccine approach involves co-display of diverse sets of RBDs from SARS-like beta coronaviruses (sarbecoviruses) on nanoparticles (mosaic-RBD-nanoparticles) that results in increased breadth of neutralizing responses in mice compared with nanoparticles presenting only SARS-CoV-2 RBDs. An advantage of this approach is that we have shown that RBD-mi3 nanoparticles retain immunogenicity after lyophilization, suggesting they could be easily stored for widespread use when needed. Thus this modular vaccine platform could provide protection from SARS-CoV-2 as well as potential future emergent coronaviruses that could cause pandemics.", "date": "2021-08", "date_type": "published", "publication": "Microscopy and Microanalysis", "volume": "27", "number": "S1", "publisher": "Cambridge University Press", "pagerange": "1112-1113", "id_number": "CaltechAUTHORS:20210930-205624907", "issn": "1431-9276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210930-205624907", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1017/s1431927621004177", "pub_year": "2021", "author_list": "Bjorkman, Pamela" }, { "id": "https://authors.library.caltech.edu/records/dgeg1-a3t08", "eprint_id": 118356, "eprint_status": "archive", "datestamp": "2023-08-22 10:46:09", "lastmod": "2026-03-29 21:24:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Karthikeyan-Smruthi", "name": { "family": "Karthikeyan", "given": "Smruthi" }, "orcid": "0000-0001-6226-4536" }, { "id": "Nguyen-Andrew", "name": { "family": "Nguyen", "given": "Andrew" } }, { "id": "McDonald-Daniel", "name": { "family": "McDonald", "given": "Daniel" } }, { "id": "Zong-Yijian", "name": { "family": "Zong", "given": "Yijian" } }, { "id": "Ronquillo-Nancy", "name": { "family": "Ronquillo", "given": "Nancy" }, "orcid": "0000-0002-2043-4688" }, { "id": "Ren-Junting", "name": { "family": "Ren", "given": "Junting" }, "orcid": "0000-0002-7492-6864" }, { "id": "Zou-Jingjing", "name": { "family": "Zou", "given": "Jingjing" } }, { "id": "Farmer-Sawyer", "name": { "family": "Farmer", "given": "Sawyer" } }, { "id": "Humphrey-Greg", "name": { "family": "Humphrey", "given": "Greg" } }, { "id": "Henderson-Diana", "name": { "family": "Henderson", "given": "Diana" } }, { "id": "Javidi-Tara", "name": { "family": "Javidi", "given": "Tara" }, "orcid": "0000-0001-7112-1043" }, { "id": "Messer-Karen-S", "name": { "family": "Messer", "given": "Karen" }, "orcid": "0000-0002-9298-2413" }, { "id": "Anderson-Cheryl", "name": { "family": "Anderson", "given": "Cheryl" } }, { "id": "Schooley-Robert", "name": { "family": "Schooley", "given": "Robert" }, "orcid": "0000-0002-2498-8426" }, { "id": "Martin-Natasha-K", "name": { "family": "Martin", "given": "Natasha K." } }, { "id": "Knight-Rob", "name": { "family": "Knight", "given": "Rob" }, "orcid": "0000-0002-0975-9019" } ] }, "title": "Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus", "ispublished": "pub", "full_text_status": "public", "keywords": "Computer Science Applications; Genetics; Molecular Biology; Modeling and Simulation; Ecology, Evolution, Behavior and Systematics; Biochemistry; Physiology; Microbiology", "note": "We thank UC San Diego's Return to Learn (RTL) program for funding the campus-wide wastewater surveillance efforts. We also thank Robert M. Neuhard and the rest of the RTL leadership team and Bradley Sollenberger of the Operational Strategic Initiatives (OSI) team for ensuring the smooth functioning of the program along with the EXCITE (EXpedited COVID-19 IdenTification Environment) CLIA lab at UCSD and the SEARCH (San Diego Epidemiology and Research for COVID Health) Alliance for processing all campus diagnostic tests. We also thank Jason Kayne, Rich Cota, Jesus Ortiz, and the Facilities management team (FM) at UCSD, Joseph Mayer from the Center for Aerosol Impacts on Chemistry of the Environment (CAICE) and Luke Arnold of the Campus Research Machine Shop (CRMS) for assistance with the installation and operation of the autosamplers; Robbie Jacobs, Shawn Knepple and their team at UCSD Logistics for assisting with our daily sampling efforts; Christopher Longhurst and the UC San Diego Health Information Services team; Brett Pollak and the UCSD Information Technology Services team for assisting with the daily notifications; Alysson M. Satterlund, Angela Song, Angela Scioscia, and Elizabeth H. Simmons of Academic Affairs for contact tracing and targeted campus messaging assistance; Jana Severson, Patrick Hochstein, Hemlata Jhaveri, the UCSD HDH team, and the UCSD Environmental Health and Safety (EHS) personnel; Jack Gilbert and the Microbiome Sample Processing Core at UC San Diego for access to qPCR equipment.", "abstract": "Wastewater-based surveillance has gained prominence and come to the forefront as a leading indicator of forecasting COVID-19 (coronavirus disease 2019) infection dynamics owing to its cost-effectiveness and its ability to inform early public health interventions. A university campus could especially benefit from wastewater surveillance, as universities are characterized by largely asymptomatic populations and are potential hot spots for transmission that necessitate frequent diagnostic testing. In this study, we employed a large-scale GIS (geographic information systems)-enabled building-level wastewater monitoring system associated with the on-campus residences of 7,614 individuals. Sixty-eight automated wastewater samplers were deployed to monitor 239 campus buildings with a focus on residential buildings. Time-weighted composite samples were collected on a daily basis and analyzed on the same day. Sample processing was streamlined significantly through automation, reducing the turnaround time by 20-fold and exceeding the scale of similar surveillance programs by 10- to 100-fold, thereby overcoming one of the biggest bottlenecks in wastewater surveillance. An automated wastewater notification system was developed to alert residents to a positive wastewater sample associated with their residence and to encourage uptake of campus-provided asymptomatic testing at no charge. This system, integrated with the rest of the \"Return to Learn\" program at the University of California (UC) San Diego-led to the early diagnosis of nearly 85% of all COVID-19 cases on campus. COVID-19 testing rates increased by 1.9 to 13\u00d7 following wastewater notifications. Our study shows the potential for a robust, efficient wastewater surveillance system to greatly reduce infection risk as college campuses and other high-risk environments reopen.", "date": "2021-08", "date_type": "published", "publication": "mSystems", "volume": "6", "number": "4", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e0079321", "id_number": "CaltechAUTHORS:20221215-540495000.23", "issn": "2379-5077", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221215-540495000.23", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of California, San Diego" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1128/msystems.00793-21", "pmcid": "PMC8409724", "pub_year": "2021", "author_list": "Karthikeyan, Smruthi; Nguyen, Andrew; et al." }, { "id": "https://authors.library.caltech.edu/records/0v15b-rxy97", "eprint_id": 110086, "eprint_status": "archive", "datestamp": "2023-08-22 10:35:26", "lastmod": "2026-03-30 08:48:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Liqiang", "name": { "family": "Wang", "given": "Liqiang" } }, { "id": "Chen-Xue", "name": { "family": "Chen", "given": "Xue" } }, { "id": "Zhang-Yibo", "name": { "family": "Zhang", "given": "Yibo" } }, { "id": "Li-Mengying", "name": { "family": "Li", "given": "Mengying" } }, { "id": "Li-Pengfei", "name": { "family": "Li", "given": "Pengfei" } }, { "id": "Jiang-Linhui", "name": { "family": "Jiang", "given": "Linhui" } }, { "id": "Xia-Yan", "name": { "family": "Xia", "given": "Yan" } }, { "id": "Li-Zhen", "name": { "family": "Li", "given": "Zhen" } }, { "id": "Li-Jiali", "name": { "family": "Li", "given": "Jiali" } }, { "id": "Wang-Lu", "name": { "family": "Wang", "given": "Lu" } }, { "id": "Hou-Tangyan", "name": { "family": "Hou", "given": "Tangyan" } }, { "id": "Liu-Weiping", "name": { "family": "Liu", "given": "Weiping" }, "orcid": "0000-0002-1173-892X" }, { "id": "Rosenfeld-Daniel", "name": { "family": "Rosenfeld", "given": "Daniel" }, "orcid": "0000-0002-0784-7656" }, { "id": "Zhu-Tong", "name": { "family": "Zhu", "given": "Tong" } }, { "id": "Zhang-Yuanhang", "name": { "family": "Zhang", "given": "Yuanhang" } }, { "id": "Chen-Jianmin", "name": { "family": "Chen", "given": "Jianmin" } }, { "id": "Wang-Shuxiao", "name": { "family": "Wang", "given": "Shuxiao" }, "orcid": "0000-0001-9727-1963" }, { "id": "Huang-Yuanlong", "name": { "family": "Huang", "given": "Yuanlong" }, "orcid": "0000-0002-6726-8904" }, { "id": "Seinfeld-J-H", "name": { "family": "Seinfeld", "given": "John H." }, "orcid": "0000-0003-1344-4068" }, { "id": "Yu-Shaocai", "name": { "family": "Yu", "given": "Shaocai" }, "orcid": "0000-0001-9718-8246" } ] }, "title": "Switching to electric vehicles can lead to significant reductions of PM_(2.5) and NO\u2082 across China", "ispublished": "pub", "full_text_status": "public", "keywords": "electric vehicles; air quality; COVID-19 lockdowns; PM2.5; NO2; China", "note": "\u00a9 2021 Elsevier Inc. \n\nReceived 21 August 2020, Revised 21 October 2020, Accepted 24 June 2021, Available online 23 July 2021.", "abstract": "Transportation contributes to around one-fifth of global greenhouse gas emissions, while also causing severe air pollution. The conversion to electric vehicles (EVs) represents a major path to decarbonize the transport sector, with potentially significant co-benefits for human health. However, the scale of such co-benefits largely remains an empirical question and lacks observational evidence. The full lockdown in China during the coronavirus disease 2019 (COVID-19) pandemic provides an unprecedented real-world experiment to evaluate emission reduction potentials of a large-scale transition to EVs. Here, we utilize ground and satellite observations of air quality during the full lockdown to constrain predictions of a comprehensive chemical transport model and find that the substantial traffic reductions are near-linearly linked to reductions of PM_(2.5) (particles with an aerodynamic diameter \u22642.5 \u03bcm) and NO\u2082. A further extrapolation of a full conversion to EVs shows a significant reduction of PM_(2.5) (30%\u201370%) and NO\u2082 (30%\u201380%) in most of China. Our findings provide fact-based evidence of potential environmental benefits generated by fully switching to EVs.", "date": "2021-07-23", "date_type": "published", "publication": "One Earth", "volume": "4", "number": "7", "publisher": "Elsevier", "pagerange": "1037-1048", "id_number": "CaltechAUTHORS:20210729-221138822", "issn": "2590-3322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210729-221138822", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.oneear.2021.06.008", "pub_year": "2021", "author_list": "Wang, Liqiang; Chen, Xue; et al." }, { "id": "https://authors.library.caltech.edu/records/s7jfw-wxw93", "eprint_id": 109801, "eprint_status": "archive", "datestamp": "2023-08-20 04:17:08", "lastmod": "2026-03-30 05:13:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Grant-Stephen-N", "name": { "family": "Grant", "given": "Stephen N." }, "orcid": "0000-0003-0923-8886" }, { "id": "Lester-H-A", "name": { "family": "Lester", "given": "Henry A." }, "orcid": "0000-0002-5470-5255" } ] }, "title": "Regulation of epithelial sodium channel activity by SARS-CoV-1 and SARS-CoV-2 proteins", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Biophysical Society. \n\nReceived 15 December 2020, Accepted 3 June 2021, Available online 29 June 2021. \n\nWe thank Drs. Christopher Barnes, Bruce N. Cohen, Douglas Eaton, Carolyn Machamer, Gerhard Thiel, Anthony West, Nael McCarty, Dennis A. Dougherty and Nathan Dascal for useful insights, and Jonathan Wang for harvesting oocytes. \n\nThis work was supported by the National Institute of Drug Abuse (DA046122 and DA049140), the National Institute of General Medical Sciences (GM-123582), and the California Tobacco-Related Disease Program (29IR0445 to D.A. Dougherty). \n\nAuthor contributions: S.N.G. designed and performed the experiments, analyzed the data, and prepared the manuscript. H.A.L. designed the experiments, analyzed the data, prepared the manuscript, and supervised the project.\n\nSupplemental Material - 1-s2.0-S0006349521004902-mmc1.pdf
", "abstract": "Severe acute respiratory syndrome (SARS) coronavirus (CoV) 2 (SARS-CoV-2), which causes the coronavirus disease 2019, encodes several proteins whose roles are poorly understood. We tested their ability either to directly form plasma membrane ion channels or to change functions of two mammalian plasma membrane ion channels, the epithelial sodium channel (ENaC) and the \u03b13\u03b24 nicotinic acetylcholine receptor. In mRNA-injected Xenopus oocytes, none of nine SARS-CoV-2 proteins or two SARS-CoV-1 proteins produced conductances, nor did co-injection of several combinations. Immunoblots for ORF8, spike (S), and envelope (E) proteins revealed that the proteins are expressed at appropriate molecular weights. In experiments on coexpression with ENaC, three tested SARS proteins (SARS-CoV-1 E, SARS-CoV-2 E, and SARS-CoV-2 S) markedly decrease ENaC currents. SARS-CoV-1 S protein decreases ENaC currents modestly. Coexpressing the E proteins but not the S proteins with \u03b13\u03b24 nicotinic acetylcholine receptors significantly reduces acetylcholine-induced currents. ENaC inhibition does not occur if the SARS-CoV protein mRNAs are injected 24 h after the ENaC mRNAs, suggesting that SARS-CoV proteins affect early step(s) in functional expression of channel proteins. Consistent with the hypothesis that the SARS-CoV-2 S protein-induced ENaC inhibition involves competition for available protease, mutating the furin cleavage site in SARS-CoV-2 S protein partially relieves inhibition of ENaC currents. Extending previous suggestions that SARS proteins affect ENaC currents via protein kinase C (PKC) activation, PKC activation via phorbol 12-myristate 13-acetate decreases ENaC and \u03b13\u03b24 activity. Phorbol 12-myristate 13-acetate application reduced membrane capacitance \u223c5%, presumably via increased endocytosis, but this decrease is much smaller than the SARS proteins' effects on conductances. Also, incubating oocytes in G\u00f6-6976, a PKC\u03b1 and PKC\u03b2 inhibitor, did not alter E or S protein-induced channel inhibition. We conclude that SARS-CoV-1 and SARS-CoV-2 proteins alter the function of human plasma membrane channels, via incompletely understood mechanisms. These interactions may play a role in the coronavirus 2019 pathophysiology.", "date": "2021-07-20", "date_type": "published", "publication": "Biophysical Journal", "volume": "120", "number": "14", "publisher": "Biophysical Society", "pagerange": "2805-2813", "id_number": "CaltechAUTHORS:20210714-140716932", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210714-140716932", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute on Drug Abuse" }, { "agency": "NIH", "grant_number": "DA046122" }, { "agency": "NIH", "grant_number": "DA049140" }, { "agency": "NIH", "grant_number": "GM-123582" }, { "agency": "California Tobacco-Related Disease Research Program", "grant_number": "29IR0445" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.bpj.2021.06.005", "pmcid": "PMC8238646", "primary_object": { "basename": "1-s2.0-S0006349521004902-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/s7jfw-wxw93/files/1-s2.0-S0006349521004902-mmc1.pdf" }, "pub_year": "2021", "author_list": "Grant, Stephen N. and Lester, Henry A." }, { "id": "https://authors.library.caltech.edu/records/kvear-yb611", "eprint_id": 109032, "eprint_status": "archive", "datestamp": "2023-08-22 10:32:26", "lastmod": "2026-03-28 23:01:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Zijun", "name": { "family": "Wang", "given": "Zijun" }, "orcid": "0000-0002-2095-2151" }, { "id": "Muecksch-Frauke", "name": { "family": "Muecksch", "given": "Frauke" }, "orcid": "0000-0002-0132-5101" }, { "id": "Schaefer-Babajew-Dennis", "name": { "family": "Schaefer-Babajew", "given": "Dennis" }, "orcid": "0000-0002-5380-2950" }, { "id": "Finkin-Shlomo", "name": { "family": "Finkin", "given": "Shlomo" }, "orcid": "0000-0003-4474-2658" }, { "id": "Viant-Charlotte", "name": { "family": "Viant", "given": "Charlotte" }, "orcid": "0000-0002-8852-2318" }, { "id": "Gaebler-Christian", "name": { "family": "Gaebler", "given": "Christian" }, "orcid": "0000-0001-7295-8128" }, { "id": "Hoffmann-Hans-Heinrich", "name": { "family": "Hoffmann", "given": "Hans-Heinrich" }, "orcid": "0000-0003-0554-0244" }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "id": "Cipolla-Melissa", "name": { "family": "Cipolla", "given": "Melissa" }, "orcid": "0000-0001-8156-2512" }, { "id": "Ramos-Victor", "name": { "family": "Ramos", "given": "Victor" }, "orcid": "0000-0001-8572-1621" }, { "id": "Oliveira-Thiago-Y", "name": { "family": "Oliveira", "given": "Thiago Y." }, "orcid": "0000-0002-2654-0879" }, { "id": "Cho-Alice", "name": { "family": "Cho", "given": "Alice" } }, { "id": "Schmidt-Fabian", "name": { "family": "Schmidt", "given": "Fabian" } }, { "id": "da-Silva-Justin", "name": { "family": "da Silva", "given": "Justin" } }, { "id": "Bednarski-Eva", "name": { "family": "Bednarski", "given": "Eva" }, "orcid": "0000-0003-4438-5590" }, { "id": "Aguado-Lauren", "name": { "family": "Aguado", "given": "Lauren" }, "orcid": "0000-0002-0036-4803" }, { "id": "Yee-Jim", "name": { "family": "Yee", "given": "Jim" } }, { "id": "Daga-Mridushi", "name": { "family": "Daga", "given": "Mridushi" } }, { "id": "Turroja-Martina", "name": { "family": "Turroja", "given": "Martina" }, "orcid": "0000-0001-9640-0559" }, { "id": "Millard-Katrina-G", "name": { "family": "Millard", "given": "Katrina G." }, "orcid": "0000-0003-2247-3178" }, { "id": "Jankovic-Mila", "name": { "family": "Jankovic", "given": "Mila" }, "orcid": "0000-0001-9696-5234" }, { "id": "Gazumyan-Anna", "name": { "family": "Gazumyan", "given": "Anna" }, "orcid": "0000-0002-5976-9717" }, { "id": "Zhao-Zhen", "name": { "family": "Zhao", "given": "Zhen" } }, { "id": "Rice-Charles-M", "name": { "family": "Rice", "given": "Charles M." }, "orcid": "0000-0003-3087-8079" }, { "id": "Bieniasz-Paul-D", "name": { "family": "Bieniasz", "given": "Paul D." }, "orcid": "0000-0002-2368-3719" }, { "id": "Caskey-Marina", "name": { "family": "Caskey", "given": "Marina" }, "orcid": "0000-0003-1727-8693" }, { "id": "Hatziioannou-Theodora", "name": { "family": "Hatziioannou", "given": "Theodora" }, "orcid": "0000-0002-7889-0766" }, { "id": "Nussenzweig-Michel-C", "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" } ] }, "title": "Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection", "ispublished": "pub", "full_text_status": "public", "keywords": "Antibodies; Antimicrobial responses; SARS-CoV-2", "note": "\u00a9 2021 Nature Publishing Group. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 02 May 2021; Accepted 04 June 2021; Published 14 June 2021. \n\nWe thank all study participants who devoted time to our research; The Rockefeller University Hospital nursing staff and Clinical Research Support Office and nursing staff; M. O. Frank, M. Bergh and R. B. Darnell for SARS-CoV-2 saliva PCR testing; P. J. Bjorkman and all members of the M.C.N. laboratory for helpful discussions and M. Jankovic for laboratory support. This work was supported by NIH grant P01-AI138398-S1 (M.C.N., C.M.R. and P.J.B.) and 2U19AI111825 (M.C.N. and C.M.R); George Mason University Fast Grants to C.M.R., 3 R01-AI091707-10S1 to C.M.R.; The G. Harold and Leila Y. Mathers Charitable Foundation to C.M.R.; NIH grant R37-AI64003 to P.D.B.; NIH grant R01AI78788 to T.H. We thank J. Vielmetter and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance. C.O.B. is supported by the HHMI Hanna Gray and Burroughs Wellcome PDEP fellowships. C.G. was supported by the Robert S. Wennett Post-Doctoral Fellowship, in part by the National Center for Advancing Translational Sciences (National Institutes of Health Clinical and Translational Science Award program, grant UL1 TR001866), and by the Shapiro\u2013Silverberg Fund for the Advancement of Translational Research. P.D.B. and M.C.N. are Howard Hughes Medical Institute Investigators. F.M. is supported by the Bulgari Women & Science Fellowship in COVID-19 Research. \n\nData availability: Data are provided in Supplementary Tables 1\u20138. The raw sequencing data have been deposited at Github (https://github.com/stratust/igpipeline). This study also uses data from https://doi.org/10.5061/dryad.35ks2 and from https://doi.org/10.1038/s41586-019-0934-8. \n\nCode availability: Computer code to process the antibody sequences and/or associated with Fig. 2 and Extended Data Fig. 5 is available at GitHub (https://github.com/stratust/igpipeline). \n\nThese authors contributed equally: Zijun Wang, Frauke Muecksch, Dennis Schaefer-Babajew, Shlomo Finkin, Charlotte Viant, Christian Gaebler \n\nAuthor Contributions: P.D.B., T.H., C.M.R. and M.C.N. conceived, designed and analysed the experiments. M. Caskey and C.G. designed clinical protocols. Z.W., F.M., D.S.-B., S.F., C.V., H.-H.H., C.O.B., A.C., F.S., J.D.S., E.B., L.A., J.Y., M.J. and Z.Z. carried out experiments. A.G. and M. Cipolla produced antibodies. D.S.-B., M.D., M.T., K.G.M., C.G. and M. Caskey recruited participants, executed clinical protocols and processed samples. T.Y.O. and V.R. performed bioinformatic analysis. Z.W., F.M., D.S.-B., C.G. and M.C.N. wrote the manuscript with input from all co-authors. \n\nCompeting interests: The Rockefeller University has filed a provisional patent application in connection with this work on which M.C.N. is an inventor (US patent 63/021,387). The patent has been licensed by Rockefeller University to Bristol Meyers Squib. Z.Z. received seed instruments and sponsored research funding from ET Healthcare. \n\nPeer review information: Nature thanks Thushan de Silva, Pei-Yong Shi and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.\n\nPublished - s41586-021-03696-9.pdf
Submitted - 2021.05.07.443175v1.full.pdf
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", "abstract": "More than one year after its inception, the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains difficult to control despite the availability of several working vaccines. Progress in controlling the pandemic is slowed by the emergence of variants that appear to be more transmissible and more resistant to antibodies. Here we report on a cohort of 63 individuals who have recovered from COVID-19 assessed at 1.3, 6.2 and 12 months after SARS-CoV-2 infection, 41% of whom also received mRNA vaccines. In the absence of vaccination, antibody reactivity to the receptor binding domain (RBD) of SARS-CoV-2, neutralizing activity and the number of RBD-specific memory B cells remain relatively stable between 6 and 12 months after infection. Vaccination increases all components of the humoral response and, as expected, results in serum neutralizing activities against variants of concern similar to or greater than the neutralizing activity against the original Wuhan Hu-1 strain achieved by vaccination of naive individuals. The mechanism underlying these broad-based responses involves ongoing antibody somatic mutation, memory B cell clonal turnover and development of monoclonal antibodies that are exceptionally resistant to SARS-CoV-2 RBD mutations, including those found in the variants of concern. In addition, B cell clones expressing broad and potent antibodies are selectively retained in the repertoire over time and expand markedly after vaccination. The data suggest that immunity in convalescent individuals will be very long lasting and that convalescent individuals who receive available mRNA vaccines will produce antibodies and memory B cells that should be protective against circulating SARS-CoV-2 variants.", "date": "2021-07-15", "date_type": "published", "publication": "Nature", "volume": "595", "number": "7867", "publisher": "Nature Publishing Group", "pagerange": "426-431", "id_number": "CaltechAUTHORS:20210510-104403619", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210510-104403619", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01-AI138398-S1" }, { "agency": "NIH", "grant_number": "2U19AI111825" }, { "agency": "George Mason University" }, { "agency": "NIH", "grant_number": "3 R01-AI091707-10S1" }, { "agency": "G. Harold and Leila Y. Mathers Charitable Foundation" }, { "agency": "NIH", "grant_number": "R37-AI64003" }, { "agency": "NIH", "grant_number": "R01AI78788" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Robert S. Wennett Postdoctoral Fellowship" }, { "agency": "National Center for Advancing Translational Sciences" }, { "agency": "NIH", "grant_number": "UL1 TR001866" }, { "agency": "Shapiro-Silverberg Fund for the Advancement of Translational Research" }, { "agency": "Bulgari Women & Science Fellowship in COVID-19 Research" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1038/s41586-021-03696-9", "pmcid": "PMC8277577", "primary_object": { "basename": "41586_2021_3696_Fig12_ESM.webp", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_Fig12_ESM.webp" }, "related_objects": [ { "basename": "41586_2021_3696_Fig13_ESM.webp", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_Fig13_ESM.webp" }, { "basename": "41586_2021_3696_Fig6_ESM.webp", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_Fig6_ESM.webp" }, { "basename": "41586_2021_3696_MOESM6_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_MOESM6_ESM.xlsx" }, { "basename": "41586_2021_3696_MOESM9_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_MOESM9_ESM.xlsx" }, { "basename": "41586_2021_3696_Fig5_ESM.webp", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_Fig5_ESM.webp" }, { "basename": "41586_2021_3696_MOESM2_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_MOESM2_ESM.xlsx" }, { "basename": "41586_2021_3696_MOESM4_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_MOESM4_ESM.xlsx" }, { "basename": "2021.05.07.443175v1.full.pdf", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/2021.05.07.443175v1.full.pdf" }, { "basename": "41586_2021_3696_Fig11_ESM.webp", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_Fig11_ESM.webp" }, { "basename": "41586_2021_3696_Fig7_ESM.webp", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_Fig7_ESM.webp" }, { "basename": "41586_2021_3696_Fig8_ESM.webp", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_Fig8_ESM.webp" }, { "basename": "41586_2021_3696_Fig9_ESM.webp", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_Fig9_ESM.webp" }, { "basename": "41586_2021_3696_MOESM5_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_MOESM5_ESM.xlsx" }, { "basename": "41586_2021_3696_Fig10_ESM.webp", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_Fig10_ESM.webp" }, { "basename": "41586_2021_3696_MOESM7_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_MOESM7_ESM.xlsx" }, { "basename": "41586_2021_3696_MOESM8_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_MOESM8_ESM.xlsx" }, { "basename": "s41586-021-03696-9.pdf", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/s41586-021-03696-9.pdf" }, { "basename": "41586_2021_3696_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_MOESM1_ESM.pdf" }, { "basename": "41586_2021_3696_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/kvear-yb611/files/41586_2021_3696_MOESM3_ESM.xlsx" } ], "pub_year": "2021", "author_list": "Wang, Zijun; Muecksch, Frauke; et al." }, { "id": "https://authors.library.caltech.edu/records/p1p7m-9mv98", "eprint_id": 108512, "eprint_status": "archive", "datestamp": "2023-10-03 22:40:33", "lastmod": "2026-03-30 05:50:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Greaney-Allison-J", "name": { "family": "Greaney", "given": "Allison J." }, "orcid": "0000-0001-7202-3349" }, { "id": "Starr-Tyler-N", "name": { "family": "Starr", "given": "Tyler N." }, "orcid": "0000-0001-6713-6904" }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "id": "Weisblum-Yiska", "name": { "family": "Weisblum", "given": "Yiska" }, "orcid": "0000-0002-9249-1745" }, { "id": "Schmidt-Fabian", "name": { "family": "Schmidt", "given": "Fabian" } }, { "id": "Caskey-Marina", "name": { "family": "Caskey", "given": "Marina" }, "orcid": "0000-0003-1727-8693" }, { "id": "Gaebler-Christian", "name": { "family": "Gaebler", "given": "Christian" }, "orcid": "0000-0001-7295-8128" }, { "id": "Cho-Alice", "name": { "family": "Cho", "given": "Alice" }, "orcid": "0000-0001-6354-6148" }, { "id": "Agudelo-Marianna", "name": { "family": "Agudelo", "given": "Marianna" }, "orcid": "0000-0003-3924-6449" }, { "id": "Finkin-Shlomo", "name": { "family": "Finkin", "given": "Shlomo" }, "orcid": "0000-0003-4474-2658" }, { "id": "Wang-Zijun", "name": { "family": "Wang", "given": "Zijun" }, "orcid": "0000-0002-2095-2151" }, { "id": "Poston-Daniel", "name": { "family": "Poston", "given": "Daniel" } }, { "id": "Muecksch-Frauke", "name": { "family": "Muecksch", "given": "Frauke" } }, { "id": "Hatziioannou-Theodora", "name": { "family": "Hatziioannou", "given": "Theodora" }, "orcid": "0000-0002-7889-0766" }, { "id": "Bieniasz-Paul-D", "name": { "family": "Bieniasz", "given": "Paul D." }, "orcid": "0000-0002-2368-3719" }, { "id": "Robbiani-Davide-F", "name": { "family": "Robbiani", "given": "Davide F." }, "orcid": "0000-0001-7379-3484" }, { "id": "Nussenzweig-Michel-C", "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Bloom-Jesse-D", "name": { "family": "Bloom", "given": "Jesse D." }, "orcid": "0000-0003-1267-3408" } ] }, "title": "Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies", "ispublished": "pub", "full_text_status": "public", "keywords": "SARS-CoV-2; Viral evolution; Viral infection", "note": "\u00a9 The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nWe thank Andrea Loes for experimental assistance and Cathy Lin for administrative support; Dolores Covarrubias, Andy Marty, and the Genomics and Flow Cytometry core facilities at the Fred Hutchinson Cancer Research Center for experimental support; J. Vielmetter, P. Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance. This work was supported by the NIAID/NIH (R01AI141707 and R01AI127893 to J.D.B., T32AI083203 to A.J.G., P01 AI138398-S1 to M.C.N. and P.J.B.) and the Gates Foundation (INV-004949). Support was also provided by the Caltech Merkin Institute for Translational Research (P.J.B.), a George Mason University Fast Grant (P.J.B.), and ATAC consortium EC 101003650 (D.F.R.); NIH grants U19 AI111825 and NIH U01 AI151698 for the United World Antiviral Research Network, UWARN (M.C.N. and D.F.R.). The Scientific Computing Infrastructure at Fred Hutch is funded by ORIP grant S10OD028685. T.N.S. is a Washington Research Foundation Innovation Fellow at the University of Washington Institute for Protein Design and a Howard Hughes Medical Institute Fellow of the Damon Runyon Cancer Research Foundation (DRG-2381-19). C.O.B. was supported by the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Postdoctoral Enrichment Program from the Burroughs Wellcome Fund. J.D.B., P.D.B., and M.C.N. are Investigators of the Howard Hughes Medical Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the US government or the other sponsors. \n\nCode availability: The complete custom code computational pipeline for escape-mapping data analysis is available at https://github.com/jbloomlab/SARS-CoV-2-RBD_MAP_Rockefeller and archived in the Zenodo repository (https://doi.org/10.5281/zenodo.4901733). Markdown summaries of the escape-mapping data analysis steps are at https://github.com/jbloomlab/SARS-CoV-2-RBD_MAP_Rockefeller/blob/main/results/summary/summary.md.\n\nAuthor Contributions:\nConceptualization: A.J.G., C.O.B., M.C.N., P.J.B. and J.D.B.; methodology: A.J.G., T.N.S. and J.D.B.; investigation: A.J.G.; software: A.J.G., T.N.S. and J.D.B.; formal analysis: A.J.G. and J.D.B.; VSV escape data: Y.W., F.S. and D.P.; resources: M.C.N., D.F.R., M.C., C.G., A.C., M.A., S.F., Z.W. and F.M.; writing\u2014original draft: A.J.G. and J.D.B.; writing\u2014review and editing: all authors; supervision: T.H., P.D.B., M.C.N., P.J.B. and J.D.B.\n\nCompeting interests: Subsequent to completion and submission of the initial version of this study, J.D.B. began consulting for Moderna on viral evolution and epidemiology. J.D.B. has the potential to receive a share of IP revenue as an inventor on a Fred Hutch optioned technology/patent (application WO2020006494) related to deep mutational scanning of viral proteins. The Rockefeller University has filed a provisional patent application related to SARS-CoV-2 monoclonal antibodies on which D.F.R. and M.C.N. are inventors. The Rockefeller University has applied for a patent relating to the replication-competent VSV/SARS-CoV-2 chimeric virus on which Y.W, F.S., T.H. and P.B. are inventors (US patent 63/036,124). The remaining authors declare no competing interests. \n\nPeer review information: Nature Communications thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.\n\nPublished - s41467-021-24435-8.pdf
Submitted - 20210317-435863v1-full.pdf
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", "abstract": "Monoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the viral spike receptor-binding domain (RBD) that escape binding by representatives of three potently neutralizing classes of anti-RBD antibodies with high-resolution structures. We compare the antibody-escape maps to similar maps for convalescent polyclonal plasmas, including plasmas from individuals from whom some of the antibodies were isolated. While the binding of polyclonal plasma antibodies are affected by mutations across multiple RBD epitopes, the plasma-escape maps most resemble those of a single class of antibodies that target an epitope on the RBD that includes site E484. Therefore, although the human immune system can produce antibodies that target diverse RBD epitopes, in practice the polyclonal response to infection is skewed towards a single class of antibodies targeting an epitope that is already undergoing rapid evolution.", "date": "2021-07-07", "date_type": "published", "publication": "Nature Communications", "volume": "12", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 4196", "id_number": "CaltechAUTHORS:20210322-133440105", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210322-133440105", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01AI141707" }, { "agency": "NIH", "grant_number": "R01AI127893" }, { "agency": "NIH", "grant_number": "T32AI083203" }, { "agency": "NIH", "grant_number": "P01 AI138398-S1" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-004949" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "George Mason University" }, { "agency": "ATAC Consortium", "grant_number": "EC 101003650" }, { "agency": "NIH", "grant_number": "U19 AI111825" }, { "agency": "NIH", "grant_number": "U01 AI151698" }, { "agency": "NIH", "grant_number": "S10OD028685" }, { "agency": "Washington Research Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-2381-19" }, { "agency": "Burroughs Wellcome Fund" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-021-24435-8", "pmcid": "PMC8263750", "primary_object": { "basename": "41467_2021_24435_MOESM4_ESM.csv", "url": "https://authors.library.caltech.edu/records/p1p7m-9mv98/files/41467_2021_24435_MOESM4_ESM.csv" }, "related_objects": [ { "basename": "41467_2021_24435_MOESM5_ESM.pdf", "url": "https://authors.library.caltech.edu/records/p1p7m-9mv98/files/41467_2021_24435_MOESM5_ESM.pdf" }, { "basename": "s41467-021-24435-8.pdf", "url": "https://authors.library.caltech.edu/records/p1p7m-9mv98/files/s41467-021-24435-8.pdf" }, { "basename": "20210317-435863v1-full.pdf", "url": "https://authors.library.caltech.edu/records/p1p7m-9mv98/files/20210317-435863v1-full.pdf" }, { "basename": "41467_2021_24435_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/p1p7m-9mv98/files/41467_2021_24435_MOESM1_ESM.pdf" }, { "basename": "41467_2021_24435_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/p1p7m-9mv98/files/41467_2021_24435_MOESM2_ESM.pdf" }, { "basename": "41467_2021_24435_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/p1p7m-9mv98/files/41467_2021_24435_MOESM3_ESM.pdf" } ], "pub_year": "2021", "author_list": "Greaney, Allison J.; Starr, Tyler N.; et al." }, { "id": "https://authors.library.caltech.edu/records/05kjw-6t056", "eprint_id": 106738, "eprint_status": "archive", "datestamp": "2024-01-29 19:48:02", "lastmod": "2026-03-30 07:57:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bloom-Joshua-S", "name": { "family": "Bloom", "given": "Joshua S." }, "orcid": "0000-0002-7241-1648" }, { "id": "Sathe-Laila", "name": { "family": "Sathe", "given": "Laila" }, "orcid": "0000-0003-1016-3295" }, { "id": "Munugala-Chetan", "name": { "family": "Munugala", "given": "Chetan" } }, { "id": "Jones-Eric-M", "name": { "family": "Jones", "given": "Eric M." } }, { "id": "Gasperini-Molly", "name": { "family": "Gasperini", "given": "Molly" }, "orcid": "0000-0003-4559-8432" }, { "id": "Lubock-Nathan-B", "name": { "family": "Lubock", "given": "Nathan B." }, "orcid": "0000-0001-8064-2465" }, { "id": "Yarza-Fauna", "name": { "family": "Yarza", "given": "Fauna" }, "orcid": "0000-0002-2512-6182" }, { "id": "Thompson-Erin-M", "name": { "family": "Thompson", "given": "Erin M." }, "orcid": "0000-0002-6085-3051" }, { "id": "Kovary-Kyle-M", "name": { "family": "Kovary", "given": "Kyle M." }, "orcid": "0000-0002-7616-2968" }, { "id": "Park-Jimin", "name": { "family": "Park", "given": "Jimin" } }, { "id": "Marquette-Dawn", "name": { "family": "Marquette", "given": "Dawn" }, "orcid": "0000-0002-3964-7683" }, { "id": "Kay-Stephania", "name": { "family": "Kay", "given": "Stephania" } }, { "id": "Lucas-Mark", "name": { "family": "Lucas", "given": "Mark" } }, { "id": "Love-TreQuan", "name": { "family": "Love", "given": "TreQuan" } }, { "id": "Booeshaghi-A-Sina", "name": { "family": "Booeshaghi", "given": "A. Sina" }, "orcid": "0000-0002-6442-4502" }, { "id": "Brandenberg-Oliver-F", "name": { "family": "Brandenberg", "given": "Oliver F." }, "orcid": "0000-0001-5662-1234" }, { "id": "Guo-Longhua", "name": { "family": "Guo", "given": "Longhua" }, "orcid": "0000-0001-9690-9750" }, { "id": "Boocock-James", "name": { "family": "Boocock", "given": "James" }, "orcid": "0000-0003-0323-8818" }, { "id": "Hochman-Myles", "name": { "family": "Hochman", "given": "Myles" }, "orcid": "0000-0001-5172-6395" }, { "id": "Simpkins-Scott-W", "name": { "family": "Simpkins", "given": "Scott W." }, "orcid": "0000-0002-5997-2838" }, { "id": "Lin-Isabella", "name": { "family": "Lin", "given": "Isabella" }, "orcid": "0000-0002-7102-6879" }, { "id": "LaPierre-Nathan", "name": { "family": "LaPierre", "given": "Nathan" }, "orcid": "0000-0003-2394-8868" }, { "id": "Hong-Duke", "name": { "family": "Hong", "given": "Duke" } }, { "id": "Zhang-Yi", "name": { "family": "Zhang", "given": "Yi" } }, { "id": "Oland-Gabriel", "name": { "family": "Oland", "given": "Gabriel" }, "orcid": "0000-0002-6941-3060" }, { "id": "Choe-Bianca-Judy", "name": { "family": "Choe", "given": "Bianca Judy" } }, { "id": "Chandrasekaran-Sukantha", "name": { "family": "Chandrasekaran", "given": "Sukantha" }, "orcid": "0000-0002-6232-5535" }, { "id": "Hilt-Evann-E", "name": { "family": "Hilt", "given": "Evann E." } }, { "id": "Butte-Manish-J", "name": { "family": "Butte", "given": "Manish J." }, "orcid": "0000-0002-4490-5595" }, { "id": "Damoiseaux-Robert", "name": { "family": "Damoiseaux", "given": "Robert" }, "orcid": "0000-0002-7611-7534" }, { "id": "Kravit-Clifford", "name": { "family": "Kravit", "given": "Clifford" }, "orcid": "0000-0002-0624-5514" }, { "id": "Cooper-Aaron-R", "name": { "family": "Cooper", "given": "Aaron R." }, "orcid": "0000-0003-4588-2513" }, { "id": "Yin-Yi", "name": { "family": "Yin", "given": "Yi" }, "orcid": "0000-0003-0963-2672" }, { "id": "Pachter-L", "name": { "family": "Pachter", "given": "Lior" }, "orcid": "0000-0002-9164-6231" }, { "id": "Garner-Omai-B", "name": { "family": "Garner", "given": "Omai B." }, "orcid": "0000-0002-7366-2692" }, { "id": "Flint-Jonathan", "name": { "family": "Flint", "given": "Jonathan" }, "orcid": "0000-0002-9427-4429" }, { "id": "Eskin-Eleazar", "name": { "family": "Eskin", "given": "Eleazar" }, "orcid": "0000-0003-1149-4758" }, { "id": "Luo-Chongyuan", "name": { "family": "Luo", "given": "Chongyuan" }, "orcid": "0000-0002-8541-0695" }, { "id": "Kosuri-Sriram", "name": { "family": "Kosuri", "given": "Sriram" }, "orcid": "0000-0002-4661-0600" }, { "id": "Kruglyak-Leonid", "name": { "family": "Kruglyak", "given": "Leonid" }, "orcid": "0000-0002-8065-3057" }, { "id": "Arboleda-Valerie-A", "name": { "family": "Arboleda", "given": "Valerie A." }, "orcid": "0000-0002-9687-9122" } ] }, "title": "Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Nature Publishing Group. \n\nReceived 20 November 2020; Accepted 20 May 2021; Published 01 July 2021. \n\nWe thank J. Semel for her support. We also thank the staff at the Held Foundation and the Carol Moss Foundation for their support of this project; staff at the UCLA David Geffen School of Medicine's Dean's Office for their support; Fast Grants Inc. for funding this work; L. Starita, B. Martin, J. Gehring, S. Srivatsan, J. Shendure and the members of the Covid Testing Scaleup Slack for their input, guidance and openness in sharing their processes; M. Berro for her guidance with the FDA EUA201963; the clinical laboratory scientists at the UCLA Clinical Microbiology laboratory for their assistance in collecting and processing the remnant specimens and data; our staff at the UCLA SwabSeq COVID19 Testing laboratory for deploying our CLIA test; and L. Yost and A. Martin for their advice and guidance during our scaling process. This work was supported by funding from the Howard Hughes Medical Institute (to L.K.) and DP5OD024579 (to V.A.A.). I.L. is supported by T32GM008042. Figures 1a,f and 3b created with BioRender.com. \n\nData availability: The main data supporting the results in this study are available within the paper and its Supplementary Information. Source data for all figures are available at GitHub (https://github.com/joshsbloom/swabseq). All protocols and primers are available under an Open COVID License online (https://www.notion.so/Octant-COVID-License-816b04b442674433a2a58bff2d8288df). Videos of the workflow for SwabSeq assay are available at Figshare (https://figshare.com/projects/Additional_SwabSeq_Data/113643). \n\nCode availability: All code can be accessed at GitHub (https://github.com/joshsbloom/swabseq). An R package to automate the diagnosis of patient samples is available at GitHub (https://github.com/joshsbloom/swabseqr). Codes for primer design and for the analysis of cross-reactivity can be found at GitHub (https://github.com/octantbio/SwabSeq). The core technology has been made available under the Open COVID Pledge, and software and data under the MIT license (UCLA) and Apache 2.0 license (Octant). \n\nAuthor Contributions: J.S.B. and V.A.A. wrote the manuscript with assistance from C.L., J.F., L.K., E.E., E.M.J., A.R.C., N.B.L., M.G. and S.Kosuri. E.M.J., A.R.C., N.B.L., M.G., S.W.S., J.S.B. and S.Kosuri designed barcodes and performed early testing and analysis of protocols and reagents. C.L., Y.Y., Y.Z., L.G., R.D. and M.J.B. provided early guidance and key automation resources. E.E., D.H., N.L. and C.K. developed the registration webapp and IT infrastructure. L.S., C.M., M.G., E.M.J., N.B.L., S.Kosuri, I.L., O.F.B., V.A.A. and J.S.B. performed and analysed experiments. A.S.B. and L.P. analysed misassignment of index barcodes. V.A.A., O.B.G., S.C., E.E.H., G.O. and B.J.C. collected and processed clinical samples. D.M. optimized operational protocols and D.M., S.Kay, M.L., T.L. and E.E. optimized scale up. E.E., L.K., J.F., C.L., Y.Y., Y.Z. and J.B. provided helpful insights into protocols, software, and development and optimization of our specimen collection and handling. F.Y., E.M.T., K.M.K., J.P. and M.H. developed the diversified S standard mixture, N1 primers and flu primers. \n\nCompeting interests: E.M.J., M.G., N.B.L., S.W.S., F.Y., E.M.T., K.M.K., J.P. and S.Kosuri are employed by and hold equity in Octant Inc., J.S.B. consults for and holds equity in Octant Inc., and A.R.C. holds equity in Octant Inc, which initially developed SwabSeq and has filed for patents for some of the work here, although they have been made available under the Open COVID License (https://www.notion.so/Octant-COVID-License-816b04b442674433a2a58bff2d8288df). \n\nPeer review information: Nature Biomedical Engineering thanks Enzo Poirier and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.\n\nSubmitted - 2020.08.04.20167874v4.full.pdf
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", "abstract": "Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24\u2009h. SwabSeq could be rapidly adapted for the detection of other pathogens.", "date": "2021-07", "date_type": "published", "publication": "Nature Biomedical Engineering", "volume": "5", "number": "7", "publisher": "Nature Publishing Group", "pagerange": "657-665", "id_number": "CaltechAUTHORS:20201119-132151980", "issn": "2157-846X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201119-132151980", "funders": { "items": [ { "agency": "Held Foundation" }, { "agency": "Carol Moss Foundation" }, { "agency": "UCLA" }, { "agency": "Fast Grants, Inc." }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "DP5OD024579" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM008042" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41551-021-00754-5", "pmcid": "PMC7480060", "primary_object": { "basename": "nihms-1957064.pdf", "url": "https://authors.library.caltech.edu/records/05kjw-6t056/files/nihms-1957064.pdf" }, "related_objects": [ { "basename": "41551_2021_754_MOESM6_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/05kjw-6t056/files/41551_2021_754_MOESM6_ESM.xlsx" }, { "basename": "41551_2021_754_MOESM7_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/05kjw-6t056/files/41551_2021_754_MOESM7_ESM.xlsx" }, { "basename": "41551_2021_754_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/05kjw-6t056/files/41551_2021_754_MOESM1_ESM.pdf" }, { "basename": "41551_2021_754_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/05kjw-6t056/files/41551_2021_754_MOESM2_ESM.pdf" }, { "basename": "41551_2021_754_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/05kjw-6t056/files/41551_2021_754_MOESM3_ESM.xlsx" }, { "basename": "41551_2021_754_MOESM4_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/05kjw-6t056/files/41551_2021_754_MOESM4_ESM.xlsx" }, { "basename": "41551_2021_754_MOESM5_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/05kjw-6t056/files/41551_2021_754_MOESM5_ESM.xlsx" } ], "pub_year": "2021", "author_list": "Bloom, Joshua S.; Sathe, Laila; et al." }, { "id": "https://authors.library.caltech.edu/records/3wp5f-r5g69", "eprint_id": 108681, "eprint_status": "archive", "datestamp": "2023-08-20 03:56:41", "lastmod": "2026-03-30 08:46:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bulchandani-Vir-Bannerjee", "name": { "family": "Bulchandani", "given": "Vir Bannerjee" }, "orcid": "0000-0002-7438-5711" }, { "id": "Shivam-Saumya", "name": { "family": "Shivam", "given": "Saumya" }, "orcid": "0000-0002-7957-153X" }, { "id": "Moudgalya-Sanjay", "name": { "family": "Moudgalya", "given": "Sanjay" } }, { "id": "Sondhi-Shivaji-L", "name": { "family": "Sondhi", "given": "S. L." } } ] }, "title": "Digital herd immunity and COVID-19", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 IOP Publishing Ltd. \n\nReceived 26 February 2021; Revised 23 March 2021; Accepted 7 April 2021; Published 23 June 2021. \n\nWe would like to thank Professor K. VijayRaghavan for interesting us in this question and for discussions of India's Aarogya Setu contact tracing app, Professor Bryan Grenfell for sharing his wisdom regarding epidemiology at an extremely hectic time and Dr. Shoibal Chakravarty for continuing discussions on all aspect of India's COVID-19 challenges.\n\nSubmitted - 2020.04.15.20066720v1.full.pdf
", "abstract": "A population can be immune to epidemics even if not all of its individual members are immune to the disease, so long as sufficiently many are immune\u2014this is the traditional notion of herd immunity. In the smartphone era a population can be immune to epidemics even if not a single one of its members is immune to the disease\u2014a notion we call \"digital herd immunity'', which is similarly an emergent characteristic of the population. This immunity arises because contact-tracing protocols based on smartphone capabilities can lead to highly efficient quarantining of infected population members and thus the extinguishing of nascent epidemics. When the disease characteristics are favorable and smartphone usage is high enough, the population is in this immune phase. As usage decreases there is a novel \"contact-tracing phase transition'' to an epidemic phase. We present and study a simple branching-process model for COVID-19 and show that digital immunity is possible regardless of the proportion of non-symptomatic transmission.", "date": "2021-07", "date_type": "published", "publication": "Physical Biology", "volume": "18", "number": "4", "publisher": "IOP", "pagerange": "Art. No. 045004", "id_number": "CaltechAUTHORS:20210409-145940364", "issn": "1478-3967", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210409-145940364", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1088/1478-3975/abf5b4", "primary_object": { "basename": "2020.04.15.20066720v1.full.pdf", "url": "https://authors.library.caltech.edu/records/3wp5f-r5g69/files/2020.04.15.20066720v1.full.pdf" }, "pub_year": "2021", "author_list": "Bulchandani, Vir Bannerjee; Shivam, Saumya; et al." }, { "id": "https://authors.library.caltech.edu/records/dxhed-gjf51", "eprint_id": 109562, "eprint_status": "archive", "datestamp": "2023-08-22 10:16:37", "lastmod": "2026-03-30 08:56:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yang-Jiani", "name": { "family": "Yang", "given": "Jiani" }, "orcid": "0000-0003-0037-2413" }, { "id": "Wen-Yifan", "name": { "family": "Wen", "given": "Yifan" }, "orcid": "0000-0003-1876-7990" }, { "id": "Wang-Yuan", "name": { "family": "Wang", "given": "Yuan" }, "orcid": "0000-0001-6657-8401" }, { "id": "Zhang-Shaojun", "name": { "family": "Zhang", "given": "Shaojun" }, "orcid": "0000-0002-2176-6174" }, { "id": "Pinto-Joseph-P", "name": { "family": "Pinto", "given": "Joseph P." }, "orcid": "0000-0001-5639-8458" }, { "id": "Pennington-Elyse-A", "name": { "family": "Pennington", "given": "Elyse A." }, "orcid": "0000-0003-1736-2342" }, { "id": "Wang-Zhou", "name": { "family": "Wang", "given": "Zhou" } }, { "id": "Wu-Ye", "name": { "family": "Wu", "given": "Ye" }, "orcid": "0000-0002-9928-1177" }, { "id": "Sander-Stanley-P", "name": { "family": "Sander", "given": "Stanley P." }, "orcid": "0000-0003-1424-3620" }, { "id": "Jiang-Jonathan-H", "name": { "family": "Jiang", "given": "Jonathan H." }, "orcid": "0000-0002-5929-8951" }, { "id": "Hao-Jiming", "name": { "family": "Hao", "given": "Jiming" } }, { "id": "Yung-Y-L", "name": { "family": "Yung", "given": "Yuk L." }, "orcid": "0000-0002-4263-2562" }, { "id": "Seinfeld-J-H", "name": { "family": "Seinfeld", "given": "John H." }, "orcid": "0000-0003-1344-4068" } ] }, "title": "From COVID-19 to future electrification: Assessing traffic impacts on air quality by a machine-learning model", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; machine learning; air pollution; traffic emissions; vehicular electrification", "note": "\u00a9 2021 National Academy of Sciences. Published under the PNAS license. \n\nContributed by John H. Seinfeld, May 3, 2021 (sent for review February 12, 2021; reviewed by Russell R. Dickerson and Alma Hodzic). \n\nY. Wang, S.P.S., J.H.J., and Y.L.Y. acknowledge support by the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. E.A.P. and J.H.S. acknowledge support by the Samsung Corporation (award SAMS.2019GRO). S.Z. acknowledges support by the National Key Research and Development Program of China (grant 2017YFC0212100), the National Natural Science Foundation of China (grant 41977180), and Ford Motor Company. J.Y. acknowledges Leo Gallagher and Daniel Kitowski at the California Department of Transportation, Thomas E. Morrell at the Caltech Library, Jin Tao for helpful information on data inputs, and Yu Zhou at Tsinghua University for useful discussions. \n\nData Availability: All study data are included in the article and/or SI Appendix. \n\nJ.Y. and Y.W. contributed equally to this work. \n\nAuthor contributions: J.Y., Y. Wang, S.Z., and J.H.S. designed research; J.Y., Y. Wen, Y. Wang, and S.Z. performed research; J.Y., Y. Wen, Y. Wang, S.Z., J.P.P., E.A.P., Z.W., Y. Wu, S.P.S., J.H.J., J.H., Y.L.Y., and J.H.S. analyzed data; J.Y., Y. Wen, and S.Z. developed the RF model; and J.Y., Y. Wen, Y. Wang, S.Z., and J.H.S. wrote the paper. \n\nReviewers: R.R.D., University of Maryland, College Park; and A.H., National Center for Atmospheric Research. \n\nThe authors declare no competing interest. \n\nThis article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2102705118/-/DCSupplemental.\n\nPublished - e2102705118.full.pdf
Supplemental Material - pnas.2102705118.sapp.pdf
", "abstract": "The large fluctuations in traffic during the COVID-19 pandemic provide an unparalleled opportunity to assess vehicle emission control efficacy. Here we develop a random-forest regression model, based on the large volume of real-time observational data during COVID-19, to predict surface-level NO\u2082, O\u2083, and fine particle concentration in the Los Angeles megacity. Our model exhibits high fidelity in reproducing pollutant concentrations in the Los Angeles Basin and identifies major factors controlling each species. During the strictest lockdown period, traffic reduction led to decreases in NO\u2082 and particulate matter with aerodynamic diameters <2.5 \u03bcm by \u201330.1% and \u201317.5%, respectively, but a 5.7% increase in O\u2083. Heavy-duty truck emissions contribute primarily to these variations. Future traffic-emission controls are estimated to impose similar effects as observed during the COVID-19 lockdown, but with smaller magnitude. Vehicular electrification will achieve further alleviation of NO\u2082 levels.", "date": "2021-06-29", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences", "volume": "118", "number": "26", "publisher": "National Academy of Sciences", "pagerange": "Art. No. e2102705118", "id_number": "CaltechAUTHORS:20210623-180037244", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210623-180037244", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NASA/JPL/Caltech" }, { "agency": "Samsung Corporation", "grant_number": "SAMS.2019GRO" }, { "agency": "National Key Research and Development Program of China", "grant_number": "2017YFC0212100" }, { "agency": "National Natural Science Foundation of China", "grant_number": "41977180" }, { "agency": "Ford Motor Company" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1073/pnas.2102705118", "pmcid": "PMC8256029", "primary_object": { "basename": "e2102705118.full.pdf", "url": "https://authors.library.caltech.edu/records/dxhed-gjf51/files/e2102705118.full.pdf" }, "related_objects": [ { "basename": "pnas.2102705118.sapp.pdf", "url": "https://authors.library.caltech.edu/records/dxhed-gjf51/files/pnas.2102705118.sapp.pdf" } ], "pub_year": "2021", "author_list": "Yang, Jiani; Wen, Yifan; et al." }, { "id": "https://authors.library.caltech.edu/records/9y8gm-q5c37", "eprint_id": 109697, "eprint_status": "archive", "datestamp": "2023-08-22 10:15:43", "lastmod": "2026-03-30 06:33:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yan-Liming", "name": { "family": "Yan", "given": "Liming" } }, { "id": "Yang-Yunxiang", "name": { "family": "Yang", "given": "Yunxiang" } }, { "id": "Li-Mingyu", "name": { "family": "Li", "given": "Mingyu" } }, { "id": "Zhang-Ying", "name": { "family": "Zhang", "given": "Ying" } }, { "id": "Zheng-Litao", "name": { "family": "Zheng", "given": "Litao" } }, { "id": "Ge-Jin", "name": { "family": "Ge", "given": "Jin" } }, { "id": "Huang-Yucen-C", "name": { "family": "Huang", "given": "Yucen C." } }, { "id": "Liu-Zhenyu", "name": { "family": "Liu", "given": "Zhenyu" } }, { "id": "Wang-Tao", "name": { "family": "Wang", "given": "Tao" } }, { "id": "Gao-Shan", "name": { "family": "Gao", "given": "Shan" } }, { "id": "Zhang-Ran", "name": { "family": "Zhang", "given": "Ran" } }, { "id": "Huang-Yuanyun-Y", "name": { "family": "Huang", "given": "Yuanyun Y." } }, { "id": "Guddat-Luke-W", "name": { "family": "Guddat", "given": "Luke W." } }, { "id": "Gao-Yan", "name": { "family": "Gao", "given": "Yan" } }, { "id": "Rao-Zihe", "name": { "family": "Rao", "given": "Zihe" } }, { "id": "Lou-Zhiyong", "name": { "family": "Lou", "given": "Zhiyong" } } ] }, "title": "Coupling of N7-methyltransferase and 3\u2032-5\u2032 exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading", "ispublished": "pub", "full_text_status": "public", "keywords": "SARS-CoV-2; replication-transcription complex; mRNA capping; proofreading; cryo-EM", "note": "\u00a9 2021 Elsevier Inc.\n\nReceived 1 April 2021, Revised 20 April 2021, Accepted 19 May 2021, Available online 24 May 2021.\n\nThis work was supported by the National Natural Science Foundation of China (U20A20135), the National Program on Key Research Project of China (2020YFA0707500 and 2017YFC0840300), Tsinghua University Spring Breeze Fund (2020Z99CFG015), and the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB37030201).\n\nAuthor contributions:\nZ.R. and Z. Lou conceived the project and designed the experiments. L.Y., Y.Y., M.L., J.G., Y.C.H., L.Z., Y.Z., S.G., Y.Y.H., and R.Z. performed sample purification, and L.Y. prepared for RTC assembly. L.Y., Y.Y., and Y.Z. for sample native electrophoretic mobility shift assays. Y.G., Z. Liu, and T.W. collected cryo-EM data. L.Y., Z. Lou, and Z.R. analyzed the data. Z.R., Z. Lou, L.Y., and L.W.G. wrote the manuscript. All authors discussed the experiments, read, and approved the manuscript.\n\nThe authors declare no competing interests.\n\nPublished - main.pdf
Supplemental Material - 1-s2.0-S0092867421006632-mmc1.pdf
Supplemental Material - 1-s2.0-S0092867421006632-mmc2.mp4
", "abstract": "The capping of mRNA and the proofreading play essential roles in SARS-CoV-2 replication and transcription. Here, we present the cryo-EM structure of the SARS-CoV-2 replication-transcription complex (RTC) in a form identified as Cap(0)-RTC, which couples a co-transcriptional capping complex (CCC) composed of nsp12 NiRAN, nsp9, the bifunctional nsp14 possessing an N-terminal exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), and nsp10 as a cofactor of nsp14. Nsp9 and nsp12 NiRAN recruit nsp10/nsp14 into the Cap(0)-RTC, forming the N7-CCC to yield cap(0) (^(7Me)GpppA) at 5\u2032 end of pre-mRNA. A dimeric form of Cap(0)-RTC observed by cryo-EM suggests an in trans backtracking mechanism for nsp14 ExoN to facilitate proofreading of the RNA in concert with polymerase nsp12. These results not only provide a structural basis for understanding co-transcriptional modification of SARS-CoV-2 mRNA but also shed light on how replication fidelity in SARS-CoV-2 is maintained.", "date": "2021-06-24", "date_type": "published", "publication": "Cell", "volume": "184", "number": "13", "publisher": "Cell Press", "pagerange": "3474-3485", "id_number": "CaltechAUTHORS:20210701-155032256", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210701-155032256", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Natural Science Foundation of China", "grant_number": "U20A20135" }, { "agency": "National Program on Key Research Project of China", "grant_number": "2020YFA0707500" }, { "agency": "National Program on Key Research Project of China", "grant_number": "2017YFC0840300" }, { "agency": "Tsinghua University", "grant_number": "2020Z99CFG015" }, { "agency": "Chinese Academy of Sciences", "grant_number": "XDB37030201" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.cell.2021.05.033", "pmcid": "PMC8142856", "primary_object": { "basename": "1-s2.0-S0092867421006632-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/9y8gm-q5c37/files/1-s2.0-S0092867421006632-mmc1.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0092867421006632-mmc2.mp4", "url": "https://authors.library.caltech.edu/records/9y8gm-q5c37/files/1-s2.0-S0092867421006632-mmc2.mp4" }, { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/9y8gm-q5c37/files/main.pdf" } ], "pub_year": "2021", "author_list": "Yan, Liming; Yang, Yunxiang; et al." }, { "id": "https://authors.library.caltech.edu/records/z9b4x-mah61", "eprint_id": 106731, "eprint_status": "archive", "datestamp": "2023-08-22 10:14:55", "lastmod": "2026-03-30 05:41:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sender-Ron", "name": { "family": "Sender", "given": "Ron" }, "orcid": "0000-0002-1165-9818" }, { "id": "Bar-On-Yinon-M", "name": { "family": "Bar-On", "given": "Yinon M." }, "orcid": "0000-0001-8477-609X" }, { "id": "Gleizer-Shmuel", "name": { "family": "Gleizer", "given": "Shmuel" }, "orcid": "0000-0001-9774-0504" }, { "id": "Bernsthein-Biana", "name": { "family": "Bernsthein", "given": "Biana" }, "orcid": "0000-0002-7957-2575" }, { "id": "Flamholz-Avi", "name": { "family": "Flamholz", "given": "Avi" }, "orcid": "0000-0002-9278-5479" }, { "id": "Phillips-R", "name": { "family": "Phillips", "given": "Rob" }, "orcid": "0000-0003-3082-2809" }, { "id": "Milo-Ron", "name": { "family": "Milo", "given": "Ron" }, "orcid": "0000-0003-1641-2299" } ] }, "title": "The total number and mass of SARS-CoV-2 virions", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; variants of concern; viral biomass; viral load; genetic diversity", "note": "\u00a9 2021 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY). \n\nEdited by Ken A. Dill, Stony Brook University, Stony Brook, NY, and approved May 10, 2021 (received for review December 13, 2020). \n\nWe thank Itai Benhar, Gidon Eshel, Shai Fuchs, Thierry Mora, Eran Segal, Maya Shamir, Ziv Shulman, Huicheng Shi, Harinder Singh, Einat Vitner, Aleksandra Walczak, and John Yin for valuable feedback on this manuscript. This research was supported by the European Research Council (Project NOVCARBFIX 646827), Israel Science Foundation (Grant 740/16), Beck-Canadian Center for Alternative Energy Research, Dana and Yossie Hollander, Ullmann Family Foundation, Helmsley Charitable Foundation, Larson Charitable Foundation, Wolfson Family Charitable Trust, Charles Rothschild, Selmo Nussenbaum, Miel de Botton (R.M.), the NIH (1R35 GM118043-01 [Maximizing Investigators' Research Award]) (R.P.), Merkin Institute for Translational Research (R.P.), the Israeli Council for Higher Education via the Weizmann Data Science Research Center, and by a research grant from Madame Olga Klein \u2013 Astrachan (R.S.). R.M. is the Charles and Louise Gartner Professional Chair. Y.M.B.-O. is an Azrieli Fellow. \n\nData Availability: All study data are included in the article, SI Appendix, and Dataset S1. \n\nR.S. and Y.M.B.-O. contributed equally to this work. \n\nAuthor contributions: R.S., Y.M.B.-O., R.P., and R.M. designed research; R.S., Y.M.B.-O., S.G., B.B., A.F., R.P., and R.M. performed research; R.S., Y.M.B.-O., S.G., B.B., A.F., R.P., and R.M. analyzed data; and R.S., Y.M.B.-O., S.G., B.B., A.F., R.P., and R.M. wrote the paper. \n\nThe authors declare no competing interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2024815118/-/DCSupplemental.\n\nPublished - e2024815118.full.pdf
Submitted - 2020.11.16.20232009v2.full.pdf
Supplemental Material - pnas.2024815118.sapp.pdf
Supplemental Material - pnas.2024815118.sd01.xlsx
", "abstract": "Quantitatively describing the time course of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection within an infected individual is important for understanding the current global pandemic and possible ways to combat it. Here we integrate the best current knowledge about the typical viral load of SARS-CoV-2 in bodily fluids and host tissues to estimate the total number and mass of SARS-CoV-2 virions in an infected person. We estimate that each infected person carries 109 to 1011 virions during peak infection, with a total mass in the range of 1 \u03bcg to 100 \u03bcg, which curiously implies that all SARS-CoV-2 virions currently circulating within human hosts have a collective mass of only 0.1 kg to 10 kg. We combine our estimates with the available literature on host immune response and viral mutation rates to demonstrate how antibodies markedly outnumber the spike proteins, and the genetic diversity of virions in an infected host covers all possible single nucleotide substitutions.", "date": "2021-06-22", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "118", "number": "25", "publisher": "National Academy of Sciences", "pagerange": "Art. No. e2024815118", "id_number": "CaltechAUTHORS:20201118-151353187", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201118-151353187", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "European Research Council (ERC)", "grant_number": "646827" }, { "agency": "Israel Science Foundation", "grant_number": "740/16" }, { "agency": "Beck-Canadian Center for Alternative Energy Research" }, { "agency": "Dana and Yossie Hollander" }, { "agency": "Ullmann Family Foundation" }, { "agency": "Helmsley Charitable Foundation" }, { "agency": "Larson Charitable Foundation" }, { "agency": "Wolfson Family Charitable Trust" }, { "agency": "Charles Rothschild" }, { "agency": "Selmo Nussenbaum" }, { "agency": "Miel de Botton" }, { "agency": "NIH", "grant_number": "1R35 GM118043-01" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "Council for Higher Education (Israel)" }, { "agency": "Weizmann Institute of Science" }, { "agency": "Madame Olga Klein" }, { "agency": "Charles and Louise Gartner Professional Chair" }, { "agency": "Azrieli Fellowship" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1073/pnas.2024815118", "pmcid": "PMC8237675", "primary_object": { "basename": "pnas.2024815118.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/z9b4x-mah61/files/pnas.2024815118.sd01.xlsx" }, "related_objects": [ { "basename": "2020.11.16.20232009v2.full.pdf", "url": "https://authors.library.caltech.edu/records/z9b4x-mah61/files/2020.11.16.20232009v2.full.pdf" }, { "basename": "e2024815118.full.pdf", "url": "https://authors.library.caltech.edu/records/z9b4x-mah61/files/e2024815118.full.pdf" }, { "basename": "pnas.2024815118.sapp.pdf", "url": "https://authors.library.caltech.edu/records/z9b4x-mah61/files/pnas.2024815118.sapp.pdf" } ], "pub_year": "2021", "author_list": "Sender, Ron; Bar-On, Yinon M.; et al." }, { "id": "https://authors.library.caltech.edu/records/0z200-msz38", "eprint_id": 107253, "eprint_status": "archive", "datestamp": "2023-08-22 10:10:46", "lastmod": "2026-03-29 18:27:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hoffmann-Magnus-A-G", "name": { "family": "Hoffmann", "given": "Magnus A. G." }, "orcid": "0000-0003-4923-9568" }, { "id": "Kieffer-Collin", "name": { "family": "Kieffer", "given": "Collin" }, "orcid": "0000-0001-9051-3819" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "In vitro characterization of engineered red blood cells as viral traps against HIV-1 and SARS-CoV-2", "ispublished": "pub", "full_text_status": "public", "keywords": "Engineered red blood cells; anti-viral therapeutics; HIV-1; SARS-CoV-2", "note": "\u00a9 2021 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).\n\nReceived 31 December 2020, Accepted 6 March 2021, Available online 10 March 2021.\n\nWe thank N.J. Huang, N. Pishesha, and H.F. Lodish for helpful discussion, advice, and reagents; P.N.P. Gnanapragasam and L.M. Kakutani for producing SARS-CoV-2 pseudovirus and setting up the SARS-CoV-2 pseudovirus neutralization assay in our laboratory; G.L. Chadwick, R. Galimidi, and A. Moradian (formerly Caltech Proteome Exploration Laboratory) for helpful discussions and reagents; G. Spigolon for guidance with light microscopy performed at the Beckman Institute Biological Imaging Facility; Z. Romero-Garcia and D.B. Kohn for the pCCL-AS3-FB plasmid; J. Voetteler and W.I. Sundquist for the CCF2-AM reagent; J.D. Bloom for 293T-ACE2 cells and plasmids for generating SARS-CoV-2 pseudovirus; and the NIH AIDS Reagent Program for reagents. BEL-A2 cell lines were created by Professor Jan Frayne, Professor David Anstee and Dr Kongtana Trakarnsanga with funding from the Wellcome Trust (grant numbers 087430/Z/08 and 102610), NHS Blood and Transplant and Department of Health (England) and were kindly provided by J. Frayne. This work was supported by the Bill and Melinda Gates Foundation grant OPP1202246, the DeLogi Trust (facilitated by Caltech), and by a generous gift from Kairos Ventures (facilitated by Caltech).\n\nAuthor contributions:\nM.A.G.H. and P.J.B. designed the research, M.A.G.H. and C.K. performed the research, M.A.G.H. and P.J.B. analyzed data, and M.A.G.H. and P.J.B. wrote the manuscript.\n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S2329050121000437-main.pdf
Submitted - 2020.12.20.423607v1.full.pdf
Supplemental Material - 1-s2.0-S2329050121000437-mmc1.pdf
", "abstract": "Engineered red blood cells (RBCs) expressing viral receptors could be used therapeutically as viral traps, as RBCs lack nuclei and other organelles required for viral replication. However, expression of viral receptors on RBCs is difficult to achieve since mature erythrocytes lack the cellular machinery to synthesize proteins. Herein, we show that the combination of a powerful erythroid-specific expression system and transgene codon optimization yields high expression levels of the HIV-1 receptors CD4 and CCR5, as well as a CD4-glycophorin A (CD4-GpA) fusion protein in erythroid progenitor cells, which efficiently differentiated into enucleated RBCs. HIV-1 efficiently entered RBCs that co-expressed CD4 and CCR5, but viral entry was not required for neutralization, as CD4 or CD4-GpA expression in the absence of CCR5 was sufficient to potently neutralize HIV-1 and prevent infection of CD4+ T cells in vitro due to the formation of high-avidity interactions with trimeric HIV-1 Env spikes on virions. To facilitate continuous large-scale production of RBC viral traps, we generated erythroblast cell lines stably expressing CD4-GpA or ACE2-GpA fusion proteins, which produced potent RBC viral traps against HIV-1 and SARS-CoV-2. Our in vitro results suggest that this approach warrants further investigation as a potential treatment against acute and chronic viral infections.", "date": "2021-06-11", "date_type": "published", "publication": "Molecular Therapy - Methods and Clinical Development", "volume": "21", "publisher": "Cell Press", "pagerange": "161-170", "id_number": "CaltechAUTHORS:20201222-101000542", "issn": "2329-0501", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201222-101000542", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Wellcome Trust", "grant_number": "087430/Z/08" }, { "agency": "Wellcome Trust", "grant_number": "102610" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "OPP1202246" }, { "agency": "Caltech De Logi Fund" }, { "agency": "Kairos Ventures" }, { "agency": "NIH" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.omtm.2021.03.003", "pmcid": "PMC7944778", "primary_object": { "basename": "2020.12.20.423607v1.full.pdf", "url": "https://authors.library.caltech.edu/records/0z200-msz38/files/2020.12.20.423607v1.full.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2329050121000437-main.pdf", "url": "https://authors.library.caltech.edu/records/0z200-msz38/files/1-s2.0-S2329050121000437-main.pdf" }, { "basename": "1-s2.0-S2329050121000437-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/0z200-msz38/files/1-s2.0-S2329050121000437-mmc1.pdf" } ], "pub_year": "2021", "author_list": "Hoffmann, Magnus A. G.; Kieffer, Collin; et al." }, { "id": "https://authors.library.caltech.edu/records/jnt7a-0x473", "eprint_id": 108862, "eprint_status": "archive", "datestamp": "2023-10-03 22:42:18", "lastmod": "2026-03-30 05:32:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Scheid-Johannes-F", "name": { "family": "Scheid", "given": "Johannes F." } }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "name": { "family": "Eraslan", "given": "Basak" }, "orcid": "0000-0003-3698-8279" }, { "name": { "family": "Hudak", "given": "Andrew" }, "orcid": "0000-0002-0241-2290" }, { "id": "Keeffe-Jennifer-R", "name": { "family": "Keeffe", "given": "Jennifer R." }, "orcid": "0000-0002-5317-6398" }, { "name": { "family": "Cosimi", "given": "Lisa A." }, "orcid": "0000-0002-5269-1881" }, { "name": { "family": "Brown", "given": "Eric M." } }, { "name": { "family": "Muecksch", "given": "Frauke" }, "orcid": "0000-0002-0132-5101" }, { "name": { "family": "Weisblum", "given": "Yiska" }, "orcid": "0000-0002-9249-1745" }, { "name": { "family": "Zhang", "given": "Shuting" } }, { "name": { "family": "Delorey", "given": "Toni" }, "orcid": "0000-0001-6614-3803" }, { "name": { "family": "Woolley", "given": "Ann E." }, "orcid": "0000-0002-2810-1618" }, { "name": { "family": "Ghantous", "given": "Fadi" }, "orcid": "0000-0002-6772-6901" }, { "name": { "family": "Park", "given": "Sung-Moo" }, "orcid": "0000-0002-7505-1617" }, { "name": { "family": "Phillips", "given": "Devan" }, "orcid": "0000-0002-9240-4912" }, { "name": { "family": "Tusi", "given": "Betsabeh" }, "orcid": "0000-0001-7072-2162" }, { "id": "Huey-Tubman-Kathryn-E", "name": { "family": "Huey-Tubman", "given": "Kathryn E." }, "orcid": "0000-0002-4683-8138" }, { "id": "Cohen-Alexander-A", "name": { "family": "Cohen", "given": "Alexander A." }, "orcid": "0000-0002-2818-656X" }, { "id": "Gnanapragasam-Priyanthi-N-P", "name": { "family": "Gnanapragasam", "given": "Priyanthi N. P." } }, { "name": { "family": "Rzasa", "given": "Kara" }, "orcid": "0000-0002-5753-7517" }, { "name": { "family": "Hatziioannou", "given": "Theodora" }, "orcid": "0000-0002-7889-0766" }, { "name": { "family": "Durney", "given": "Michael A." } }, { "name": { "family": "Gu", "given": "Xiebin" }, "orcid": "0000-0003-2626-3733" }, { "name": { "family": "Tada", "given": "Takuya" }, "orcid": "0000-0003-0779-9954" }, { "name": { "family": "Landau", "given": "Nathaniel R." }, "orcid": "0000-0002-9997-1004" }, { "id": "West-Anthony-P-Jr", "name": { "family": "West", "given": "Anthony P., Jr." }, "orcid": "0000-0003-4213-5184" }, { "name": { "family": "Rozenblatt-Rosen", "given": "Orit" }, "orcid": "0000-0001-6313-3570" }, { "name": { "family": "Seaman", "given": "Michael S." }, "orcid": "0000-0001-6444-3562" }, { "name": { "family": "Baden", "given": "Lindsey R." } }, { "name": { "family": "Graham", "given": "Daniel B." }, "orcid": "0000-0002-8403-8115" }, { "name": { "family": "Deguine", "given": "Jacques" }, "orcid": "0000-0001-9218-3040" }, { "name": { "family": "Bieniasz", "given": "Paul D." }, "orcid": "0000-0002-2368-3719" }, { "name": { "family": "Regev", "given": "Aviv" }, "orcid": "0000-0003-3293-3158" }, { "name": { "family": "Hung", "given": "Deborah" }, "orcid": "0000-0003-4262-0673" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Xavier", "given": "Ramnik J." }, "orcid": "0000-0002-5630-5167" } ] }, "title": "B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV", "ispublished": "pub", "full_text_status": "public", "keywords": "single B cell genomics; COVID-19; monoclonal antibodies; SARS-CoV cross-neutralization; memory B cells; cryo-electron microscopy; disordered CDRH3", "note": "\u00a9 2021 Elsevier Inc. \n\nReceived 18 December 2020, Revised 26 February 2021, Accepted 19 April 2021, Available online 24 April 2021. \n\nWe thank all study participants who devoted time to our research and the clinical staff. We thank Heather Kang for editorial assistance with the manuscript and figures. We thank the Biogen, Broad Institute of MIT and Harvard, and Partners HealthCare COVID-19 biobank for support with patient samples. We thank members of the Bjorkman, Xavier, and Bieniasz laboratories for helpful discussions. We thank Liat Amir-Zilberstein and Novalia Pishesha for support with sample processing and Christy Lavine (BIDMC) for assistance with pseudovirus assays. We thank Harry Gristick (Caltech) for technical assistance with SPR binding experiments and Kawther Abu Elneel and Jenna Pfiffner-Borges for arranging and coordinating laboratory space during the COVID-19 pandemic. We thank Patricia Rogers and Natan Pirete (Broad Institute) for support with cell sorting, Reuben Ryan Cano (Broad Institute) for help with size exclusion chromatography, and the Nussenzweig laboratory (Rockefeller University) for providing plasmids for mAbs mGO53, JB40, and ED38. We thank Pauline Hoffman, Leesa Kakutani, Yu (Erica) Lee, Jost Vielmetter, and the Caltech Beckman Institute Protein Expression Center for expression and purification of antigens and support for automated assays and Drs. Songye Chen and Andrey Malyutin (Caltech) for maintaining electron microscopes. Cell sorting was performed at the Flow Cytometry Facility of the Broad Institute, sequencing of pre-constructed DNA libraries was performed at the Genomics Platform (Broad Institute), and electron microscopy was performed in the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support the Molecular Observatory (Dr. Jens Kaiser, director) and Drs. Silvia Russi, Aina Cohen, and Clyde Smith and the beamline staff at SSRL for data collection assistance. This work was supported by NIH (P01-AI138398-S1 and P50 8 P50 AI150464-13 to P.J.B.; DK43351 and U19 AI142784 to R.J.X.; and DA046100, AI122390, and AI120898 to N.R.L.), the Caltech Merkin Institute for Translational Research (to P.J.B.), George Mason University Fast Grant (to P.J.B.), the Manton Foundation (to R.J.X. and A.R.), the Center for Microbiome Informatics and Therapeutics (CMIT) at Massachusetts Institute of Technology (MIT) (to R.J.X.), and the Klarman Cell Observatory. Work at the Broad Institute was supported by a gift from an anonymous donor. C.O.B was supported by the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Postdoctoral Enrichment Program from the Burroughs Wellcome Fund. P.D.B. is a Howard Hughes Medical Institute Investigator. A.R. was a Howard Hughes Medical Institute Investigator while doing this research. T.T. was supported by the Vilcek/Goldfarb Fellowship Endowment Fund. \n\nAuthor contributions: J.F.S., C.O.B., B.E., D.G., P.J.B., J.D., A.R., D.H., and R.J.X. conceived the study and analyzed data. A.E.W., L.A.C., R.J.X., D.H., and J.D. established and orchestrated the patient cohort. J.F.S. established and performed cell staining and sorting, B.E. performed computational analysis with guidance from A.R. and B.E. J.F.S. analyzed repertoire and transcriptome data with guidance from A.R. J.F.S. and A.H. performed mAb cloning, production, purification, and binding characterization. C.O.B. performed protein characterization and crystallographic and cryo-EM studies and analyzed structures. T.D., D.P., O.R.-R., and A.R. developed and performed scRNA-seq library preparation and coordinated single-cell RNA-seq. J.F.S., E.B., S.P., and B.T. performed patient sample processing. K.H.T. purified proteins. J.R.K. and A.A.C. performed and analyzed ELISAs. J.R.K. performed SPR binding and polyreactivity assays. M.A.D. and X.G. assisted with size exclusion chromatography. P.N.G., F.M., Y.W., T.H., F.G., S.Z., D.H., M.S.S., and P.D.B. developed and performed in vitro neutralization assays. A.P.W. analyzed mAb sequences. T.T. and N.R.L. conceived and designed ACE2-CH3 protein purification. J.F.S., C.O.B., B.E., J.D., A.R., P.J.B., and R.J.X. wrote the paper with contributions from other authors. \n\nDeclaration of interests: A provisional patent for the novel SARS-CoV-2 mAbs described in this study has been filed. The authors listed on that application are R.J.X., J.F.S., C.O.B., P.J.B., and B.E. The Broad Institute has filed multiple patents in the area of single cell RNA-seq on which A.R. and O.R.-R. are named inventors. Rockefeller University has applied for a patent relating to the replication competent VSV/SARS-CoV-2 chimeric virus on which Y.W., T.H., and P.D.B. are listed as inventors (US patent 63/036,124). R.J.X. is co-founder and equity holder of Jnana Therapeutics. R.J.X. and A.R. are co-founders and equity holders of Celsius Therapeutics. A.R. is an equity holder in Immunitas and was an SAB member of ThermoFisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics, and Asimov. A.R. and O.R.-R. are employees of Genentech (member of the Roche Group) since August and October 2020, respectively. These companies did not provide support for this work.\n\nPublished - 1-s20-S0092867421005353-main.pdf
Accepted Version - 1-s20-S0092867421005353-acceptedmain.pdf
Supplemental Material - 1-s20-S0092867421005353-mmc1.pdf
", "abstract": "Monoclonal antibodies (mAbs) are a focus in vaccine and therapeutic design to counteract severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Here, we combined B cell sorting with single-cell VDJ and RNA sequencing (RNA-seq) and mAb structures to characterize B cell responses against SARS-CoV-2. We show that the SARS-CoV-2-specific B cell repertoire consists of transcriptionally distinct B cell populations with cells producing potently neutralizing antibodies (nAbs) localized in two clusters that resemble memory and activated B cells. Cryo-electron microscopy structures of selected nAbs from these two clusters complexed with SARS-CoV-2 spike trimers show recognition of various receptor-binding domain (RBD) epitopes. One of these mAbs, BG10-19, locks the spike trimer in a closed conformation to potently neutralize SARS-CoV-2, the recently arising mutants B.1.1.7 and B.1.351, and SARS-CoV and cross-reacts with heterologous RBDs. Together, our results characterize transcriptional differences among SARS-CoV-2-specific B cells and uncover cross-neutralizing Ab targets that will inform immunogen and therapeutic design against coronaviruses.", "date": "2021-06-10", "date_type": "published", "publication": "Cell", "volume": "184", "number": "12", "publisher": "Cell Press", "pagerange": "3205-3221", "id_number": "CaltechAUTHORS:20210429-090704273", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210429-090704273", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01-AI138398-S1" }, { "agency": "NIH", "grant_number": "P50 8 P50 AI150464-13" }, { "agency": "NIH", "grant_number": "DK43351" }, { "agency": "NIH", "grant_number": "U19 AI142784" }, { "agency": "NIH", "grant_number": "DA046100" }, { "agency": "NIH", "grant_number": "AI122390" }, { "agency": "NIH", "grant_number": "AI120898" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "George Mason University" }, { "agency": "Manton Foundation" }, { "agency": "Massachusetts Institute of Technology (MIT)" }, { "agency": "Klarman Cell Observatory" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Vilcek/Goldfarb Fellowship Endowment Fund" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Caltech Beckman Institute" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cell.2021.04.032", "pmcid": "PMC8064835", "primary_object": { "basename": "1-s20-S0092867421005353-main.pdf", "url": "https://authors.library.caltech.edu/records/jnt7a-0x473/files/1-s20-S0092867421005353-main.pdf" }, "related_objects": [ { "basename": "1-s20-S0092867421005353-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/jnt7a-0x473/files/1-s20-S0092867421005353-mmc1.pdf" }, { "basename": "1-s20-S0092867421005353-acceptedmain.pdf", "url": "https://authors.library.caltech.edu/records/jnt7a-0x473/files/1-s20-S0092867421005353-acceptedmain.pdf" } ], "pub_year": "2021", "author_list": "Scheid, Johannes F.; Barnes, Christopher O.; et al." }, { "id": "https://authors.library.caltech.edu/records/95vdh-wqp47", "eprint_id": 111883, "eprint_status": "archive", "datestamp": "2023-08-20 03:39:24", "lastmod": "2026-03-30 14:15:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Miyazaki-Kayuzuki", "name": { "family": "Miyazaki", "given": "Kayuzuki" }, "orcid": "0000-0002-1466-4655" }, { "id": "Bowman-Kevin-W", "name": { "family": "Bowman", "given": "Kevin" }, "orcid": "0000-0002-8659-1117" }, { "id": "Sekiya-Takashi", "name": { "family": "Sekiya", "given": "Takashi" }, "orcid": "0000-0002-5666-6026" }, { "id": "Takigawa-Masayuki", "name": { "family": "Takigawa", "given": "Masayuki" }, "orcid": "0000-0002-5666-6026" }, { "id": "Neu-Jessica-L", "name": { "family": "Neu", "given": "Jessica L." } }, { "id": "Sudo-Kengo", "name": { "family": "Sudo", "given": "Kengo" }, "orcid": "0000-0002-5013-4168" }, { "id": "Osterman-Gregory-B", "name": { "family": "Osterman", "given": "Greg" }, "orcid": "0000-0002-6339-7434" }, { "id": "Eskes-Henk", "name": { "family": "Eskes", "given": "Henk" }, "orcid": "0000-0002-8743-4455" } ] }, "title": "Global Tropospheric Ozone Responses to Reduced NO\u2093 Emissions Linked to the COVID-19 Worldwide Lockdowns", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). \n\nSubmitted 17 November 2020. Accepted 21 April 2021. Published 9 June 2021.\n\nWe acknowledge the use of data products from the National Aeronautics and Space Administration (NASA) Aura and EOS Terra and Aqua satellite missions. We also acknowledge the free use of the tropospheric NO\u2082 column data from the SCIAMACHY, GOME-2, and OMI sensors from www.qa4ecv.eu and from TROPOMI. The OpenAQ surface ozone data were obtained through EPA and the World Air Quality Index Project. The TROPOMI NO\u2082 algorithm and data processors have been developed by KNMI under the NSO TROPOMI Science Contract, in cooperation with ESA. Sentinel-5 Precursor is an ESA mission on behalf of the European Commission (EC). The Earth Simulator was used for model simulations with support of the Japan Agency for Marine-Earth Science and Technology. Part of this work was conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract with the NASA. \n\nK.M. and K.B. acknowledge the support of the NASA Atmospheric Composition: Aura Science Team Program (19-AURAST19-0044) and the TROPESS project. \n\nAuthor contributions: K.M., K.B., and J.L.N. designed the research; all the authors performed research and wrote and edited the paper. Competing interests: The authors declare that they have no competing interests. \n\nData and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The basic concentration and emission data used in the study can be downloaded freely from https://tes.jpl.nasa.gov/chemical-reanalysis/.\n\nPublished - sciadv.abf7460.pdf
Supplemental Material - abf7460_data_file_s1.xlsx
Supplemental Material - abf7460_sm.pdf
Supplemental Material - sciadv.abf7460_data_file_s1.zip
", "abstract": "Efforts to stem the transmission of coronavirus disease 2019 (COVID-19) led to rapid, global ancillary reductions in air pollutant emissions. Here, we quantify the impact on tropospheric ozone using a multiconstituent chemical data assimilation system. Anthropogenic NOGlobal Tropospheric Ozone Responses to Reduced No\u2093 Emissions Linked to the COVID-19 Worldwide Lockdowns emissions dropped by at least 15% globally and 18 to 25% regionally in April and May 2020, which decreased free tropospheric ozone by up to 5 parts per billion, consistent with independent satellite observations. The global total tropospheric ozone burden declined by 6TgO\u2083 (\u223c2%) in May and June 2020, largely due to emission reductions in Asia and the Americas that were amplified by regionally high ozone production efficiencies (up to 4 TgO\u2083/TgN). Our results show that COVID-19 mitigation left a global atmospheric imprint that altered atmospheric oxidative capacity and climate radiative forcing, providing a test of the efficacy of NO\u2093 emissions controls for co-benefiting air quality and climate.", "date": "2021-06-09", "date_type": "published", "publication": "Science Advances", "volume": "7", "number": "24", "publisher": "American Association for the Advancement of Science", "pagerange": "Art. No. eabf7460", "id_number": "CaltechAUTHORS:20211116-003049409", "issn": "2375-2548", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211116-003049409", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NASA/JPL/Caltech" } ] }, "local_group": { "items": [ { "id": "Keck-Institute-for-Space-Studies" }, { "id": "COVID-19" } ] }, "doi": "10.1126/sciadv.abf7460", "pmcid": "PMC8189586", "primary_object": { "basename": "sciadv.abf7460_data_file_s1.zip", "url": "https://authors.library.caltech.edu/records/95vdh-wqp47/files/sciadv.abf7460_data_file_s1.zip" }, "related_objects": [ { "basename": "sciadv.abf7460.pdf", "url": "https://authors.library.caltech.edu/records/95vdh-wqp47/files/sciadv.abf7460.pdf" }, { "basename": "abf7460_data_file_s1.xlsx", "url": "https://authors.library.caltech.edu/records/95vdh-wqp47/files/abf7460_data_file_s1.xlsx" }, { "basename": "abf7460_sm.pdf", "url": "https://authors.library.caltech.edu/records/95vdh-wqp47/files/abf7460_sm.pdf" } ], "pub_year": "2021", "author_list": "Miyazaki, Kayuzuki; Bowman, Kevin; et al." }, { "id": "https://authors.library.caltech.edu/records/tcca5-cff90", "eprint_id": 108318, "eprint_status": "archive", "datestamp": "2023-08-22 10:00:26", "lastmod": "2026-03-30 08:42:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Livanos-Alexandra-E", "name": { "family": "Livanos", "given": "Alexandra E." } }, { "name": { "family": "Jha", "given": "Divya" } }, { "name": { "family": "Cossarini", "given": "Francesca" } }, { "name": { "family": "Gonzalez-Reiche", "given": "Ana S." } }, { "name": { "family": "Tokuyama", "given": "Minami" } }, { "name": { "family": "Aydillo", "given": "Teresa" } }, { "name": { "family": "Parigi", "given": "Tommaso L." } }, { "id": "Ladinsky-Mark-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "name": { "family": "Ramos", "given": "Irene" } }, { "name": { "family": "Dunleavy", "given": "Katie" } }, { "name": { "family": "Lee", "given": "Brian" } }, { "name": { "family": "Dixon", "given": "Rebekah E." } }, { "name": { "family": "Chen", "given": "Steven T." } }, { "name": { "family": "Martinez-Delgado", "given": "Gustavo" } }, { "name": { "family": "Nagula", "given": "Satish" } }, { "name": { "family": "Bruce", "given": "Emily A." } }, { "name": { "family": "Ko", "given": "Huaibin M." } }, { "name": { "family": "Glicksberg", "given": "Benjamin S." } }, { "name": { "family": "Nadkarni", "given": "Girish" } }, { "name": { "family": "Pujadas", "given": "Elisabet" } }, { "name": { "family": "Reidy", "given": "Jason" } }, { "name": { "family": "Naymagon", "given": "Steven" } }, { "name": { "family": "Grinspan", "given": "Ari" } }, { "name": { "family": "Ahmad", "given": "Jawad" } }, { "name": { "family": "Tankelevich", "given": "Michael" } }, { "name": { "family": "Bram", "given": "Yaron" } }, { "name": { "family": "Gordon", "given": "Ronald" } }, { "name": { "family": "Sharma", "given": "Keshav" } }, { "name": { "family": "Houldsworth", "given": "Jane" } }, { "name": { "family": "Britton", "given": "Graham J." } }, { "name": { "family": "Chen-Liaw", "given": "Alice" } }, { "name": { "family": "Spindler", "given": "Matthew P." } }, { "name": { "family": "Plitt", "given": "Tamar" } }, { "name": { "family": "Wang", "given": "Pei" } }, { "name": { "family": "Cerutti", "given": "Andrea" } }, { "name": { "family": "Faith", "given": "Jeremiah J." } }, { "name": { "family": "Colombel", "given": "Jean-Frederic" } }, { "name": { "family": "Kenigsberg", "given": "Ephraim" } }, { "name": { "family": "Argmann", "given": "Carmen" } }, { "name": { "family": "Merad", "given": "Miriam" } }, { "name": { "family": "Gnjatic", "given": "Sacha" } }, { "name": { "family": "Harpaz", "given": "Noam" } }, { "name": { "family": "Danese", "given": "Silvio" } }, { "name": { "family": "Cordon-Cardo", "given": "Carlos" } }, { "name": { "family": "Rahman", "given": "Adeeb" } }, { "name": { "family": "Schwartz", "given": "Robert E." } }, { "name": { "family": "Kumta", "given": "Nikhil A." } }, { "name": { "family": "Aghemo", "given": "Alessio" } }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Petralia", "given": "Francesca" } }, { "name": { "family": "van Bakel", "given": "Harm" } }, { "name": { "family": "Garcia-Sastre", "given": "Adolfo" } }, { "name": { "family": "Mehandru", "given": "Saurabh" }, "orcid": "0000-0001-9781-2969" } ] }, "title": "Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; SARS-CoV-2; GI symptoms; GI infection; outcomes; host immune response", "note": "\u00a9 2021 by the AGA Institute. \n\nReceived 20 November 2020, Revised 22 February 2021, Accepted 23 February 2021, Available online 4 March 2021. \n\nThe authors would like to thank the clinical staff, physicians, and patients who participated in this study. The authors also thank Dr Randy Albrecht for support with the BSL 3 facility and procedures at the Icahn School of Medicine at Mount Sinai. \n\nCRediT Authorship Contributions: Alexandra E. Livanos, MD (Investigation: Equal); Divya Jha, PhD (Investigation: Equal); Francesca Cossarini, MD (Investigation: Equal); Ana S. Gonzalez-Reiche, PhD (Investigation: Equal); Minami Tokuyama, BS (Investigation: Equal); Teresa Aydillo, PhD (Investigation: Equal); Tommaso L. Parigi, MD (Investigation: Equal); Mark S. Ladinsky, PhD (Formal analysis: Supporting); Irene Ramos, PhD (Investigation: Supporting); Katie Dunleavy, MD (Investigation: Supporting); Brian Lee, BS (Investigation: Supporting); Rebekah Dixon, BS (Investigation: Supporting); Steven T. Chen, BS (Investigation: Supporting); Gustavo Martinez-Delgado, PhD (Investigation: Supporting); Satish Nagula, MD (Investigation: Supporting); Emily A. Bruce, PhD (Data curation: Supporting); Huaibin M. Ko, MD (Investigation: Supporting); Benjamin S. Glicksberg, PhD (Investigation: Supporting); Girish Nadkarni, MD (Investigation: Supporting); Elisabet Pujadas, MD (Investigation: Supporting); Jason Reidy, MS (Investigation: Supporting); Steven Naymagon, MD (Investigation: Supporting); Ari Grinspan, MD (Investigation: Supporting); Jawad Ahmad, MD (Investigation: Supporting); Michael Tankelevich, BS (Investigation: Supporting); Yaron Bram, PhD (Data curation: Supporting); Ronald Gordon, MD (Investigation: Supporting); Keshav Sharma, MS (Investigation: Supporting); Jane Houldsworth, BS (Investigation: Supporting); Graham J. Britton, PhD (Investigation: Supporting); Alice Chen-Liaw, BS (Investigation: Supporting); Matthew P. Spindler, BS (Investigation: Supporting); Tamar Plitt, BS (Investigation: Supporting); Pei Wang, PhD (Supporting: Supporting); Andrea Cerutti, MD, PhD (Supporting: Supporting); Jeremiah J. Faith, PhD (Supporting: Supporting); Jean-Frederic Colombel, MD (Supporting: Supporting); Ephraim Kenigsberg, PhD (Supporting: Supporting); Carmen Argmann, PhD (Supporting: Supporting); Miriam Merad, MD, PhD (Supporting: Supporting); Sacha Gnjatic, PhD (Supporting: Supporting); Noam Harpaz, MD (Supporting: Supporting); Silvio Danese, MD, PhD (Supporting: Supporting); Carlos Cordon-Cardo, MD, PhD (Supporting: Supporting); Adeeb Rahman, PhD (Supporting: Supporting); Robert E. Schwartz, MD, PhD (Data curation: Supporting; Formal analysis: Supporting; Investigation: Supporting); Nikhil A. Kumta, MD (Supporting: Supporting); Alessio Aghemo, MD, PhD (Supporting: Supporting); Pamela J. Bjorkman, PhD (Formal analysis: Supporting; Investigation: Supporting); Francesca Petralia, PhD (Supporting: Supporting); Harm van Bakel, PhD (Supporting: Supporting); Adolfo Garcia-Sastre, PhD (Supervision: Supporting); Saurabh Mehandru, MD (Investigation: Lead; Writing \u2013 original draft: Lead; Writing \u2013 review & editing: Lead). \n\nConflicts of interest: These authors disclose the following: Girish Nadkarni reports employment with, consultancy agreements with, and ownership interest in Pensieve Health and Renalytix AI; has received consulting fees from AstraZeneca, BioVie, GLG Consulting, and Reata; and has served as a scientific advisor or member of Pensieve Health and Renalytix AI. Jeremiah J. Faith has served on the scientific advisor board of Vedanta Biosciences and has received grants from Janssen (unrelated to this work). Jean-Frederic Colombel has served as a consultant for AbbVie, Amgen, Arena Pharmaceuticals, Boehringer Ingelheim, Celgene Corporations, Celltrion, Eli Lilly, and Enterome (all unrelated to this work). Sacha Gnjatic has received research grants from Bristol Myers Squibb, Genentech, Immune Design, Agenus, and Janssen and has served as a consultant for Merck, OncoMed, and Neon Therapeutics. Noam Harpaz has served as a consultant for Lilly USA and has received a pathology service contract with AbbVie and Celgene. Silvio Danese has served as a consultant for Ely Lilly, Enthera, Ferring Pharmaceuticals, Gilead, Hospira, Inotrem, Janssen, Johnson & Johnson, Merck Sharp & Dohme Mundipharma, Mylan, Pfizer, Roche, Sandoz, Sublimity Therapeutics, Takeda, TiGenix, UCB, and Vifor. Robert E. Schwartz has served on the scientific advisory board of Miromatrix Inc and is a consultant and speaker for Alnylam Inc. Nikhil A. Kumta has served as a consultant for Apollo Endosurgery, Boston Scientific, Gyrus AMCI, and Olympus. The remaining authors disclose no conflicts. \n\nThis research was partly funded by National Institutes of Health (NIH)/National Institute of Diabetes and Digestive and Kidney Diseases 123749 0S1 (to Saurabh Mehandru). Additional support was provided by the Center for Research for Influenza Pathogenesis, a National Institute of Allergy and Infectious Diseases (NIAID)\u2013supported Center of Excellence for Influenza Research and Surveillance (contract no. HHSN272201400008C), and NIAID R01AI113186 (to Harm van Bakel). Additionally, the work was supported by the generous support of the JPB Foundation, the Open Philanthropy Project (research grant 2020-215611 [5384]), the Defense Advanced Research Projects Agency, and anonymous donors to Adolfo Garcia-Sastre. Minami Tokuyama was funded by the Digestive Disease Research Foundation. Ana S. Gonzalez-Reiche is supported in part by a Robin Chemers Neustein Postdoctoral Fellowship Award. The research carried out by Harm van Bakel and Ana S. Gonzalez-Reiche was supported by the Office of Research Infrastructure of the NIH under awards S10OD018522 and S10OD026880. Robert E. Schwartz is funded by NCI R01CA234614, NIAID 2R01AI107301, and NIDDK R01DK121072 and is supported as an Irma Hirschl Trust Research Award Scholar. Emily A. Bruce is supported by NIH grant P20GM125498 (awarded to University of Vermont Translational Global Infectious Disease Research Center). Pamela J. Bjorkman and Mark S. Ladinsky are supported by George Mason University Fast Grants. Steven T. Chen is supported by grant F30CA243210. Graham J. Britton is supported by a Research Fellowship Award from the Crohn's and Colitis Foundation of America. Matthew P. Spindler is supported by NIH T32 5T32AI007605. Sacha Gnjatic is supported by grants U24 CA224319, U01 DK124165, and P01 CA190174.\n\nAccepted Version - main.pdf
Supplemental Material - 1-s2.0-S0016508521004613-mmc1.xlsx
Supplemental Material - 1-s2.0-S0016508521004613-mmc10.xlsx
Supplemental Material - 1-s2.0-S0016508521004613-mmc2.mp4
Supplemental Material - 1-s2.0-S0016508521004613-mmc3.mp4
Supplemental Material - 1-s2.0-S0016508521004613-mmc4.xlsx
Supplemental Material - 1-s2.0-S0016508521004613-mmc5.xlsx
Supplemental Material - 1-s2.0-S0016508521004613-mmc6.xlsx
Supplemental Material - 1-s2.0-S0016508521004613-mmc7.xlsx
Supplemental Material - 1-s2.0-S0016508521004613-mmc8.xlsx
Supplemental Material - 1-s2.0-S0016508521004613-mmc9.xlsx
", "abstract": "Background & Aims: Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of COVID-19, we investigated intestinal infection with SARS-CoV-2, its effect on pathogenesis, and clinical significance. \n\nMethods: Human intestinal biopsy tissues were obtained from patients with COVID-19 (n = 19) and uninfected control individuals (n = 10) for microscopic examination, cytometry by time of flight analyses, and RNA sequencing. Additionally, disease severity and mortality were examined in patients with and without GI symptoms in 2 large, independent cohorts of hospitalized patients in the United States (N = 634) and Europe (N = 287) using multivariate logistic regressions. \n\nResults: COVID-19 case patients and control individuals in the biopsy cohort were comparable for age, sex, rates of hospitalization, and relevant comorbid conditions. SARS-CoV-2 was detected in small intestinal epithelial cells by immunofluorescence staining or electron microscopy in 15 of 17 patients studied. High-dimensional analyses of GI tissues showed low levels of inflammation, including down-regulation of key inflammatory genes including IFNG, CXCL8, CXCL2, and IL1B and reduced frequencies of proinflammatory dendritic cells compared with control individuals. Consistent with these findings, we found a significant reduction in disease severity and mortality in patients presenting with GI symptoms that was independent of sex, age, and comorbid illnesses and despite similar nasopharyngeal SARS-CoV-2 viral loads. Furthermore, there was reduced levels of key inflammatory proteins in circulation in patients with GI symptoms. \n\nConclusions: These data highlight the absence of a proinflammatory response in the GI tract despite detection of SARS-CoV-2. In parallel, reduced mortality in patients with COVID-19 presenting with GI symptoms was observed. A potential role of the GI tract in attenuating SARS-CoV-2\u2013associated inflammation needs to be further examined.", "date": "2021-06", "date_type": "published", "publication": "Gastroenterology", "volume": "160", "number": "7", "publisher": "AGA Institute", "pagerange": "2435-2450", "id_number": "CaltechAUTHORS:20210305-070228450", "issn": "0016-5085", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210305-070228450", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "123749 0S1" }, { "agency": "Center for Research for Influenza Pathogenesis", "grant_number": "HHSN272201400008C" }, { "agency": "NIH", "grant_number": "R01AI113186" }, { "agency": "JPB Foundation" }, { "agency": "Open Philanthropy Project", "grant_number": "2020-215611 (5384)" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Digestive Disease Research Foundation" }, { "agency": "Robin Chemers Neustein Postdoctoral Fellowship Award" }, { "agency": "NIH", "grant_number": "S10OD018522" }, { "agency": "NIH", "grant_number": "S10OD026880" }, { "agency": "NIH", "grant_number": "R01CA234614" }, { "agency": "NIH", "grant_number": "2R01AI107301" }, { "agency": "NIH", "grant_number": "R01DK121072" }, { "agency": "Irma Hirschl Trust Research Award" }, { "agency": "NIH", "grant_number": "P20GM125498" }, { "agency": "George Mason University" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F30CA243210" }, { "agency": "Crohn's and Colitis Foundation of America" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 5T32AI007605" }, { "agency": "NIH", "grant_number": "U24 CA224319" }, { "agency": "NIH", "grant_number": "U01 DK124165" }, { "agency": "NIH", "grant_number": "P01 CA190174" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1053/j.gastro.2021.02.056", "pmcid": "PMC7931673", "primary_object": { "basename": "1-s2.0-S0016508521004613-mmc10.xlsx", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc10.xlsx" }, "related_objects": [ { "basename": "1-s2.0-S0016508521004613-mmc1.xlsx", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc1.xlsx" }, { "basename": "1-s2.0-S0016508521004613-mmc3.mp4", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc3.mp4" }, { "basename": "1-s2.0-S0016508521004613-mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc4.xlsx" }, { "basename": "1-s2.0-S0016508521004613-mmc5.xlsx", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc5.xlsx" }, { "basename": "1-s2.0-S0016508521004613-mmc6.xlsx", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc6.xlsx" }, { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/main.pdf" }, { "basename": "1-s2.0-S0016508521004613-mmc2.mp4", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc2.mp4" }, { "basename": "1-s2.0-S0016508521004613-mmc7.xlsx", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc7.xlsx" }, { "basename": "1-s2.0-S0016508521004613-mmc8.xlsx", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc8.xlsx" }, { "basename": "1-s2.0-S0016508521004613-mmc9.xlsx", "url": "https://authors.library.caltech.edu/records/tcca5-cff90/files/1-s2.0-S0016508521004613-mmc9.xlsx" } ], "pub_year": "2021", "author_list": "Livanos, Alexandra E.; Jha, Divya; et al." }, { "id": "https://authors.library.caltech.edu/records/b7m61-8rn51", "eprint_id": 108344, "eprint_status": "archive", "datestamp": "2023-10-03 22:39:15", "lastmod": "2026-03-30 05:27:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "De-Gasparo-Raoul", "name": { "family": "De Gasparo", "given": "Raoul" } }, { "name": { "family": "Pedotti", "given": "Mattia" }, "orcid": "0000-0003-1370-9505" }, { "name": { "family": "Simonelli", "given": "Luca" }, "orcid": "0000-0001-6331-7716" }, { "name": { "family": "Nickl", "given": "Petr" } }, { "name": { "family": "Muecksch", "given": "Frauke" }, "orcid": "0000-0002-0132-5101" }, { "name": { "family": "Cassaniti", "given": "Irene" }, "orcid": "0000-0002-3385-2088" }, { "name": { "family": "Percivalle", "given": "Elena" }, "orcid": "0000-0002-3355-1410" }, { "name": { "family": "Lorenzi", "given": "Julio C. 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This work was also supported by SNF grant 31003A_182270 (L.V.); Lions Club Monteceneri (L.V.); George Mason University Fast Grant and IRB start-up funds (D.F.R.); NIH U01 AI151698 for the United World Antiviral Research Network (UWARN) (D.F.R. and M.C.N.); NIH grant P01-AI138398-S1 (M.C.N. and P.J.B.); 2U19AI111825 (M.C.N. and D.F.R.); the Caltech Merkin Institute for Translational Research and P50 AI150464 (P.J.B.); R37-AI64003 (P.D.B.); and R01AI78788 (T.H.); P.D.B. and M.C.N. are Howard Hughes Medical Institute Investigators. The study was also supported by the Czech Academy of Sciences and Czech Ministry of Agriculture (RVO 68378050 (R.S.) and RVO0518 (D.R.)); Czech Ministry of Education, Youth and Sports and the European Regional Development Fund (LM2018126; CZ.1.05/2.1.00/19.0395 and CZ.1.05/1.1.00/02.0109 (R.S.) and CZ.02.1.01/0.0/0.0/15_003/0000495 (D.R.)); Czech Science Foundation (20-14325S (D.R.)); the Bulgari Women & Science Fellowship in COVID-19 Research (F. Muecksch); the EU Joint Research Centre Exploratory Research program ('NanoMicrobials\u2032; D. Magr\u00ec); and by Ricerca Finalizzata from Ministry of Health, Italy (grant no. GR-2013-02358399 (A.P.)). We are grateful for the high-performance computing resources that were provided by S. Bassini of CINECA to M. Hust, F. Bertoglio, F. Bognuda and E. Restivo. We thank V. Zatecka, V. Martinkova and L. Kutlikova for technical assistance; and V. Babak for help with statistical analyses. We are grateful to the late F. Diederich for their mentorship. \n\nData availability: The data that support the findings of this study are available within the Article and its Supplementary Information. Any other data are available from the corresponding author upon reasonable request. Published data were taken from GenBank (https://www.ncbi.nlm.nih.gov/genbank/), UniProt (https://www.uniprot.org/), PDB (https://www.rcsb.org/) and the ViPR database (https://www.viprbrc.org/). Source data are provided with this paper. \n\nThese authors contributed equally: Raoul De Gasparo, Mattia Pedotti. \n\nAuthor Contributions: R.D.G, M. Pedotti, L.S., F. Muecksch, J.C.C.L., F. Mazzola, D. Magr\u00ec, I.C., E.P., S.D.G., M. Palus, D. Mehn, S. Gioria, C.O.B., F. Bianchini, J.C.S., F.G. and S. Gaiarsa designed and carried out experiments and analysed results, and produced plasmids, antibodies and viral proteins. P.N., T.M., J.H., V.H, B.M., N.P., A.F., J.T., V.I., M. Palus, D.Z., P.B., I.B., P.S. and D.R., performed mouse experiments and analysed the results. L.V., D.F.R., D.R., Q.P.-H., F. Baldanti, A.P., L.C., P.J.B., M.C.N., P.D.B. and T.H. conceived and designed study and experiments, and analysed the results. P.N., T.M., R.N., O.P., J.P., J.R. and R.S. conceived and designed the mouse model. L.V., D.F.R., D.R. and R.D.G. wrote the manuscript, with input from all co-authors. \n\nCompeting interests: The Institute for Research in Biomedicine has filed a provisional European patent application in connection with this work, on which L.V. is inventor (PCT/EP2020/085342). The Rockefeller University has filed a provisional US patent application (US 63/021,387) on coronavirus antibodies, on which D.F.R. and M.C.N. are inventors. \n\nPeer review information: Nature thanks Stanley Perlman and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.\n\nIn this Article, authors Raoul De Gasparo and Mattia Pedotti should not be linked to affiliation 15, 'Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA' and should instead be linked to the equal contribution footnote, 16. In addition, affiliation 14 should read 'Universit\u00e0 degli Studi di Pavia, Pavia, Italy'. The Article has been corrected online.\n\nDe Gasparo, R., Pedotti, M., Simonelli, L. et al. Publisher Correction: Bispecific IgG neutralizes SARS-CoV-2 variants and prevents escape in mice. Nature (2021). https://doi.org/10.1038/s41586-021-03719-5\n\nSubmitted - 20210122-427567v2.full.pdf
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", "abstract": "Neutralizing antibodies that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein are among the most promising approaches against COVID-19. A bispecific IgG1-like molecule (CoV-X2) has been developed on the basis of C121 and C135, two antibodies derived from donors who had recovered from COVID-19. Here we show that CoV-X2 simultaneously binds two independent sites on the RBD and, unlike its parental antibodies, prevents detectable spike binding to the cellular receptor of the virus, angiotensin-converting enzyme 2 (ACE2). Furthermore, CoV-X2 neutralizes wild-type SARS-CoV-2 and its variants of concern, as well as escape mutants generated by the parental monoclonal antibodies. We also found that in a mouse model of SARS-CoV-2 infection with lung inflammation, CoV-X2 protects mice from disease and suppresses viral escape. Thus, the simultaneous targeting of non-overlapping RBD epitopes by IgG-like bispecific antibodies is feasible and effective, and combines the advantages of antibody cocktails with those of single-molecule approaches.", "date": "2021-05-20", "date_type": "published", "publication": "Nature", "volume": "593", "number": "7859", "publisher": "Nature Publishing Group", "pagerange": "424-428", "id_number": "CaltechAUTHORS:20210308-130543968", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210308-130543968", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "European Research Council (ERC)", "grant_number": "101003650" }, { "agency": "Swiss National Science Foundation (SNSF)", "grant_number": "31003A_182270" }, { "agency": "Lions Club Monteceneri" }, { "agency": "George Mason University" }, { "agency": "NIH", "grant_number": "U01 AI151698" }, { "agency": "NIH", "grant_number": "P01-AI138398-S1" }, { "agency": "NIH", "grant_number": "2U19AI111825" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "NIH", "grant_number": "P50 AI150464" }, { "agency": "NIH", "grant_number": "R37-AI64003" }, { "agency": "NIH", "grant_number": "R01AI78788" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Czech Academy of Sciences" }, { "agency": "Ministry of Agriculture (Czech Republic)", "grant_number": "RVO 68378050" }, { "agency": "Ministry of Agriculture (Czech Republic)", "grant_number": "RVO0518" }, { "agency": "Ministry of Education, Youth and Sports (Czech Republic)" }, { "agency": "European Regional Development Fund", "grant_number": "LM2018126" }, { "agency": "European Regional Development Fund", "grant_number": "CZ.1.05/2.1.00/19.0395" }, { "agency": "European Regional Development Fund", "grant_number": "CZ.1.05/1.1.00/02.0109" }, { "agency": "European Regional Development Fund", "grant_number": "CZ.02.1.01/0.0/0.0/15_003/0000495" }, { "agency": "Czech Science Foundation", "grant_number": "20-14325S" }, { "agency": "Bulgari Women & Science Fellowship in COVID-19 Research" }, { "agency": "European Union Joint Research Centre Exploratory Research Program" }, { "agency": "Ricerca Finalizzata", "grant_number": "GR-2013-02358399" }, { "agency": "Ministero della Salute (Italy)" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41586-021-03461-y", "pmcid": "PMC8330819", "primary_object": { "basename": "41586_2021_3461_Tab1_ESM.jpg", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_Tab1_ESM.jpg" }, "related_objects": [ { "basename": "20210122-427567v2.full.pdf", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/20210122-427567v2.full.pdf" }, { "basename": "41586_2021_3461_Fig10_ESM.webp", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_Fig10_ESM.webp" }, { "basename": "41586_2021_3461_Fig6_ESM.webp", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_Fig6_ESM.webp" }, { "basename": "41586_2021_3461_Fig7_ESM.webp", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_Fig7_ESM.webp" }, { "basename": "41586_2021_3461_Fig9_ESM.webp", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_Fig9_ESM.webp" }, { "basename": "41586_2021_3461_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_MOESM1_ESM.pdf" }, { "basename": "41586_2021_3461_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_MOESM2_ESM.pdf" }, { "basename": "41586_2021_3461_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_MOESM3_ESM.xlsx" }, { "basename": "41586_2021_3461_Fig3_ESM.webp", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_Fig3_ESM.webp" }, { "basename": "41586_2021_3461_Fig4_ESM.webp", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_Fig4_ESM.webp" }, { "basename": "41586_2021_3461_Fig5_ESM.webp", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_Fig5_ESM.webp" }, { "basename": "41586_2021_3461_Fig8_ESM.webp", "url": "https://authors.library.caltech.edu/records/b7m61-8rn51/files/41586_2021_3461_Fig8_ESM.webp" } ], "pub_year": "2021", "author_list": "De Gasparo, Raoul; Pedotti, Mattia; et al." }, { "id": "https://authors.library.caltech.edu/records/brdw0-qey65", "eprint_id": 105297, "eprint_status": "archive", "datestamp": "2023-08-20 03:15:42", "lastmod": "2026-03-30 14:06:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ma-Jianxin", "name": { "family": "Ma", "given": "Jianxin" } }, { "id": "Qi-Xiao", "name": { "family": "Qi", "given": "Xiao" } }, { "id": "Chen-Haoxuan", "name": { "family": "Chen", "given": "Haoxuan" }, "orcid": "0000-0001-8398-9093" }, { "id": "Li-Xinyue", "name": { "family": "Li", "given": "Xinyue" }, "orcid": "0000-0002-0822-4960" }, { "id": "Zhang-Zheng", "name": { "family": "Zhang", "given": "Zheng" } }, { "id": "Wang-Haibin", "name": { "family": "Wang", "given": "Haibin" } }, { "id": "Sun-Lingli", "name": { "family": "Sun", "given": "Lingli" } }, { "id": "Zhang-Lu", "name": { "family": "Zhang", "given": "Lu" } }, { "id": "Guo-Jiazhen", "name": { "family": "Guo", "given": "Jiazhen" } }, { "id": "Morawska-Lidia", "name": { "family": "Morawska", "given": "Lidia" }, "orcid": "0000-0002-0594-9683" }, { "id": "Grinshpun-Sergey-A", "name": { "family": "Grinshpun", "given": "Sergey A." }, "orcid": "0000-0003-4339-927X" }, { "id": "Biswas-Pratim", "name": { "family": "Biswas", "given": "Pratim" }, "orcid": "0000-0003-1104-3738" }, { "id": "Flagan-R-C", "name": { "family": "Flagan", "given": "Richard C." }, "orcid": "0000-0001-5690-770X" }, { "id": "Yao-Maosheng", "name": { "family": "Yao", "given": "Maosheng" }, "orcid": "0000-0002-1442-8054" } ] }, "title": "Coronavirus Disease 2019 Patients in Earlier Stages Exhaled Millions of Severe Acute Respiratory Syndrome Coronavirus 2 Per Hour", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19, SARS-CoV-2, exhaled breath, airborne transmission", "note": "\u00a9 The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nReceived: 15 July 2020; Editorial decision: 24 August 2020; Accepted: 26 August 2020; Published: 28 August 2020; Corrected and typeset: 08 October 2020. \n\nThe authors thank the local Center for Disease Prevention and Control medical stuff for their assistance in recruiting patients. \n\nThis research was supported by the National Natural Science Foundation of China (NSFC; 22040101) and the NSFC Distinguished Young Scholars Fund (21725701 to M. Y.). \n\nAuthor contributions. M. Y. and J. M. contributed to the study design. J. M., M. Y., X. Q., Z. Z., H. W., L. S., and J. G. contributed to sample collection and experiments. J. M., X. Q., and M. Y. contributed to patients' recruitment and clinical management. M. Y., J. M., X. L., H. C., L. Z., L. M., S. A. G., P. B., and R. C. F. contributed to data analysis, data interpretation, figure preparation, and literature search. M. Y. wrote the manuscript draft, and all authors revised the manuscript. All authors reviewed and approved the final version of the report. \n\nPotential conflicts of interest. The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest.\n\nSubmitted - 2020.05.31.20115154v1.full.pdf
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", "abstract": "Coronavirus disease 2019 (COVID-19) patients exhaled millions of severe acute respiratory syndrome coronavirus 2 RNA copies per hour, which plays an important role in COVID-19 transmission. Exhaled breath had a higher positive rate (26.9%, n = 52) than surface (5.4%, n = 242) and air (3.8%, n = 26) samples.", "date": "2021-05-15", "date_type": "published", "publication": "Clinical Infectious Diseases", "volume": "72", "number": "10", "publisher": "Oxford University Press", "pagerange": "e652-e654", "id_number": "CaltechAUTHORS:20200909-135124154", "issn": "1058-4838", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200909-135124154", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Natural Science Foundation of China", "grant_number": "22040101" }, { "agency": "National Natural Science Foundation of China", "grant_number": "21725701" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1093/cid/ciaa1283", "pmcid": "PMC7499537", "primary_object": { "basename": "2020.05.31.20115154v1.full.pdf", "url": "https://authors.library.caltech.edu/records/brdw0-qey65/files/2020.05.31.20115154v1.full.pdf" }, "related_objects": [ { "basename": "ciaa1283_suppl_supplementary_material.docx", "url": "https://authors.library.caltech.edu/records/brdw0-qey65/files/ciaa1283_suppl_supplementary_material.docx" }, { "basename": "ciaa1283_suppl_supplementary_table.xlsx", "url": "https://authors.library.caltech.edu/records/brdw0-qey65/files/ciaa1283_suppl_supplementary_table.xlsx" }, { "basename": "ciaa1283_suppl_supplementary_video_1.mp4", "url": "https://authors.library.caltech.edu/records/brdw0-qey65/files/ciaa1283_suppl_supplementary_video_1.mp4" }, { "basename": "ciaa1283_suppl_supplementary_video_2.mp4", "url": "https://authors.library.caltech.edu/records/brdw0-qey65/files/ciaa1283_suppl_supplementary_video_2.mp4" } ], "pub_year": "2021", "author_list": "Ma, Jianxin; Qi, Xiao; et al." }, { "id": "https://authors.library.caltech.edu/records/40sg9-d3h73", "eprint_id": 109115, "eprint_status": "archive", "datestamp": "2023-08-20 03:15:14", "lastmod": "2026-03-28 21:09:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bloom-Jesse-D", "name": { "family": "Bloom", "given": "Jesse D." }, "orcid": "0000-0003-1267-3408" }, { "id": "Chan-Yujia-Alina", "name": { "family": "Chan", "given": "Yujia Alina" } }, { "id": "Baric-Ralph-S", "name": { "family": "Baric", "given": "Ralph S." } }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Cobey-Sarah", "name": { "family": "Cobey", "given": "Sarah" } }, { "id": "Deverman-Benjamin-E", "name": { "family": "Deverman", "given": "Benjamin E." }, "orcid": "0000-0002-6223-9303" }, { "id": "Fisman-David-N", "name": { "family": "Fisman", "given": "David N." } }, { "id": "Gupta-Ravindra", "name": { "family": "Gupta", "given": "Ravindra" } }, { "id": "Iwasaki-Akiko", "name": { "family": "Iwasaki", "given": "Akiko" } }, { "id": "Lipsitch-Marc", "name": { "family": "Lipsitch", "given": "Marc" } }, { "id": "Medzhitov-Ruslan", "name": { "family": "Medzhitov", "given": "Ruslan" } }, { "id": "Neher-Richard-A", "name": { "family": "Neher", "given": "Richard A." } }, { "id": "Nielsen-Rasmus", "name": { "family": "Nielsen", "given": "Rasmus" } }, { "id": "Patterson-Nick", "name": { "family": "Patterson", "given": "Nick" } }, { "id": "Stearns-Tim", "name": { "family": "Stearns", "given": "Tim" } }, { "id": "van-Nimwegen-Erik", "name": { "family": "van Nimwegen", "given": "Erik" } }, { "id": "Worobey-Michael", "name": { "family": "Worobey", "given": "Michael" } }, { "id": "Relman-David-A", "name": { "family": "Relman", "given": "David A." } } ] }, "title": "Investigate the origins of COVID-19", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 American Association for the Advancement of Science.\nThis is an article distributed under the terms of the Science Journals Default License.\n\nAccepted Version - nihms-1834584.pdf
", "abstract": "On 30 December 2019, the Program for Monitoring Emerging Diseases notified the world about a pneumonia of unknown cause in Wuhan, China (1). Since then, scientists have made remarkable progress in understanding the causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), its transmission, pathogenesis, and mitigation by vaccines, therapeutics, and non-pharmaceutical interventions. Yet more investigation is still needed to determine the origin of the pandemic. Theories of accidental release from a lab and zoonotic spillover both remain viable. Knowing how COVID-19 emerged is critical for informing global strategies to mitigate the risk of future outbreaks.", "date": "2021-05-14", "date_type": "published", "publication": "Science", "volume": "372", "number": "6543", "publisher": "American Association for the Advancement of Science", "pagerange": "694", "id_number": "CaltechAUTHORS:20210513-115757419", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210513-115757419", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/science.abj0016", "pmcid": "PMC9520851", "primary_object": { "basename": "nihms-1834584.pdf", "url": "https://authors.library.caltech.edu/records/40sg9-d3h73/files/nihms-1834584.pdf" }, "pub_year": "2021", "author_list": "Bloom, Jesse D.; Chan, Yujia Alina; et al." }, { "id": "https://authors.library.caltech.edu/records/r2x9d-af674", "eprint_id": 106665, "eprint_status": "archive", "datestamp": "2023-08-20 03:11:55", "lastmod": "2026-03-30 07:17:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "G\u00fcnther-Sebastian", "name": { "family": "G\u00fcnther", "given": "Sebastian" }, "orcid": "0000-0002-7329-6653" }, { "name": { "family": "Reinke", "given": "Patrick Y. A." }, "orcid": "0000-0002-7354-0839" }, { "name": { "family": "Fern\u00e1ndez-Garc\u00eda", "given": "Yaiza" }, "orcid": "0000-0002-9592-2141" }, { "name": { "family": "Lieske", "given": "Julia" } }, { "name": { "family": "Lane", "given": "Thomas J." } }, { "name": { "family": "Ginn", "given": "Helen M." }, "orcid": "0000-0002-7894-4939" }, { "name": { "family": "Koua", "given": "Faisal H. 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Parts of this research were carried out at PETRA III at beamline P11. Further MX data were collected at beamline P13 and P14 operated by EMBL. We thank the DESY machine group, in particular Mario Wunderlich, Kim Heuck, Arne Brinkmann, Olaf Goldbeck, J\u00fcrgen Haar, Torsten Schulz, Gunnar Priebe, Maximilian Holz, Bj\u00f6rn Lemcke, Klaus Knaack, Oliver Seebauer, Philipp Willanzheimer, Rolf Jonas, and Nicole Engling. We thank Thomas Dietrich, Simon Geile, Filip Guicking, Heshmat Noei, and Tim Pakendorf from DESY, and Bianca Di Fabrizio and Sebastian K\u00fchn from BNITM for assistance. This research was supported in part through the Maxwell computational resources operated at DESY. We acknowledge the use of the XBI biological sample preparation laboratory at European XFEL, enabled by the XBI User Consortium. \n\nWe acknowledge financial support from the EXSCALATE4CoV EU-H2020 Emergency Project (101003551), the Cluster of Excellence \"Advanced Imaging of Matter\" of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - project ID 390715994, the Helmholtz Association Impulse and Networking funds (projects ExNet-0002 and InternLabs-0011 \"HIR3X\"), the Federal Ministry of Education and Research (BMBF) via projects 05K16GUA, 05K19GU4, 05K20BI1, 05K20FL1, 16GW0277 and 031B0405D), and the Joachim-Herz-Stiftung Hamburg (project Infecto-Physics). CE and MR acknowledge financial support from grant-No. HIDSS-0002 DASHH (Data Science in Hamburg - HELMHOLTZ Graduate School for the Structure of Matter). RC is supported by DFG grants INST 187/621-1 and INST 187/686-1. DT is supported by the Slovenian Research Agency (ARRS; research program P1-0048, Infrastructural program IO-0048). BS was supported by an Exploration Grant from the Boehringer Ingelheim Foundation. The Heinrich Pette Institute, Leibniz Institute for Experimental Virology was supported by the Free and Hanseatic City of Hamburg and the Federal Ministry of Health. CU and BK were supported by EU Horizon 2020 ERC StG-2017 759661, BMBF RTK Struktur 01KI20391, BMBF Visavix 05K16BH1 and the Leibniz Association SAW-2014-HPI-4 grant. \n\nAuthor Contributions: SeG, PR, YFG, WB, PG, ARB, RC, DT, AZ, HNC, ARP, CB, AM designed research. SeG, PR, TJL, WH, HNC, ARP, CB, AM wrote manuscript. SeG, PR, JL, FHMK, SM, WB, ID, BS, HGie, BNB, MB, PLX, NW, HA, NU, SF, BAF, MS, HB, JK, GEPM, ARM, FG, VH, PF, MW, ECS, PM, HT, TB participated in sample preparation. PR performed crystallization experiments. SeG, PR, JL, TJL, OY, SS, AT, MGr, HF, FT, MGa, YG, CFL, SA, AP, GB, DVS, GP, TRS, IB, SP performed X-ray data collection. TJL, HGin, DO, OY, LG, MD, TAW, FS, CR, DM, JZD, IK, CS, RS, HUH, DCFM contributed to X-ray data management. SeG, PR, JL, TJL, HGin, FHMK, WE, DO, AH, VS, JH, JM, JB, JW, CF, MSW, AC, DT, WH, AM performed X-ray data analysis. KL, BK, CU, RC performed and analyzed MS experiments. YFG, BEP, StG performed and analyzed antiviral activity assays. PG, BE, MK, MGA, SN, CG, LZ, XS, KK, AU, JL, RH performed and analyzed ligand binding studies and protein activity assays. CE, JPZ, MR performed computational binding studies. \n\nCompeting Interests: MR is stakeholder of BioSolveIT GmbH, licensor of the software HYDE. \n\nData and materials availability: The coordinates and structure factors for all described crystal structures of SARS-CoV-2 Mpro in complex with compounds are deposited in the PDB with accession codes 6YNQ, 6YVF, 7A1U, 7ABU, 7ADW, 7AF0, 7AGA, 7AHA, 7AK4, 7AKU, 7AMJ, 7ANS, 7AOL, 7AP6, 7APH, 7AQE, 7AQI, 7AQJ, 7AR5, 7AR6, 7ARF, 7AVD, 7AWR, 7AWS, 7AWU, 7AWW, 7AX6, 7AXM, 7AXO, 7AY7, 7B83 and 7NEV. Code used in this analysis has been previously published (10). The code for forcing adherence to the Wilson distribution is included in the Vagabond refinement package (https://vagabond.hginn.co.uk/) under a GPLv3 license. Compounds from the Fraunhofer IME Repurposing collection were obtained from the Fraunhofer Institute for Molecular Biology and Applied Ecology under a Material Transfer Agreement. Compounds from the Safe-in-man Library were kindly provided by Domp\u00e9 Farmaceutici S.p.A. Other materials are available from SeG or AM upon request. This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.\n\nPublished - 642.full.pdf
Submitted - 2020.11.12.378422v2.full.pdf
Supplemental Material - abf7945-Guenther-SM.pdf
Supplemental Material - abf7945_Guenther_Reproducibility-Checklist.pdf
Supplemental Material - abf7945_Guenther_Table-S1.xlsx
Supplemental Material - abf7945_Guenther_Table-S3.pdf
Supplemental Material - abf7945_Guenther_Table-S4.xlsx
Supplemental Material - abf7945_Guenther_Table-S7.xlsx
", "abstract": "The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (M^(pro)), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to M^(pro). In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.", "date": "2021-05-07", "date_type": "published", "publication": "Science", "volume": "372", "number": "6542", "publisher": "American Association for the Advancement of Science", "pagerange": "642-646", "id_number": "CaltechAUTHORS:20201113-100151878", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201113-100151878", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "European Union", "grant_number": "EXSCALATE4CoV" }, { "agency": "European Union", "grant_number": "101003551" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "EXC 2056" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "390715994" }, { "agency": "Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF)", "grant_number": "ExNet-0002" }, { "agency": "Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF)", "grant_number": "InternLabs-0011 \"HIR3X\"" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)", "grant_number": "05K16GUA" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)", "grant_number": "05K19GU4" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)", "grant_number": "05K20BI1" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)", "grant_number": "05K20FL1" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)", "grant_number": "16GW0277" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)", "grant_number": "031B0405D" }, { "agency": "Joachim-Herz-Stiftung Hamburg" }, { "agency": "Helmholtz Graduate School for the Structure of Matter", "grant_number": "HIDSS-0002" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "187/621-1" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "187/686-1" }, { "agency": "Slovenian Research Agency", "grant_number": "P1-0048" }, { "agency": "Slovenian Research Agency", "grant_number": "IO-0048" }, { "agency": "Boehringer Ingelheim Foundation" }, { "agency": "City of Hamburg" }, { "agency": "Bundesgesundheitsministerium" }, { "agency": "European Research Council (ERC)", "grant_number": "759661" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)", "grant_number": "01KI2039" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)", "grant_number": "05K16BH1" }, { "agency": "Leibniz Association", "grant_number": "SAW-2014-HPI-4" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1126/science.abf7945", "pmcid": "PMC8224385", "primary_object": { "basename": "abf7945_Guenther_Table-S3.pdf", "url": "https://authors.library.caltech.edu/records/r2x9d-af674/files/abf7945_Guenther_Table-S3.pdf" }, "related_objects": [ { "basename": "abf7945_Guenther_Table-S4.xlsx", "url": "https://authors.library.caltech.edu/records/r2x9d-af674/files/abf7945_Guenther_Table-S4.xlsx" }, { "basename": "abf7945_Guenther_Table-S7.xlsx", "url": "https://authors.library.caltech.edu/records/r2x9d-af674/files/abf7945_Guenther_Table-S7.xlsx" }, { "basename": "2020.11.12.378422v2.full.pdf", "url": "https://authors.library.caltech.edu/records/r2x9d-af674/files/2020.11.12.378422v2.full.pdf" }, { "basename": "642.full.pdf", "url": "https://authors.library.caltech.edu/records/r2x9d-af674/files/642.full.pdf" }, { "basename": "abf7945_Guenther_Reproducibility-Checklist.pdf", "url": "https://authors.library.caltech.edu/records/r2x9d-af674/files/abf7945_Guenther_Reproducibility-Checklist.pdf" }, { "basename": "abf7945-Guenther-SM.pdf", "url": "https://authors.library.caltech.edu/records/r2x9d-af674/files/abf7945-Guenther-SM.pdf" }, { "basename": "abf7945_Guenther_Table-S1.xlsx", "url": "https://authors.library.caltech.edu/records/r2x9d-af674/files/abf7945_Guenther_Table-S1.xlsx" } ], "pub_year": "2021", "author_list": "G\u00fcnther, Sebastian; Reinke, Patrick Y. 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Keith" } }, { "id": "Safford-Hannah", "name": { "family": "Safford", "given": "Hannah" }, "orcid": "0000-0001-9283-2602" }, { "id": "Sherchan-Samendra-P", "name": { "family": "Sherchan", "given": "Samendra P." }, "orcid": "0000-0002-0092-7928" }, { "id": "Shuster-William", "name": { "family": "Shuster", "given": "William" }, "orcid": "0000-0001-7688-0110" }, { "id": "Stalder-Thibault", "name": { "family": "Stalder", "given": "Thibault" }, "orcid": "0000-0002-8368-1889" }, { "id": "Wheeler-Robert-T", "name": { "family": "Wheeler", "given": "Robert T." }, "orcid": "0000-0003-3223-7021" }, { "id": "Korfmacher-Katrina-S", "name": { "family": "Korfmacher", "given": "Katrina Smith" }, "orcid": "0000-0002-8926-4082" } ] }, "title": "Wastewater Surveillance for SARS-CoV-2 on College Campuses: Initial Efforts, Lessons Learned, and Research Needs", "ispublished": "pub", "full_text_status": "public", "keywords": "Health, Toxicology and Mutagenesis; Public Health, Environmental and Occupational Health", "note": "\u00a9 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). \n\n(This article belongs to the Section Infectious Disease Epidemiology).\n\nThe authors would like to thank these individuals for their important contributions to this research and information about their colleges' wastewater surveillance systems: Aaron Best, Walter Betancourt, Cindi K. Brinkman, Logan Bullough, Lifang Chiang, Erik R. Coats, Ryan Dupont, David Freedman, Elmer Johnson, Rob Knight, Karl Korfmacher, Erin K. Lipp, Erin A. Mack, Christopher Maroney, Simona Matsoyan, Alan Palmer, Ian Pepper, Shalina Shahin, Lachlan Squair, Eva M. Top, and Rogelio Zuniga-Montanez. The content of this manuscript is solely the responsibility of the authors and does not necessarily represent the views of contributors, interviewees, or institutions included in the study. \n\nThis research was funded by the National Institute of Environmental Health Sciences, grant P30 ES001247 (to K.S.K.), and by the Catena Foundation (to K.L.N. and S.H.L.). The APC was supported by the Catena Foundation. \n\nAuthor Contributions. Conceptualization, S.H.-L., K.S.K., and K.L.N.; Methodology, S.H.-L., K.S.K., and K.L.N.; Validation, S.H.-L., K.S.K., S.K.D.L., T.S.R., S.M.P., J.L.R., C.B., H.S., T.D.C., P.J.M., D.K.R., T.S., K.M., A.B. (Aaron Bivins), A.B. (Andrea Bruder), S.P., H.N.B., P.B., D.A.L., S.K., R.T.W., W.S., and S.P.S.; Formal Analysis, S.H.-L. and K.S.K.; Investigation, S.H.-L., K.S.K., K.L.N., S.K.D.L., T.S.R., S.M.P., J.L.R., C.B., H.S., T.D.C., P.J.M., D.K.R., T.S., K.M., A.B. (Aaron Bivins), A.B. (Andrea Bruder), S.P., H.N.B., P.B., D.A.L., S.K., R.T.W., W.S., and S.P.S.; Resources, K.S.K. and K.L.N.; Data Curation, S.H.-L., K.S.K., S.K.D.L., T.S.R., S.M.P., J.L.R., C.B., H.S., T.D.C., P.J.M., D.K.R., T.S., K.M., A.B. (Aaron Bivins), A.B. (Andrea Bruder), S.P., H.N.B., P.B., D.A.L., S.K., R.T.W., W.S., and S.P.S.; Writing\u2014Original Draft Preparation, S.H.-L. and K.S.K.; Writing\u2014Review and Editing, S.H.-L., K.S.K., S.K.D.L., T.S.R., S.M.P., J.L.R., C.B., H.S., T.D.C., P.J.M., D.K.R., T.S., K.M., A.B. (Aaron Bivins), A.B. (Andrea Bruder), S.P., H.N.B., P.B., D.A.L., S.K., R.T.W., W.S., and S.P.S.; Visualization, K.S.K.; Supervision, K.S.K. and K.L.N.; Project Administration, S.H.-L. and K.S.K.; Funding Acquisition, K.S.K. and K.L.N. All authors have read and agreed to the published version of the manuscript. \n\nInstitutional Review Board Statement. The study was conducted according to the guidelines of the Declaration of Helsinki, and approved by the Institutional Review Boards of the University of California, Berkeley, CPHS protocol no. 2020-11-13796, approved 18 November 2020 and the University of Rochester, study ID STUDY00005616, approved 25 November 2020. \n\nInformed Consent Statement. All subjects gave their informed consent for inclusion in the study. Written participant consent was waived due to the determination of \"exempt\" status by the Institutional Review Boards at University of Rochester and the University of California Berkeley. \n\nThe authors declare no conflict of interest.", "abstract": "Wastewater surveillance for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging approach to help identify the risk of a coronavirus disease (COVID-19) outbreak. This tool can contribute to public health surveillance at both community (wastewater treatment system) and institutional (e.g., colleges, prisons, and nursing homes) scales. This paper explores the successes, challenges, and lessons learned from initial wastewater surveillance efforts at colleges and university systems to inform future research, development and implementation. We present the experiences of 25 college and university systems in the United States that monitored campus wastewater for SARS-CoV-2 during the fall 2020 academic period. We describe the broad range of approaches, findings, resources, and impacts from these initial efforts. These institutions range in size, social and political geographies, and include both public and private institutions. Our analysis suggests that wastewater monitoring at colleges requires consideration of local information needs, sewage infrastructure, resources for sampling and analysis, college and community dynamics, approaches to interpretation and communication of results, and follow-up actions. Most colleges reported that a learning process of experimentation, evaluation, and adaptation was key to progress. This process requires ongoing collaboration among diverse stakeholders including decision-makers, researchers, faculty, facilities staff, students, and community members.", "date": "2021-05-01", "date_type": "published", "publication": "International Journal of Environmental Research and Public Health", "volume": "18", "number": "9", "publisher": "MDPI", "pagerange": "Art. No. 4455", "id_number": "CaltechAUTHORS:20221215-540206000.10", "issn": "1660-4601", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221215-540206000.10", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P30 ES001247" }, { "agency": "Catena Foundation" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.3390/ijerph18094455", "pmcid": "PMC8122720", "pub_year": "2021", "author_list": "Harris-Lovett, Sasha; Nelson, Kara L.; et al." }, { "id": "https://authors.library.caltech.edu/records/j5494-5pq97", "eprint_id": 107591, "eprint_status": "archive", "datestamp": "2023-10-03 22:35:14", "lastmod": "2026-03-30 07:34:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Zijun", "name": { "family": "Wang", "given": "Zijun" }, "orcid": "0000-0002-2095-2151" }, { "name": { "family": "Schmidt", "given": "Fabian" } }, { "name": { "family": "Weisblum", "given": "Yiska" }, "orcid": "0000-0002-9249-1745" }, { "name": { "family": "Muecksch", "given": "Frauke" } }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "name": { "family": "Finkin", "given": "Shlomo" }, "orcid": "0000-0003-4474-2658" }, { "name": { "family": "Schaefer-Babajew", "given": "Dennis" }, "orcid": "0000-0002-5380-2950" }, { "name": { "family": "Cipolla", "given": "Melissa" }, "orcid": "0000-0001-8156-2512" }, { "name": { "family": "Gaebler", "given": "Christian" }, "orcid": "0000-0001-7295-8128" }, { "name": { "family": "Lieberman", "given": "Jenna A." }, "orcid": "0000-0002-5376-6697" }, { "name": { "family": "Oliveira", "given": "Thiago Y." }, "orcid": "0000-0002-2654-0879" }, { "id": "Yang-Zhi", "name": { "family": "Yang", "given": "Zhi" }, "orcid": "0000-0001-8680-3784" }, { "id": "Abernathy-Morgan-E", "name": { "family": "Abernathy", "given": "Morgan E." } }, { "id": "Huey-Tubman-Kathryn-E", "name": { "family": "Huey-Tubman", "given": "Kathryn E." }, "orcid": "0000-0002-4683-8138" }, { "name": { "family": "Hurley", "given": "Arlene" }, "orcid": "0000-0003-0575-0233" }, { "name": { "family": "Turroja", "given": "Martina" }, "orcid": "0000-0001-9640-0559" }, { "name": { "family": "West", "given": "Kamille A." }, "orcid": "0000-0001-8152-804X" }, { "name": { "family": "Gordon", "given": "Kristie" } }, { "name": { "family": "Millard", "given": "Katrina G." }, "orcid": "0000-0003-2247-3178" }, { "name": { "family": "Ramos", "given": "Victor" }, "orcid": "0000-0001-8572-1621" }, { "name": { "family": "Da Silva", "given": "Justin" } }, { "name": { "family": "Xu", "given": "Jianliang" } }, { "name": { "family": "Colbert", "given": "Robert A." }, "orcid": "0000-0001-6237-4575" }, { "name": { "family": "Patel", "given": "Roshni" } }, { "name": { "family": "Dizon", "given": "Juan" } }, { "name": { "family": "Unson-O'Brien", "given": "Cecille" } }, { "name": { "family": "Shimeliovich", "given": "Irina" } }, { "name": { "family": "Gazumyan", "given": "Anna" }, "orcid": "0000-0002-5976-9717" }, { "name": { "family": "Caskey", "given": "Marina" }, "orcid": "0000-0003-1727-8693" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Casellas", "given": "Rafael" }, "orcid": "0000-0001-9282-2287" }, { "name": { "family": "Hatziioannou", "given": "Theodora" }, "orcid": "0000-0002-7889-0766" }, { "name": { "family": "Bieniasz", "given": "Paul D." }, "orcid": "0000-0002-2368-3719" }, { "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" } ] }, "title": "mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants", "ispublished": "pub", "full_text_status": "public", "keywords": "Antibodies; Antimicrobial responses; SARS-CoV-2", "note": "\u00a9 The Author(s), under exclusive licence to Springer Nature Limited 2021. \n\nReceived 15 January 2021; Accepted 03 February 2021; Published 10 February 2021. \n\nWe thank all study participants who devoted time to our research; Drs. Barry Coller and Sarah Schlesinger, the Rockefeller University Hospital Clinical Research Support Office and nursing staff; Charles M. Rice and all members of the M.C.N. laboratory for helpful discussions and Ma\u0161a Jankovic for laboratory support; and Dr. Jost Vielmetter and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance. Electron microscopy was performed in the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy and we thank Drs. Songye Chen and Andrey Malyutin for technical assistance. This work was supported by NIH grant P01-AI138398-S1 (M.C.N. and P.J.B.) and 2U19AI111825 (M.C.N.); the Caltech Merkin Institute for Translational Research and P50 AI150464-13 (P.J.B.), a George Mason University Fast Grant (P.J.B.); R37-AI64003 to P.D.B.; R01AI78788 to T.H.; We thank Dr. Jost Vielmetter and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance C.O.B. is supported by the HHMI Hanna Gray and Burroughs Wellcome PDEP fellowships. C.G. was supported by the Robert S. Wennett Post-Doctoral Fellowship, in part by the National Center for Advancing Translational Sciences (National Institutes of Health Clinical and Translational Science Award program, grant UL1 TR001866), and by the Shapiro-Silverberg Fund for the Advancement of Translational Research. P.D.B. and M.C.N. are Howard Hughes Medical Institute Investigators. \n\nData availability statement: Data are provided in Extended Data Tables 1-7. The raw sequencing data and computer scripts associated with Fig. 2 have been deposited at Github (https://github.com/stratust/igpipeline). This study also uses data from \"A Public Database of Memory and Naive B-Cell Receptor Sequences\", PDB (6VYB and 6NB6) and from \"High frequency of shared clonotypes in human B cell receptor repertoires\". Cryo-EM maps associated with data reported in this manuscript will be deposited in the Electron Microscopy Data Bank (EMDB: https://www.ebi.ac.uk/pdbe/emdb/) under accession codes EMD-23393 (C601-S), EMD-23394 (C603-S), EMD-23395 (C643-S), EMD-23396 (C663-S), EMD-23397 (C666-S), EMD-23398 (C669-S), and EMD-23399 (C670-S). \n\nCode availability statement: Computer code to process the antibody sequences is available at GitHub (https://github.com/stratust/igpipeline). \n\nAuthor contributions: These authors contributed equally: Zijun Wang, Fabian Schmidt, Yiska Weisblum, Frauke Muecksch, Christopher O. Barnes, Shlomo Finkin, Dennis Schaefer-Babajew, Melissa Cipolla, Christian Gaebler, Jenna A. Lieberman. \n\nP.D.B., P.J.B., R.C., T.H., M.C.N., Z.W., F.S., Y.W., F.M., C.O.B, S.F., D.S.B., M.Cipolla. conceived, designed and analyzed the experiments. M.Caskey, C.G., J.A.L., K.W., D.S.B. designed clinical protocols Z.W., F.S., Y.W., F.M., C.O.B., S.F., D.S.B., M.Cipolla, J.D.S., A.G., Z.Y., M.E.A., K.E.H. carried out experiments. C.G., M.Caskey, K.W.D., R.A.C., A.H., K.G.M. recruited participants and executed clinical protocols. I.S., R.P, J.D., J.X. and C.U.O. processed clinical samples. T.Y.O. and V.R. performed bioinformatic analysis. R.C., P.D.B., P.J.B., T.H., and M.C.N. wrote the manuscript with input from all co-authors. \n\nCompeting interests: The Rockefeller University has filed a provisional patent application in connection with this work on which Z.W. and M.C.N. are inventors (US patent 63/199, 676). \n\nPeer review information: Nature thanks the anonymous reviewers for their contribution to the peer review of this work.\n\nSubmitted - 20210115-426911v2full.pdf
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", "abstract": "Here we report on the antibody and memory B cell responses in a cohort of 20 volunteers who received either the Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccines. Eight weeks after the second vaccine injection volunteers showed high levels of IgM, and IgG anti-SARS-CoV-2 spike protein (S) and receptor binding domain (RBD) binding titers. Moreover, the plasma neutralizing activity, and the relative numbers of RBD-specific memory B cells were equivalent to individuals who recovered from natural infection. However, activity against SARS-CoV-2 variants encoding E484K or N501Y or the K417N:E484K:N501Y combination was reduced by a small but significant margin. Vaccine-elicited monoclonal antibodies (mAbs) potently neutralize SARS-CoV-2, targeting a number of different RBD epitopes in common with mAbs isolated from infected donors. However, neutralization by 14 of the 17 most potent mAbs tested was reduced or abolished by either K417N, or E484K, or N501Y mutations. Notably, the same mutations were selected when recombinant vesicular stomatitis virus (rVSV)/SARS-CoV-2 S was cultured in the presence of the vaccine elicited mAbs. Taken together the results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants, and that mRNA vaccines may need to be updated periodically to avoid potential loss of clinical efficacy.", "date": "2021-04-22", "date_type": "published", "publication": "Nature", "volume": "592", "number": "7855", "publisher": "Nature Publishing Group", "pagerange": "616-622", "id_number": "CaltechAUTHORS:20210120-121820490", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210120-121820490", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01-AI138398-S1" }, { "agency": "NIH", "grant_number": "2U19AI111825" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "NIH", "grant_number": "P50 AI150464-13" }, { "agency": "George Mason University" }, { "agency": "NIH", "grant_number": "R37-AI64003" }, { "agency": "NIH", "grant_number": "R01AI78788" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Robert S. Wennett Postdoctoral Fellowship" }, { "agency": "NIH", "grant_number": "UL1 TR001866" }, { "agency": "Shapiro-Silverberg Fund for the Advancement of Translational Research" } ] }, "local_group": { "items": [ { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41586-021-03324-6", "pmcid": "PMC7836122", "primary_object": { "basename": "41586_2021_3324_MOESM4_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/j5494-5pq97/files/41586_2021_3324_MOESM4_ESM.xlsx" }, "related_objects": [ { "basename": "41586_2021_3324_MOESM5_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/j5494-5pq97/files/41586_2021_3324_MOESM5_ESM.xlsx" }, { "basename": "41586_2021_3324_MOESM6_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/j5494-5pq97/files/41586_2021_3324_MOESM6_ESM.xlsx" }, { "basename": "41586_2021_3324_MOESM8_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/j5494-5pq97/files/41586_2021_3324_MOESM8_ESM.xlsx" }, { "basename": "41586_2021_3324_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/j5494-5pq97/files/41586_2021_3324_MOESM1_ESM.pdf" }, { "basename": "41586_2021_3324_MOESM2_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/j5494-5pq97/files/41586_2021_3324_MOESM2_ESM.xlsx" }, { "basename": "41586_2021_3324_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/j5494-5pq97/files/41586_2021_3324_MOESM3_ESM.xlsx" }, { "basename": "41586_2021_3324_MOESM7_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/j5494-5pq97/files/41586_2021_3324_MOESM7_ESM.xlsx" }, { "basename": "20210115-426911v2full.pdf", "url": "https://authors.library.caltech.edu/records/j5494-5pq97/files/20210115-426911v2full.pdf" } ], "pub_year": "2021", "author_list": "Wang, Zijun; Schmidt, Fabian; et al." }, { "id": "https://authors.library.caltech.edu/records/9avj8-66164", "eprint_id": 108905, "eprint_status": "archive", "datestamp": "2023-08-22 09:36:57", "lastmod": "2026-03-29 14:51:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fan-Hao", "name": { "family": "Fan", "given": "Hao" }, "orcid": "0000-0002-6947-9609" }, { "id": "Wang-Yuan", "name": { "family": "Wang", "given": "Yuan" }, "orcid": "0000-0001-6657-8401" }, { "id": "Zhao-Chuanfeng", "name": { "family": "Zhao", "given": "Chuanfeng" }, "orcid": "0000-0002-5196-3996" }, { "id": "Yang-Yikun", "name": { "family": "Yang", "given": "Yikun" }, "orcid": "0000-0001-7427-6876" }, { "id": "Yang-Xingchuan", "name": { "family": "Yang", "given": "Xingchuan" } }, { "id": "Sun-Yue", "name": { "family": "Sun", "given": "Yue" } }, { "id": "Jiang-Shuyi", "name": { "family": "Jiang", "given": "Shuyi" } } ] }, "title": "The Role of Primary Emission and Transboundary Transport in the Air Quality Changes During and After the COVID\u201019 Lockdown in China", "ispublished": "pub", "full_text_status": "public", "keywords": "air pollutants; China; COVID\u201019; emission; lockdown", "note": "\u00a9 2021. American Geophysical Union. \n\nIssue Online: 09 April 2021; Version of Record online: 09 April 2021; Accepted manuscript online: 27 March 2021; Manuscript accepted: 15 March 2021; Manuscript revised: 11 March 2021; Manuscript received: 09 October 2020. \n\nThis work was supported by the National Natural Science Foundation of China (Grants 41925022, 91837204), the State Key Laboratory of Earth Surface Processes and Resource Ecology, and the Fundamental Research Funds for the Central Universities. \n\nData Availability Statement: The air pollutant observation data and reanalysis data used in this article can be obtained from https://zenodo.org/record/4074307.\n\nPublished - 2020GL091065.pdf
Supplemental Material - 2020gl091065-sup-0001-supporting_information_si-s01.docx
", "abstract": "In late January 2020, China's rapid and strict control measures to curb the COVID\u201019 spread led to a sharp halt in socio\u2010economic activity and a significant reduction in emissions. Using the ground\u2010based observational data, the authors synergistically quantify the nation\u2010wide variations of major air pollutant as well as meteorology during and after the lockdown. Their concentrations (except O\u2083) exhibited significant reduction during February and March 2020, by more than 24% during the lockdown compared with the earlier time period and by more than 17% compared with that in the same period in 2019. In contrast, ozone increased rapidly by about 60% across the country during the lockdown. Abnormal increases in carbon monoxide and particulate matter concentrations in southwest China are attributed to the severe wildfires in Southeast Asia. The concentration of air pollutants bounced back rapidly after the full\u2010scale reopen in March 2020, indicating the decisive role of emissions in the pollution formation.", "date": "2021-04-16", "date_type": "published", "publication": "Geophysical Research Letters", "volume": "48", "number": "7", "publisher": "American Geophysical Union", "pagerange": "Art. No. e2020GL091065", "id_number": "CaltechAUTHORS:20210430-124915477", "issn": "0094-8276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210430-124915477", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Natural Science Foundation of China", "grant_number": "41925022" }, { "agency": "National Natural Science Foundation of China", "grant_number": "91837204" }, { "agency": "State Key Laboratory of Earth Surface Processes and Resource Ecology" }, { "agency": "Fundamental Research Funds for the Central Universities" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1029/2020gl091065", "primary_object": { "basename": "2020gl091065-sup-0001-supporting_information_si-s01.docx", "url": "https://authors.library.caltech.edu/records/9avj8-66164/files/2020gl091065-sup-0001-supporting_information_si-s01.docx" }, "related_objects": [ { "basename": "2020GL091065.pdf", "url": "https://authors.library.caltech.edu/records/9avj8-66164/files/2020GL091065.pdf" } ], "pub_year": "2021", "author_list": "Fan, Hao; Wang, Yuan; et al." }, { "id": "https://authors.library.caltech.edu/records/3n2h6-vbx03", "eprint_id": 106451, "eprint_status": "archive", "datestamp": "2023-10-03 22:33:01", "lastmod": "2026-03-30 06:34:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gaebler-Christian", "name": { "family": "Gaebler", "given": "Christian" }, "orcid": "0000-0001-7295-8128" }, { "name": { "family": "Wang", "given": "Zijun" }, "orcid": "0000-0002-2095-2151" }, { "name": { "family": "Lorenzi", "given": "Julio C. C." } }, { "name": { "family": "Muecksch", "given": "Frauke" } }, { "name": { "family": "Finkin", "given": "Shlomo" }, "orcid": "0000-0003-4474-2658" }, { "name": { "family": "Tokuyama", "given": "Minami" } }, { "name": { "family": "Cho", "given": "Alice" } }, { "name": { "family": "Jankovic", "given": "Mila" } }, { "name": { "family": "Schaefer-Babajew", "given": "Dennis" }, "orcid": "0000-0002-5380-2950" }, { "name": { "family": "Oliveira", "given": "Thiago Y." }, "orcid": "0000-0002-2654-0879" }, { "name": { "family": "Cipolla", "given": "Melissa" }, "orcid": "0000-0001-8156-2512" }, { "name": { "family": "Viant", "given": "Charlotte" } }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "name": { "family": "Bram", "given": "Yaron" } }, { "name": { "family": "Breton", "given": "Ga\u00eblle" } }, { "name": { "family": "H\u00e4ggl\u00f6f", "given": "Thomas" } }, { "name": { "family": "Mendoza", "given": "Pilar" } }, { "name": { "family": "Hurley", "given": "Arlene" }, "orcid": "0000-0003-0575-0233" }, { "name": { "family": "Turroja", "given": "Martina" }, "orcid": "0000-0001-9640-0559" }, { "name": { "family": "Gordon", "given": "Kristie" } }, { "name": { "family": "Millard", "given": "Katrina G." }, "orcid": "0000-0003-2247-3178" }, { "name": { "family": "Ramos", "given": "Victor" }, "orcid": "0000-0001-8572-1621" }, { "name": { "family": "Schmidt", "given": "Fabian" } }, { "name": { "family": "Weisblum", "given": "Yiska" }, "orcid": "0000-0002-9249-1745" }, { "name": { "family": "Jha", "given": "Divya" } }, { "name": { "family": "Tankelevich", "given": "Michael" } }, { "name": { "family": "Martinez-Delgado", "given": "Gustavo" } }, { "name": { "family": "Yee", "given": "Jim" } }, { "name": { "family": "Patel", "given": "Roshni" } }, { "name": { "family": "Dizon", "given": "Juan" } }, { "name": { "family": "Unson-O'Brien", "given": "Cecille" } }, { "name": { "family": "Shimeliovich", "given": "Irina" } }, { "name": { "family": "Robbiani", "given": "Davide F." }, "orcid": "0000-0001-7379-3484" }, { "name": { "family": "Zhao", "given": "Zhen" } }, { "name": { "family": "Gazumyan", "given": "Anna" }, "orcid": "0000-0002-5976-9717" }, { "name": { "family": "Schwartz", "given": "Robert E." } }, { "name": { "family": "Hatziioannou", "given": "Theodora" }, "orcid": "0000-0002-7889-0766" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Mehandru", "given": "Saurabh" } }, { "name": { "family": "Bieniasz", "given": "Paul D." }, "orcid": "0000-0002-2368-3719" }, { "name": { "family": "Caskey", "given": "Marina" }, "orcid": "0000-0003-1727-8693" }, { "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" } ] }, "title": "Evolution of antibody immunity to SARS-CoV-2", "ispublished": "pub", "full_text_status": "public", "keywords": "Antimicrobial responses; Humoral immunity; SARS-CoV-2", "note": "\u00a9 2021 Nature Publishing Group. \n\nReceived 03 November 2020; Accepted 06 January 2021; Published 18 January 2021. \n\nWe thank all study participants who devoted time to our research; B. Coller and S. Schlesinger, the Rockefeller University Hospital Clinical Research Support Office and nursing staff; M. Okawa Frank and R. B. Darnell for SARS-CoV-2 saliva PCR testing; C. M. Rice and all members of the M.C.N. laboratory for helpful discussions; M. Jankovic for laboratory support; and J. Vielmetter and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance. This work was supported by NIH grant P01-AI138398-S1 (M.C.N. and P.J.B.) and 2U19AI111825 (M.C.N.).; the Caltech Merkin Institute for Translational Research and P50 AI150464-13 (P.J.B.), George Mason University Fast Grant (D.F.R. and P.J.B.) and the European ATAC grant EC 101003650 (D.F.R.); R37-AI64003 to P.D.B.; R01AI78788 to T. Hatziioannou; NCI R01CA234614, NIAID 2R01AI107301, NIDDK R01DK121072 and 1RO3DK117252 to R.E.S., NIH NIDDK R01 DK123749 01S1 to S.M. C.O.B. is supported by the HHMI Hanna Gray and Burroughs Wellcome PDEP fellowships. R.E.S. is an Irma Hirschl Trust Research Award Scholar. M.T. is supported by the Digestive Disease Research Foundation (DDRF). C.G. was supported by the Robert S. Wennett Post-Doctoral Fellowship, in part by the National Center for Advancing Translational Sciences (National Institutes of Health Clinical and Translational Science Award programme, grant UL1 TR001866), and by the Shapiro\u2013Silverberg Fund for the Advancement of Translational Research. P.D.B. and M.C.N. are Howard Hughes Medical Institute Investigators. \n\nData availability: Data are provided in Supplementary Tables 1\u20138. The raw sequencing data and computer scripts associated with Fig. 2 have been deposited at https://github.com/stratust/igpipeline. This study also uses data from a DRYAD accession linked to ref. 57 (https://doi.org/10.5061/dryad.35ks2), the Protein Data Bank (accession codes 6VYB and 6NB6) and ref. 53. \n\nCode availability: Computer code to process the antibody sequences is available at GitHub (https://github.com/stratust/igpipeline). \n\nAuthor Contributions: C.G., P.D.B., P.J.B., T. Hatziioannou, S.M. and M.C.N. conceived, designed and analysed the experiments. D.F.R., M. Caskey and C.G. designed clinical protocols. Z.W., J.C.C.L., F.M., S.F., M. Tokuyama, A.C., M.J., D.S.-B., F.S., Y.W., T. H\u00e4ggl\u00f6f, P.M., G.B., C.V., C.O.B., K.G., D.J., J.Y., G.M.-D., Y.B., R.E.S. and Z.Z. carried out experiments. A.G. and M. Cipolla produced antibodies. A.H., D.S.-B., M. Turroja, K.G.M., M. Tankelevich, C.G. and M. Caskey recruited participants and executed clinical protocols. I.S., R.P, J.D. and C.U.-O. processed clinical samples. T.Y.O. and V.R. performed bioinformatic analysis. C.G, P.D.B., P.J.B., T. Hatziioannou, S.M. and M.C.N. wrote the manuscript with input from all co-authors. \n\nCompeting interests: The Rockefeller University has filed a provisional patent application in connection with this work on which D.F.R. and M.C.N. are inventors (US patent 63/021,387). R.E.S. is on the scientific advisory board of Miromatrix Inc and is a consultant and speaker for Alnylam Inc. S.M. has served as a consultant for Takeda Pharmaceuticals, Morphic and Glaxo Smith Kline. Z.Z. received seed instruments and sponsored travel from ET Healthcare. \n\nPeer review information: Nature thanks Michael Laue, Stanley Perlman and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.\n\nAccepted Version - nihms-1705497.pdf
Submitted - 20201103-367391v2-full.pdf
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", "abstract": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected 78 million individuals and is responsible for over 1.7 million deaths to date. Infection is associated with the development of variable levels of antibodies with neutralizing activity, which can protect against infection in animal models. Antibody levels decrease with time, but, to our knowledge, the nature and quality of the memory B cells that would be required to produce antibodies upon reinfection has not been examined. Here we report on the humoral memory response in a cohort of 87 individuals assessed at 1.3 and 6.2 months after infection with SARS-CoV-2. We find that titres of IgM and IgG antibodies against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 decrease significantly over this time period, with IgA being less affected. Concurrently, neutralizing activity in plasma decreases by fivefold in pseudotype virus assays. By contrast, the number of RBD-specific memory B cells remains unchanged at 6.2 months after infection. Memory B cells display clonal turnover after 6.2 months, and the antibodies that they express have greater somatic hypermutation, resistance to RBD mutations and increased potency, indicative of continued evolution of the humoral response. Immunofluorescence and PCR analyses of intestinal biopsies obtained from asymptomatic individuals at 4 months after the onset of coronavirus disease 2019 (COVID-19) revealed the persistence of SARS-CoV-2 nucleic acids and immunoreactivity in the small bowel of 7 out of 14 individuals. We conclude that the memory B cell response to SARS-CoV-2 evolves between 1.3 and 6.2 months after infection in a manner that is consistent with antigen persistence.", "date": "2021-03-25", "date_type": "published", "publication": "Nature", "volume": "591", "number": "7851", "publisher": "Nature Publishing Group", "pagerange": "639-644", "id_number": "CaltechAUTHORS:20201105-121857214", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201105-121857214", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01-AI138398-S1" }, { "agency": "NIH", "grant_number": "2U19AI111825" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "NIH", "grant_number": "P50 AI150464-13" }, { "agency": "George Mason University" }, { "agency": "European ATAC Consortium", "grant_number": "EC 101003650" }, { "agency": "NIH", "grant_number": "R37-AI64003" }, { "agency": "NIH", "grant_number": "R01AI78788" }, { "agency": "NIH", "grant_number": "R01CA234614" }, { "agency": "NIH", "grant_number": "2R01AI107301" }, { "agency": "NIH", "grant_number": "R01DK121072" }, { "agency": "NIH", "grant_number": "1RO3DK117252" }, { "agency": "NIH", "grant_number": "R01 DK123749 01S1" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Irma Hirschl Trust Research Award" }, { "agency": "Digestive Disease Research Foundation" }, { "agency": "Robert S. Wennett Postdoctoral Fellowship" }, { "agency": "NIH", "grant_number": "UL1 TR001866" }, { "agency": "Shapiro-Silverberg Fund for the Advancement of Translational Research" } ] }, "local_group": { "items": [ { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41586-021-03207-w", "pmcid": "PMC8221082", "primary_object": { "basename": "41586_2021_3207_Fig12_ESM.webp", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig12_ESM.webp" }, "related_objects": [ { "basename": "41586_2021_3207_Fig13_ESM.webp", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig13_ESM.webp" }, { "basename": "41586_2021_3207_Fig6_ESM.jpeg", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig6_ESM.jpeg" }, { "basename": "41586_2021_3207_Fig7_ESM.jpg", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig7_ESM.jpg" }, { "basename": "41586_2021_3207_Fig9_ESM.jpg", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig9_ESM.jpg" }, { "basename": "41586_2021_3207_MOESM4_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_MOESM4_ESM.xlsx" }, { "basename": "41586_2021_3207_MOESM9_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_MOESM9_ESM.xlsx" }, { "basename": "41586_2021_3207_Fig10_ESM.jpg", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig10_ESM.jpg" }, { "basename": "41586_2021_3207_Fig15_ESM.webp", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig15_ESM.webp" }, { "basename": "41586_2021_3207_Fig8_ESM.jpg", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig8_ESM.jpg" }, { "basename": "41586_2021_3207_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_MOESM3_ESM.xlsx" }, { "basename": "41586_2021_3207_MOESM7_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_MOESM7_ESM.xlsx" }, { "basename": "nihms-1705497.pdf", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/nihms-1705497.pdf" }, { "basename": "20201103-367391v2-full.pdf", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/20201103-367391v2-full.pdf" }, { "basename": "41586_2021_3207_Fig11_ESM.jpg", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig11_ESM.jpg" }, { "basename": "41586_2021_3207_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_MOESM1_ESM.pdf" }, { "basename": "41586_2021_3207_MOESM2_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_MOESM2_ESM.xlsx" }, { "basename": "41586_2021_3207_MOESM5_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_MOESM5_ESM.xlsx" }, { "basename": "41586_2021_3207_MOESM8_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_MOESM8_ESM.xlsx" }, { "basename": "41586_2021_3207_Fig14_ESM.webp", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_Fig14_ESM.webp" }, { "basename": "41586_2021_3207_MOESM6_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/3n2h6-vbx03/files/41586_2021_3207_MOESM6_ESM.xlsx" } ], "pub_year": "2021", "author_list": "Gaebler, Christian; Wang, Zijun; et al." }, { "id": "https://authors.library.caltech.edu/records/74cpm-pe049", "eprint_id": 106739, "eprint_status": "archive", "datestamp": "2023-08-20 02:01:49", "lastmod": "2026-03-30 06:12:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bain-William-G", "name": { "family": "Bain", "given": "William G." }, "orcid": "0000-0001-8506-0552" }, { "id": "Pe\u00f1aloza-Hern\u00e1n-F", "name": { "family": "Pe\u00f1aloza", "given": "Hern\u00e1n F." }, "orcid": "0000-0002-1593-678X" }, { "id": "Ladinsky-Mark-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "van-der-Geest-Rick", "name": { "family": "van der Geest", "given": "Rick" }, "orcid": "0000-0002-1973-5934" }, { "id": "Sullivan-Mara", "name": { "family": "Sullivan", "given": "Mara" }, "orcid": "0000-0003-3772-1998" }, { "id": "Ross-Mark", "name": { "family": "Ross", "given": "Mark" } }, { "id": "Kitsios-Georgios-D", "name": { "family": "Kitsios", "given": "Georgios D." } }, { "id": "Meth\u00e9-Barbara-A", "name": { "family": "Meth\u00e9", "given": "Barbara A." }, "orcid": "0000-0001-8711-1448" }, { "id": "McVerry-Bryan-J", "name": { "family": "McVerry", "given": "Bryan J." }, "orcid": "0000-0002-1175-4874" }, { "id": "Morris-Alison", "name": { "family": "Morris", "given": "Alison" }, "orcid": "0000-0002-7290-6536" }, { "id": "Watson-Alan-M", "name": { "family": "Watson", "given": "Alan M." } }, { "id": "Watkins-Simon-C", "name": { "family": "Watkins", "given": "Simon C." } }, { "id": "St-Croix-Claudette-M", "name": { "family": "St. Croix", "given": "Claudette M." }, "orcid": "0000-0003-0794-4939" }, { "id": "Stolz-Donna-B", "name": { "family": "Stolz", "given": "Donna B." }, "orcid": "0000-0002-1833-7010" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Lee-Janet-S", "name": { "family": "Lee", "given": "Janet S." } } ] }, "title": "Lower Respiratory Tract Myeloid Cells Harbor SARS-Cov-2 and Display an Inflammatory Phenotype", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Published by Elsevier Inc. under license from the American College of Chest Physicians. Under an Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). \n\nReceived 19 September 2020, Revised 26 October 2020, Accepted 28 October 2020, Available online 18 November 2020. \n\nThis work was supported by Career Development Award Number IK2 BX004886 from the United States Department of Veterans Affairs Biomedical Laboratory R&D (BLRD) Service (W. Bain); the National Heart, Lung, and Blood Institute of the National Institutes of Health under Award Numbers K23 HL129987 (G. Kitsios); P01HL114453 (J. Lee, B. McVerry); and R01 HL136143, R01 HL142084, K24 HL143285 (J. Lee) and R21 HL143091 (B. A. Meth\u00e9); and the UPMC Immune Therapy and Transplant Center (A. Morris). Electron and confocal microscopy at the University of Pittsburgh Center for Biologic Imaging was supported by National Institutes of Health Office of the Director awards S10OD010625 and S10OD019973 (S. Watkins). Electron tomography at the California Institute of Technology was supported by a George Mason University Fast Grant (P. Bjorkman), National Institute of Allergy and Infectious Diseases (NIAID) Grant 2 P50 AI150464 (P. Bjorkman). Electron microscopy was performed with a TF-30 electron microscope that is maintained by the California Institute of Technology Kavli Nanoscience Institute. \n\nAuthor contributions: W. Bain takes responsibility for the content of this manuscript. W. Bain enrolled patients, collected samples, performed the experiments, designed, analyzed, and interpreted the data, and wrote the manuscript. H. Pe\u00f1aloza and M. Ladinsky performed the experiments and designed and interpreted the data. R. van der Geest, M. Sullivan, and M. Ross performed the experiments and revised the work for important intellectual content. G. Kitsios enrolled patients, collected samples, provided critical input to the design of the experiments, and revised the work for important intellectual content. B. A. Meth\u00e9, B. McVerry, and A. Morris provided critical input to design of the experiments and revised the work for important intellectual content. A. Watson and S. Watkins provided critical input to the design of the experiments, expert imaging input, and revised the work for important intellectual content. C. St Croix and D. Stolz performed the experiments, designed and interpreted the data, and revised the work for important intellectual content. P. Bjorkman conceived, designed, interpreted the data, and revised the work for important intellectual content. J. Lee conceived, designed, analyzed, interpreted the data, and wrote the manuscript. \n\nRole of sponsors: The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health, Department of Veterans Affairs, or any other sponsoring agency. \n\nOther contributions: The authors thank the patients and patient families who have enrolled in the University of Pittsburgh Acute Lung Injury Registry; the physicians, nurses, respiratory therapists, and other staff at the University of Pittsburgh Medical Center Presbyterian and Shadyside Hospital ICUs for assistance with coordination and collection of endotracheal aspirate samples; Nicole Bensen, BS, and Caitlin Schaefer, MPH, at the University of Pittsburgh for assistance with identifying and consenting patients and their families and for assistance with collection of endotracheal aspirate samples; and Heather Michael, BS, and Lauren Furguiele, BS, at the University of Pittsburgh for assistance with processing endotracheal aspirate samples.\n\nPublished - 1-s2.0-S0012369220351576-main.pdf
Submitted - 2020.08.11.20171967v1.full.pdf
", "abstract": "Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) pneumonia may induce an aberrant immune response with brisk recruitment of myeloid cells into the airspaces. Although the clinical implications are unclear, others have suggested that infiltrating myeloid cells may contribute to morbidity and mortality rates during SARS-CoV-2 infection. However, few reports have characterized myeloid cells from the lower respiratory tract, which appears to be the primary site of viral-induced disease, during severe SARS-CoV-2 pneumonia.", "date": "2021-03", "date_type": "published", "publication": "CHEST", "volume": "159", "number": "3", "publisher": "Elsevier", "pagerange": "963-966", "id_number": "CaltechAUTHORS:20201119-133947323", "issn": "0012-3692", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201119-133947323", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Veterans Affairs", "grant_number": "IK2 BX004886" }, { "agency": "NIH", "grant_number": "K23 HL129987" }, { "agency": "NIH", "grant_number": "P01HL114453" }, { "agency": "NIH", "grant_number": "R01 HL136143" }, { "agency": "NIH", "grant_number": "R01 HL142084" }, { "agency": "NIH", "grant_number": "K24 HL143285" }, { "agency": "NIH", "grant_number": "R21 HL143091" }, { "agency": "University of Pittsburgh" }, { "agency": "NIH", "grant_number": "S10OD010625" }, { "agency": "NIH", "grant_number": "S10OD019973" }, { "agency": "George Mason University" }, { "agency": "NIH", "grant_number": "2 P50 AI150464" } ] }, "local_group": { "items": [ { "id": "Kavli-Nanoscience-Institute" }, { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.chest.2020.10.083", "pmcid": "PMC7671922", "primary_object": { "basename": "1-s2.0-S0012369220351576-main.pdf", "url": "https://authors.library.caltech.edu/records/74cpm-pe049/files/1-s2.0-S0012369220351576-main.pdf" }, "related_objects": [ { "basename": "2020.08.11.20171967v1.full.pdf", "url": "https://authors.library.caltech.edu/records/74cpm-pe049/files/2020.08.11.20171967v1.full.pdf" } ], "pub_year": "2021", "author_list": "Bain, William G.; Pe\u00f1aloza, Hern\u00e1n F.; et al." }, { "id": "https://authors.library.caltech.edu/records/jk4kd-j8n07", "eprint_id": 107358, "eprint_status": "archive", "datestamp": "2023-08-20 01:52:52", "lastmod": "2026-03-30 06:03:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ming-Yi", "name": { "family": "Ming", "given": "Yi" }, "orcid": "0000-0002-5324-1305" }, { "id": "Lin-Pu", "name": { "family": "Lin", "given": "Pu" }, "orcid": "0000-0003-2577-6094" }, { "id": "Naik-Vaishali", "name": { "family": "Naik", "given": "Vaishali" }, "orcid": "0000-0002-2254-1700" }, { "id": "Paulot-Fabien", "name": { "family": "Paulot", "given": "Fabien" }, "orcid": "0000-0001-7534-4922" }, { "id": "Horowitz-Larry-W", "name": { "family": "Horowitz", "given": "Larry W." }, "orcid": "0000-0002-5886-3314" }, { "id": "Ginoux-Paul-A", "name": { "family": "Ginoux", "given": "Paul A." }, "orcid": "0000-0003-3642-2988" }, { "id": "Ramaswamy-Venkatachalam", "name": { "family": "Ramaswamy", "given": "V." }, "orcid": "0000-0002-1984-6423" }, { "id": "Loeb-Norman-G", "name": { "family": "Loeb", "given": "Norman G." }, "orcid": "0000-0002-2538-9644" }, { "id": "Shen-Zhaoyi", "name": { "family": "Shen", "given": "Zhaoyi" }, "orcid": "0000-0002-0444-4720" }, { "id": "Singer-Clare-E", "name": { "family": "Singer", "given": "Clare E." }, "orcid": "0000-0002-1708-0997" }, { "id": "Ward-Ryan-X", "name": { "family": "Ward", "given": "Ryan X." }, "orcid": "0000-0003-2317-3310" }, { "id": "Zhang-Zhibo", "name": { "family": "Zhang", "given": "Zhibo" }, "orcid": "0000-0001-9491-1654" }, { "id": "Bellouin-Nicolas", "name": { "family": "Bellouin", "given": "Nicolas" }, "orcid": "0000-0003-2109-9559" } ] }, "title": "Assessing the Influence of COVID\u201019 on the Shortwave Radiative Fluxes Over the East Asian Marginal Seas", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020. The Authors. This article has been contributed to by US Government employees and their work is in the public domain in the USA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. \n\nIssue Online: 02 February 2021; Version of Record online: 02 February 2021; Accepted manuscript online: 29 December 2020; Manuscript accepted: 23 December 2020; Manuscript revised: 21 December 2020; Manuscript received: 12 November 2020. \n\nThe authors thank L. Donner and D. Paynter for their helpful comments on an early draft. Z. Shen acknowledges support from the Ronald and Maxine Linde Challenge for Climate Science Fund. C. E. Singer acknowledges support from the NSF Graduate Research Fellowship under Grant No. DGE\u20101745301. R. X. Ward. acknowledges fellowship support from the Resnick Sustainability Institute at Caltech. \n\nData Availability Statement: The AQUA/MODIS MYD08 L3 Global 1 Deg. data set was acquired from the Level\u20101 and Atmosphere Archive and Distribution System (LAADS) Distributed Active Archive Center (DAAC), located in the Goddard Space Flight Center in Greenbelt, Maryland (https://ladsweb.nascom.nasa.gov/). The CERES data were obtained from the NASA Langley Research Center Atmospheric Science Data Center (https://doi.org/10.5067/TERRA-AQUA/CERES/EBAF-TOA_L3B004.1). Primary AM4 simulation results that may be used to produce the plots are available are available online (https://data.caltech.edu/records/1666).\n\nPublished - 2020GL091699.pdf
Supplemental Material - 2020gl091699-sup-0001-supporting_information_si-s01.docx
", "abstract": "The Coronavirus Disease 2019 (COVID\u201019) pandemic led to a widespread reduction in aerosol emissions. Using satellite observations and climate model simulations, we study the underlying mechanisms of the large decreases in solar clear\u2010sky reflection (3.8 W m\u207b\u00b2 or 7%) and aerosol optical depth (0.16 W m\u207b\u00b2 or 32%) observed over the East Asian Marginal Seas in March 2020. By separating the impacts from meteorology and emissions in the model simulations, we find that about one\u2010third of the clear\u2010sky anomalies can be attributed to pandemic\u2010related emission reductions, and the rest to weather variability and long\u2010term emission trends. The model is skillful at reproducing the observed interannual variations in solar all\u2010sky reflection, but no COVID\u201019 signal is discerned. The current observational and modeling capabilities will be critical for monitoring, understanding, and predicting the radiative forcing and climate impacts of the ongoing crisis.", "date": "2021-02-16", "date_type": "published", "publication": "Geophysical Research Letters", "volume": "48", "number": "3", "publisher": "American Geophysical Union", "pagerange": "Art. No. e2020GL091699", "id_number": "CaltechAUTHORS:20210107-101118570", "issn": "0094-8276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210107-101118570", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ronald And Maxine Linde Center for Global Environmental Science" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" }, { "agency": "Resnick Sustainability Institute" } ] }, "local_group": { "items": [ { "id": "Resnick-Sustainability-Institute" }, { "id": "COVID-19" } ] }, "doi": "10.1029/2020gl091699", "primary_object": { "basename": "2020GL091699.pdf", "url": "https://authors.library.caltech.edu/records/jk4kd-j8n07/files/2020GL091699.pdf" }, "related_objects": [ { "basename": "2020gl091699-sup-0001-supporting_information_si-s01.docx", "url": "https://authors.library.caltech.edu/records/jk4kd-j8n07/files/2020gl091699-sup-0001-supporting_information_si-s01.docx" } ], "pub_year": "2021", "author_list": "Ming, Yi; Lin, Pu; et al." }, { "id": "https://authors.library.caltech.edu/records/srcxm-mek65", "eprint_id": 106725, "eprint_status": "archive", "datestamp": "2023-10-03 22:33:46", "lastmod": "2026-03-30 17:20:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cohen-Alexander-A", "name": { "family": "Cohen", "given": "Alexander A." }, "orcid": "0000-0002-2818-656X" }, { "id": "Gnanapragasam-Priyanthi-N-P", "name": { "family": "Gnanapragasam", "given": "Priyanthi N. P." } }, { "id": "Lee-Yu-E", "name": { "family": "Lee", "given": "Yu E." } }, { "id": "Hoffman-Pauline-R", "name": { "family": "Hoffman", "given": "Pauline R." }, "orcid": "0000-0002-9260-3356" }, { "id": "Ou-Susan", "name": { "family": "Ou", "given": "Susan" }, "orcid": "0000-0002-8803-5296" }, { "id": "Kakutani-Leesa-M", "name": { "family": "Kakutani", "given": "Leesa M." } }, { "id": "Keeffe-Jennifer-R", "name": { "family": "Keeffe", "given": "Jennifer R." }, "orcid": "0000-0002-5317-6398" }, { "id": "Wu-Hung-Jen", "name": { "family": "Wu", "given": "Hung-Jen" }, "orcid": "0000-0003-1764-1966" }, { "id": "Howarth-Mark", "name": { "family": "Howarth", "given": "Mark" }, "orcid": "0000-0001-8870-7147" }, { "id": "West-Anthony-P-Jr", "name": { "family": "West", "given": "Anthony P., Jr." }, "orcid": "0000-0003-4213-5184" }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "id": "Nussenzweig-Michel-C", "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice", "ispublished": "pub", "full_text_status": "public", "keywords": "neutralizing antibodies, receptor-binding domain, sarbecoviruses, vaccine, zoonotic coronaviruses", "note": "\u00a9 2021 American Association for the Advancement of Science.\nThis work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.\n\nReceived 12 November 2020; accepted 7 January 2021\nPublished online 12 January 2021.\n\nWe thank K. Brune (Genie Biotech) for advice about mi3 production; J. Bloom (Fred Hutchinson) and P. Bieniasz (Rockefeller University) for neutralization assay reagents; J. Vielmetter and Caltech's Beckman Institute Protein Expression Center for protein production; A. Flyak for help with flow cytometry; M. Murphy for figures; COVID-19 plasma donors, B. Coller, S. Schlesinger, and the Rockefeller University Hospital Clinical Research Support Office and nursing staff; and A. Flyak and A. DeLaitsch for critical reading of the manuscript.\n\nFunding:\nSupported by NIH grant P01-AI138938-S1 (P.J.B. and M.C.N.), the Caltech Merkin Institute for Translational Research (P.J.B.), a George Mason University Fast Grant (P.J.B.), and the Medical Research Council (MR/P001351/1) (M.H.) (this UK-funded award is part of the EDCTP2 program supported by the European Union). M.C.N. is a Howard Hughes Medical Institute Investigator. \n\nAuthor contributions: \nA.A.C., C.O.B., and P.J.B. conceived and designed experiments; A.A.C., P.N.P.G., Y.E.L., P.R.H., S.O., and L.M.K. performed experiments; H.-J.W. generated and validated SpyCatcher003-mi3; M.H. supervised the generation and validation of SpyCatcher003-mi3; and A.A.C., J.R.K., A.P.W., C.O.B., M.C.N., and P.J.B. analyzed data and wrote the paper with contributions from other authors.\n\nCompeting interests: \nM.H. is an inventor on a patent on SpyTag/SpyCatcher (EP2534484) and a patent application on SpyTag003:SpyCatcher003 (UK Intellectual Property Office 1706430.4), as well as a SpyBiotech cofounder, shareholder, and consultant. P.J.B. and A.A.C. are inventors on a provisional application from the California Institute of Technology that covers the mosaic nanoparticles described in this work. \n\nData and materials availability: \nAll data are available in the main text or the supplementary materials. Materials are available upon request to the corresponding author with a signed material transfer agreement.\n\nPublished - science-abf6840.pdf
Submitted - 20201117-387092v3full.pdf
Supplemental Material - abf6840_Cohen_SM.pdf
Supplemental Material - abf6840_Reproducibility-Checklist.pdf
", "abstract": "Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles with four to eight distinct RBDs). Mice immunized with RBD nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic RBD nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs relative to sera from immunizations with homotypic SARS-CoV-2\u2013RBD nanoparticles or COVID-19 convalescent human plasmas. Moreover, after priming, sera from mosaic RBD\u2013immunized mice neutralized heterologous pseudotyped coronaviruses as well as or better than sera from homotypic SARS-CoV-2\u2013RBD nanoparticle immunizations, demonstrating no loss of immunogenicity against particular RBDs resulting from co-display. A single immunization with mosaic RBD nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses.", "date": "2021-02-12", "date_type": "published", "publication": "Science", "volume": "371", "number": "6530", "publisher": "American Association for the Advancement of Science", "pagerange": "735-741", "id_number": "CaltechAUTHORS:20201118-120755714", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201118-120755714", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01-AI138938-S1" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "George Mason University" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/P001351/1" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/science.abf6840", "pmcid": "PMC7928838", "primary_object": { "basename": "20201117-387092v3full.pdf", "url": "https://authors.library.caltech.edu/records/srcxm-mek65/files/20201117-387092v3full.pdf" }, "related_objects": [ { "basename": "abf6840_Cohen_SM.pdf", "url": "https://authors.library.caltech.edu/records/srcxm-mek65/files/abf6840_Cohen_SM.pdf" }, { "basename": "abf6840_Reproducibility-Checklist.pdf", "url": "https://authors.library.caltech.edu/records/srcxm-mek65/files/abf6840_Reproducibility-Checklist.pdf" }, { "basename": "science-abf6840.pdf", "url": "https://authors.library.caltech.edu/records/srcxm-mek65/files/science-abf6840.pdf" } ], "pub_year": "2021", "author_list": "Cohen, Alexander A.; Gnanapragasam, Priyanthi N. P.; et al." }, { "id": "https://authors.library.caltech.edu/records/npa4g-rjj03", "eprint_id": 106296, "eprint_status": "archive", "datestamp": "2023-08-22 08:41:59", "lastmod": "2026-03-30 08:19:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhou-Lian", "name": { "family": "Zhou", "given": "Lian" } }, { "id": "Yao-Maosheng", "name": { "family": "Yao", "given": "Maosheng" }, "orcid": "0000-0002-1442-8054" }, { "id": "Zhang-Xiang", "name": { "family": "Zhang", "given": "Xiang" }, "orcid": "0000-0003-4462-3798" }, { "id": "Hu-Bicheng", "name": { "family": "Hu", "given": "Bicheng" } }, { "id": "Li-Xinyue", "name": { "family": "Li", "given": "Xinyue" }, "orcid": "0000-0002-0822-4960" }, { "id": "Chen-Haoxuan", "name": { "family": "Chen", "given": "Haoxuan" }, "orcid": "0000-0001-8398-9093" }, { "id": "Zhang-Lu", "name": { "family": "Zhang", "given": "Lu" } }, { "id": "Liu-Yun", "name": { "family": "Liu", "given": "Yun" } }, { "id": "Du-Meng", "name": { "family": "Du", "given": "Meng" } }, { "id": "Sun-Bochao", "name": { "family": "Sun", "given": "Bochao" } }, { "id": "Jiang-Yunyu", "name": { "family": "Jiang", "given": "Yunyu" } }, { "id": "Zhou-Kai", "name": { "family": "Zhou", "given": "Kai" } }, { "id": "Hong-Jie", "name": { "family": "Hong", "given": "Jie" } }, { "id": "Yu-Na", "name": { "family": "Yu", "given": "Na" } }, { "id": "Ding-Zhen", "name": { "family": "Ding", "given": "Zhen" } }, { "id": "Xu-Yan", "name": { "family": "Xu", "given": "Yan" } }, { "id": "Hu-Min", "name": { "family": "Hu", "given": "Min" } }, { "id": "Morawska-Lidia", "name": { "family": "Morawska", "given": "Lidia" }, "orcid": "0000-0002-0594-9683" }, { "id": "Grinshpun-Sergey-A", "name": { "family": "Grinshpun", "given": "Sergey A." }, "orcid": "0000-0003-4339-927X" }, { "id": "Biswas-Pratim", "name": { "family": "Biswas", "given": "Pratim" }, "orcid": "0000-0003-1104-3738" }, { "id": "Flagan-R-C", "name": { "family": "Flagan", "given": "Richard C." }, "orcid": "0000-0001-5690-770X" }, { "id": "Zhu-Baoli", "name": { "family": "Zhu", "given": "Baoli" } }, { "id": "Liu-Wenqing", "name": { "family": "Liu", "given": "Wenqing" } }, { "id": "Zhang-Yuanhang", "name": { "family": "Zhang", "given": "Yuanhang" } } ] }, "title": "Breath-, air- and surface-borne SARS-CoV-2 in hospitals", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; SARS-CoV-2; Exhaled breath; Airborne transmission; Surface-borne", "note": "\u00a9 2020 Elsevier Ltd. \n\nReceived 4 September 2020, Revised 5 October 2020, Accepted 6 October 2020, Available online 15 October 2020. \n\nThis research was equally supported by the Chinese Academy of Engineering Grant (2020-ZD-15), and a National Natural Science Foundation of China (NSFC) grant (22040101) (PI: M. Yao) dedicated to the COVID-19 pandemic. This work was also partially supported by the NSFC Distinguished Young Scholars Fund Awarded to M. Yao (21725701), and the Scientific Research Fund of Jiangsu Provincial Health Committee (S2017002).\n\nCRediT authorship contribution statement:\nLian Zhou: Data curation, Resources, Validation, Investigation. Maosheng Yao: Supervision, Conceptualization, Methodology, Data interpretation, Formal analysis, Resources, Investigation, Funding acquisition. Xiang Zhang: Data curation, Resources, Validation, Investigation. Bicheng Hu: Data curation, Resources, Validation, Investigation. Xinyue Li: Data curation, Resources, Validation, Investigation. Haoxuan Chen: Data curation, Resources, Validation, Investigation. Lu Zhang: Data curation, Resources, Validation, Investigation. Yun Liu: Data curation, Resources, Validation, Investigation. Meng Du: Data curation, Resources, Validation, Investigation. Bochao Sun: Data curation, Resources, Validation, Investigation. Yunyu Jiang: Data curation, Resources, Validation, Investigation. Kai Zhou: Data curation, Resources, Validation, Investigation. Jie Hong: Data curation, Resources, Validation, Investigation. Na Yu: Data curation, Resources, Validation, Investigation. Zhen Ding: Data curation, Resources, Validation, Investigation. Yan Xu: Data curation, Resources, Validation, Investigation. Min Hu: Data interpretation, Investigation, Writing - original draft, Writing - review & editing, Formal analysis, Validation. Lidia Morawska: Data interpretation, Investigation, Writing - original draft, Writing - review & editing, Formal analysis, Validation. Sergey A. Grinshpun: Data interpretation, Investigation, Writing - original draft, Writing - review & editing, Formal analysis, Validation. Pratim Biswas: Data interpretation, Investigation, Writing - original draft, Writing - review & editing, Formal analysis, Validation. Richard C. Flagan: Data interpretation, Investigation, Writing - original draft, Writing - review & editing, Formal analysis, Validation. Baoli Zhu: Supervision, Conceptualization, Methodology, Data interpretation, Formal analysis, Resources, Investigation, Funding acquisition. Wenqing Liu: Supervision, Conceptualization, Methodology, Data interpretation, Formal analysis, Resources, Investigation, Funding acquisition. Yuanhang Zhang: Supervision, Conceptualization, Methodology, Data interpretation, Formal analysis, Resources, Investigation, Funding acquisition.\n\nDeclaration of competing interest:\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nPublished - 1-s2.0-S0021850220301786-main.pdf
Submitted - 2020.05.31.20115196v1.full.pdf
Supplemental Material - 1-s2.0-S0021850220301786-mmc1.docx
Supplemental Material - 1-s2.0-S0021850220301786-mmc2.xlsx
Supplemental Material - 1-s2.0-S0021850220301786-mmc3.pdf
", "abstract": "The COVID-19 pandemic has brought an unprecedented crisis to the global health sector. When discharging COVID-19 patients in accordance with throat or nasal swab protocols using RT-PCR, the potential risk of reintroducing the infection source to humans and the environment must be resolved. Here, 14 patients including 10 COVID-19 subjects were recruited; exhaled breath condensate (EBC), air samples and surface swabs were collected and analyzed for SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR) in four hospitals with applied natural ventilation and disinfection practices in Wuhan. Here we discovered that 22.2% of COVID-19 patients (n = 9), who were ready for hospital discharge based on current guidelines, had SARS-CoV-2 in their exhaled breath (~10\u2075 RNA copies/m\u00b3). Although fewer surface swabs (3.1%, n = 318) tested positive, medical equipment such as face shield frequently contacted/used by healthcare workers and the work shift floor were contaminated by SARS-CoV-2 (3\u20138 viruses/cm\u00b2). Three of the air samples (n = 44) including those collected using a robot-assisted sampler were detected positive by a digital PCR with a concentration level of 9\u2013219 viruses/m\u00b3. RT-PCR diagnosis using throat swab specimens had a failure rate of more than 22% in safely discharging COVID-19 patients who were otherwise still exhaling the SARS-CoV-2 by a rate of estimated ~1400 RNA copies per minute into the air. Direct surface contact might not represent a major transmission route, and lower positive rate of air sample (6.8%) was likely due to natural ventilation (1.6\u20133.3 m/s) and regular disinfection practices. While there is a critical need for strengthening hospital discharge standards in preventing re-emergence of COVID-19 spread, use of breath sample as a supplement specimen could further guard the hospital discharge to ensure the safety of the public and minimize the pandemic re-emergence risk.", "date": "2021-02", "date_type": "published", "publication": "Journal of Aerosol Science", "volume": "152", "publisher": "Elsevier", "pagerange": "Art. No. 105693", "id_number": "CaltechAUTHORS:20201027-093242333", "issn": "0021-8502", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201027-093242333", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Chinese Academy of Engineering", "grant_number": "2020-ZD-15" }, { "agency": "National Natural Science Foundation of China", "grant_number": "22040101" }, { "agency": "National Natural Science Foundation of China", "grant_number": "21725701" }, { "agency": "Scientific Research Fund of Jiangsu Provincial Health Committee", "grant_number": "S2017002" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.jaerosci.2020.105693", "pmcid": "PMC7557302", "primary_object": { "basename": "1-s2.0-S0021850220301786-main.pdf", "url": "https://authors.library.caltech.edu/records/npa4g-rjj03/files/1-s2.0-S0021850220301786-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0021850220301786-mmc1.docx", "url": "https://authors.library.caltech.edu/records/npa4g-rjj03/files/1-s2.0-S0021850220301786-mmc1.docx" }, { "basename": "1-s2.0-S0021850220301786-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/npa4g-rjj03/files/1-s2.0-S0021850220301786-mmc2.xlsx" }, { "basename": "1-s2.0-S0021850220301786-mmc3.pdf", "url": "https://authors.library.caltech.edu/records/npa4g-rjj03/files/1-s2.0-S0021850220301786-mmc3.pdf" }, { "basename": "2020.05.31.20115196v1.full.pdf", "url": "https://authors.library.caltech.edu/records/npa4g-rjj03/files/2020.05.31.20115196v1.full.pdf" } ], "pub_year": "2021", "author_list": "Zhou, Lian; Yao, Maosheng; et al." }, { "id": "https://authors.library.caltech.edu/records/q1065-dze64", "eprint_id": 106291, "eprint_status": "archive", "datestamp": "2023-08-22 08:32:29", "lastmod": "2026-03-30 09:19:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Min-Jihong", "name": { "family": "Min", "given": "Jihong" }, "orcid": "0000-0002-5788-1473" }, { "id": "Sempionatto-Juliane-R", "name": { "family": "Sempionatto", "given": "Juliane R." }, "orcid": "0000-0003-2431-9019" }, { "id": "Teymourian-Hazhir", "name": { "family": "Teymourian", "given": "Hazhir" }, "orcid": "0000-0003-0025-4732" }, { "id": "Wang-Joseph", "name": { "family": "Wang", "given": "Joseph" } }, { "id": "Gao-Wei", "name": { "family": "Gao", "given": "Wei" }, "orcid": "0000-0002-8503-4562" } ] }, "title": "Wearable electrochemical biosensors in North America", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Wearable biosensors; Flexible electronics; Electrochemistry; Personalized medicine; COVID-19; Telemedicine", "note": "\u00a9 2020 Elsevier B.V. \n\nReceived 28 May 2020, Revised 18 October 2020, Accepted 19 October 2020, Available online 26 October 2020. \n\nThis work was supported by National Institutes of Health grant 5R21NR018271 the Translational Research Institute for Space Health through NASA NNX16AO69A, NASA Cooperative Agreement 80NSSC20M0167 (Caltech) and the Center of Wearable Sensors at University of California San Diego (UCSD). \n\nAuthor contributions: J.M., J.R.S., and H.T. contributed equally. All the authors co-wrote the paper.\n\nThe authors declare that they have no known financial or personal competing interests that could have influence the work reported in this paper.", "abstract": "Tremendous research and commercialization efforts around the world are focused on developing novel wearable electrochemical biosensors that can noninvasively and continuously screen for biochemical markers in body fluids for the prognosis, diagnosis and management of diseases, as well as the monitoring of fitness. Researchers in North America are leading the development of innovative wearable platforms that can comfortably comply to the human body and efficiently sample fluids such as sweat, interstitial fluids, tear and saliva for the electrochemical detection of biomarkers through various sensing approaches such as potentiometric ion selective electrodes and amperometric enzymatic sensors. We start this review with a historical timeline overviewing the major milestones in the development of wearable electrochemical sensors by North American institutions. We then describe how such research efforts have led to pioneering developments and are driving the advancement and commercialization of wearable electrochemical sensors: from minimally invasive continuous glucose monitors for chronic disease management to non-invasive sweat electrolyte sensors for dehydration monitoring in fitness applications. While many countries across the globe have contributed significantly to this rapidly emerging field, their contributions are beyond the scope of this review. Furthermore, we share our perspective on the promising future of wearable electrochemical sensors in applications spanning from remote and personalized healthcare to wellness.", "date": "2021-01-15", "date_type": "published", "publication": "Biosensors and Bioelectronics", "volume": "172", "publisher": "Elsevier", "pagerange": "Art. No. 112750", "id_number": "CaltechAUTHORS:20201027-083652858", "issn": "0956-5663", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201027-083652858", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "5R21NR018271" }, { "agency": "NASA", "grant_number": "NNX16AO69A" }, { "agency": "NASA", "grant_number": "80NSSC20M0167" }, { "agency": "University of California, San Diego" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.bios.2020.112750", "pub_year": "2021", "author_list": "Min, Jihong; Sempionatto, Juliane R.; et al." }, { "id": "https://authors.library.caltech.edu/records/h7qgk-gdv25", "eprint_id": 106872, "eprint_status": "archive", "datestamp": "2023-08-20 01:20:15", "lastmod": "2026-03-29 20:10:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Flyak-Andrew-I", "name": { "family": "Flyak", "given": "Andrew I." }, "orcid": "0000-0002-8722-479X" } ] }, "title": "SARS-CoV-2 B cell receptor signatures in at-risk populations", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 American Society for Clinical Investigation. \n\nPublished November 20, 2020. \n\nAIF is supported by a research funding from the National Institutes of Health grant K99 AI153465 (content is solely the responsibility of the author and does not necessarily represent the official views of the NIH). AIF acknowledges Pamela J. Bjorkman for critical reading of the manuscript. \n\nThe author has declared that no conflict of interest exists.\n\nPublished - jci-131-144685.pdf
", "abstract": "Many individuals possess B cells capable of recognizing epitopes on the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this issue of the JCI, Paschold and Simnica et al. interrogated the frequency of SARS-CoV-2\u2013specific B cell receptor rearrangements in healthy subjects based on age and cancer status. The authors found that while SARS-CoV-2\u2013specific antibody signatures can be identified in the repertoires of young, healthy individuals, such sequences are less frequent in elderly subjects or patients with cancer. Overall, this study sheds light on B cell repertoire restrictions that might lead to an unfavorable clinical course of coronavirus disease 2019 infection in at-risk populations.", "date": "2021-01-04", "date_type": "published", "publication": "Journal of Clinical Investigation", "volume": "131", "number": "1", "publisher": "American Society for Clinical Investigation", "pagerange": "Art. No. e144685", "id_number": "CaltechAUTHORS:20201202-081646342", "issn": "0021-9738", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201202-081646342", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "K99 AI153465" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1172/JCI144685", "pmcid": "PMC7773361", "primary_object": { "basename": "jci-131-144685.pdf", "url": "https://authors.library.caltech.edu/records/h7qgk-gdv25/files/jci-131-144685.pdf" }, "pub_year": "2021", "author_list": "Flyak, Andrew I." }, { "id": "https://authors.library.caltech.edu/records/e6gze-wmh58", "eprint_id": 106736, "eprint_status": "archive", "datestamp": "2023-08-20 01:13:08", "lastmod": "2026-03-30 06:50:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Crits-Christoph-Alexander", "name": { "family": "Crits-Christoph", "given": "Alexander" } }, { "id": "Kantor-Rose-S", "name": { "family": "Kantor", "given": "Rose S." }, "orcid": "0000-0002-5402-8979" }, { "id": "Olm-Matthew-R", "name": { "family": "Olm", "given": "Matthew R." }, "orcid": "0000-0001-5540-350X" }, { "id": "Whitney-Oscar-N", "name": { "family": "Whitney", "given": "Oscar N." }, "orcid": "0000-0002-4858-2615" }, { "id": "Al-Shayeb-Basem", "name": { "family": "Al-Shayeb", "given": "Basem" }, "orcid": "0000-0002-3120-3201" }, { "id": "Lou-Yue-Clare", "name": { "family": "Lou", "given": "Yue Clare" } }, { "id": "Flamholz-Avi", "name": { "family": "Flamholz", "given": "Avi" }, "orcid": "0000-0002-9278-5479" }, { "id": "Kennedy-Lauren-C", "name": { "family": "Kennedy", "given": "Lauren C." }, "orcid": "0000-0002-4451-2361" }, { "id": "Greenwald-Hannah", "name": { "family": "Greenwald", "given": "Hannah" } }, { "id": "Hinkle-Adrian", "name": { "family": "Hinkle", "given": "Adrian" } }, { "id": "Hetzel-Jonathan", "name": { "family": "Hetzel", "given": "Jonathan" } }, { "id": "Spitzer-Sara", "name": { "family": "Spitzer", "given": "Sara" } }, { "id": "Koble-Jeffery", "name": { "family": "Koble", "given": "Jeffery" } }, { "id": "Tan-Asako", "name": { "family": "Tan", "given": "Asako" } }, { "id": "Hyde-Fred", "name": { "family": "Hyde", "given": "Fred" } }, { "id": "Schroth-Gary-P", "name": { "family": "Schroth", "given": "Gary" }, "orcid": "0000-0002-3055-056X" }, { "id": "Kuersten-Scott", "name": { "family": "Kuersten", "given": "Scott" } }, { "id": "Banfield-Jillian-F", "name": { "family": "Banfield", "given": "Jillian F." } }, { "id": "Nelson-Kara-L", "name": { "family": "Nelson", "given": "Kara L." } } ] }, "title": "Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants", "ispublished": "pub", "full_text_status": "public", "keywords": "coronavirus, environmental microbiology, genomics, metagenomics", "note": "\u00a9 2021 Crits-Christoph et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived 21 September 2020; Accepted 15 December 2020; Published 19 January 2021. \n\nWe gratefully acknowledge the originating and submitting laboratories of SARS-CoV-2 genomes in the GISAID EpiCoV database (www.gisaid.org) that were used for our comparisons to clinical samples and in particular the Innovative Genomics Institute SARS-CoV-2 Sequencing Group for Alameda County genomes. We also gratefully acknowledge Vinson Fan for assistance with RT-qPCR and the laboratory of Robert Tjian for sharing materials. \n\nFunding was provided to K.L.N. and J.F.B. by a Rapid Research Response grant from the Innovative Genomics Institute (IGI) and a seed grant from the Center for Information Technology Research in the Interest of Society (CITRIS) at UC Berkeley. \n\nData availability: Sequencing data for this project has been released under NCBI BioProject ID PRJNA661613. Processed data, reproducible code, and workflows for the analyses performed are available at https://github.com/alexcritschristoph/wastewater_sarscov2.\n\nPublished - mBio-2021-Crits-Christoph-e02703-20.full.pdf
Submitted - 2020.09.13.20193805v1.full.pdf
Supplemental Material - inline-supplementary-material-1.xlsx
Supplemental Material - inline-supplementary-material-2.xlsx
Supplemental Material - inline-supplementary-material-3.xlsx
Supplemental Material - inline-supplementary-material-4.xlsx
", "abstract": "Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.", "date": "2021-01", "date_type": "published", "publication": "mBio", "volume": "12", "number": "1", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e02703-20", "id_number": "CaltechAUTHORS:20201119-100731171", "issn": "2150-7511", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201119-100731171", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Innovative Genomics Institute (IGI)" }, { "agency": "University of California, Berkeley" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1128/mBio.02703-20", "pmcid": "PMC7845645", "primary_object": { "basename": "inline-supplementary-material-4.xlsx", "url": "https://authors.library.caltech.edu/records/e6gze-wmh58/files/inline-supplementary-material-4.xlsx" }, "related_objects": [ { "basename": "mBio-2021-Crits-Christoph-e02703-20.full.pdf", "url": "https://authors.library.caltech.edu/records/e6gze-wmh58/files/mBio-2021-Crits-Christoph-e02703-20.full.pdf" }, { "basename": "2020.09.13.20193805v1.full.pdf", "url": "https://authors.library.caltech.edu/records/e6gze-wmh58/files/2020.09.13.20193805v1.full.pdf" }, { "basename": "inline-supplementary-material-1.xlsx", "url": "https://authors.library.caltech.edu/records/e6gze-wmh58/files/inline-supplementary-material-1.xlsx" }, { "basename": "inline-supplementary-material-2.xlsx", "url": "https://authors.library.caltech.edu/records/e6gze-wmh58/files/inline-supplementary-material-2.xlsx" }, { "basename": "inline-supplementary-material-3.xlsx", "url": "https://authors.library.caltech.edu/records/e6gze-wmh58/files/inline-supplementary-material-3.xlsx" } ], "pub_year": "2021", "author_list": "Crits-Christoph, Alexander; Kantor, Rose S.; et al." }, { "id": "https://authors.library.caltech.edu/records/bvvsg-p6b11", "eprint_id": 107531, "eprint_status": "archive", "datestamp": "2023-08-22 08:18:12", "lastmod": "2026-03-29 18:26:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "B\u00e1rcena-Montserrat", "name": { "family": "B\u00e1rcena", "given": "Montserrat" } }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "id": "Beck-Martin", "name": { "family": "Beck", "given": "Martin" } }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Canard-Bruno", "name": { "family": "Canard", "given": "Bruno" } }, { "id": "Gao-George-F", "name": { "family": "Gao", "given": "George F." } }, { "id": "Ga-Yunyun", "name": { "family": "Gao", "given": "Yunyun" } }, { "id": "Hilgenfeld-Rolf", "name": { "family": "Hilgenfeld", "given": "Rolf" } }, { "id": "Hummer-Gerhard", "name": { "family": "Hummer", "given": "Gerhard" } }, { "id": "Patwardhan-Ardan", "name": { "family": "Patwardhan", "given": "Ardan" } }, { "id": "Santoni-Gianluca", "name": { "family": "Santoni", "given": "Gianluca" } }, { "id": "Saphire-Erica-Ollmann", "name": { "family": "Saphire", "given": "Erica Ollmann" }, "orcid": "0000-0002-1206-7451" }, { "id": "Schaffitzel-Christiane", "name": { "family": "Schaffitzel", "given": "Christiane" } }, { "id": "Schendel-Sharon-L", "name": { "family": "Schendel", "given": "Sharon L." } }, { "id": "Smith-Janet-L", "name": { "family": "Smith", "given": "Janet" } }, { "id": "Thorn-Andrea", "name": { "family": "Thorn", "given": "Andrea" } }, { "id": "Veesler-David", "name": { "family": "Veesler", "given": "David" }, "orcid": "0000-0002-6019-8675" }, { "id": "Zhang-Peijun", "name": { "family": "Zhang", "given": "Peijun" } }, { "id": "Zhou-Qiang", "name": { "family": "Zhou", "given": "Qiang" } } ] }, "title": "Structural biology in the fight against COVID-19", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Cryoelectron microscopy; Immunology; Virology; X-ray crystallography", "note": "\u00a9 2021 Nature Publishing Group. \n\nPublished 12 January 2021. \n\nCompeting interests: C.S. declares that patent applications describing methods and material compositions based on the presented observations have been filed. D.V. is a consultant for Vir Biotechnology Inc. The Veesler laboratory has received a sponsored research agreement from Vir Biotechnology Inc. All other authors declare no competing interests.", "abstract": "How can structural biology help us understand and combat SARS-CoV-2? Researchers in the field share their experiences and opinions and point to the challenges that lie ahead.", "date": "2021-01", "date_type": "published", "publication": "Nature Structural & Molecular Biology", "volume": "28", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "2-7", "id_number": "CaltechAUTHORS:20210119-071807621", "issn": "1545-9993", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210119-071807621", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41594-020-00544-8", "pub_year": "2021", "author_list": "B\u00e1rcena, Montserrat; Barnes, Christopher O.; et al." }, { "id": "https://authors.library.caltech.edu/records/qv39b-hpn10", "eprint_id": 107532, "eprint_status": "archive", "datestamp": "2023-08-22 08:18:19", "lastmod": "2026-03-28 22:38:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Weissgerber-Tracey", "name": { "family": "Weissgerber", "given": "Tracey" }, "orcid": "0000-0002-7490-2600" }, { "id": "Riedel-Nico", "name": { "family": "Riedel", "given": "Nico" }, "orcid": "0000-0002-3808-1163" }, { "id": "Kilicoglu-Halil", "name": { "family": "Kilicoglu", "given": "Halil" } }, { "id": "Labb\u00e9-Cyril", "name": { "family": "Labb\u00e9", "given": "Cyril" } }, { "id": "Eckmann-Peter", "name": { "family": "Eckmann", "given": "Peter" } }, { "id": "ter-Riet-Gerben", "name": { "family": "ter Riet", "given": "Gerben" }, "orcid": "0000-0002-2231-7637" }, { "id": "Byrne-Jennifer", "name": { "family": "Byrne", "given": "Jennifer" }, "orcid": "0000-0002-8923-0587" }, { "id": "Cabanac-Guillaume", "name": { "family": "Cabanac", "given": "Guillaume" } }, { "id": "Capes-Davis-Amanda", "name": { "family": "Capes-Davis", "given": "Amanda" } }, { "id": "Favier-Bertrand", "name": { "family": "Favier", "given": "Bertrand" } }, { "id": "Saladi-Shyam-M", "name": { "family": "Saladi", "given": "Shyam" }, "orcid": "0000-0001-9701-3059" }, { "id": "Grabitz-Peter", "name": { "family": "Grabitz", "given": "Peter" } }, { "id": "Bannach-Brown-Alexandra", "name": { "family": "Bannach-Brown", "given": "Alexandra" } }, { "id": "Schulz-Robert", "name": { "family": "Schulz", "given": "Robert" }, "orcid": "0000-0002-4830-309X" }, { "id": "McCann-Sarah", "name": { "family": "McCann", "given": "Sarah" }, "orcid": "0000-0003-4737-2349" }, { "id": "Bernard-Rene", "name": { "family": "Bernard", "given": "Rene" }, "orcid": "0000-0003-3265-2372" }, { "id": "Bandrowski-Anita", "name": { "family": "Bandrowski", "given": "Anita" }, "orcid": "0000-0002-5497-0243" } ] }, "title": "Automated screening of COVID-19 preprints: can we help authors to improve transparency and reproducibility?", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Medical research; Research data", "note": "\u00a9 2021 Nature Publishing Group. \n\nPublished 11 January 2021. \n\nSciScore was funded by the US National Institutes of Health (OD024432, DA039832, DK097771, MH119094, and HHSN276201700124P). The development and application of Seek & Blastn is supported by grants from the US Office of Research Integrity, grant ID ORIIR180038-01-00 (J.A.B., C.L.), and from the National Health and Medical Research Council of Australia, Ideas grant ID APP1184263 (J.A.B., C.L., A.C.D.). Development of Limitation-Recognizer was partially supported by the intramural research program of the NIH and National Library of Medicine.\n \nCompeting interests: A.B. is a cofounder of SciCrunch Inc.", "abstract": "The COVID-19 pandemic has thrust preprints into the spotlight, attracting attention from the media and the public, as well as from scientists. Preprints are articles not yet published in a peer-reviewed journal, and as such they offer a unique opportunity to improve reporting. The Automated Screening Working Group (https://scicrunch.org/ASWG/about/COVIDPreprint) aims to provide rapid feedback that may help authors of COVID-19 preprints to improve their transparency and reproducibility.", "date": "2021-01", "date_type": "published", "publication": "Nature Medicine", "volume": "27", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "6-7", "id_number": "CaltechAUTHORS:20210119-072728244", "issn": "1078-8956", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210119-072728244", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "OD024432" }, { "agency": "NIH", "grant_number": "DA039832" }, { "agency": "NIH", "grant_number": "DK097771" }, { "agency": "NIH", "grant_number": "MH119094" }, { "agency": "NIH", "grant_number": "HHSN276201700124P" }, { "agency": "Department of Health and Human Services", "grant_number": "ORIIR180038-01-00" }, { "agency": "National Health and Medical Research Council of Australia", "grant_number": "APP1184263" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1038/s41591-020-01203-7", "pub_year": "2021", "author_list": "Weissgerber, Tracey; Riedel, Nico; et al." }, { "id": "https://authors.library.caltech.edu/records/7cm2m-kkz63", "eprint_id": 107073, "eprint_status": "archive", "datestamp": "2023-09-25 22:46:46", "lastmod": "2026-03-30 17:11:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lukas-Heather", "name": { "family": "Lukas", "given": "Heather" } }, { "id": "Xu-Changhao", "name": { "family": "Xu", "given": "Changhao" } }, { "id": "Yu-You", "name": { "family": "Yu", "given": "You" }, "orcid": "0000-0001-7059-7023" }, { "id": "Gao-Wei", "name": { "family": "Gao", "given": "Wei" }, "orcid": "0000-0002-8503-4562" } ] }, "title": "Emerging Telemedicine Tools for Remote COVID-19 Diagnosis, Monitoring, and Management", "ispublished": "pub", "full_text_status": "public", "keywords": "Anatomy, Infectious diseases,Sensors, Testing and assessment, Biomarkers", "note": "\u00a9 2020 American Chemical Society. This article is made available via the ACS COVID-19 subset for unrestricted RESEARCH re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. \n\nPublication Date: December 14, 2020. \n\nThis project was supported by the Merkin Institute for Translational Research at Caltech, COVID-19 Research Funding from the Tobacco Related-Disease Research Program (TRDRP), the Translational Research Institute for Space Health through NASA NNX16AO69A, and an American Heart Association grant no. 19TPA34850157. \n\nThe authors declare no competing financial interest.\n\nPublished - acsnano.0c08494.pdf
", "abstract": "The management of the COVID-19 pandemic has relied on cautious contact tracing, quarantine, and sterilization protocols while we await a vaccine to be made widely available. Telemedicine or mobile health (mHealth) is well-positioned during this time to reduce potential disease spread and prevent overloading of the healthcare system through at-home COVID-19 screening, diagnosis, and monitoring. With the rise of mass-fabricated electronics for wearable and portable sensors, emerging telemedicine tools have been developed to address shortcomings in COVID-19 diagnostics, monitoring, and management. In this Perspective, we summarize current implementations of mHealth sensors for COVID-19, highlight recent technological advances, and provide an overview on how these tools may be utilized to better control the COVID-19 pandemic.", "date": "2020-12-22", "date_type": "published", "publication": "ACS Nano", "volume": "14", "number": "12", "publisher": "American Chemical Society", "pagerange": "16180-16193", "id_number": "CaltechAUTHORS:20201214-130923880", "issn": "1936-0851", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201214-130923880", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "California Tobacco-Related Disease Research Program" }, { "agency": "NASA", "grant_number": "NNX16AO69A" }, { "agency": "American Heart Association", "grant_number": "19TPA34850157" } ] }, "local_group": { "items": [ { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" } ] }, "doi": "10.1021/acsnano.0c08494", "pmcid": "PMC7754783", "primary_object": { "basename": "acsnano.0c08494.pdf", "url": "https://authors.library.caltech.edu/records/7cm2m-kkz63/files/acsnano.0c08494.pdf" }, "pub_year": "2020", "author_list": "Lukas, Heather; Xu, Changhao; et al." }, { "id": "https://authors.library.caltech.edu/records/nv9je-zaz95", "eprint_id": 106875, "eprint_status": "archive", "datestamp": "2023-08-22 08:05:06", "lastmod": "2026-03-30 05:59:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tada-Takuya", "name": { "family": "Tada", "given": "Takuya" }, "orcid": "0000-0003-0779-9954" }, { "id": "Fan-Chen", "name": { "family": "Fan", "given": "Chen" } }, { "id": "Chen-Jennifer-S", "name": { "family": "Chen", "given": "Jennifer S." }, "orcid": "0000-0002-7808-2670" }, { "id": "Kaur-Ramanjit", "name": { "family": "Kaur", "given": "Ramanjit" }, "orcid": "0000-0002-4627-415X" }, { "id": "Stapleford-Kenneth-A", "name": { "family": "Stapleford", "given": "Kenneth A." }, "orcid": "0000-0002-7796-2254" }, { "id": "Gristick-Harry-B", "name": { "family": "Gristick", "given": "Harry" }, "orcid": "0000-0002-1957-2821" }, { "id": "Dcosta-Belinda-M", "name": { "family": "Dcosta", "given": "Belinda M." } }, { "id": "Wilen-Craig-B", "name": { "family": "Wilen", "given": "Craig B." }, "orcid": "0000-0003-2495-9403" }, { "id": "Nimigean-Crina-M", "name": { "family": "Nimigean", "given": "Crina M." }, "orcid": "0000-0002-6254-4447" }, { "id": "Landau-Nathaniel-R", "name": { "family": "Landau", "given": "Nathaniel R." }, "orcid": "0000-0002-9997-1004" } ] }, "title": "An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2", "ispublished": "pub", "full_text_status": "public", "keywords": "SARS-CoV-2; soluble ACE2; microbody; spike protein; lentiviral pseudotype; D614G; Fc fusion; ACE2 transgenic; coronavirus; entry inhibitor", "note": "\u00a9 2020 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nReceived 11 August 2020, Revised 26 October 2020, Accepted 24 November 2020, Available online 1 December 2020. Published: December 22, 2020. \n\nWe thank Michael Letko and Vincent Munster (NIH) for \u03b2 coronavirus spike protein expression vectors. The work was funded by grants from the NIH (DA046100, AI122390, and AI120898 to N.R.L.; RO1 GM124451 to C.M.N.) and Pamela J. Bjorkman in support of H.G. (P01-AI38398-S1). C.B.W. was supported by the NIH (grant K08 AI128043), Burroughs Wellcome Fund, Ludwig Family Foundation, and the Mathers Charitable Foundation. T.T. was supported by the Vilcek/Goldfarb Fellowship Endowment Fund. J.S.C. was supported by NIH grants T32GM007205 and F30HL149151. \n\nAuthor Contributions: Conceptualization and Methodology, T.T., N.R.L., C.M.N., and C.B.W.; Investigation, T.T., C.F., J.S.C., R.K., K.A.S., H.G., and B.M.D.; Writing \u2013 Original Draft, T.T.; Writing \u2013 Review & Editing, N.R.L.; Funding Acquisition, N.R.L., C.M.N., C.B.W.; Resources, N.R.L., C.M.N., and C.B.W.; and Supervision, N.R.L. \n\nDeclaration of Interests: A provisional patent application has been filed with the US Patent and Trademark Office.\n\nPublished - 1-s2.0-S2211124720315175-main.pdf
Supplemental Material - 1-s2.0-S2211124720315175-mmc1.pdf
Supplemental Material - 1-s2.0-S2211124720315175-mmc2.xlsx
Supplemental Material - 1-s2.0-S2211124720315175-mmc3.xlsx
Supplemental Material - 1-s2.0-S2211124720315175-mmc4.xlsx
", "abstract": "Soluble forms of angiotensin-converting enzyme 2 (ACE2) have recently been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We report on an improved soluble ACE2, termed a \"microbody,\" in which the ACE2 ectodomain is fused to Fc domain 3 of the immunoglobulin (Ig) heavy chain. The protein is smaller than previously described ACE2-Ig Fc fusion proteins and contains an H345A mutation in the ACE2 catalytic active site that inactivates the enzyme without reducing its affinity for the SARS-CoV-2 spike. The disulfide-bonded ACE2 microbody protein inhibits entry of SARS-CoV-2 spike protein pseudotyped virus and replication of live SARS-CoV-2 in vitro and in a mouse model. Its potency is 10-fold higher than soluble ACE2, and it can act after virus bound to the cell. The microbody inhibits the entry of \u03b2 coronaviruses and virus with the variant D614G spike. The ACE2 microbody may be a valuable therapeutic for coronavirus disease 2019 (COVID-19) that is active against viral variants and future coronaviruses.", "date": "2020-12-22", "date_type": "published", "publication": "Cell Reports", "volume": "33", "number": "12", "publisher": "Cell Press", "pagerange": "Art. No. 108528", "id_number": "CaltechAUTHORS:20201202-101233646", "issn": "2211-1247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201202-101233646", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "DA046100" }, { "agency": "NIH", "grant_number": "AI122390" }, { "agency": "NIH", "grant_number": "AI120898" }, { "agency": "NIH", "grant_number": "RO1 GM124451" }, { "agency": "NIH", "grant_number": "P01-AI38398-S1" }, { "agency": "NIH", "grant_number": "K08 AI128043" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Ludwig Family Foundation" }, { "agency": "Mathers Charitable Foundation" }, { "agency": "Vilcek/Goldfarb Fellowship Endowment Fund" }, { "agency": "NIH", "grant_number": "T32GM007205" }, { "agency": "NIH", "grant_number": "F30HL149151" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.celrep.2020.108528", "pmcid": "PMC7705358", "primary_object": { "basename": "1-s2.0-S2211124720315175-main.pdf", "url": "https://authors.library.caltech.edu/records/nv9je-zaz95/files/1-s2.0-S2211124720315175-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2211124720315175-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/nv9je-zaz95/files/1-s2.0-S2211124720315175-mmc1.pdf" }, { "basename": "1-s2.0-S2211124720315175-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/nv9je-zaz95/files/1-s2.0-S2211124720315175-mmc2.xlsx" }, { "basename": "1-s2.0-S2211124720315175-mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/nv9je-zaz95/files/1-s2.0-S2211124720315175-mmc3.xlsx" }, { "basename": "1-s2.0-S2211124720315175-mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/nv9je-zaz95/files/1-s2.0-S2211124720315175-mmc4.xlsx" } ], "pub_year": "2020", "author_list": "Tada, Takuya; Fan, Chen; et al." }, { "id": "https://authors.library.caltech.edu/records/jvh7d-16y03", "eprint_id": 106816, "eprint_status": "archive", "datestamp": "2023-08-22 08:03:00", "lastmod": "2026-03-30 08:12:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Parker-Harrison-A", "name": { "family": "Parker", "given": "H. A." }, "orcid": "0000-0002-0041-2764" }, { "id": "Hasheminassab-Sina", "name": { "family": "Hasheminassab", "given": "S." }, "orcid": "0000-0002-4422-8547" }, { "id": "Crounse-John-D", "name": { "family": "Crounse", "given": "J. D." }, "orcid": "0000-0001-5443-729X" }, { "id": "Roehl-Coleen-M", "name": { "family": "Roehl", "given": "C. M." }, "orcid": "0000-0001-5383-8462" }, { "id": "Wennberg-P-O", "name": { "family": "Wennberg", "given": "P. O." }, "orcid": "0000-0002-6126-3854" } ] }, "title": "Impacts of Traffic Reductions Associated With COVID-19 on Southern California Air Quality", "ispublished": "pub", "full_text_status": "public", "keywords": "air quality; lockdown; COVID\u201019; South Coast Air Basin; ozone; nitrogen dioxide", "note": "\u00a9 2020 The Authors. This is an open access article under the terms of the Creative Commons Attribution\u2010NonCommercial\u2010NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non\u2010commercial and no modifications or adaptations are made. \n\nIssue Online: 01 December 2020; Version of Record online: 01 December 2020; Accepted manuscript online: 23 November 2020; Manuscript accepted: 10 November 2020; Manuscript revised: 05 November 2020; Manuscript received: 01 August 2020. \n\nThe views expressed in this document are solely those of the authors and do not necessarily reflect those of the South Coast AQMD. The CITAQS facility was funded by Caltech's Linde Center for Global Environmental Science and the Resnick Sustainability Institute. We thank NASA via NNX17AE15G for support of retrievals of CH\u2082O from the Caltech TCCON station. Harrison Parker thanks the Rose Hill Foundation for initial support of his graduate fellowship. \n\nData Availability Statement: Data from the CITAQS are available by request and will be available online to the public in the near future. All data from the AQMD sites are available through the California Air Resources Board Air Quality Data Query Tool (https://www.arb.ca.gov/aqmis2/aqdselect.php). Data from the CalNex campaign are available online (https://www.esrl.noaa.gov/csl/projects/calnex/). TROPOMI data used in this research are available through the Sentinel\u20105P Data Hub (https://s5phub.copernicus.eu/). Traffic data used here are available through the Caltrans PeMS program (https://pems.dot.ca.gov/). Weather data are available online or by contacting the corresponding author (https://tccon\u2010weather.caltech.edu/).\n\nPublished - 2020GL090164.pdf
Supplemental Material - grl61597-sup-0001-2020gl090164-si-s01.pdf
", "abstract": "On 19 March 2020, California put in place Stay\u2010At\u2010Home orders to reduce the spread of SARS\u2010CoV\u20102. As a result, decreases up to 50% in traffic occurred across the South Coast Air Basin (SoCAB). We report that, compared to the 19 March to 30 June period of the last 5\u2009years, the 2020 concentrations of PM_(2.5) and NO_x showed an overall reduction across the basin. O\u2083 concentrations decreased in the western part of the basin and generally increased in the downwind areas. The NO_x decline in 2020 (approximately 27% basin\u2010wide) is in addition to ongoing declines over the last two decades (on average 4% less than the \u22126.8% per year afternoon NO\u2082 concentration decrease) and provides insight into how air quality may respond over the next few years of continued vehicular reductions. The modest changes in O\u2083 suggests additional mitigation will be necessary to comply with air quality standards.", "date": "2020-12-16", "date_type": "published", "publication": "Geophysical Research Letters", "volume": "47", "number": "23", "publisher": "American Geophysical Union", "pagerange": "Art. No. e2020GL090164", "id_number": "CaltechAUTHORS:20201124-133212486", "issn": "0094-8276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201124-133212486", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ronald And Maxine Linde Center for Global Environmental Science" }, { "agency": "Resnick Sustainability Institute" }, { "agency": "NASA", "grant_number": "NNX17AE15G" }, { "agency": "Rose Hills Foundation" } ] }, "local_group": { "items": [ { "id": "Resnick-Sustainability-Institute" }, { "id": "COVID-19" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1029/2020gl090164", "pmcid": "PMC7744837", "primary_object": { "basename": "2020GL090164.pdf", "url": "https://authors.library.caltech.edu/records/jvh7d-16y03/files/2020GL090164.pdf" }, "related_objects": [ { "basename": "grl61597-sup-0001-2020gl090164-si-s01.pdf", "url": "https://authors.library.caltech.edu/records/jvh7d-16y03/files/grl61597-sup-0001-2020gl090164-si-s01.pdf" } ], "pub_year": "2020", "author_list": "Parker, H. A.; Hasheminassab, S.; et al." }, { "id": "https://authors.library.caltech.edu/records/pgm54-cy870", "eprint_id": 107080, "eprint_status": "archive", "datestamp": "2023-08-22 08:00:33", "lastmod": "2026-03-28 23:39:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stratton-Catherine", "name": { "family": "Stratton", "given": "Catherine" }, "orcid": "0000-0002-1841-4565" }, { "id": "Kadakia-Shevali", "name": { "family": "Kadakia", "given": "Shevali" } }, { "id": "Balikuddembe-Joseph-K", "name": { "family": "Balikuddembe", "given": "Joseph K." } }, { "id": "Peterson-Mark", "name": { "family": "Peterson", "given": "Mark" } }, { "id": "Hajjioui-Abderrazak", "name": { "family": "Hajjioui", "given": "Abderrazak" }, "orcid": "0000-0002-2311-5543" }, { "id": "Cooper-Rory", "name": { "family": "Cooper", "given": "Rory" } }, { "id": "Hong-Bo-Young", "name": { "family": "Hong", "given": "Bo-Young" } }, { "id": "Pandiyan-Uma", "name": { "family": "Pandiyan", "given": "Uma" } }, { "id": "Mu\u00f1oz-Velasco-Laura-Paulina", "name": { "family": "Mu\u00f1oz-Velasco", "given": "Laura Paulina" } }, { "id": "Joseph-James", "name": { "family": "Joseph", "given": "James" } }, { "id": "Krassioukov-Andrei", "name": { "family": "Krassioukov", "given": "Andrei" }, "orcid": "0000-0002-0022-7972" }, { "id": "Tripathi-Deo-Rishi", "name": { "family": "Tripathi", "given": "Deo Rishi" } }, { "id": "Tuakli-Wosornu-Yetsa-A", "name": { "family": "Tuakli-Wosornu", "given": "Yetsa A." }, "orcid": "0000-0001-5557-6953" } ] }, "title": "Access denied: the shortage of digitized fitness resources for people with disabilities", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Accessibility; inclusive; home exercise; people with disabilities; digital resources", "note": "\u00a9 2020 Informa UK Limited, trading as Taylor & Francis Group. \n\nReceived 3 August 2020; Revised 18 November 2020; Accepted 19 November 2020; Published online: 11 Dec 2020. \n\nNo potential conflict of interest was reported by the author(s).", "abstract": "Purpose: The COVID-19 pandemic has drastically impacted every aspect of life, including how people exercise and access fitness resources. Prior to COVID-19, the global burden of disease attributable to sedentary behavior disproportionately affected the health of people with disabilities (PWD). This pre-existing gap has only widened during COVID-19 due to limited disability-friendly digital exercise resources. The purpose of this work is to examine this gap in accessibility to digital fitness resources, and re-frame the notion of accessibility to suit the contemporary context. \n\nMaterials and methods: Using machine learning, video titles/descriptions about home exercise ordered by relevance populated on YouTube between 1 January 2020 and 30 June 2020 were examined. \n\nResults: Using the search terms, \"home exercise,\" \"home-based exercise,\" \"exercise no equipment,\" \"workout no equipment,\" \"exercise at home,\" or \"at-home exercise,\" 700 videos ordered by relevance included 28 (4%) that were inclusive of participants with disabilities. Unfortunately, most digital fitness resources are therefore inaccessible to PWD. The global pause the pandemic has induced may be the right moment to construct a comprehensive, indexed digital library of home-based fitness video content for the disabled. There is a further need for more nuanced understandings of accessibility as technological advancements continue. \n\nImplications for Rehabilitation: Physical activity is incredibly important to the quality of life and health of all people. \n\nPhysical activity levels, however, remain lower among persons with disabilities. \n\nAccess to disability-friendly resources remains a challenge and worsened by the circumstances of COVID-19 due to an apparent lack of digital fitness resources for persons with disabilities. \n\nA broader and comprehensive definition of accessibility must recognize digital advances and access to physical activity for persons with disabilities must feature digital resources.", "date": "2020-12-11", "date_type": "published", "publication": "Disability and Rehabilitation", "volume": "44", "number": "13", "publisher": "Informa UK Limited", "pagerange": "3301-3303", "id_number": "CaltechAUTHORS:20201215-075622224", "issn": "0963-8288", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201215-075622224", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1080/09638288.2020.1854873", "pub_year": "2020", "author_list": "Stratton, Catherine; Kadakia, Shevali; et al." }, { "id": "https://authors.library.caltech.edu/records/r5anw-4eh31", "eprint_id": 103585, "eprint_status": "archive", "datestamp": "2023-08-22 07:58:55", "lastmod": "2026-03-30 13:53:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Booeshaghi-A-Sina", "name": { "family": "Booeshaghi", "given": "A. Sina" }, "orcid": "0000-0002-6442-4502" }, { "id": "Lubock-Nathan-B", "name": { "family": "Lubock", "given": "Nathan B." }, "orcid": "0000-0001-8064-2465" }, { "id": "Cooper-Aaron-R", "name": { "family": "Cooper", "given": "Aaron R." }, "orcid": "0000-0003-4588-2513" }, { "id": "Simpkins-Scott-W", "name": { "family": "Simpkins", "given": "Scott W." }, "orcid": "0000-0002-5997-2838" }, { "id": "Bloom-Joshua-S", "name": { "family": "Bloom", "given": "Joshua S." }, "orcid": "0000-0002-7241-1648" }, { "id": "Gehring-Jase", "name": { "family": "Gehring", "given": "Jase" }, "orcid": "0000-0002-3894-9495" }, { "id": "Luebbert-Laura", "name": { "family": "Luebbert", "given": "Laura" }, "orcid": "0000-0003-1379-2927" }, { "id": "Kosuri-Sriram", "name": { "family": "Kosuri", "given": "Sriram" }, "orcid": "0000-0002-4661-0600" }, { "id": "Pachter-L", "name": { "family": "Pachter", "given": "Lior" }, "orcid": "0000-0002-9164-6231" } ] }, "title": "Reliable and accurate diagnostics from highly multiplexed sequencing assays", "ispublished": "pub", "full_text_status": "public", "keywords": "Computational biology and bioinformatics; Infectious diseases", "note": "\u00a9 2020 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 02 November 2020; Accepted 24 November 2020; Published 10 December 2020. \n\nWe thank P\u00e1ll Melsted for assistance with bustools. \n\nAuthor Contributions: A.S.B. and L.P. developed the kallisto|bustools approach to processing and analyzing HMSA data. A.S.B. adapted kallisto and bustools to process SwabSeq, LAMP-seq, covE-seq, and TRB-seq data. A.S.B. performed the analyses and collected results for the paper. N.L. developed the bcl2fastq\u2009+\u2009starcode processing approach with assistance from A.R.C., S.W.S., and J.S.B. J.G. assisted with technical aspects of the SwabSeq assay and in assessing the kallisto|bustools workflow results. L.L. created Fig. 1 and explored the sample index structures of LAMP-seq, TRB-seq, and SwabSeq. S.K., N.L.B., A.R.C., S.W.S. and J.S.B. developed SwabSeq. A.S.B., L.L., and L.P. wrote the manuscript. \n\nCompeting interests: A.S.B., J.G., L.L., and L.P. declare no conflicts of interest. S.K., N.L.B., A.R.C., S.W.S. and J.S.B. are employees of Ocant, which developed SwabSeq. SwabSeq is released under the terms of the Octant Covid License20.\n\nPublished - s41598-020-78942-7.pdf
Submitted - 2020.05.13.20100131v1.full.pdf
Supplemental Material - 41598_2020_78942_MOESM1_ESM.docx
Supplemental Material - 41598_2020_78942_MOESM2_ESM.docx
", "abstract": "Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA.", "date": "2020-12-10", "date_type": "published", "publication": "Scientific Reports", "volume": "10", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 21759", "id_number": "CaltechAUTHORS:20200601-101849395", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200601-101849395", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41598-020-78942-7", "pmcid": "PMC7730459", "primary_object": { "basename": "s41598-020-78942-7.pdf", "url": "https://authors.library.caltech.edu/records/r5anw-4eh31/files/s41598-020-78942-7.pdf" }, "related_objects": [ { "basename": "2020.05.13.20100131v1.full.pdf", "url": "https://authors.library.caltech.edu/records/r5anw-4eh31/files/2020.05.13.20100131v1.full.pdf" }, { "basename": "41598_2020_78942_MOESM1_ESM.docx", "url": "https://authors.library.caltech.edu/records/r5anw-4eh31/files/41598_2020_78942_MOESM1_ESM.docx" }, { "basename": "41598_2020_78942_MOESM2_ESM.docx", "url": "https://authors.library.caltech.edu/records/r5anw-4eh31/files/41598_2020_78942_MOESM2_ESM.docx" } ], "pub_year": "2020", "author_list": "Booeshaghi, A. Sina; Lubock, Nathan B.; et al." }, { "id": "https://authors.library.caltech.edu/records/2fw6n-rc071", "eprint_id": 106510, "eprint_status": "archive", "datestamp": "2023-10-03 22:33:20", "lastmod": "2026-03-30 07:33:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Linsky-Thomas-W", "name": { "family": "Linsky", "given": "Thomas W." }, "orcid": "0000-0002-1632-3395" }, { "name": { "family": "Vergara", "given": "Renan" }, "orcid": "0000-0002-3680-5105" }, { "name": { "family": "Codina", "given": "Nuria" }, "orcid": "0000-0003-3945-2242" }, { "name": { "family": "Nelson", "given": "Jorgen W." }, "orcid": "0000-0002-0202-2460" }, { "name": { "family": "Walker", "given": "Matthew J." }, "orcid": "0000-0001-5541-9245" }, { "name": { "family": "Su", "given": "Wen" }, "orcid": "0000-0002-2291-6349" }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "name": { "family": "Hsiang", "given": "Tien-Ying" }, "orcid": "0000-0002-4316-4561" }, { "name": { "family": "Esser-Nobis", "given": "Katharina" }, "orcid": "0000-0002-9027-0391" }, { "name": { "family": "Yu", "given": "Kevin" }, "orcid": "0000-0002-6725-0413" }, { "name": { "family": "Reneer", "given": "Z. Beau" }, "orcid": "0000-0002-5685-000X" }, { "name": { "family": "Hou", "given": "Yixuan J." }, "orcid": "0000-0002-8323-7243" }, { "name": { "family": "Priya", "given": "Tanu" } }, { "name": { "family": "Mitsumoto", "given": "Masaya" } }, { "name": { "family": "Pong", "given": "Avery" } }, { "name": { "family": "Lau", "given": "Uland Y." }, "orcid": "0000-0002-4758-6884" }, { "name": { "family": "Mason", "given": "Marsha L." }, "orcid": "0000-0002-8968-2196" }, { "name": { "family": "Chen", "given": "Jerry" }, "orcid": "0000-0001-5276-6735" }, { "name": { "family": "Chen", "given": "Alex" } }, { "name": { "family": "Berrocal", "given": "Tania" }, "orcid": "0000-0002-9411-9197" }, { "name": { "family": "Peng", "given": "Hong" } }, { "name": { "family": "Clairmont", "given": "Nicole S." } }, { "name": { "family": "Castellanos", "given": "Javier" } }, { "name": { "family": "Lin", "given": "Yu-Ru" } }, { "name": { "family": "Josephson-Day", "given": "Anna" }, "orcid": "0000-0003-4136-1622" }, { "name": { "family": "Baric", "given": "Ralph S." }, "orcid": "0000-0001-6827-8701" }, { "name": { "family": "Fuller", "given": "Deborah H." }, "orcid": "0000-0001-7315-2441" }, { "name": { "family": "Walkey", "given": "Carl D." } }, { "name": { "family": "Ross", "given": "Ted M." } }, { "name": { "family": "Swanson", "given": "Ryan" }, "orcid": "0000-0003-3403-3591" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Gale", "given": "Michael" }, "orcid": "0000-0002-6332-7436" }, { "name": { "family": "Blancas-Mejia", "given": "Luis M." }, "orcid": "0000-0002-2516-2482" }, { "name": { "family": "Yen", "given": "Hui-Ling" }, "orcid": "0000-0003-2493-3609" }, { "name": { "family": "Silva", "given": "Daniel-Adriano" }, "orcid": "0000-0002-3195-9009" } ] }, "title": "De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived 31 July 2020; accepted 29 October 2020. Published online 5 November 2020. \n\nWe thank M. Dougan, L. Aberman, U. Ulge, J. Rathbun, and J. Drachman for useful discussions and comments on this manuscript; Neoleukin Therapeutics, Inc. (\"Neoleukin\") for supporting this work; S. Chen and A. Malyutin (Caltech) for maintaining electron microscopes; and J. Vielmetter and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance. All of the computational resources for the de novo protein design were provided by Neoleukin's high-performance \"Neo\" computational cluster. Funding: This work was supported by NIH grants AI145296 and AI127463 and a Department of Defense grant subcontract to M.G.; NIH grant P50 8 P50 AI150464-13 and the Caltech Merkin Institute for Translational Research to P.J.B.; the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Post-doctoral Enrichment Program from the Burroughs Wellcome Fund to C.O.B; NIH NIAID grant HHSN272201400006C to H.-L.Y.; and NIH grant R01 AI089728 to R.S.B. Electron microscopy was performed at the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy. This project was also supported by the North Carolina Policy Collaboratory at the University of North Carolina at Chapel Hill with funding from the North Carolina Coronavirus Relief Fund established and appropriated by the North Carolina General Assembly. T.M.R. is supported by the Georgia Research Alliance as an Eminent Scholar. \"Neoleukin\" is a trademark of Neoleukin Therapeutics, Inc. The views and opinions expressed in this article are those of the authors and do not necessarily reflect the position of Neoleukin. Author contributions: T.W.L. designed and coordinated the research, developed computational design methods, designed de novo protein decoys of ACE2, characterized designs, and wrote the manuscript. R.V. designed de novo proteins, performed molecular biology, characterized and optimized the designs, and wrote the manuscript. N.C. designed de novo proteins, characterized and optimized the designs, and wrote the manuscript. J.W.N. designed de novo proteins, characterized and optimized the designs, performed molecular biology, performed SSM experiments, and wrote the manuscript. M.J.W. designed de novo proteins, performed molecular biology, characterized and optimized the designs, and wrote the manuscript. W.S. performed neutralization assays with the live SARS-CoV-2 virus in Vero E6 cells and edited the manuscript. C.O.B. performed cryo-EM data collection and structure solutions and analyzed the structure together with P.J.B. T.-Y.H. performed cell-neutralization assays with the live SARS-CoV-2 NanoLuc virus in Calu-3 cells. K.E.-N. performed cell-neutralization assays with the live SARS-CoV-2 NanoLuc virus in Calu-3 cells. Y.J.H. developed the nLUC reporter virus. K.Y. designed and performed ACE2 competition assays and developed methods to quantify the de novo designs in tissue lysates. T.P. designed, purified, and characterized de novo proteins. M.M. designed de novo proteins. A.P. designed de novo proteins and performed binding characterizations. U.Y.L. designed de novo proteins. M.L.M. performed pharmacokinetic studies in mice, coordinated the research for cross-reactivity binding assay, and edited the manuscript. J.C. performed pharmacokinetic studies in mice. Z.B.R. and T.M.R. performed the SARS-CoV-2 viral protection studies in hamsters. A.C. performed the ACE2 enzymatic assay and cytotoxicity assays with VeroE6. T.B. purified and characterized de novo proteins. H.P. performed mass spectrometry. N.S.C. performed molecular biology. J.Ca. developed and implemented computational tools for collaborative de novo protein design. Y.-R.L. designed de novo proteins. A.J.-D. coordinated project operations and wrote the manuscript. R.S.B. coordinated the development of the nLUC reporter virus and edited the manuscript. C.D.W. coordinated the research for ACE2 competition assays and methods to quantify the de novo designs and edited the manuscript. R.S. coordinated the research for in vitro neutralization testing, in vivo viral challenge modeling, and in vivo pharmacokinetics of the de novo proteins and edited the manuscript. D.H.F. designed the in vivo experiments. M.G. coordinated and directed the research for in vitro NanoLuc SARS-CoV-2 neutralization and edited the manuscript. L.M.B.-M. designed de novo proteins, coordinated the purification and characterization of the de novo proteins, and edited the manuscript. H.-L.Y. coordinated the research for in vitro SARS-CoV-2 neutralization and edited the manuscript. D.-A.S. generated the original idea to design the de novo decoys to neutralize SARS-CoV-2, designed the research, developed computational design selection strategies, wrote the manuscript, and directed the effort. Competing interests: T.W.L., N.C., J.W.N., and D.-A.S. are inventors on provisional patent applications for the de novo decoys described in this work. D.-A.S. and C.D.W. are cofounders of Neoleukin Therapeutics. Neoleukin authors own options and/or stock in the company. Data and materials availability: PyRosetta code used to generate initial perturbations for mobile secondary structure elements is available in the supplemental materials, appendix A. The cryo-EM maps generated from cryo-EM studies of the CTC-445.2-S 6P complex (states 1 to 4) have been deposited at the Electron Microscopy Databank (EMDB 786 http://www.emdataresource.org/) under the following accession codes: EMD-22913 (state 1), EMD-22914 (state 2), EMD-22915 (state 3), and EMD-22916 (state 4). The atomic coordinates for the CTC-445.2-S 6P complex (state 4) have been deposited at the PDB (http://www.rcsb.org/) under the accession code 7KL9. Neoleukin materials may be made available to academic noncommercial researchers through a material transfer agreement upon request.\n\nPublished - science-abe0075.pdf
Supplemental Material - abe0075-Linsky-FR-SM-Reproducibility-Checklist.pdf
Supplemental Material - abe0075-Linsky-FR-SM.pdf
", "abstract": "We developed a de novo protein design strategy to swiftly engineer decoys for neutralizing pathogens that exploit extracellular host proteins to infect the cell. Our pipeline allowed the design, validation, and optimization of de novo hACE2 decoys to neutralize SARS-CoV-2. The best decoy, CTC-445.2, binds with low nanomolar affinity and high specificity to the RBD of the spike protein. Cryo-EM shows that the design is accurate and can simultaneously bind to all three RBDs of a single spike protein. Because the decoy replicates the spike protein target interface in hACE2, it is intrinsically resilient to viral mutational escape. A bivalent decoy, CTC-445.2d, shows ~10-fold improvement in binding. CTC-445.2d potently neutralizes SARS-CoV-2 infection of cells in vitro and a single intranasal prophylactic dose of decoy protected Syrian hamsters from a subsequent lethal SARS-CoV-2 challenge.", "date": "2020-12-04", "date_type": "published", "publication": "Science", "volume": "370", "number": "6521", "publisher": "American Association for the Advancement of Science", "pagerange": "1208-1214", "id_number": "CaltechAUTHORS:20201109-112630767", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201109-112630767", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AI145296" }, { "agency": "NIH", "grant_number": "AI127463" }, { "agency": "Department of Defense" }, { "agency": "NIH", "grant_number": "P50 8 P50 AI150464-13" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "NIH", "grant_number": "HHSN272201400006C" }, { "agency": "NIH", "grant_number": "R01 AI089728" }, { "agency": "North Carolina Coronavirus Relief Fund" }, { "agency": "Georgia Research Alliance" } ] }, "local_group": { "items": [ { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/science.abe0075", "pmcid": "PMC7920261", "primary_object": { "basename": "abe0075-Linsky-FR-SM.pdf", "url": "https://authors.library.caltech.edu/records/2fw6n-rc071/files/abe0075-Linsky-FR-SM.pdf" }, "related_objects": [ { "basename": "abe0075-Linsky-FR-SM-Reproducibility-Checklist.pdf", "url": "https://authors.library.caltech.edu/records/2fw6n-rc071/files/abe0075-Linsky-FR-SM-Reproducibility-Checklist.pdf" }, { "basename": "science-abe0075.pdf", "url": "https://authors.library.caltech.edu/records/2fw6n-rc071/files/science-abe0075.pdf" } ], "pub_year": "2020", "author_list": "Linsky, Thomas W.; Vergara, Renan; et al." }, { "id": "https://authors.library.caltech.edu/records/e6v3e-hke90", "eprint_id": 105754, "eprint_status": "archive", "datestamp": "2023-09-25 22:43:38", "lastmod": "2026-03-30 16:17:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Torrente-Rodr\u00edguez-Rebeca-M", "name": { "family": "Torrente-Rodr\u00edguez", "given": "Rebeca M." }, "orcid": "0000-0002-2153-172X" }, { "id": "Lukas-Heather-L", "name": { "family": "Lukas", "given": "Heather" }, "orcid": "0000-0002-8160-9066" }, { "id": "Tu-Jiaobing", "name": { "family": "Tu", "given": "Jiaobing" }, "orcid": "0000-0002-7653-6640" }, { "id": "Min-Jihong", "name": { "family": "Min", "given": "Jihong" }, "orcid": "0000-0002-5788-1473" }, { "id": "Yang-Yiran", "name": { "family": "Yang", "given": "Yiran" }, "orcid": "0000-0001-8770-8746" }, { "id": "Xu-Changhao", "name": { "family": "Xu", "given": "Changhao" }, "orcid": "0000-0002-6817-3341" }, { "id": "Rossiter-Harry-B", "name": { "family": "Rossiter", "given": "Harry B." }, "orcid": "0000-0002-7884-0726" }, { "id": "Gao-Wei", "name": { "family": "Gao", "given": "Wei" }, "orcid": "0000-0002-8503-4562" } ] }, "title": "SARS-CoV-2 RapidPlex: A Graphene-Based Multiplexed Telemedicine Platform for Rapid and Low-Cost COVID-19 Diagnosis and Monitoring", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Elsevier Inc. \n\nAccepted: September 29, 2020; Received in revised form: September 20, 2020; Received: September 1, 2020. \n\nThis project was supported by the Merkin Institute for Translational Research at Caltech, Emergency COVID-19 Research Seed Funding and COVID-19 Continuation Funding from Tobacco-Related Disease Research Program (TRDRP), TRDRP High Impact Pilot Research Award, National Institutes of Health (5R21NR018271), and the Translational Research Institute through NASA NNX16AO69A. J.T. was supported by the National Science Scholarship from the Agency for Science, Technology and Research (A\u2217STAR), Singapore. We gratefully acknowledge critical support and infrastructure provided for this work by the Kavli Nanoscience Institute at Caltech. \n\nAuthor Contributions: W.G., R.M.T.-R., and H.L. initiated the concept and designed the experiments; R.M.T.-R., H.L., and J.T. led the experiments and collected the overall data; Y.Y. performed electrode fabrication and characterization; J.M. performed the circuit design and platform test; C.X. contributed to sensor characterization; W.G., R.M.T.-R., and H.L. contributed the data analysis and co-wrote the paper. All authors provided the feedback on the manuscript. \n\nThe authors declare no competing interests.\n\nAccepted Version - PIIS2590238520305531.pdf
Supplemental Material - 1-s2.0-S2590238520305531-mmc1.pdf
", "abstract": "The COVID-19 pandemic is an ongoing global challenge for public health systems. Ultrasensitive and early identification of infection is critical in preventing widespread COVID-19 infection by presymptomatic and asymptomatic individuals, especially in the community and in-home settings. We demonstrate a multiplexed, portable, wireless electrochemical platform for ultra-rapid detection of COVID-19: the SARS-CoV-2 RapidPlex. It detects viral antigen nucleocapsid protein, IgM and IgG antibodies, as well as the inflammatory biomarker C-reactive protein, based on our mass-producible laser-engraved graphene electrodes. We demonstrate ultrasensitive, highly selective, and rapid electrochemical detection in the physiologically relevant ranges. We successfully evaluated the applicability of our SARS-CoV-2 RapidPlex platform with COVID-19-positive and COVID-19-negative blood and saliva samples. Based on this pilot study, our multiplexed immunosensor platform may allow for high-frequency at-home testing for COVID-19 telemedicine diagnosis and monitoring.", "date": "2020-12-02", "date_type": "published", "publication": "Matter", "volume": "3", "number": "6", "publisher": "Cell Press", "pagerange": "1981-1998", "id_number": "CaltechAUTHORS:20201002-102234974", "issn": "2590-2385", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201002-102234974", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "California Tobacco-Related Disease Research Program" }, { "agency": "NIH", "grant_number": "5R21NR018271" }, { "agency": "NASA", "grant_number": "NNX16AO69A" }, { "agency": "Agency for Science, Technology and Research (A*STAR)" } ] }, "local_group": { "items": [ { "id": "Kavli-Nanoscience-Institute" }, { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" } ] }, "doi": "10.1016/j.matt.2020.09.027", "pmcid": "PMC7535803", "primary_object": { "basename": "1-s2.0-S2590238520305531-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/e6v3e-hke90/files/1-s2.0-S2590238520305531-mmc1.pdf" }, "related_objects": [ { "basename": "PIIS2590238520305531.pdf", "url": "https://authors.library.caltech.edu/records/e6v3e-hke90/files/PIIS2590238520305531.pdf" } ], "pub_year": "2020", "author_list": "Torrente-Rodr\u00edguez, Rebeca M.; Lukas, Heather; et al." }, { "id": "https://authors.library.caltech.edu/records/zkmqd-chz53", "eprint_id": 106750, "eprint_status": "archive", "datestamp": "2023-08-20 00:36:21", "lastmod": "2026-03-30 06:35:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Contreras-Sebasti\u00e1n", "name": { "family": "Contreras", "given": "Sebasti\u00e1n" }, "orcid": "0000-0001-8909-774X" }, { "id": "Villavicencio-H-Andr\u00e9s", "name": { "family": "Villavicencio", "given": "H. Andr\u00e9s" } }, { "id": "Medina-Ortiz-David", "name": { "family": "Medina-Ortiz", "given": "David" }, "orcid": "0000-0002-8369-5746" }, { "id": "Saavedra-Claudia-P", "name": { "family": "Saavedra", "given": "Claudia P." } }, { "id": "Olivera-Nappa-\u00c1lvaro", "name": { "family": "Olivera-Nappa", "given": "\u00c1lvaro" }, "orcid": "0000-0001-6053-7019" } ] }, "title": "Real-Time Estimation of R_t for Supporting Public-Health Policies Against COVID-19", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19, public-health policies, epidemiologic modeling, SARS-CoV-2, effective reproduction\nnumber R_t", "note": "\u00a9 2020 Contreras, Villavicencio, Medina-Ortiz, Saavedra and Olivera-Nappa. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. \n\nReceived: 13 May 2020; Accepted: 30 November 2020; Published: 22 December 2020. \n\nThis manuscript has been released as a pre-print at https://www.medrxiv.org/content/10.1101/2020.04.23.20076984v1 (26). This research has been financed mainly by the Centre for Biotechnology and Bioengineering\u2014CeBiB (PIA project FB0001, Conicyt, Chile). DM-O gratefully acknowledges Conicyt, Chile, for Ph.D. fellowship 21181435. The authors thank Prof. Francisco Melo for the helpful discussions on previous versions of our manuscript. \n\nData Availability Statement: Publicly available datasets were analyzed in this study. This data can be found at: https://www.worldometers.info/coronavirus/; https://www.gob.cl/coronavirus/cifrasoficiales/. \n\nAuthor Contributions: SC, DM-O, and HV: conceptualization, methodology, and investigation. \u00c1O-N, SC, and CS: validation. SC, DM-O, HV, and \u00c1O-N: writing, review, and editing. \u00c1O-N and CS: supervision and project administration. \u00c1O-N: funding resources. All authors contributed to the article and approved the submitted version. \n\nThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.\n\nPublished - fpubh-08-556689.pdf
Submitted - 2020.04.23.20076984v1.full.pdf
", "abstract": "In the absence of a consensus protocol to slow down the spread of SARS-CoV-2, policymakers need real-time indicators to support decisions in public health matters. The Effective Reproduction Number (R_t) represents the number of secondary infections generated per each case and can be dramatically modified by applying effective interventions. However, current methodologies to calculate R_t from data remain somewhat cumbersome, thus raising a barrier between its timely calculation and application by policymakers. In this work, we provide a simple mathematical formulation for obtaining the effective reproduction number in real-time using only and directly daily official case reports, obtained by modifying the equations describing the viral spread. We numerically explore the accuracy and limitations of the proposed methodology, which was demonstrated to provide accurate, timely, and intuitive results. We illustrate the use of our methodology to study the evolution of the pandemic in different iconic countries, and to assess the efficacy and promptness of different public health interventions.", "date": "2020-12", "date_type": "published", "publication": "Frontiers in Public Health", "volume": "8", "publisher": "Frontiers Media", "pagerange": "Art. No. 556689", "id_number": "CaltechAUTHORS:20201120-072926742", "issn": "2296-2565", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201120-072926742", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Centre for Biotechnology and Bioengineering" }, { "agency": "Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica (CONICYT)", "grant_number": "FB0001" }, { "agency": "Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica (CONICYT)", "grant_number": "21181435" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.3389/fpubh.2020.556689", "pmcid": "PMC7783316", "primary_object": { "basename": "fpubh-08-556689.pdf", "url": "https://authors.library.caltech.edu/records/zkmqd-chz53/files/fpubh-08-556689.pdf" }, "related_objects": [ { "basename": "2020.04.23.20076984v1.full.pdf", "url": "https://authors.library.caltech.edu/records/zkmqd-chz53/files/2020.04.23.20076984v1.full.pdf" } ], "pub_year": "2020", "author_list": "Contreras, Sebasti\u00e1n; Villavicencio, H. Andr\u00e9s; et al." }, { "id": "https://authors.library.caltech.edu/records/y8day-6fg33", "eprint_id": 106277, "eprint_status": "archive", "datestamp": "2023-08-22 07:42:41", "lastmod": "2026-03-30 16:39:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Turner-Alexander-J", "name": { "family": "Turner", "given": "Alexander J." }, "orcid": "0000-0003-1406-7372" }, { "id": "Kim-Jinsol", "name": { "family": "Kim", "given": "Jinsol" } }, { "id": "Fitzmaurice-Helen", "name": { "family": "Fitzmaurice", "given": "Helen" }, "orcid": "0000-0002-1631-5491" }, { "id": "Newman-Catherine", "name": { "family": "Newman", "given": "Catherine" } }, { "id": "Worthington-Kevin", "name": { "family": "Worthington", "given": "Kevin" } }, { "id": "Chan-Katherine", "name": { "family": "Chan", "given": "Katherine" }, "orcid": "0000-0002-1976-1438" }, { "id": "Wooldridge-Paul-J", "name": { "family": "Wooldridge", "given": "Paul J." }, "orcid": "0000-0003-2711-5900" }, { "id": "K\u00f6hler-Philipp", "name": { "family": "K\u00f6hler", "given": "Philipp" }, "orcid": "0000-0002-7820-1318" }, { "id": "Frankenberg-C", "name": { "family": "Frankenberg", "given": "Christian" }, "orcid": "0000-0002-0546-5857" }, { "id": "Cohen-Ronald-C", "name": { "family": "Cohen", "given": "Ronald C." }, "orcid": "0000-0001-6617-7691" } ] }, "title": "Observed impacts of COVID-19 on urban CO\u2082 emissions", "ispublished": "pub", "full_text_status": "public", "keywords": "urban CO2; COVID; traffic; emissions; SIF; inversion", "note": "\u00a9 2020 American Geophysical Union. \n\nIssue Online: 13 November 2020; Version of Record online: 13 November 2020; Accepted manuscript online: 30 October 2020; Manuscript accepted: 27 October 2020; Manuscript revised: 29 September 2020; Manuscript received: 24 July 2020. \n\nWe thank B. Fasoli for recent developments to the STILT model and sharing pre\u2010processing code, E. Delaria for developing a temperature calibration, P. Vannucci and A. Lall for feedback, and former members of the BEACO\u2082N project for establishing the network: A. A. Shusterman, V. Teige, and K. Lieschke. The author acknowledges ideas and advice from the participants in the COVID\u201019 and Earth System Science workshop organized by the W.M. Keck Institute for Space Studies. We are grateful to the team that has realized the TROPOMI instrument, consisting of the partnership between Airbus Defence and Space, KNMI, SRON, and TNO, commissioned by NSO and ESA. A. J. T. was supported as a Miller Fellow with the Miller Institute for Basic Research in Science at UC Berkeley. This research was funded by grants from the Koret Foundation and University of California, Berkeley. Part of this research was funded by the NASA Carbon Cycle Science program (grant NNX17AE14G). TROPOMI SIF data generation by P. K. and C. F. is funded by the Earth Science U.S. Participating Investigator program (grant NNX15AH95G). This research used the Savio computational cluster resource provided by the Berkeley Research Computing program at the University of California, Berkeley (supported by the UC Berkeley Chancellor, Vice Chancellor for Research, and Chief Information Officer). \n\nThe authors declare no competing interests. \n\nData Availability Statement: CO2 data are available online (http://beacon.berkeley.edu/). Code has been deposited in GitHub (https://www.github.com/alexjturner/UrbanInversion).\n\nPublished - 2020GL090037.pdf
Submitted - essoar.10504138.1.pdf
Supplemental Material - grl_61488_2020gl090037-sup-0001-text_si-s01.pdf
", "abstract": "Governments restricted mobility and effectively shuttered much of the global economy in response to the COVID\u201019 pandemic. Six San Francisco Bay Area counties were the first region in the United States to issue a \"shelter\u2010in\u2010place\" order asking non\u2010essential workers to stay home. Here we use CO\u2082 observations from 35 Berkeley Environment, Air\u2010quality and CO\u2082 Network (BEACO\u2082N) nodes and an atmospheric transport model to quantify changes in urban CO\u2082 emissions due to the order. We infer hourly emissions at 900\u2010m spatial resolution for 6\u2009weeks before and 6\u2009weeks during the order. We observe a 30% decrease in anthropogenic CO\u2082 emissions during the order and show that this decrease is primarily due to changes in traffic (\u201348%) with pronounced changes to daily and weekly cycles; non\u2010traffic emissions show small changes (\u20138%). These findings provide a glimpse into a future with reduced CO\u2082 emissions through electrification of vehicles.", "date": "2020-11-28", "date_type": "published", "publication": "Geophysical Research Letters", "volume": "47", "number": "22", "publisher": "American Geophysical Union", "pagerange": "Art. No. e2020GL090037", "id_number": "CaltechAUTHORS:20201026-102351517", "issn": "0094-8276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201026-102351517", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Miller Institute for Basic Research in Science" }, { "agency": "Koret Foundation" }, { "agency": "University of California, Berkeley" }, { "agency": "NASA", "grant_number": "NNX17AE14G" }, { "agency": "NASA", "grant_number": "NNX15AH95G" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1029/2020GL090037", "primary_object": { "basename": "2020GL090037.pdf", "url": "https://authors.library.caltech.edu/records/y8day-6fg33/files/2020GL090037.pdf" }, "related_objects": [ { "basename": "essoar.10504138.1.pdf", "url": "https://authors.library.caltech.edu/records/y8day-6fg33/files/essoar.10504138.1.pdf" }, { "basename": "grl_61488_2020gl090037-sup-0001-text_si-s01.pdf", "url": "https://authors.library.caltech.edu/records/y8day-6fg33/files/grl_61488_2020gl090037-sup-0001-text_si-s01.pdf" } ], "pub_year": "2020", "author_list": "Turner, Alexander J.; Kim, Jinsol; et al." }, { "id": "https://authors.library.caltech.edu/records/mhfrj-pvr73", "eprint_id": 105913, "eprint_status": "archive", "datestamp": "2023-08-20 00:27:46", "lastmod": "2026-03-30 06:14:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Banerjee-Abhik-K", "name": { "family": "Banerjee", "given": "Abhik K." }, "orcid": "0000-0001-9127-5461" }, { "id": "Blanco-Mario-R", "name": { "family": "Blanco", "given": "Mario R." }, "orcid": "0000-0002-9852-2231" }, { "id": "Bruce-Emily-A", "name": { "family": "Bruce", "given": "Emily A." } }, { "id": "Honson-Drew-D", "name": { "family": "Honson", "given": "Drew D." } }, { "id": "Chen-Linlin-M", "name": { "family": "Chen", "given": "Linlin M." } }, { "id": "Chow-Amy-Y", "name": { "family": "Chow", "given": "Amy" } }, { "id": "Bhat-Prashant", "name": { "family": "Bhat", "given": "Prashant" }, "orcid": "0000-0003-3832-4871" }, { "id": "Ollikainen-Noah", "name": { "family": "Ollikainen", "given": "Noah" }, "orcid": "0000-0002-1174-2400" }, { "id": "Quinodoz-Sofia-A", "name": { "family": "Quinodoz", "given": "Sofia A." }, "orcid": "0000-0003-1862-5204" }, { "id": "Loney-Colin", "name": { "family": "Loney", "given": "Colin" } }, { "id": "Thai-Jasmine", "name": { "family": "Thai", "given": "Jasmine" } }, { "id": "Miller-Zachary-D", "name": { "family": "Miller", "given": "Zachary D." } }, { "id": "Lin-Aaron-E", "name": { "family": "Lin", "given": "Aaron E." } }, { "id": "Schmidt-Madaline-M", "name": { "family": "Schmidt", "given": "Madaline M." } }, { "id": "Stewart-Douglas-G", "name": { "family": "Stewart", "given": "Douglas G." } }, { "id": "Goldfarb-Daniella", "name": { "family": "Goldfarb", "given": "Daniella" }, "orcid": "0000-0001-5714-7159" }, { "id": "De-Lorenzo-Giuditta", "name": { "family": "De Lorenzo", "given": "Giuditta" } }, { "id": "Rihn-Suzannah-J", "name": { "family": "Rihn", "given": "Suzannah J." } }, { "id": "Voorhees-R-M", "name": { "family": "Voorhees", "given": "Rebecca" }, "orcid": "0000-0003-1640-2293" }, { "id": "Botten-Jason-W", "name": { "family": "Botten", "given": "Jason W." } }, { "id": "Majumdar-Devdoot-S", "name": { "family": "Majumdar", "given": "Devdoot" }, "orcid": "0000-0002-2541-3851" }, { "id": "Guttman-M", "name": { "family": "Guttman", "given": "Mitchell" }, "orcid": "0000-0003-4748-9352" } ] }, "title": "SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Published by Elsevier. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nReceived 18 June 2020, Revised 26 August 2020, Accepted 2 October 2020, Available online 8 October 2020. \n\nWe thank Fritz Roth for clones; Marko Jovanovic, Bil Clemons, Shu-ou Shan, and Jamie Wangen for guidance and discussions; Joanna Jachowicz for analyses; Shawna Hiley for editing; Inna-Marie Strazhnik for figures; and Scott Tighe, Pheobe Laaguiby, Roxana del Rio-Guerra, Joyce Oetjen, Philip Eisenhauer, Arvind H. Patel, and Arthur Wickenhagen for technical help. This work was supported by NIH F30HL136080 (to A.K.B.); P20GM125498 and P30GM118228-04 (to E.A.B.); NIH GM7616-40 and F30CA247447 (to P.B.); UM1HL120877 and U54GM115516 (to D.M.); R41AI132047 and U01AI1141997 (to J.W.B.); U01 DA040612 and U01 HL130007 (to M.G.); the USC MD/PhD Program (to A.K.B.); UCLA-Caltech MSTP (to P.B.); American Cancer Society PF-17-240-01 (to N.O.); Wellcome Trust 201366/Z/16/Z (to S.J.R.); the Office of the Vice President for Research at UVM (to J.W.B.); Heritage Medical Research Institute (to M.G. and R.V.); and NYSCF, CZI, and Caltech (to M.G.). M.G. is a NYSCF-Robertson Investigator.\n\nData and Code Availability:\nAll datasets generated during this study are available at NCBI Short Read Archive: Bioproject PRJNA665692 (viral protein purifications) and PRJNA665581 (nascent and total RNA-Seq). Table S1 is available at Mendeley data archive, Mendeley Data: http://dx.doi.org/10.17632/zg7wp4xd5v.1\n\nAuthor Contributions:\nA.K.B. conceived the project and performed protein and 5EU purification, sequencing, NSP1 and 5\u2032 leader flow cytometry, and analyses. M.R.B. developed and optimized viral protein purification methods, optimized and performed translation assays and splicing assays, and led development and execution of biochemical assays and functional experiments. E.A.B. led virus work, designed and performed experiments, and provided guidance and support regarding analyses, ideas, and discussions of the paper. D.D.H. performed NSP1 translational assays and imaging experiments. L.M.C. performed 5\u2032 leader experiments. A.C. performed membrane reporter and puromycin experiments. P.B. developed 5EU selection and splicing analyses. N.O., S.A.Q., A.E.L., R.V., and M.G. performed analyses. D.G.S., D.G., G.D.L., and S.J.R. generated viral antibodies and performed viral infection. C.L. performed imaging and analysis. J.T., Z.D.M., and M.M.S. performed experiments. R.M.V. provided guidance regarding ribosome and SRP structure and function. J.W.B. provided guidance and reagents for virus work. D.M. and M.G. led the project, supervised experiments and analyses, and wrote the paper.\n\nDeclaration of Interests:\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S0092867420313106-main.pdf
Supplemental Material - 1-s2.0-S0092867420313106-mmc1.xlsx
Supplemental Material - 1-s2.0-S0092867420313106-mmc2.pdf
", "abstract": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently identified coronavirus that causes the respiratory disease known as coronavirus disease 2019 (COVID-19). Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis. Here, we comprehensively define the interactions between SARS-CoV-2 proteins and human RNAs. NSP16 binds to the mRNA recognition domains of the U1 and U2 splicing RNAs and acts to suppress global mRNA splicing upon SARS-CoV-2 infection. NSP1 binds to 18S ribosomal RNA in the mRNA entry channel of the ribosome and leads to global inhibition of mRNA translation upon infection. Finally, NSP8 and NSP9 bind to the 7SL RNA in the signal recognition particle and interfere with protein trafficking to the cell membrane upon infection. Disruption of each of these essential cellular functions acts to suppress the interferon response to viral infection. Our results uncover a multipronged strategy utilized by SARS-CoV-2 to antagonize essential cellular processes to suppress host defenses.", "date": "2020-11-25", "date_type": "published", "publication": "Cell", "volume": "183", "number": "5", "publisher": "Cell Press", "pagerange": "1325-1339", "id_number": "CaltechAUTHORS:20201008-083809040", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201008-083809040", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F30HL136080" }, { "agency": "NIH", "grant_number": "P20GM125498" }, { "agency": "NIH", "grant_number": "P30GM118228-04" }, { "agency": "NIH", "grant_number": "GM7616-40" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F30CA247447" }, { "agency": "NIH", "grant_number": "UM1HL120877" }, { "agency": "NIH", "grant_number": "U54GM115516" }, { "agency": "NIH", "grant_number": "R41AI132047" }, { "agency": "NIH", "grant_number": "U01AI1141997" }, { "agency": "NIH", "grant_number": "U01 DA040612" }, { "agency": "NIH", "grant_number": "U01 HL130007" }, { "agency": "USC MD/PhD Program" }, { "agency": "UCLA-Caltech Medical Scientist Training Program" }, { "agency": "American Cancer Society", "grant_number": "PF-17-240-01" }, { "agency": "Wellcome Trust", "grant_number": "201366/Z/16/Z" }, { "agency": "University of Vermont" }, { "agency": "Heritage Medical Research Institute" }, { "agency": "New York Stem Cell Foundation" }, { "agency": "Chan Zuckerberg Initiative" }, { "agency": "Caltech" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" }, { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cell.2020.10.004", "pmcid": "PMC7543886", "primary_object": { "basename": "1-s2.0-S0092867420313106-main.pdf", "url": "https://authors.library.caltech.edu/records/mhfrj-pvr73/files/1-s2.0-S0092867420313106-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0092867420313106-mmc1.xlsx", "url": "https://authors.library.caltech.edu/records/mhfrj-pvr73/files/1-s2.0-S0092867420313106-mmc1.xlsx" }, { "basename": "1-s2.0-S0092867420313106-mmc2.pdf", "url": "https://authors.library.caltech.edu/records/mhfrj-pvr73/files/1-s2.0-S0092867420313106-mmc2.pdf" } ], "pub_year": "2020", "author_list": "Banerjee, Abhik K.; Blanco, Mario R.; et al." }, { "id": "https://authors.library.caltech.edu/records/j29fh-xtv32", "eprint_id": 107242, "eprint_status": "archive", "datestamp": "2023-08-20 00:24:44", "lastmod": "2026-03-28 23:04:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yun-Kyongsik", "name": { "family": "Yun", "given": "Kyongsik" }, "orcid": "0000-0002-6103-7187" }, { "id": "Lee-Jeong-Seok", "name": { "family": "Lee", "given": "Jeong Seok" } }, { "id": "Kim-Eun-Young", "name": { "family": "Kim", "given": "Eun Young" } }, { "id": "Chandra-Himanshu", "name": { "family": "Chandra", "given": "Himanshu" } }, { "id": "Oh-Baek-Lok", "name": { "family": "Oh", "given": "Baek-Lok" } }, { "id": "Oh-Jihoon", "name": { "family": "Oh", "given": "Jihoon" } } ] }, "title": "Severe COVID-19 Illness: Risk Factors and Its Burden on Critical Care Resources", "ispublished": "pub", "full_text_status": "public", "keywords": "ECMO\u2014extracorporeal membrane oxygenation, ventilator, severity, COVID-19, hydroxychloroquine", "note": "\u00a9 2020 Yun, Lee, Kim, Chandra, Oh and Oh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.\n\nReceived: 18 August 2020; Accepted: 12 October 2020;\nPublished: 19 November 2020.\n\nWe thank the medical professionals dedicated to treating patients with COVID-19 in Korea, and the Ministry of Health and Welfare and the Health Insurance Review and Assessment Service of Korea for promptly sharing valuable national health insurance claim data.\n\nData Availability Statement:\nThe datasets generated in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://hira-covid19.net/.\n\nEthics Statement:\nThe studies involving human participants were reviewed and approved by The Catholic University of Korea (KC20ZISI0259). Written informed consent for participation was not required for this study in accordance with the national legislation and the institutional requirements.\n\nAuthor Contributions:\nKY, B-LO, and JO conceived of the presented idea. KY, HC, and B-LO performed and analyzed the dataset. JO, JL, and HC verified the analytical methods. B-LO and JO supervised the findings of this work. All authors discussed the results and contributed to the final manuscript.\n\nFunding:\nThis work was partially supported by the Seoul National University Hospital Research Fund (0320202160).\n\nConflict of Interest:\nJL was employed by GENOME INSIGHT Inc.\n\nThe remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.\n\nPublished - fmed-07-583060.pdf
Supplemental Material - 5212337.zip
", "abstract": "In South Korea, the first confirmed case of coronavirus 2019 (COVID-19) was detected on January 20, 2020. After a month, the number of confirmed cases surged, as community transmission occurred. The local hospitals experienced severe shortages in medical resources such as mechanical ventilators and extracorporeal membrane oxygenation (ECMO) equipment. With the medical claims data of 7,590 COVID-19 confirmed patients, this study examined how the demand for major medical resources and medications changed during the outbreak and subsequent stabilization period of COVID-19 in South Korea. We also aimed to investigate how the underlying diseases and demographic factors affect disease severity. Our findings revealed that the risk of being treated with a mechanical ventilator or ECMO (critical condition) was almost twice as high in men, and a previous history of hypertension, diabetes, and psychiatric diseases increased the risk for progressing to critical condition [Odds Ratio (95% CI), 1.60 (1.14\u20132.24); 1.55 (1.55\u20132.06); 1.73 (1.25\u20132.39), respectively]. Although chronic pulmonary disease did not significantly increase the risk for severity of the illness, patients with a Charlson comorbidity index score of \u22655 and those treated in an outbreak area had an increased risk of developing a critical condition [3.82 (3.82\u20138.15); 1.59 (1.20\u20132.09), respectively]. Our results may help clinicians predict the demand for medical resources during the spread of COVID-19 infection and identify patients who are likely to develop severe disease.", "date": "2020-11-19", "date_type": "published", "publication": "Frontiers in Medicine", "volume": "7", "publisher": "Frontiers Media SA", "pagerange": "Art. No. 583060", "id_number": "CaltechAUTHORS:20201221-133546033", "issn": "2296-858X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201221-133546033", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Seoul National University Hospital Research Fund", "grant_number": "0320202160" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.3389/fmed.2020.583060", "pmcid": "PMC7711126", "primary_object": { "basename": "5212337.zip", "url": "https://authors.library.caltech.edu/records/j29fh-xtv32/files/5212337.zip" }, "related_objects": [ { "basename": "fmed-07-583060.pdf", "url": "https://authors.library.caltech.edu/records/j29fh-xtv32/files/fmed-07-583060.pdf" } ], "pub_year": "2020", "author_list": "Yun, Kyongsik; Lee, Jeong Seok; et al." }, { "id": "https://authors.library.caltech.edu/records/w04vt-43h07", "eprint_id": 106144, "eprint_status": "archive", "datestamp": "2023-08-22 06:57:40", "lastmod": "2026-03-30 16:05:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Liu-Zhu", "name": { "family": "Liu", "given": "Zhu" }, "orcid": "0000-0002-8968-7050" }, { "name": { "family": "Ciais", "given": "Philippe" }, "orcid": "0000-0001-8560-4943" }, { "name": { "family": "Deng", "given": "Zhu" }, "orcid": "0000-0002-6409-9578" }, { "name": { "family": "Lei", "given": "Ruixue" }, "orcid": "0000-0001-6226-7075" }, { "name": { "family": "Davis", "given": "Steven J." }, "orcid": "0000-0002-9338-0844" }, { "name": { "family": "Feng", "given": "Sha" }, "orcid": "0000-0002-2376-0868" }, { "name": { "family": "Zheng", "given": "Bo" }, "orcid": "0000-0001-8344-3445" }, { "name": { "family": "Cui", "given": "Duo" } }, { "name": { "family": "Dou", "given": "Xinyu" }, "orcid": "0000-0001-7783-6971" }, { "name": { "family": "Zhu", "given": "Biqing" }, "orcid": "0000-0001-9360-6797" }, { "name": { "family": "Guo", "given": "Rui" }, "orcid": "0000-0001-5536-0669" }, { "name": { "family": "Ke", "given": "Piyu" }, "orcid": "0000-0003-0353-6313" }, { "name": { "family": "Sun", "given": "Taochun" }, "orcid": "0000-0003-3640-6005" }, { "name": { "family": "Lu", "given": "Chenxi" } }, { "name": { "family": "He", "given": "Pan" } }, { "id": "Wang-Yuan", "name": { "family": "Wang", "given": "Yuan" }, "orcid": "0000-0001-6657-8401" }, { "name": { "family": "Yue", "given": "Xu" }, "orcid": "0000-0002-8861-8192" }, { "name": { "family": "Wang", "given": "Yilong" } }, { "name": { "family": "Lei", "given": "Yadong" } }, { "name": { "family": "Zhou", "given": "Hao" } }, { "name": { "family": "Cai", "given": "Zhaonan" } }, { "name": { "family": "Wu", "given": "Yuhui" } }, { "name": { "family": "Guo", "given": "Runtao" } }, { "name": { "family": "Han", "given": "Tingxuan" } }, { "name": { "family": "Xue", "given": "Jinjun" }, "orcid": "0000-0002-6794-1361" }, { "name": { "family": "Boucher", "given": "Olivier" } }, { "name": { "family": "Boucher", "given": "Eulalie" }, "orcid": "0000-0002-6070-2544" }, { "name": { "family": "Chevallier", "given": "Fr\u00e9d\u00e9ric" }, "orcid": "0000-0002-4327-3813" }, { "name": { "family": "Tanaka", "given": "Katsumasa" }, "orcid": "0000-0001-9601-6442" }, { "name": { "family": "Wei", "given": "Yimin" }, "orcid": "0000-0002-8476-7334" }, { "name": { "family": "Zhong", "given": "Haiwang" } }, { "name": { "family": "Kang", "given": "Chongqing" } }, { "name": { "family": "Zhang", "given": "Ning" } }, { "name": { "family": "Chen", "given": "Bin" } }, { "name": { "family": "Xi", "given": "Fengming" } }, { "name": { "family": "Liu", "given": "Miaomiao" } }, { "name": { "family": "Br\u00e9on", "given": "Fran\u00e7ois-Marie" }, "orcid": "0000-0003-2128-739X" }, { "name": { "family": "Lu", "given": "Yonglong" }, "orcid": "0000-0002-3338-4210" }, { "name": { "family": "Zhang", "given": "Qiang" }, "orcid": "0000-0002-8376-131X" }, { "name": { "family": "Guan", "given": "Dabo" } }, { "name": { "family": "Gong", "given": "Peng" }, "orcid": "0000-0003-1513-3765" }, { "name": { "family": "Kammen", "given": "Daniel M." }, "orcid": "0000-0003-2984-7777" }, { "name": { "family": "He", "given": "Kebin" } }, { "name": { "family": "Schellnhuber", "given": "Hans Joachim" } } ] }, "title": "Near-real-time monitoring of global CO\u2082 emissions reveals the effects of the COVID-19 pandemic", "ispublished": "pub", "full_text_status": "public", "keywords": "Atmospheric science; Climate sciences; Environmental sciences; Environmental social sciences", "note": "\u00a9 The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 09 June 2020; Accepted 17 September 2020; Published 14 October 2020. \n\nZL acknowledges funding from the National Natural Science Foundation of China (grant 71874097 and 41921005), Beijing Natural Science Foundation (JQ19032), and Qiushi Foundation. CB is supported by the National Science Fund for Distinguished Young Scholars of China (71725005), Beijing Outstanding Scientist Program (BJJWZYJH01201910027031). N.Z. is supported by the National Natural Science Foundation of China (71822402 and 91746112) and National Key R&D Program of China (2018YFC0213600). P.G. is thankful to Cyrus Tang foundation and Delos LLC. Asia for donations to support his research at Tsinghua University. M.M.L. is thankful to The Science Fund for Creative Research Groups \"Environmental Risk Management (ERM)\" granted by NSFC (71921003). H.Z. and C.K. are thankful to National High-End Think Tank Construction Project of National Governance and Global Governance Institute of Tsinghua University (2020WTF044). X.Y. is supported by the National Key Research and Development Program of China (2017YFA0603802). Y.L. was supported by National Natural Science Foundation of China (No. 71761147001), This research is partially supported by Tsinghua University Initiative Scientific Research Program (2020Z99CFG012). Authors acknowledge Paul O. Wennberg for insightful comments that helped improve this paper and Jingjing Chen and Qi Pan for the help of data collection. \n\nData availability: All data generated or analyzed during this study are included in this article (data available at https://www.carbonmonitor.org or https://www.carbonmonitor.org.cn). \n\nAOD from MODIS: https://ladsweb.modaps.eosdis.nasa.gov/missions-and-measurements/products/MOD04_L2/ \n\nNO2 from OMI: http://www.temis.nl/airpollution/no2col/no2regioomimonth_qa.php \n\nXCO2 from GOSAT: https://data2.gosat.nies.go.jp/GosatDataArchiveService/usr/download/DownloadPage/view. \n\nCode availability: All code generated during and/or analyzed during the current study are available from the corresponding author upon reasonable request. \n\nThese authors contributed equally: Zhu Liu, Philippe Ciais, Zhu Deng. \n\nAuthor Contributions: Z.L. and P.C. designed the research, Z.D. coordinated the data processing. Z.L., P.C., Z.D., R.L., S.J.D., S.F., B.Z., D.C., X.D., B.Z., R.G., P.K., T.S., C.L., P.H., Y.Wang, X.Y., Y.W., Y.L., H.Z., Z.C., Y.Wu, Runtao G., T.H., J.X., O.B., E.B., F.C., K.T., H.Z., C.K. contributed to data collecting, analysis, Z.L., P.C., Z.D., R.L., S.J.D., S.F., B.Z., D.C., X.D., B.Z., R.G., P.K., T.S., C.L., P.H., Y.Wang, X.Y., Y.W., Y.L., H.Z., Z.C., Y.Wu, Runtao G., T.H., J.X., O.B., E.B., F.C., K.T., Y.W., H.Z., C.K., N.Z., B.C., F.X., M.L., F.M., Y.L., Q.Z., D.G., P.G., D.M., K.H. and H.J.S. contributed to paper writing. \n\nAuthors declare no competing interests. \n\nPeer review information: Nature Communications thanks Daniel Moran, Thomas Wiedmann, and Yoshiki Yamagata for their contribution to the peer review of this work.\n\nLiu, Z., Ciais, P., Deng, Z. et al. Author Correction: Near-real-time monitoring of global CO2 emissions reveals the effects of the COVID-19 pandemic. Nat Commun 11, 6292 (2020). https://doi.org/10.1038/s41467-020-20254-5\n\nPublished - s41467-020-18922-7.pdf
Supplemental Material - 41467_2020_18922_MOESM1_ESM.pdf
Erratum - s41467-020-20254-5.pdf
", "abstract": "The COVID-19 pandemic is impacting human activities, and in turn energy use and carbon dioxide (CO\u2082) emissions. Here we present daily estimates of country-level CO2 emissions for different sectors based on near-real-time activity data. The key result is an abrupt 8.8% decrease in global CO\u2082 emissions (\u22121551 Mt CO\u2082) in the first half of 2020 compared to the same period in 2019. The magnitude of this decrease is larger than during previous economic downturns or World War II. The timing of emissions decreases corresponds to lockdown measures in each country. By July 1st, the pandemic's effects on global emissions diminished as lockdown restrictions relaxed and some economic activities restarted, especially in China and several European countries, but substantial differences persist between countries, with continuing emission declines in the U.S. where coronavirus cases are still increasing substantially.", "date": "2020-10-14", "date_type": "published", "publication": "Nature Communications", "volume": "11", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 5172", "id_number": "CaltechAUTHORS:20201019-102845933", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201019-102845933", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Natural Science Foundation of China", "grant_number": "71874097" }, { "agency": "National Natural Science Foundation of China", "grant_number": "41921005" }, { "agency": "Beijing Natural Science Foundation", "grant_number": "JQ19032" }, { "agency": "Qiushi Foundation" }, { "agency": "National Science Fund for Distinguished Young Scholars of China", "grant_number": "71725005" }, { "agency": "Beijing Outstanding Scientist Program", "grant_number": "BJJWZYJH01201910027031" }, { "agency": "National Natural Science Foundation of China", "grant_number": "71822402" }, { "agency": "National Natural Science Foundation of China", "grant_number": "91746112" }, { "agency": "National Key Research and Development Program of China", "grant_number": "2018YFC0213600" }, { "agency": "Cyrus Tang Foundation" }, { "agency": "Delos LLC" }, { "agency": "Science Fund for Creative Research Groups" }, { "agency": "National Natural Science Foundation of China", "grant_number": "71921003" }, { "agency": "Tsinghua University", "grant_number": "2020WTF044" }, { "agency": "National Key Research and Development Program", "grant_number": "2017YFA0603802" }, { "agency": "National Natural Science Foundation of China", "grant_number": "71761147001" }, { "agency": "Tsinghua University", "grant_number": "2020Z99CFG012" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1038/s41467-020-18922-7", "pmcid": "PMC7560733", "primary_object": { "basename": "41467_2020_18922_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/w04vt-43h07/files/41467_2020_18922_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "s41467-020-18922-7.pdf", "url": "https://authors.library.caltech.edu/records/w04vt-43h07/files/s41467-020-18922-7.pdf" }, { "basename": "s41467-020-20254-5.pdf", "url": "https://authors.library.caltech.edu/records/w04vt-43h07/files/s41467-020-20254-5.pdf" } ], "pub_year": "2020", "author_list": "Liu, Zhu; Ciais, Philippe; et al." }, { "id": "https://authors.library.caltech.edu/records/znbwp-rb862", "eprint_id": 104225, "eprint_status": "archive", "datestamp": "2023-08-19 23:48:30", "lastmod": "2026-03-29 16:37:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ames-A-D", "name": { "family": "Ames", "given": "Aaron D." }, "orcid": "0000-0003-0848-3177" }, { "id": "Moln\u00e1r-Tam\u00e1s-G", "name": { "family": "Moln\u00e1r", "given": "Tam\u00e1s G." }, "orcid": "0000-0002-9379-7121" }, { "id": "Singletary-Andrew-W", "name": { "family": "Singletary", "given": "Andrew W." }, "orcid": "0000-0001-6635-4256" }, { "id": "Orosz-G\u00e1bor", "name": { "family": "Orosz", "given": "G\u00e1bor" }, "orcid": "0000-0002-9000-3736" } ] }, "title": "Safety-Critical Control of Active Interventions for COVID-19 Mitigation", "ispublished": "pub", "full_text_status": "public", "keywords": "Safety-Critical Control, Epidemiology, Non-Pharmaceutical Intervention, COVID-19", "note": "\u00a9 2020 IEEE. This work is licensed under a Creative Commons Attribution 4.0 License. \n\nThis work was supported in part by the National Science Foundation, Cyber-Physical Systems (CPS) Award 1932091. \n\nThe authors would like to thank Franca Hoffmann for her insights into compartmental epidemiological models and G\u00e1bor St\u00e9p\u00e1n for discussions regarding non-pharmaceutical interventions in Europe.\n\nPublished - 09217519.pdf
Submitted - 2009.10262.pdf
Submitted - 2020.06.17.20133264v1.full.pdf
", "abstract": "The world has recently undergone the most ambitious mitigation effort in a century, consisting of wide-spread quarantines aimed at preventing the spread of COVID-19. The use of influential epidemiological models of COVID-19 helped to encourage decision makers to take drastic non-pharmaceutical interventions. Yet, inherent in these models are often assumptions that the active interventions are static, e.g., that social distancing is enforced until infections are minimized, which can lead to inaccurate predictions that are ever evolving as new data is assimilated. We present a methodology to dynamically guide the active intervention by shifting the focus from viewing epidemiological models as systems that evolve in autonomous fashion to control systems with an \"input\" that can be varied in time in order to change the evolution of the system. We show that a safety-critical control approach to COVID-19 mitigation gives active intervention policies that formally guarantee the safe evolution of compartmental epidemiological models. This perspective is applied to current US data on cases while taking into account reduction of mobility, and we find that it accurately describes the current trends when time delays associated with incubation and testing are incorporated. Optimal active intervention policies are synthesized to determine future mitigations necessary to bound infections, hospitalizations, and death, both at national and state levels. We therefore provide means in which to model and modulate active interventions with a view toward the phased reopenings that are currently beginning across the US and the world in a decentralized fashion. This framework can be converted into public policies, accounting for the fractured landscape of COVID-19 mitigation in a safety-critical fashion.", "date": "2020-10-08", "date_type": "published", "publication": "IEEE Access", "volume": "8", "publisher": "IEEE", "pagerange": "188454-188474", "id_number": "CaltechAUTHORS:20200706-130358309", "issn": "2169-3536", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200706-130358309", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CNS-1932091" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1109/ACCESS.2020.3029558", "pmcid": "PMC8545284", "primary_object": { "basename": "09217519.pdf", "url": "https://authors.library.caltech.edu/records/znbwp-rb862/files/09217519.pdf" }, "related_objects": [ { "basename": "2009.10262.pdf", "url": "https://authors.library.caltech.edu/records/znbwp-rb862/files/2009.10262.pdf" }, { "basename": "2020.06.17.20133264v1.full.pdf", "url": "https://authors.library.caltech.edu/records/znbwp-rb862/files/2020.06.17.20133264v1.full.pdf" } ], "pub_year": "2020", "author_list": "Ames, Aaron D.; Moln\u00e1r, Tam\u00e1s G.; et al." }, { "id": "https://authors.library.caltech.edu/records/kz5wn-h6515", "eprint_id": 105013, "eprint_status": "archive", "datestamp": "2023-08-19 23:35:12", "lastmod": "2026-03-29 00:01:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Reutrakul-Sirimon", "name": { "family": "Reutrakul", "given": "Sirimon" }, "orcid": "0000-0002-0686-1069" }, { "id": "Genco-Matthew", "name": { "family": "Genco", "given": "Matthew" } }, { "id": "Salinas-Harley", "name": { "family": "Salinas", "given": "Harley" } }, { "id": "Sargis-Robert-M", "name": { "family": "Sargis", "given": "Robert M." }, "orcid": "0000-0001-7061-2983" }, { "id": "Paul-Carlie", "name": { "family": "Paul", "given": "Carlie" } }, { "id": "Eisenberg-Yuval", "name": { "family": "Eisenberg", "given": "Yuval" } }, { "id": "Fang-Jiali", "name": { "family": "Fang", "given": "Jiali" } }, { "id": "Caskey-Rachel-N", "name": { "family": "Caskey", "given": "Rachel N." } }, { "id": "Henkle-Sarah", "name": { "family": "Henkle", "given": "Sarah" } }, { "id": "Fatoorehchi-Sam", "name": { "family": "Fatoorehchi", "given": "Sam" } }, { "id": "Osta-Amanda", "name": { "family": "Osta", "given": "Amanda" } }, { "id": "Srivastava-Pavan", "name": { "family": "Srivastava", "given": "Pavan" } }, { "id": "Johnson-Alexia", "name": { "family": "Johnson", "given": "Alexia" } }, { "id": "Messmer-Sarah-E", "name": { "family": "Messmer", "given": "Sarah E." } }, { "id": "Barnes-Michelle", "name": { "family": "Barnes", "given": "Michelle" } }, { "id": "Pratuangtham-Sarida", "name": { "family": "Pratuangtham", "given": "Sarida" } }, { "id": "Layden-Brian-T", "name": { "family": "Layden", "given": "Brian T." }, "orcid": "0000-0003-2176-5654" } ] }, "title": "Feasibility of Inpatient Continuous Glucose Monitoring During the COVID-19 Pandemic: Early Experience", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2020 by the American Diabetes Association. \n\nReceived 18 June 2020 and accepted 23 June 2020. \n\nThis article is part of a special article collection available at https://care.diabetesjournals.org/collection/diabetes-and-COVID19. \n\nThe authors thank the nursing staff of 7East, University of Illinois Hospital & Health Sciences System, and the endocrinology fellows for their assistance in the study and their dedicated care for the COVID-19\u2013positive patients. They acknowledge Rebecca S. Monson and Kirstie K. Danielson (University of Illinois at Chicago) for their assistance in the study. \n\nThis study was supported by the Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Illinois at Chicago. Dexcom provided equipment support. \n\nDexcom had no role in the study design, data collection, or analysis. \n\nNo potential conflicts of interest relevant to this article were reported. \n\nAuthor Contributions: S.R. designed the study, researched and analyzed the data, and wrote and edited the manuscript. M.G., H.S., C.P., J.F., R.N.C., S.H., S.F., A.O., P.S., A.J., S.E.M., and M.B. researched data and reviewed and edited the manuscript. S.P. analyzed the data and contributed to the discussion. R.M.S., Y.E., and B.T.L. designed the study, contributed to the discussion, and reviewed and edited the manuscript. S.R. is the guarantor of this work and, as such, had full access to all the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.", "abstract": "Continuous glucose monitoring (CGM) systems have been explored in a few studies for non\u2013intensive care unit (ICU) patients (1\u20133). During the coronavirus disease 2019 (COVID-19) pandemic, shortage of personal protective equipment (PPE) became a concern. On 1 April 2020, the U.S. Food and Drug Administration announced it would not object to the use of CGM systems to assist with COVID-19 patient monitoring (4). This study was conducted to explore the feasibility of using CGM in noncritically ill patients hospitalized with COVID-19.", "date": "2020-10", "date_type": "published", "publication": "Diabetes Care", "volume": "43", "number": "10", "publisher": "American Diabetes Association", "pagerange": "e137-e138", "id_number": "CaltechAUTHORS:20200818-151255840", "issn": "0149-5992", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200818-151255840", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Illinois, Chicago" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.2337/dc20-1503", "pub_year": "2020", "author_list": "Reutrakul, Sirimon; Genco, Matthew; et al." }, { "id": "https://authors.library.caltech.edu/records/14qcy-ft037", "eprint_id": 104400, "eprint_status": "archive", "datestamp": "2023-08-19 23:34:35", "lastmod": "2026-03-30 15:53:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kozak-John-J", "name": { "family": "Kozak", "given": "John J." } }, { "id": "Gray-H-B", "name": { "family": "Gray", "given": "Harry B." }, "orcid": "0000-0002-7937-7876" }, { "id": "Garza-L\u00f3pez-Roberto-A", "name": { "family": "Garza-L\u00f3pez", "given": "Roberto A." } } ] }, "title": "Structural stability of the SARS-CoV-2 main protease: Can metal ions affect function?", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2020 Elsevier Inc. \n\nReceived 26 May 2020, Revised 8 July 2020, Accepted 10 July 2020, Available online 16 July 2020. \n\nWork at Caltech was supported by the NIH (DK019038) and the Arnold and Mabel Beckman Foundation. Support at Pomona College was provided by the Howard Hughes Medical Institute Research Program and a Sontag Research Fellowship Award. Molecular graphics and analyses performed with UCSF Chimera, developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from NIH P41-GM103311. \n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.", "abstract": "We have investigated the structural stability of the SARS (Severe acute respiratory syndrome)-CoV-2 main protease monomer (Mpro). We quantified the spatial and angular changes in the structure using two independent analyses, one based on a spatial metrics (\u03b4, ratio), the second on angular metrics. The order of unfolding of the 10 helices in Mpro is characterized by beta vs alpha plots similar to those of cytochromes and globins. The longest turning region is anomalous in the earliest stage of unfolding. In an investigation of excluded-volume effects, we found that the maximum spread in average molecular-volume values for Mpro, cytochrome c-b\u2085\u2086\u2082, cytochrome c', myoglobin, and cytoglobin is ~10 \u0173. This apparent universality is a consequence of the dominant contributions from six residues: ALA, ASP, GLU, LEU, LYS and VAL. Of the seven Mpro histidines, residues 41, 163, 164, and 246 are in stable H-bonded regions; metal ion binding to one or more of these residues could break up the H-bond network, thereby affecting protease function. Our analysis also indicated that metal binding to cysteine residues 44 and 145 could disable the enzyme.", "date": "2020-10", "date_type": "published", "publication": "Journal of Inorganic Biochemistry", "volume": "211", "publisher": "Elsevier", "pagerange": "Art. No. 111179", "id_number": "CaltechAUTHORS:20200716-094538897", "issn": "0162-0134", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200716-094538897", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "DK019038" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Sontag Foundation" }, { "agency": "University of California, San Francisco" }, { "agency": "NIH", "grant_number": "P41-GM103311" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.jinorgbio.2020.111179", "pmcid": "PMC7365078", "pub_year": "2020", "author_list": "Kozak, John J.; Gray, Harry B.; et al." }, { "id": "https://authors.library.caltech.edu/records/d0v8s-00052", "eprint_id": 104231, "eprint_status": "archive", "datestamp": "2023-08-22 06:30:01", "lastmod": "2026-03-30 07:57:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Contreras-Sebasti\u00e1n", "name": { "family": "Contreras", "given": "Sebasti\u00e1n" }, "orcid": "0000-0001-8909-774X" }, { "id": "Biron-Lattes-Juan-Pablo", "name": { "family": "Biron-Lattes", "given": "Juan Pablo" } }, { "id": "Villavicencio-H-Andr\u00e9s", "name": { "family": "Villavicencio", "given": "H. Andr\u00e9s" } }, { "id": "Medina-Ortiz-David", "name": { "family": "Medina-Ortiz", "given": "David" }, "orcid": "0000-0002-8369-5746" }, { "id": "Llanovarced-Kawles-Nyna", "name": { "family": "Llanovarced-Kawles", "given": "Nyna" } }, { "id": "Olivera-Nappa-\u00c1lvaro", "name": { "family": "Olivera-Nappa", "given": "\u00c1lvaro" }, "orcid": "0000-0001-6053-7019" } ] }, "title": "Statistically-based methodology for revealing real contagion trends and correcting delay-induced errors in the assessment of COVID-19 pandemic", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; SARS-CoV-2; Public health; Statistics; ARIMA models; Data analysis", "note": "\u00a9 2020 Elsevier Ltd. \n\nReceived 26 May 2020, Revised 19 June 2020, Accepted 2 July 2020, Available online 3 July 2020. \n\nThe authors gratefully acknowledge support from the Chilean National Agency for Research and development through ANID PIA Grant AFB180004, and the Centre for Biotechnology and Bioengineering - CeBiB (PIA project FB0001, Conicyt, Chile). DM-O gratefully acknowledges Conicyt, Chile, for PhD fellowship 21181435.\n\nCRediT authorship contribution statement:\nSebasti\u00e1n Contreras: Conceptualization, Methodology, Investigation, Writing - original draft, Visualization, Writing - review & editing, Supervision. Juan Pablo Biron-Lattes: Validation, Investigation, Writing - original draft, Writing - review & editing. H. Andr\u00e9s Villavicencio: Conceptualization, Investigation, Writing - original draft, Supervision. David Medina-Ortiz: Validation, Writing - review & editing. Nyna Llanovarced-Kawles: Investigation, Writing - original draft. \u00c1lvaro Olivera-Nappa: Validation, Writing - review & editing, Supervision, Project administration, Funding acquisition. \n\nThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.\n\nPublished - 1-s2.0-S0960077920304847-main.pdf
Accepted Version - main.pdf
", "abstract": "COVID-19 pandemic has reshaped our world in a timescale much shorter than what we can understand. Particularities of SARS-CoV-2, such as its persistence in surfaces and the lack of a curative treatment or vaccine against COVID-19, have pushed authorities to apply restrictive policies to control its spreading. As data drove most of the decisions made in this global contingency, their quality is a critical variable for decision-making actors, and therefore should be carefully curated. In this work, we analyze the sources of error in typically reported epidemiological variables and usual tests used for diagnosis, and their impact on our understanding of COVID-19 spreading dynamics. We address the existence of different delays in the report of new cases, induced by the incubation time of the virus and testing-diagnosis time gaps, and other error sources related to the sensitivity/specificity of the tests used to diagnose COVID-19. Using a statistically-based algorithm, we perform a temporal reclassification of cases to avoid delay-induced errors, building up new epidemiologic curves centered in the day where the contagion effectively occurred. We also statistically enhance the robustness behind the discharge/recovery clinical criteria in the absence of a direct test, which is typically the case of non-first world countries, where the limited testing capabilities are fully dedicated to the evaluation of new cases. Finally, we applied our methodology to assess the evolution of the pandemic in Chile through the Effective Reproduction Number R_t, identifying different moments in which data was misleading governmental actions. In doing so, we aim to raise public awareness of the need for proper data reporting and processing protocols for epidemiological modelling and predictions.", "date": "2020-10", "date_type": "published", "publication": "Chaos, Solitons, and Fractals", "volume": "139", "publisher": "Elsevier", "pagerange": "Art. No. 110087", "id_number": "CaltechAUTHORS:20200706-145145631", "issn": "0960-0779", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200706-145145631", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica (CONICYT)", "grant_number": "AFB180004" }, { "agency": "Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica (CONICYT)", "grant_number": "FB0001" }, { "agency": "Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica (CONICYT)", "grant_number": "21181435" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.chaos.2020.110087", "pmcid": "PMC7341964", "primary_object": { "basename": "1-s2.0-S0960077920304847-main.pdf", "url": "https://authors.library.caltech.edu/records/d0v8s-00052/files/1-s2.0-S0960077920304847-main.pdf" }, "related_objects": [ { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/d0v8s-00052/files/main.pdf" } ], "pub_year": "2020", "author_list": "Contreras, Sebasti\u00e1n; Biron-Lattes, Juan Pablo; et al." }, { "id": "https://authors.library.caltech.edu/records/ax3gh-dfg43", "eprint_id": 104578, "eprint_status": "archive", "datestamp": "2023-08-19 23:19:52", "lastmod": "2026-03-29 20:44:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lecocq-Thomas", "name": { "family": "Lecocq", "given": "Thomas" }, "orcid": "0000-0002-4988-6477" }, { "name": { "family": "Hicks", "given": "Stephen P." }, "orcid": "0000-0002-7476-3284" }, { "name": { "family": "Van Noten", "given": "Koen" }, "orcid": "0000-0001-8933-4426" }, { "name": { "family": "van Wijk", "given": "Kasper" }, "orcid": "0000-0003-4994-8030" }, { "name": { "family": "Koelemeijer", "given": "Paula" } }, { "name": { "family": "De Plaen", "given": "Raphael S. M." }, "orcid": "0000-0003-3477-2001" }, { "name": { "family": "Massin", "given": "Fr\u00e9d\u00e9rick" }, "orcid": "0000-0002-7532-5139" }, { "name": { "family": "Hillers", "given": "Gregor" }, "orcid": "0000-0003-2341-1892" }, { "name": { "family": "Anthony", "given": "Robert E." } }, { "name": { "family": "Apoloner", "given": "Maria-Theresia" }, "orcid": "0000-0002-4006-1284" }, { "name": { "family": "Arroyo-Sol\u00f3rzano", "given": "Mario" }, "orcid": "0000-0002-1653-2680" }, { "name": { "family": "Assink", "given": "Jelle D." }, "orcid": "0000-0002-4990-6845" }, { "name": { "family": "B\u00fcy\u00fckakp\u0131nar", "given": "Pinar" }, "orcid": "0000-0001-8461-674X" }, { "name": { "family": "Cannata", "given": "Andrea" }, "orcid": "0000-0002-0028-5822" }, { "name": { "family": "Cannavo", "given": "Flavio" }, "orcid": "0000-0001-7550-8579" }, { "name": { "family": "Carrasco", "given": "Sebastian" }, "orcid": "0000-0002-6207-8757" }, { "name": { "family": "Caudron", "given": "Corentin" }, "orcid": "0000-0002-3748-0007" }, { "name": { "family": "Chaves", "given": "Esteban J." }, "orcid": "0000-0002-5724-1513" }, { "name": { "family": "Cornwell", "given": "David G." }, "orcid": "0000-0002-9843-7811" }, { "name": { "family": "Craig", "given": "David" }, "orcid": "0000-0001-9414-1725" }, { "name": { "family": "den Ouden", "given": "Olivier F. C." } }, { "name": { "family": "Diaz", "given": "Jordi" }, "orcid": "0000-0003-1801-0541" }, { "name": { "family": "Donner", "given": "Stefanie" }, "orcid": "0000-0001-7351-8079" }, { "name": { "family": "Evangelidis", "given": "Christos P." }, "orcid": "0000-0001-8733-8984" }, { "name": { "family": "Evers", "given": "L\u00e4slo" }, "orcid": "0000-0003-2825-6211" }, { "name": { "family": "Fauville", "given": "Benoit" } }, { "name": { "family": "Fernandez", "given": "Gonzalo A." }, "orcid": "0000-0001-8284-9566" }, { "name": { "family": "Giannopoulos", "given": "Dimitrios" }, "orcid": "0000-0002-8314-0759" }, { "name": { "family": "Gibbons", "given": "Steven J." }, "orcid": "0000-0002-7822-0244" }, { "name": { "family": "Girona", "given": "T\u00e1rsilo" }, "orcid": "0000-0001-6422-0422" }, { "name": { "family": "Grecu", "given": "Bogdan" }, "orcid": "0000-0002-7662-996X" }, { "name": { "family": "Grunberg", "given": "Marc" }, "orcid": "0000-0002-1307-7790" }, { "name": { "family": "Het\u00e9nyi", "given": "Gy\u00f6rgy" }, "orcid": "0000-0001-9036-4761" }, { "name": { "family": "Horleston", "given": "Anna" }, "orcid": "0000-0002-6748-6522" }, { "name": { "family": "Inza", "given": "Adolfo" }, "orcid": "0000-0001-5381-9042" }, { "name": { "family": "Irving", "given": "Jessica C. E." }, "orcid": "0000-0002-0866-8246" }, { "name": { "family": "Jamalreyhani", "given": "Mohammadreza" }, "orcid": "0000-0003-4181-7175" }, { "name": { "family": "Kafka", "given": "Alan" }, "orcid": "0000-0001-6643-1602" }, { "name": { "family": "Koymans", "given": "Mathijs R." } }, { "id": "Labedz-Celeste-R", "name": { "family": "Labedz", "given": "Celeste R." }, "orcid": "0000-0001-7339-2170" }, { "name": { "family": "Larose", "given": "Eric" } }, { "name": { "family": "Lindsey", "given": "Nathaniel J." }, "orcid": "0000-0001-9522-6683" }, { "name": { "family": "McKinnon", "given": "Mika" }, "orcid": "0000-0002-9274-0377" }, { "name": { "family": "Megies", "given": "Tobias" }, "orcid": "0000-0002-5033-9921" }, { "name": { "family": "Miller", "given": "Meghan S." }, "orcid": "0000-0001-5494-2296" }, { "name": { "family": "Minarik", "given": "William" }, "orcid": "0000-0001-5509-5543" }, { "name": { "family": "Moresi", "given": "Louis" }, "orcid": "0000-0003-3685-174X" }, { "name": { "family": "M\u00e1rquez-Ram\u00edrez", "given": "V\u00edctor H." }, "orcid": "0000-0003-1494-2229" }, { "name": { "family": "M\u00f6llhoff", "given": "Martin" }, "orcid": "0000-0003-1848-1554" }, { "name": { "family": "Nesbitt", "given": "Ian M." }, "orcid": "0000-0001-5828-6070" }, { "name": { "family": "Niyogi", "given": "Shankho" }, "orcid": "0000-0002-8362-4569" }, { "name": { "family": "Ojeda", "given": "Javier" }, "orcid": "0000-0002-7188-8356" }, { "name": { "family": "Oth", "given": "Adrien" }, "orcid": "0000-0003-4859-6504" }, { "name": { "family": "Proud", "given": "Simon" }, "orcid": "0000-0003-3880-6774" }, { "name": { "family": "Pulli", "given": "Jay" } }, { "name": { "family": "Retailleau", "given": "Lise" }, "orcid": "0000-0002-0711-4540" }, { "name": { "family": "Rintam\u00e4ki", "given": "Annukka E." } }, { "name": { "family": "Satriano", "given": "Claudio" }, "orcid": "0000-0002-3039-2530" }, { "name": { "family": "Savage", "given": "Martha K." }, "orcid": "0000-0002-2080-0676" }, { "name": { "family": "Shani-Kadmiel", "given": "Shahar" }, "orcid": "0000-0003-2215-6164" }, { "name": { "family": "Sleeman", "given": "Reinoud" }, "orcid": "0000-0002-1928-5056" }, { "name": { "family": "Sokos", "given": "Efthimios" }, "orcid": "0000-0002-7742-7251" }, { "name": { "family": "Stammler", "given": "Klaus" } }, { "name": { "family": "Stott", "given": "Alexander E." }, "orcid": "0000-0001-6121-705X" }, { "name": { "family": "Subedi", "given": "Shiba" }, "orcid": "0000-0002-7009-7333" }, { "name": { "family": "S\u00f8rensen", "given": "Mathilde B." }, "orcid": "0000-0002-8589-7480" }, { "name": { "family": "Taira", "given": "Taka'aki" }, "orcid": "0000-0002-6170-797X" }, { "name": { "family": "Tapia", "given": "Mar" } }, { "name": { "family": "Turhan", "given": "Fatih" }, "orcid": "0000-0003-4612-7421" }, { "name": { "family": "van der Pluijm", "given": "Ben" }, "orcid": "0000-0001-7737-2791" }, { "name": { "family": "Vanstone", "given": "Mark" }, "orcid": "0000-0002-4836-6154" }, { "name": { "family": "Vergne", "given": "Jerome" }, "orcid": "0000-0003-1731-9360" }, { "name": { "family": "Vuorinen", "given": "Tommi A. T." }, "orcid": "0000-0002-8186-012X" }, { "name": { "family": "Warren", "given": "Tristram" }, "orcid": "0000-0003-3877-0046" }, { "name": { "family": "Wassermann", "given": "Joachim" }, "orcid": "0000-0002-4088-1792" }, { "name": { "family": "Xiao", "given": "Han" }, "orcid": "0000-0001-8727-8053" } ] }, "title": "Global quieting of high-frequency seismic noise due to COVID-19 pandemic lockdown measures", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 American Association for the Advancement of Science. \n\nReceived 10 June 2020; accepted 14 July 2020. Published online 23 July 2020. \n\nWe sincerely thank two anonymous reviewers, T. Nissen-Meyer, and J. Slate for their comments, which have improved the manuscript. We are extremely grateful to all seismic network managers, operators, and technicians who have helped facilitate the raw global seismic dataset (24). We also kindly acknowledge all of the passionate community seismologists for running their \"home\" seismometers and contributing, indirectly, to a better understanding of Earth. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. government. We dedicate this community-led study to all essential workers who have kept our countries going during these difficult times. \n\nP.K. was funded by a Royal Society University Research Fellowship (URF\\R1\\180377). P.B. and M.J. acknowledge support from the International Training Course \"Seismology and Seismic Hazard Assessment\" funded by the GeoForschungsZentrum Potsdam (GFZ) and the German Federal Foreign Office through the German Humanitarian Assistance program (grant S08-60 321.50 ALL 03/19). P.B. also acknowledges financial support from the Bo\u011fazi\u00e7i University Research Fund (BAP 15683). O.F.C.d.O acknowledges funding from a Young Investigator Grant from the Human Frontier Science Program (HFSP project RGY0072/2017). C.P.E. and E.S. acknowledge funding from the HELPOS Project \"Hellenic Plate Observing System\" (MIS 5002697). L.E. and S.S.-K. acknowledge funding from a VIDI project from the Dutch Research Council (NWO project 864.14.005). G.A.F. acknowledges contributions from the Observatorio San Calixto, which is supported by the Air Force Technical Application Center (AFTAC). C.R.L. acknowledges funding from the NSF Graduate Research Fellowship Program (grant DGE\u20101745301). V.-H.M. and R.D.P. acknowledge support from grant CONACYT-299766. R.D.P. acknowledges support from the UNAM-DGAPA postdoctoral scholarship. J.O. acknowledges support from the Agencia Nacional de Investigaci\u00f3n y Desarrollo (Scholarship ANID-PFCHA/Doctorado Nacional/2020-21200903). S.P. acknowledges financial support from the Natural Environment Research Council (NE/R013144/1). A.E.R. acknowledges support from the K.H. Renlund foundation. M.K.S. acknowledges the New Zealand Earthquake Commission (EQC project 20796). H.X. acknowledges support from a Multidisciplinary Research on the Coronavirus and its Impacts (MRCI) grant from UC Santa Barbara. The Australian Seismometers in Schools data used in this research are supported by AuScope, enabled by the Australian Commonwealth NCRIS program. A.O. acknowledges support from the project RESIST, funded by the Belgian Federal Science Policy (contract SR/00/305) and the Luxembourg National Research Fund. \n\nAuthor contributions: T.L. designed and led the research. T.L., S.P.H., K.V.N., K.v.W., P.K., and R.S.M.D.P. processed and visualized the data and drafted the manuscript. F.M. contributed to the software development and provided the supplementary movie. G.H. thoroughly edited and reviewed the manuscript. All authors processed seismic data, took part in discussions, and performed a full interactive review of the original and revised manuscripts. \n\nThe authors declare no competing interests. \n\nData and materials availability: The raw data used to compute the hiFSAN were obtained from different networks and data providers (24). The computed data and codes used to analyze and plot Figs. 1 to 4 are available from the companion repository: https://github.com/ThomasLecocq/2020_Science_GlobalQuieting and (40).\n\nSupplemental Material - abd2438_Lecocq_SM.pdf
Supplemental Material - abd2438_Lecocq_Table_S1.csv
Supplemental Material - abd2438_Lecocq_Table_S2.csv
Supplemental Material - abd2438_Lecocq_Table_S3.csv
Supplemental Material - abd2438s1.mp4
", "abstract": "Human activity causes vibrations that propagate into the ground as high-frequency seismic waves. Measures to mitigate the coronavirus disease 2019 (COVID-19) pandemic caused widespread changes in human activity, leading to a months-long reduction in seismic noise of up to 50%. The 2020 seismic noise quiet period is the longest and most prominent global anthropogenic seismic noise reduction on record. Although the reduction is strongest at surface seismometers in populated areas, this seismic quiescence extends for many kilometers radially and hundreds of meters in depth. This quiet period provides an opportunity to detect subtle signals from subsurface seismic sources that would have been concealed in noisier times and to benchmark sources of anthropogenic noise. A strong correlation between seismic noise and independent measurements of human mobility suggests that seismology provides an absolute, real-time estimate of human activities.", "date": "2020-09-11", "date_type": "published", "publication": "Science", "volume": "369", "number": "6509", "publisher": "American Association for the Advancement of Science", "pagerange": "1338-1343", "id_number": "CaltechAUTHORS:20200727-071931607", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200727-071931607", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Royal Society", "grant_number": "URF\\R1\\180377" }, { "agency": "GeoForschungsZentrum Potsdam (GFZ)", "grant_number": "S08-60 321.50 ALL 03/19" }, { "agency": "Federal Foreign Office (Germany)" }, { "agency": "Bo\u011fazi\u00e7i University", "grant_number": "BAP 15683" }, { "agency": "Human Frontier Science Program", "grant_number": "RGY0072/2017" }, { "agency": "HELPOS Project", "grant_number": "MIS 5002697" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "864.14.005" }, { "agency": "Observatorio San Calixto" }, { "agency": "Air Force Technical Application Center (AFTAC)" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE\u20101745301" }, { "agency": "Consejo Nacional de Ciencia y Tecnolog\u00eda (CONACYT)", "grant_number": "299766" }, { "agency": "Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM)" }, { "agency": "Agencia Nacional de Investigaci\u00f3n y Desarrollo", "grant_number": "2020-21200903" }, { "agency": "Natural Environment Research Council (NERC)", "grant_number": "NE/R013144/1" }, { "agency": "K. H. Renlund Foundation" }, { "agency": "New Zealand Earthquake Commission", "grant_number": "20796" }, { "agency": "University of California, Santa Barbara" }, { "agency": "AuScope" }, { "agency": "Commonwealth of Australia" }, { "agency": "Belgian Federal Science Policy Office (BELSPO)", "grant_number": "SR/00/305" }, { "agency": "Luxembourg National Research Fund" } ] }, "local_group": { "items": [ { "id": "Seismological-Laboratory" }, { "id": "COVID-19" } ] }, "doi": "10.1126/science.abd2438", "primary_object": { "basename": "abd2438_Lecocq_SM.pdf", "url": "https://authors.library.caltech.edu/records/ax3gh-dfg43/files/abd2438_Lecocq_SM.pdf" }, "related_objects": [ { "basename": "abd2438_Lecocq_Table_S1.csv", "url": "https://authors.library.caltech.edu/records/ax3gh-dfg43/files/abd2438_Lecocq_Table_S1.csv" }, { "basename": "abd2438_Lecocq_Table_S2.csv", "url": "https://authors.library.caltech.edu/records/ax3gh-dfg43/files/abd2438_Lecocq_Table_S2.csv" }, { "basename": "abd2438_Lecocq_Table_S3.csv", "url": "https://authors.library.caltech.edu/records/ax3gh-dfg43/files/abd2438_Lecocq_Table_S3.csv" }, { "basename": "abd2438s1.mp4", "url": "https://authors.library.caltech.edu/records/ax3gh-dfg43/files/abd2438s1.mp4" } ], "pub_year": "2020", "author_list": "Lecocq, Thomas; Hicks, Stephen P.; et al." }, { "id": "https://authors.library.caltech.edu/records/sv55p-d9s19", "eprint_id": 103905, "eprint_status": "archive", "datestamp": "2023-08-22 06:12:37", "lastmod": "2026-03-30 15:39:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Liqiang", "name": { "family": "Wang", "given": "Liqiang" } }, { "id": "Li-Mengying", "name": { "family": "Li", "given": "Mengying" } }, { "id": "Yu-Shaocai", "name": { "family": "Yu", "given": "Shaocai" }, "orcid": "0000-0001-9718-8246" }, { "id": "Chen-Xue", "name": { "family": "Chen", "given": "Xue" } }, { "id": "Li-Zhen", "name": { "family": "Li", "given": "Zhen" } }, { "id": "Zhang-Yibo", "name": { "family": "Zhang", "given": "Yibo" } }, { "id": "Jiang-Linhui", "name": { "family": "Jiang", "given": "Linhui" } }, { "id": "Xia-Yan", "name": { "family": "Xia", "given": "Yan" } }, { "id": "Li-Jiali", "name": { "family": "Li", "given": "Jiali" } }, { "id": "Liu-Weiping", "name": { "family": "Liu", "given": "Weiping" }, "orcid": "0000-0002-1173-892X" }, { "id": "Liu-Pengfei", "name": { "family": "Liu", "given": "Pengfei" }, "orcid": "0000-0002-6714-7387" }, { "id": "Lichtfouse-Eric", "name": { "family": "Lichtfouse", "given": "Eric" }, "orcid": "0000-0002-8535-8073" }, { "id": "Rosenfeld-Daniel", "name": { "family": "Rosenfeld", "given": "Daniel" }, "orcid": "0000-0002-0784-7656" }, { "id": "Seinfeld-J-H", "name": { "family": "Seinfeld", "given": "John H." }, "orcid": "0000-0003-1344-4068" } ] }, "title": "Unexpected rise of ozone in urban and rural areas, and sulfur dioxide in rural areas during the coronavirus city lockdown in Hangzhou, China: implications for air quality", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; Hangzhou; Lockdown; Air quality; Emission reductions; Coronavirus; PM2.5; PM10; SO2; CO; NO2; O3", "note": "\u00a9 2020 Springer Nature Switzerland AG. \n\nReceived 13 May 2020; Accepted 01 June 2020; Published 12 June 2020. \n\nThis work was partially supported by the Department of Science and Technology of China (Nos. 2016YFC0202702, 2018YFC0213506, and 2018YFC0213503), National Research Program for Key Issues in Air Pollution Control in China (No. DQGG0107), and National Natural Science Foundation of China (Nos. 21577126 and 41561144004). Part of this work was also supported by the \"Zhejiang 1000 Talent Plan\" and Research Center for Air Pollution and Health in Zhejiang University. Pengfei Li is supported by Initiation Fund for Introducing Talents of Hebei Agricultural University (412201904). \n\nLiqiang Wang and Mengying Li these authors contributed equally to this work.\n\nPublished - Wang2020_Article_UnexpectedRiseOfOzoneInUrbanAn.pdf
Supplemental Material - 10311_2020_1028_MOESM1_ESM.docx
", "abstract": "The outbreak of coronavirus named COVID-19, initially identified in Wuhan, China in December 2019, has spread rapidly at the global scale. Most countries have rapidly stopped almost all activities including industry, services and transportation of goods and people, thus decreasing air pollution in an unprecedented way, and providing a unique opportunity to study air pollutants. While satellite data have provided visual evidence for the global reduction in air pollution such as nitrogen dioxide (NO\u2082) worldwide, precise and quantitative information is missing at the local scale. Here we studied changes in particulate matter (PM_(2.5), PM\u2081\u2080), carbon monoxide (CO), NO\u2082, sulfur dioxide (SO\u2082) and ozone (O\u2083) at 10 urban sites in Hangzhou, a city of 7.03 million inhabitants, and at 1 rural site, before city lockdown, January 1\u201323, during city lockdown, January 24-February 15, and during resumption, February 16\u201328, in 2020. Results show that city lockdown induced a sharp decrease in PM_(2.5), PM\u2081\u2080, CO, and NO\u2082 concentrations at both urban and rural sites. The NO\u2082 decrease is explained by reduction in traffic emissions in the urban areas, and by lower regional transport in rural areas during lockdown, as expected. SO\u2082 concentrations decreased from 6.3 to 5.3 \u03bcg m\u207b\u00b3 in the city, but increased surprisingly from 4.7 to 5.8 \u03bcg m\u207b\u00b3 at the rural site: this increase is attributed both to higher coal consumption for heating and emissions from traditional fireworks of the Spring Eve and Lantern Festivals during lockdown. Unexpectedly, O\u2083 concentrations increased by 145% from 24.6 to 60.6 \u03bcg m\u207b\u00b3 in the urban area, and from 42.0 to 62.9 \u03bcg m\u207b\u00b3 in the rural area during the lockdown. This finding is explained by the weakening of chemical titration of O\u2083 by NO due to reductions of NO_x fresh emissions during the non-photochemical reaction period from 20:00 PM to 9:00 AM (local time). During the lockdown, compared to the same period in 2019, the daily average concentrations in the city decreased by 42.7% for PM_(2.5), 47.9% for PM\u2081\u2080, 28.6% for SO\u2082, 22.3% for CO and 58.4% for NO\u2082, which is obviously explained by the absence of city activities. Overall, we observed not only the expected reduction in some atmospheric pollutants (PM, SO\u2082, CO, NO\u2082), but also unexpected increases in SO\u2082 in the rural areas and of ozone (O\u2083) in both urban and rural areas, the latter being paradoxically due to the reduction in nitrogen oxide levels. In other words, the city lockdown has improved air quality by reducing PM_(2.5), PM\u2081\u2080, CO, and NO\u2082, but has also decreased air quality by augmenting O\u2083 and SO\u2082.", "date": "2020-09", "date_type": "published", "publication": "Environmental Chemistry Letters", "volume": "18", "number": "5", "publisher": "Springer", "pagerange": "1713-1723", "id_number": "CaltechAUTHORS:20200615-082327667", "issn": "1610-3653", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200615-082327667", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Science and Technology (China)", "grant_number": "2016YFC0202702" }, { "agency": "Department of Science and Technology (China)", "grant_number": "2018YFC0213506" }, { "agency": "Department of Science and Technology (China)", "grant_number": "2018YFC0213503" }, { "agency": "National Research Program for Key Issues in Air Pollution Control in China", "grant_number": "DQGG0107" }, { "agency": "National Natural Science Foundation of China", "grant_number": "21577126" }, { "agency": "National Natural Science Foundation of China", "grant_number": "41561144004" }, { "agency": "Zhejiang 1000 Talent Plan" }, { "agency": "Zhejiang University" }, { "agency": "Hebei Agricultural University", "grant_number": "412201904" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1007/s10311-020-01028-3", "pmcid": "PMC7292245", "primary_object": { "basename": "10311_2020_1028_MOESM1_ESM.docx", "url": "https://authors.library.caltech.edu/records/sv55p-d9s19/files/10311_2020_1028_MOESM1_ESM.docx" }, "related_objects": [ { "basename": "Wang2020_Article_UnexpectedRiseOfOzoneInUrbanAn.pdf", "url": "https://authors.library.caltech.edu/records/sv55p-d9s19/files/Wang2020_Article_UnexpectedRiseOfOzoneInUrbanAn.pdf" } ], "pub_year": "2020", "author_list": "Wang, Liqiang; Li, Mengying; et al." }, { "id": "https://authors.library.caltech.edu/records/s31gs-9cc18", "eprint_id": 105444, "eprint_status": "archive", "datestamp": "2023-10-03 22:28:01", "lastmod": "2026-03-29 20:39:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wise-Toby", "name": { "family": "Wise", "given": "Toby" }, "orcid": "0000-0002-9021-3282" }, { "id": "Zbozinek-Tomislav-D", "name": { "family": "Zbozinek", "given": "Tomislav D." }, "orcid": "0000-0003-0187-671X" }, { "id": "Michelini-Giorgia", "name": { "family": "Michelini", "given": "Giorgia" }, "orcid": "0000-0002-0887-7582" }, { "id": "Hagan-Cindy-C", "name": { "family": "Hagan", "given": "Cindy C." }, "orcid": "0000-0002-4576-7120" }, { "id": "Mobbs-D", "name": { "family": "Mobbs", "given": "Dean" }, "orcid": "0000-0003-1175-3772" } ] }, "title": "Changes in risk perception and self-reported protective behaviour during the first week of the COVID-19 pandemic in the United States", "ispublished": "pub", "full_text_status": "public", "keywords": "coronavirus, COVID-19, risk perception, protective behaviour, pandemic", "note": "\u00a9 2020 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. \n\nManuscript received 01/05/2020; Manuscript accepted 07/09/2020; Published online 16/09/2020. \n\nEthics: The study was approved by the Institutional Review Board (IRB) at the California Institute of Technology and subjects provided informed consent. \n\nData accessibility: All analysis code was written in Python and is available along with data at https://github.com/tobywise/covid19-risk-perception. \n\nAuthors' contributions: All authors designed the study. T.W. collected and analysed the data and drafted the manuscript. All authors critically revised the manuscript. \n\nWe declare we have no competing interests. \n\nThis work was supported by the US National Institute of Mental Health grant no. 2P50MH094258 and a Chen Institute Award (grant no. P2026052); Merkin Institute grant DM1.COV19R1 and Templeton Foundation grant TWCF0366 (both to D.M.). T.W. is supported by a Wellcome Trust Sir Henry Wellcome Fellowship (grant no. 206460/17/Z). T.D.Z. is supported by the National Science Foundation (grant no. 1911441).\n\nPublished - rsos-200742.pdf
Supplemental Material - rsos200742_si_001.pdf
", "abstract": "Efforts to change behaviour are critical in minimizing the spread of highly transmissible pandemics such as COVID-19. However, it is unclear whether individuals are aware of disease risk and alter their behaviour early in the pandemic. We investigated risk perception and self-reported engagement in protective behaviours in 1591 United States-based individuals cross-sectionally and longitudinally over the first week of the pandemic. Subjects demonstrated growing awareness of risk and reported engaging in protective behaviours with increasing frequency but underestimated their risk of infection relative to the average person in the country. Social distancing and hand washing were most strongly predicted by the perceived probability of personally being infected. However, a subgroup of individuals perceived low risk and did not engage in these behaviours. Our results highlight the importance of risk perception in early interventions during large-scale pandemics.", "date": "2020-09", "date_type": "published", "publication": "Royal Society Open Science", "volume": "7", "number": "9", "publisher": "Royal Society", "pagerange": "Art. No. 200742", "id_number": "CaltechAUTHORS:20200918-083207183", "issn": "2054-5703", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200918-083207183", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "2P50MH094258" }, { "agency": "Tianqiao and Chrissy Chen Institute for Neuroscience", "grant_number": "P2026052" }, { "agency": "Caltech Merkin Institute for Translational Research", "grant_number": "DM1.COV19R1" }, { "agency": "John Templeton Foundation", "grant_number": "TWCF0366" }, { "agency": "Wellcome Trust", "grant_number": "206460/17/Z" }, { "agency": "NSF", "grant_number": "BCS-1911441" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" } ] }, "doi": "10.1098/rsos.200742", "pmcid": "PMC7540790", "primary_object": { "basename": "rsos200742_si_001.pdf", "url": "https://authors.library.caltech.edu/records/s31gs-9cc18/files/rsos200742_si_001.pdf" }, "related_objects": [ { "basename": "rsos-200742.pdf", "url": "https://authors.library.caltech.edu/records/s31gs-9cc18/files/rsos-200742.pdf" } ], "pub_year": "2020", "author_list": "Wise, Toby; Zbozinek, Tomislav D.; et al." }, { "id": "https://authors.library.caltech.edu/records/r4hfq-2n392", "eprint_id": 103263, "eprint_status": "archive", "datestamp": "2023-09-25 22:18:33", "lastmod": "2026-03-30 05:25:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Robbiani-Davide-F", "name": { "family": "Robbiani", "given": "Davide F." }, "orcid": "0000-0001-7379-3484" }, { "name": { "family": "Gaebler", "given": "Christian" }, "orcid": "0000-0001-7295-8128" }, { "name": { "family": "Muecksch", "given": "Frauke" } }, { "name": { "family": "Lorenzi", "given": "Julio C. C." } }, { "name": { "family": "Wang", "given": "Zijun" } }, { "name": { "family": "Cho", "given": "Alice" } }, { "name": { "family": "Agudelo", "given": "Marianna" } }, { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "name": { "family": "Gazumyan", "given": "Anna" } }, { "name": { "family": "Finkin", "given": "Shlomo" }, "orcid": "0000-0003-4474-2658" }, { "name": { "family": "H\u00e4ggl\u00f6f", "given": "Thomas" }, "orcid": "0000-0002-7751-0928" }, { "name": { "family": "Oliveira", "given": "Thiago Y." } }, { "name": { "family": "Viant", "given": "Charlotte" } }, { "name": { "family": "Hurley", "given": "Arlene" }, "orcid": "0000-0003-0575-0233" }, { "name": { "family": "Hoffmann", "given": "Hans-Heinrich" } }, { "name": { "family": "Millard", "given": "Katrina G." } }, { "name": { "family": "Kost", "given": "Rhonda G." } }, { "name": { "family": "Gordon", "given": "Kristie" } }, { "name": { "family": "Cipolla", "given": "Melissa" } }, { "name": { "family": "Bianchini", "given": "Filippo" } }, { "name": { "family": "Chen", "given": "Spencer T." } }, { "name": { "family": "Ramos", "given": "Victor" } }, { "name": { "family": "Patel", "given": "Roshni" } }, { "name": { "family": "Dizon", "given": "Juan" } }, { "name": { "family": "Shimeliovich", "given": "Irina" } }, { "name": { "family": "Mendoza", "given": "Pilar" } }, { "name": { "family": "Hartweger", "given": "Harald" } }, { "name": { "family": "Nogueira", "given": "Lilian" } }, { "name": { "family": "Pack", "given": "Maggi" } }, { "name": { "family": "Horowitz", "given": "Jill" } }, { "name": { "family": "Schmidt", "given": "Fabian" } }, { "name": { "family": "Weisblum", "given": "Yiska" }, "orcid": "0000-0002-9249-1745" }, { "name": { "family": "Michailidis", "given": "Eleftherios" } }, { "name": { "family": "Ashbrook", "given": "Alison W." } }, { "name": { "family": "Waltari", "given": "Eric" } }, { "name": { "family": "Pak", "given": "John E." } }, { "id": "Huey-Tubman-Kathryn-E", "name": { "family": "Huey-Tubman", "given": "Kathryn E." }, "orcid": "0000-0002-4683-8138" }, { "id": "Koranda-Nicholas", "name": { "family": "Koranda", "given": "Nicholas" } }, { "id": "Hoffman-Pauline-R", "name": { "family": "Hoffman", "given": "Pauline R." } }, { "id": "West-Anthony-P-Jr", "name": { "family": "West", "given": "Anthony P., Jr." } }, { "name": { "family": "Rice", "given": "Charles M." }, "orcid": "0000-0003-3087-8079" }, { "name": { "family": "Hatziioannou", "given": "Theodora" }, "orcid": "0000-0002-7889-0766" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "name": { "family": "Bieniasz", "given": "Paul D." }, "orcid": "0000-0002-2368-3719" }, { "name": { "family": "Caskey", "given": "Marina" }, "orcid": "0000-0003-1727-8693" }, { "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" } ] }, "title": "Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Springer Nature Limited. \n\nReceived 03 May 2020. Accepted 12 June 2020. Published 18 June 2020. \n\nOnline content: Any methods, additional references, Nature Research reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at https://doi.org/10.1038/s41586-020-2456-9 \n\nWe thank all study participants who devoted time to our research; Drs. Barry Coller and Sarah Schlesinger, the Rockefeller University Hospital Clinical Research Support Office and nursing staff. Dr. Joseph L. DeRisi for facilitating interactions with the Chan Zuckerberg BioHub. All members of the M.C.N. laboratory for helpful discussions, Drs. Amelia Escolano, Ga\u00eblle Breton and Bernardo Reis, and Ma\u0161a Jankovic for laboratory support, and Dr. Jost Vielmetter and the Protein Expression Center in the Beckman Institute at Caltech. This work was supported by NIH grant P01-AI138398-S1 (M.C.N., C.M.R., P.J.B.) and 2U19AI111825 (M.C.N. and C.M.R).; the Caltech Merkin Institute for Translational Research and P50 AI150464 (P.J.B.), George Mason University Fast Grant (D.F.R. and P.J.B.) and the European ATAC consortium EC 101003650 (D.F.R.); 3 R01-AI091707-10S1 to C.M.R.; R37-AI64003 to P.D.B.; R01AI78788 to T.H.; The G. Harold and Leila Y. Mathers Charitable Foundation to C.M.R.. Electron microscopy was performed in the Caltech Beckman Institute Resource Center for Transmission Electron Microscpy (Drs. Songye Chen and Andrey Malyutin, Directors). C.G. was supported by the Robert S. Wennett Post-Doctoral Fellowship, in part by the National Center for Advancing Translational Sciences (National Institutes of Health Clinical and Translational Science Award program, grant UL1 TR001866), and by the Shapiro-Silverberg Fund for the Advancement of Translational Research. P.D.B. and M.C.N. are Howard Hughes Medical Institute Investigators. \n\nAuthor contributions: D.F.R., P.D.B., P.J.B., T.H., C.M.R. and M.C.N. conceived, designed and analyzed the experiments. D.F.R., M.C. and C.G. designed clinical protocols. F.M., J.C.C.L., Z.W., A.C., M.A., C.O.B., S.F., T.H., C.V., K.G., F.B., S.T.C., P.M., H.H., L.N., F.S., Y.W., H.-H.H., E.M., A.W.A., K.E.H.T., N.K. and P.R.H. carried out experiments. A.G. and M.C. produced antibodies. C.O.B., J.P. and E.W. produced SARS-CoV-2 proteins. A.H., R.K., J.H., K.G.M., C.G. and M.C. recruited participants and executed clinical protocols. R.P., J.D., M.P. and I.S. processed clinical samples. \n\nData availability: Data are provided in SI Tables 1, 3, 4, 5 and 6; and in Figure 3 has associated raw sequencing data deposited at Github (https://github.com/stratust/igpipeline). This study also includes A Public Database of Memory and Naive B-Cell Receptor Sequences (https://datadryad.org/stash/dataset/doi:10.5061/dryad.35ks2), PDB datasets 6VYB and 6NB6 and Sequence Read Archive SRP010970. \n\nCode availability: Computer code to process the antibody sequences is available at GitHub (https://github.com/stratust/igpipeline).\n\nAccepted Version - nihms-1603863.pdf
Submitted - 2020.05.13.092619v2.full.pdf
", "abstract": "During the COVID-19 pandemic, SARS-CoV-2 infected millions of people and claimed hundreds of thousands of lives. Virus entry into cells depends on the receptor binding domain (RBD) of the SARS-CoV-2 spike protein (S). Although there is no vaccine, it is likely that antibodies will be essential for protection. However, little is known about the human antibody response to SARS-CoV-2. Here we report on 149 COVID-19 convalescent individuals. Plasmas collected an average of 39 days after the onset of symptoms had variable half-maximal pseudovirus neutralizing titres: less than 1:50 in 33% and below 1:1,000 in 79%, while only 1% showed titres above 1:5,000. Antibody sequencing revealed expanded clones of RBD-specific memory B cells expressing closely related antibodies in different individuals. Despite low plasma titres, antibodies to three distinct epitopes on RBD neutralized at half-maximal inhibitory concentrations (IC\u2085\u2080 values) as low as single digit nanograms per millitre. Thus, most convalescent plasmas obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.", "date": "2020-08-20", "date_type": "published", "publication": "Nature", "volume": "584", "number": "7821", "publisher": "Nature Publishing Group", "pagerange": "437-442", "id_number": "CaltechAUTHORS:20200518-082748284", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200518-082748284", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01-AI138398-S1" }, { "agency": "NIH", "grant_number": "2U19AI111825" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "NIH", "grant_number": "P50 AI150464" }, { "agency": "George Mason University" }, { "agency": "ATAC Consortium", "grant_number": "EC 101003650" }, { "agency": "NIH", "grant_number": "3 R01- AI091707-10S1" }, { "agency": "NIH", "grant_number": "R37-AI64003" }, { "agency": "NIH", "grant_number": "R01AI78788" }, { "agency": "G. Harold and Leila Y. Mathers Charitable Foundation" }, { "agency": "Robert S. Wennett Postdoctoral Fellowship" }, { "agency": "NIH", "grant_number": "UL1 TR001866" }, { "agency": "Shapiro-Silverberg Fund" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41586-020-2456-9", "pmcid": "PMC7263513", "primary_object": { "basename": "2020.05.13.092619v2.full.pdf", "url": "https://authors.library.caltech.edu/records/r4hfq-2n392/files/2020.05.13.092619v2.full.pdf" }, "related_objects": [ { "basename": "nihms-1603863.pdf", "url": "https://authors.library.caltech.edu/records/r4hfq-2n392/files/nihms-1603863.pdf" } ], "pub_year": "2020", "author_list": "Robbiani, Davide F.; Gaebler, Christian; et al." }, { "id": "https://authors.library.caltech.edu/records/gyrhz-xxc89", "eprint_id": 103584, "eprint_status": "archive", "datestamp": "2023-09-25 22:21:40", "lastmod": "2026-03-30 05:53:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Barnes-Christopher-O", "name": { "family": "Barnes", "given": "Christopher O." }, "orcid": "0000-0003-2754-5951" }, { "id": "West-Anthony-P-Jr", "name": { "family": "West", "given": "Anthony P., Jr." } }, { "id": "Huey-Tubman-Kathryn-E", "name": { "family": "Huey-Tubman", "given": "Kathryn E." }, "orcid": "0000-0002-4683-8138" }, { "id": "Hoffmann-Magnus-A-G", "name": { "family": "Hoffmann", "given": "Magnus A. G." }, "orcid": "0000-0003-4923-9568" }, { "id": "Sharaf-Naima-G", "name": { "family": "Sharaf", "given": "Naima G." }, "orcid": "0000-0002-3662-9228" }, { "id": "Hoffman-Pauline-R", "name": { "family": "Hoffman", "given": "Pauline R." } }, { "id": "Koranda-Nicholas", "name": { "family": "Koranda", "given": "Nicholas" } }, { "id": "Gristick-Harry-B", "name": { "family": "Gristick", "given": "Harry B." }, "orcid": "0000-0002-1957-2821" }, { "id": "Gaebler-Christian", "name": { "family": "Gaebler", "given": "Christian" }, "orcid": "0000-0001-7295-8128" }, { "id": "Muecksch-Frauke", "name": { "family": "Muecksch", "given": "Frauke" } }, { "id": "Cetrulo-Lorenzi-Julio-C", "name": { "family": "Cetrulo Lorenzi", "given": "Julio C." }, "orcid": "0000-0003-2492-3961" }, { "id": "Finkin-Shlomo", "name": { "family": "Finkin", "given": "Shlomo" }, "orcid": "0000-0003-4474-2658" }, { "id": "H\u00e4ggl\u00f6f-Thomas", "name": { "family": "H\u00e4ggl\u00f6f", "given": "Thomas" }, "orcid": "0000-0002-7751-0928" }, { "id": "Hurley-Arlene", "name": { "family": "Hurley", "given": "Arlene" }, "orcid": "0000-0003-0575-0233" }, { "id": "Millard-Katrina-G", "name": { "family": "Millard", "given": "Katrina G." } }, { "id": "Weisblum-Yiska", "name": { "family": "Weisblum", "given": "Yiska" }, "orcid": "0000-0002-9249-1745" }, { "id": "Schmidt-Fabian", "name": { "family": "Schmidt", "given": "Fabian" } }, { "id": "Hatziioannou-Theodora", "name": { "family": "Hatziioannou", "given": "Theodora" }, "orcid": "0000-0002-7889-0766" }, { "id": "Bieniasz-Paul-D", "name": { "family": "Bieniasz", "given": "Paul D." }, "orcid": "0000-0002-2368-3719" }, { "id": "Caskey-Marina", "name": { "family": "Caskey", "given": "Marina" }, "orcid": "0000-0003-1727-8693" }, { "id": "Robbiani-Davide-F", "name": { "family": "Robbiani", "given": "Davide F." }, "orcid": "0000-0001-7379-3484" }, { "id": "Nussenzweig-Michel-C", "name": { "family": "Nussenzweig", "given": "Michel C." }, "orcid": "0000-0003-0592-8564" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies", "ispublished": "pub", "full_text_status": "public", "keywords": "Coronavirus; COVID-19; electron microscopy; ELISA; Fab; IgG; convalescent plasma; MERS-CoV; SARS-CoV; SARS-CoV-2", "note": "\u00a9 2020 The Author(s). Published by Elsevier Under a Creative This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).\n\nReceived 11 May 2020, Revised 27 May 2020, Accepted 15 June 2020, Available online 24 June 2020. \n\nWe gratefully acknowledge all labs and authors for making SARS-CoV-2 genome sequence data available for this research. We thank all study participants who devoted time to our research, Drs. Barry Coller and Sarah Schlesinger, and the Rockefeller University Hospital Clinical Research Support Office and nursing staff. We thank the Global Initiative on Sharing Avian Influenza Data (GISAID) and the originating and submitting laboratories for sharing the SARS-CoV-2 genome sequences; see Table S4 for a list of sequence contributors. We thank members of the Bjorkman, Nussenzweig, and Bienasz laboratories for helpful discussions, Drs. John Pak (Chan Zuckerberg Biohub) and Florian Krammer (Icahn School of Medicine at Mount Sinai) for CoV expression plasmids, Drs. Songye Chen and Andrey Malyutin (Caltech) for maintaining electron microscopes, Dr. Jost Vielmetter and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance, and Ms. Marta Murphy for help with figures. Electron microscopy was performed in the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support the Molecular Observatory (Dr. Jens Kaiser, director), and Drs. Silvia Russi, Aina Cohen, and Clyde Smith and the beamline staff at SSRL for data collection assistance. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences (DE-AC02-76SF00515). The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the NIH, National Institute of General Medical Sciences (P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. This work was supported by NIH (P01-AI138938-S1 to P.J.B. and M.C.N., P50 8 P50 AI150464-13 to P.J.B., and 2U19AI111825 to M.C.N.), the Caltech Merkin Institute for Translational Research (to P.J.B.), George Mason University Fast Grants (to P.J.B. and D.F.R.), and the Bill and Melinda Gates Foundation Collaboration for AIDS Vaccine Discovery (CAVD) (INV-002143 to P.J.B. and M.C.N.). C.O.B was supported by the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Postdoctoral Enrichment Program from the Burroughs Wellcome Fund. C.G. is a fellow of the Robert S. Wennett and Mario Cader-Frech Foundation and was supported in part by the National Center for Advancing Translational Sciences (NCATS, National Institutes of Health Clinical and Translational Science Award [CTSA] program) (UL1 TR001866), and by the Shapiro-Silverberg Fund for the Advancement of Translational Research. P.D.B. and M.C.N. are Howard Hughes Medical Institute Investigators.\n\nAuthor Contributions:\nC.O.B., A.P.W., D.F.R., M.C.N., and P.J.B. conceived the study and analyzed data. C.O.B. performed protein characterization, nsEMPEM, and cryo-EM and interpreted structures. N.G.S. and C.O.B. performed and analyzed crystallographic structures. C.O.B. and K.E.H.-T. prepared plasma IgGs and Fabs. M.A.G.H., K.E.H.-T., N.G.S., and C.O.B. performed and analyzed ELISAs. P.R.H. and N.K. expressed and purified proteins. A.P.W. and H.B.G. performed computational modeling. A.P.W. analyzed antibody sequences. F.M., J.C.C.L., Y.W., F.S., T.H., and P.D.B. developed and performed in vitro neutralization assays. C.G., S.F., A.H., K.G.M., M.C., and D.F.R. collected and processed human plasma samples. C.O.B., A.P.W., M.C.N., and P.J.B. wrote the paper with contributions from other authors.\n\nDeclaration of Interests:\nIn connection with this work, The Rockefeller University has filed a provisional patent application on which D.F.R. and M.C.N. are inventors.\n\nPublished - 1-s2.0-S0092867420307571-main.pdf
Submitted - 2020.05.28.121533v1.full.pdf
Supplemental Material - 1-s2.0-S0092867420307571-mmc1.pdf
Supplemental Material - 1-s2.0-S0092867420307571-mmc2.xlsx
", "abstract": "Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal IgGs and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1^A and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4\u00c5 cryo-EM structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses and that characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.", "date": "2020-08-20", "date_type": "published", "publication": "Cell", "volume": "182", "number": "4", "publisher": "Cell Press", "pagerange": "828-842", "id_number": "CaltechAUTHORS:20200601-100510853", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200601-100510853", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-76SF00515" }, { "agency": "NIH", "grant_number": "P41GM103393" }, { "agency": "NIH", "grant_number": "P01-AI138398-S1" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "NIH", "grant_number": "P50 8 P50 AI150464-13" }, { "agency": "NIH", "grant_number": "2U19AI111825" }, { "agency": "George Mason University" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "INV-002143" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Robert S. Wennett and Mario Cader-Frech Foundation" }, { "agency": "NIH", "grant_number": "UL1 TR001866" }, { "agency": "Shapiro-Silverberg Fund" } ] }, "local_group": { "items": [ { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cell.2020.06.025", "pmcid": "PMC7311918", "primary_object": { "basename": "1-s2.0-S0092867420307571-main.pdf", "url": "https://authors.library.caltech.edu/records/gyrhz-xxc89/files/1-s2.0-S0092867420307571-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0092867420307571-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/gyrhz-xxc89/files/1-s2.0-S0092867420307571-mmc1.pdf" }, { "basename": "1-s2.0-S0092867420307571-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/gyrhz-xxc89/files/1-s2.0-S0092867420307571-mmc2.xlsx" }, { "basename": "2020.05.28.121533v1.full.pdf", "url": "https://authors.library.caltech.edu/records/gyrhz-xxc89/files/2020.05.28.121533v1.full.pdf" } ], "pub_year": "2020", "author_list": "Barnes, Christopher O.; West, Anthony P., Jr.; et al." }, { "id": "https://authors.library.caltech.edu/records/6e46y-xz920", "eprint_id": 103957, "eprint_status": "archive", "datestamp": "2023-08-19 22:53:00", "lastmod": "2026-03-30 08:23:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Le-Tianhao", "name": { "family": "Le", "given": "Tianhao" }, "orcid": "0000-0002-6600-8270" }, { "id": "Wang-Yuan", "name": { "family": "Wang", "given": "Yuan" }, "orcid": "0000-0001-6657-8401" }, { "id": "Liu-Lang", "name": { "family": "Liu", "given": "Lang" }, "orcid": "0000-0002-1092-0615" }, { "id": "Yang-Jiani", "name": { "family": "Yang", "given": "Jiani" } }, { "id": "Yung-Y-L", "name": { "family": "Yung", "given": "Yuk L." }, "orcid": "0000-0002-4263-2562" }, { "id": "Li-Guohui", "name": { "family": "Li", "given": "Guohui" } }, { "id": "Seinfeld-J-H", "name": { "family": "Seinfeld", "given": "John H." }, "orcid": "0000-0003-1344-4068" } ] }, "title": "Unexpected air pollution with marked emission reductions during the COVID-19 outbreak in China", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 The Authors. This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material. \n\nReceived for publication March 16, 2020. Accepted for publication June 9, 2020. \n\nWe are grateful to Chao Liu and Alexei Lyapustin for helpful discussions on the satellite products, and Yuxuan Wang and Yuanlong Huang for chemistry analysis. \n\nY.W. and Y.L.Y. acknowledge the support of the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Additional support was provided by the NSF AGS-1700727 grant. G.L. and L.L. acknowledge the National Key R&D Plan Grant 2017YFC0210000 and the Strategic Priority Research Program of Chinese Academy of Sciences Grant XDB40030203. \n\nAuthor contributions: Y.W. conceived and designed the research. T.L., Y.W., and Y.L.Y. performed the data analyses and produced the figures. L.L, Y.W., and G.L. performed and analyzed the WRF-Chem simulations. J.Y. and L.L. obtained the ground-based pollution data. Y.W. and J.H.S wrote the paper. All authors contributed to the scientific discussions and preparation of the manuscript. \n\nThe authors declare no competing interests. \n\nData and materials availability: All data are available in the manuscript or the supplementary materials.\n\nPublished - 702.full.pdf
Supplemental Material - abb7431_Le_SM.pdf
", "abstract": "The absence of motor vehicle traffic and suspended manufacturing during the coronavirus disease 2019 (COVID-19) pandemic in China enabled assessment of the efficiency of air pollution mitigation. Up to 90% reduction of certain emissions during the city-lockdown period can be identified from satellite and ground-based observations. Unexpectedly, extreme particulate matter levels simultaneously occurred in northern China. Our synergistic observation analyses and model simulations show that anomalously high humidity promoted aerosol heterogeneous chemistry, along with stagnant airflow and uninterrupted emissions from power plants and petrochemical facilities, contributing to severe haze formation. Also, because of nonlinear production chemistry and titration of ozone in winter, reduced nitrogen oxides resulted in ozone enhancement in urban areas, further increasing the atmospheric oxidizing capacity and facilitating secondary aerosol formation.", "date": "2020-08-07", "date_type": "published", "publication": "Science", "volume": "369", "number": "6504", "publisher": "American Association for the Advancement of Science", "pagerange": "702-706", "id_number": "CaltechAUTHORS:20200622-104138262", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200622-104138262", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NASA/JPL/Caltech" }, { "agency": "NSF", "grant_number": "AGS-1700727" }, { "agency": "National Key Research and Development Program of China", "grant_number": "2017YFC0210000" }, { "agency": "Chinese Academy of Sciences", "grant_number": "XDB40030203" } ] }, "local_group": { "items": [ { "id": "Astronomy-Department" }, { "id": "COVID-19" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1126/science.abb7431", "primary_object": { "basename": "702.full.pdf", "url": "https://authors.library.caltech.edu/records/6e46y-xz920/files/702.full.pdf" }, "related_objects": [ { "basename": "abb7431_Le_SM.pdf", "url": "https://authors.library.caltech.edu/records/6e46y-xz920/files/abb7431_Le_SM.pdf" } ], "pub_year": "2020", "author_list": "Le, Tianhao; Wang, Yuan; et al." }, { "id": "https://authors.library.caltech.edu/records/y1qv7-23k59", "eprint_id": 104749, "eprint_status": "archive", "datestamp": "2023-08-19 22:39:18", "lastmod": "2026-03-30 06:41:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Weatherbee-B-A-T", "name": { "family": "Weatherbee", "given": "Bailey A. T." } }, { "id": "Glover-D-M", "name": { "family": "Glover", "given": "David M." }, "orcid": "0000-0003-0956-0103" }, { "id": "Zernicka-Goetz-M", "name": { "family": "Zernicka-Goetz", "given": "Magdalena" }, "orcid": "0000-0002-7004-2471" } ] }, "title": "Expression of SARS-CoV-2 receptor ACE2 and the protease TMPRSS2 suggests susceptibility of the human embryo in the first trimester", "ispublished": "pub", "full_text_status": "public", "keywords": "TMPRSS2, SARS-CoV-2, receptor ACE2", "note": "\u00a9 2020 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. \n\nReceived: 9 June 2020; Accepted: 30 June 2020; Published: 05 August 2020. \n\nData accessibility: Single cell RNA-sequencing data are deposited in Gene Expression Omnibus (GEO) under accession numbers GSE136447 and GSE109555. \n\nWe declare we have no competing interests. \n\nD.M.G. and M.Z.-G. are grateful to Caltech for start-up funding. Work in the M.Z.-G. laboratory is also funded by grants from the Wellcome Trust (207415/Z/17/Z); Open Philanthropy; the Weston Havens Foundation; and the Curci Foundation. B.A.T.W. is supported by the Gates Cambridge Trust.\n\nPublished - rsob.200162.pdf
", "abstract": "While initially recognized as causing respiratory disease, the SARS-CoV-2 virus also affects many other organs leading to other complications. It has emerged that advanced age and obesity are risk factors for complications but questions concerning the potential effects on fetal health and successful pregnancy for those infected with SARS-CoV-2 remain largely unanswered. Here, we examine human pre-gastrulation embryos to determine the expression patterns of the genes ACE2, encoding the SARS-CoV-2 receptor, and TMPRSS2, encoding a protease that cleaves both the viral spike protein and the ACE2 receptor to facilitate infection. We show expression and co-expression of these genes in the trophoblast of the blastocyst and syncytiotrophoblast and hypoblast of the implantation stages, which develop into tissues that interact with the maternal blood supply for nutrient exchange. Expression of ACE2 and TMPRSS2 in these tissues raises the possibility for vertical transmission and indicates that further work is required to understand potential risks to implantation, placental health and fetal health that require further study.", "date": "2020-08", "date_type": "published", "publication": "Open Biology", "volume": "10", "number": "8", "publisher": "Royal Society", "pagerange": "200162", "id_number": "CaltechAUTHORS:20200805-090719433", "issn": "2046-2441", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200805-090719433", "funders": { "items": [ { "agency": "Caltech" }, { "agency": "Wellcome Trust", "grant_number": "207415/Z/17/Z" }, { "agency": "Open Philanthropy" }, { "agency": "Weston Havens Foundation" }, {}, { "agency": "University of Cambridge" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1098/rsob.200162", "pmcid": "PMC7479935", "primary_object": { "basename": "rsob.200162.pdf", "url": "https://authors.library.caltech.edu/records/y1qv7-23k59/files/rsob.200162.pdf" }, "pub_year": "2020", "author_list": "Weatherbee, Bailey A. T.; Glover, David M.; et al." }, { "id": "https://authors.library.caltech.edu/records/aan98-s5736", "eprint_id": 105167, "eprint_status": "archive", "datestamp": "2023-08-19 22:28:44", "lastmod": "2026-03-29 00:30:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Medina-Ortiz-David", "name": { "family": "Medina-Ortiz", "given": "David" }, "orcid": "0000-0002-8369-5746" }, { "id": "Contreras-Sebasti\u00e1n", "name": { "family": "Contreras", "given": "Sebasti\u00e1n" }, "orcid": "0000-0001-8909-774X" }, { "id": "Barrera-Saavedra-Yasna", "name": { "family": "Barrera-Saavedra", "given": "Yasna" } }, { "id": "Cabas-Mora-Gabriel", "name": { "family": "Cabas-Mora", "given": "Gabriel" } }, { "id": "Olivera-Nappa-\u00c1lvaro", "name": { "family": "Olivera-Nappa", "given": "\u00c1lvaro" }, "orcid": "0000-0001-6053-7019" } ] }, "title": "Country-Wise Forecast Model for the Effective Reproduction Number R_t of Coronavirus Disease", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19, SARS-CoV-2, effective reproduction number Rt, public-health policies, epidemiologic modeling", "note": "\u00a9 2020 Medina-Ortiz, Contreras, Barrera-Saavedra, Cabas-Mora and Olivera-Nappa. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. \n\nReceived: 02 May 2020; Accepted: 02 July 2020; Published: 17 July 2020. \n\nThe authors gratefully acknowledge support from the Centre for Biotechnology and Bioengineering-CeBiB (PIA project FB0001, Conicyt, Chile). DM-O gratefully acknowledges Conicyt, Chile, for Ph.D. fellowship 21181435. DM-O greatly thanks Cristofer Quiroz for his support in the search for databases and related services for the development of forecast models. \n\nData Availability Statement: Publicly available datasets were analyzed in this study. This data can be found here: https://www.worldometers.info/coronavirus/, https://www.gob.cl/coronavirus/cifrasoficiales/, and https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data. \n\nAuthor Contributions: DM-O and SC: conceptualization. DM-O: methodology. \u00c1O-N, DM-O, and SC: validation and writing, review, and editing. DM-O, SC, GC-M, and YB-S: investigation. \u00c1O-N and DM-O: supervision and project administration. \u00c1O-N: funding resources. All authors contributed to the article and approved the submitted version. \n\nThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.\n\nPublished - fphy-08-00304.pdf
", "abstract": "Due to the particularities of SARS-CoV-2, public health policies have played a crucial role in the control of the COVID-19 pandemic. Epidemiological parameters for assessing the stage of the outbreak, such as the Effective Reproduction Number (R_t), are not always straightforward to calculate, raising barriers between the scientific community and non-scientific decision-making actors. The combination of estimators of R_t with elaborated Machine Learning-based forecasting techniques provides a way to support decision-making when assessing governmental plans of action. In this work, we develop forecast models applying logistic growth strategies and auto-regression techniques based on Auto-Regressive Integrated Moving Average (ARIMA) models for each country that records information about the COVID-19 outbreak. Using the forecast for the main variables of the outbreak, namely the number of infected (I), recovered (R), and dead (D) individuals, we provide a real-time estimation of R_t and its temporal evolution within a timeframe. With such models, we evaluate R_t trends at the continental and country levels, providing a clear picture of the effect governmental actions have had on the spread. We expect this methodology of combining forecast models for raw data to calculate R_t to serve as valuable input to support decision-making related to controlling the spread of SARS-CoV-2.", "date": "2020-07-17", "date_type": "published", "publication": "Frontiers in Physics", "volume": "8", "publisher": "Frontiers Media SA", "pagerange": "Art. No. 304", "id_number": "CaltechAUTHORS:20200831-105818791", "issn": "2296-424X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200831-105818791", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica (CONICYT)", "grant_number": "PIA FB0001" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.3389/fphy.2020.00304", "primary_object": { "basename": "fphy-08-00304.pdf", "url": "https://authors.library.caltech.edu/records/aan98-s5736/files/fphy-08-00304.pdf" }, "pub_year": "2020", "author_list": "Medina-Ortiz, David; Contreras, Sebasti\u00e1n; et al." }, { "id": "https://authors.library.caltech.edu/records/yx447-7d045", "eprint_id": 104698, "eprint_status": "archive", "datestamp": "2023-08-19 22:10:41", "lastmod": "2026-03-29 20:49:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fang-Jennifer", "name": { "family": "Fang", "given": "Jennifer" } }, { "id": "Liu-Yiju-T", "name": { "family": "Liu", "given": "Yiju T." } }, { "id": "Lee-Ernest-Y", "name": { "family": "Lee", "given": "Ernest Y." }, "orcid": "0000-0001-5144-2552" }, { "id": "Yadav-Kabir", "name": { "family": "Yadav", "given": "Kabir" } } ] }, "title": "Telehealth Solutions for In-hospital Communication with Patients Under Isolation During COVID-19", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Fang et al. This is an open access article\ndistributed in accordance with the terms of the Creative Commons Attribution (CC BY 4.0) License. See: http://creativecommons.org/licenses/by/4.0/. \n\nSubmitted May 12, 2020; Revision received May 29, 2020; Accepted May 27, 2020. Electronically published June 23, 2020. \n\nWe thank Dan Pipe-Mazo for his technical assistance\nduring this project, and Shir Aharon and Steven Okai for\nhelping test various app and device settings. We thank Linda\nRodgers and Ron Lam for showing us Apple Configurator. \n\nBy the WestJEM article submission agreement, all authors are required to disclose all affiliations, funding sources and financial or management relationships that could be perceived as potential sources of bias. No author has professional or financial relationships with any companies that are relevant to this study. There are no conflicts of interest or sources of funding to declare.\n\nPublished - eScholarship_UC_item_0nb053tn.pdf
Supplemental Material - 48165-Supplement_2.docx
Supplemental Material - 48165-Supplement_3.docx
Supplemental Material - Supplement1.docx
", "abstract": "The coronavirus disease 2019 (COVID-19) pandemic is a public health crisis that has quickly overwhelmed our healthcare system. It has led to significant shortages in personal protective equipment (PPE), ventilators, and intensive care unit beds across the nation. As the initial entry point for patients with suspected COVID illness, emergency departments (ED) have had to adapt quickly to prioritize the safety of patients and providers while still delivering optimal, timely patient care. COVID-19 has presented many challenges for the ED that also extend to all inpatient services. Some of these key challenges are the fundamental tasks of communicating with patients in respiratory isolation while minimizing PPE usage and enabling all patients who have been affected by hospitals' visitor restrictions to connect with their families. We discuss the design principles behind implementing a robust in-hospital telehealth system for patient-provider and patient-family communication, provide a review of the strengths and weaknesses of potential videoconferencing options, and deliver concise, step-by-step guides for setting up a secure, low-cost, user-friendly solution that can be rapidly deployed.", "date": "2020-07", "date_type": "published", "publication": "Western Journal of Emergency Medicine", "volume": "21", "number": "4", "publisher": "Western Journal of Emergency Medicine", "pagerange": "801-806", "id_number": "CaltechAUTHORS:20200803-094606578", "issn": "1936-900X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200803-094606578", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.5811/westjem.2020.5.48165", "pmcid": "PMC7390554", "primary_object": { "basename": "48165-Supplement_2.docx", "url": "https://authors.library.caltech.edu/records/yx447-7d045/files/48165-Supplement_2.docx" }, "related_objects": [ { "basename": "48165-Supplement_3.docx", "url": "https://authors.library.caltech.edu/records/yx447-7d045/files/48165-Supplement_3.docx" }, { "basename": "eScholarship_UC_item_0nb053tn.pdf", "url": "https://authors.library.caltech.edu/records/yx447-7d045/files/eScholarship_UC_item_0nb053tn.pdf" }, { "basename": "Supplement1.docx", "url": "https://authors.library.caltech.edu/records/yx447-7d045/files/Supplement1.docx" } ], "pub_year": "2020", "author_list": "Fang, Jennifer; Liu, Yiju T.; et al." }, { "id": "https://authors.library.caltech.edu/records/j45c4-raz41", "eprint_id": 103773, "eprint_status": "archive", "datestamp": "2023-08-22 05:29:55", "lastmod": "2026-03-29 14:25:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Contreras-Sebasti\u00e1n", "name": { "family": "Contreras", "given": "Sebasti\u00e1n" }, "orcid": "0000-0001-8909-774X" }, { "id": "Villavicencio-H-Andr\u00e9s", "name": { "family": "Villavicencio", "given": "H. Andr\u00e9s" } }, { "id": "Medina-Ortiz-D", "name": { "family": "Medina-Ortiz", "given": "David" }, "orcid": "0000-0002-8369-5746" }, { "id": "Biron-Lattes-Juan-Pablo", "name": { "family": "Biron-Lattes", "given": "Juan Pablo" } }, { "id": "Olivera-Nappa-\u00c1lvaro", "name": { "family": "Olivera-Nappa", "given": "\u00c1lvaro" }, "orcid": "0000-0001-6053-7019" } ] }, "title": "A multi-group SEIRA model for the spread of COVID-19 among heterogeneous populations", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19 pandemic; SARS-CoV2; Multigroup model; Public-health; SEIRA models", "note": "\u00a9 2020 Elsevier Ltd. \n\nReceived 23 April 2020, Accepted 20 May 2020, Available online 25 May 2020. \n\nThe authors gratefully acknowledge support from the Chilean National Agency for Research and development through ANID PIA Grant AFB180004, and the Centre for Biotechnology and Bioengineering - CeBiB (PIA project FB0001, Conicyt, Chile). DM-O gratefully acknowledges Conicyt, Chile, for PhD fellowship 21181435. \n\nCRediT authorship contribution statement - \nSebasti\u00e1n Contreras: Conceptualization, Methodology, Investigation, Writing - original draft, Writing - review & editing, Supervision. H. Andr\u00e9s Villavicencio: Methodology, Validation, Investigation, Writing - original draft, Writing - review & editing. David Medina-Ortiz: Validation, Investigation, Writing - original draft, Writing - review & editing. Juan Pablo Biron-Lattes: Validation, Writing - original draft, Writing - review & editing. \u00c1lvaro Olivera-Nappa: Validation, Writing - original draft, Writing - review & editing, Supervision, Project administration, Funding acquisition. \n\nThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.\n\nSubmitted - 2004.13452.pdf
", "abstract": "The outbreak and propagation of COVID-19 have posed a considerable challenge to modern society. In particular, the different restrictive actions taken by governments to prevent the spread of the virus have changed the way humans interact and conceive interaction. Due to geographical, behavioral, or economic factors, different sub-groups among a population are more (or less) likely to interact, and thus to spread/acquire the virus. In this work, we present a general multi-group SEIRA model for representing the spread of COVID-19 among a heterogeneous population and test it in a numerical case of study. By highlighting its applicability and the ease with which its general formulation can be adapted to particular studies, we expect our model to lead us to a better understanding of the evolution of this pandemic and to better public-health policies to control it.", "date": "2020-07", "date_type": "published", "publication": "Chaos, Solitons, and Fractals", "volume": "136", "publisher": "Elsevier", "pagerange": "Art. No. 109925", "id_number": "CaltechAUTHORS:20200608-115356852", "issn": "0960-0779", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200608-115356852", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica (CONICYT)", "grant_number": "AFB180004" }, { "agency": "Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica (CONICYT)", "grant_number": "FB0001" }, { "agency": "Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica (CONICYT)", "grant_number": "21181435" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1016/j.chaos.2020.109925", "pmcid": "PMC7247502", "primary_object": { "basename": "2004.13452.pdf", "url": "https://authors.library.caltech.edu/records/j45c4-raz41/files/2004.13452.pdf" }, "pub_year": "2020", "author_list": "Contreras, Sebasti\u00e1n; Villavicencio, H. Andr\u00e9s; et al." }, { "id": "https://authors.library.caltech.edu/records/hzqf2-3ap31", "eprint_id": 110714, "eprint_status": "archive", "datestamp": "2023-08-22 05:33:17", "lastmod": "2026-03-29 14:27:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Esbin-Meagan-N", "name": { "family": "Esbin", "given": "Meagan N." }, "orcid": "0000-0002-2157-3831" }, { "id": "Whitney-Oscar-N", "name": { "family": "Whitney", "given": "Oscar N." }, "orcid": "0000-0002-4858-2615" }, { "id": "Chong-Shasha", "name": { "family": "Chong", "given": "Shasha" }, "orcid": "0000-0002-5372-311X" }, { "id": "Maurer-Anna", "name": { "family": "Maurer", "given": "Anna" }, "orcid": "0000-0003-2768-7757" }, { "id": "Darzacq-Xavier", "name": { "family": "Darzacq", "given": "Xavier" }, "orcid": "0000-0003-2537-8395" }, { "id": "Tjian-Robert", "name": { "family": "Tjian", "given": "Robert" }, "orcid": "0000-0003-0539-8217" } ] }, "title": "Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection", "ispublished": "pub", "full_text_status": "public", "keywords": "CRISPR; LAMP; RT-PCR; covid-19; sars-cov-2", "note": "\u00a9 2020 Esbin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society. This article, published in RNA, is available undera Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. \n\nFreely available online through the RNA Open Access option. \n\nWe thank all of the members of the Tjian and Darzacq laboratory for their reading, insights, and helpful discussions on this review. We would expressly like to thank the Tjian and Darzacq COVID-19 response team for their unpublished findings relevant to COVID-19 testing presented here. The authors gratefully acknowledge funding from the Howard Hughes Medical Institute (grant CC34430 to R.T. and M.N.E.) and the National Institutes of Health (NIH training program grant T32GM098218 to M.N.E. and NIH training program grant T32GM007232 to O.N.W.). \n\nAuthor contributions: M.N.E. developed the concept; M.N.E., O.N.W., and S.C. contributed to the design and writing of the review; and A.M. prepared the figures. All authors contributed to the reading, collection, and analysis of sources for this review.\n\nPublished - RNA-2020-Esbin-771-83.pdf
Supplemental Material - Supplemental_Table_Legends.docx
Supplemental Material - Supplemental_Table_S1_.xlsx
Supplemental Material - Supplemental_Table_S2_.xlsx
", "abstract": "The current COVID-19 pandemic presents a serious public health crisis, and a better understanding of the scope and spread of the virus would be aided by more widespread testing. Nucleic-acid-based tests currently offer the most sensitive and early detection of COVID-19. However, the \"gold standard\" test pioneered by the U.S. Centers for Disease Control and Prevention takes several hours to complete and requires extensive human labor, materials such as RNA extraction kits that could become in short supply, and relatively scarce qPCR machines. It is clear that a huge effort needs to be made to scale up current COVID-19 testing by orders of magnitude. There is thus a pressing need to evaluate alternative protocols, reagents, and approaches to allow nucleic-acid testing to continue in the face of these potential shortages. There has been a tremendous explosion in the number of papers written within the first weeks of the pandemic evaluating potential advances, comparable reagents, and alternatives to the \"gold-standard\" CDC RT-PCR test. Here we present a collection of these recent advances in COVID-19 nucleic acid testing, including both peer-reviewed and preprint articles. Due to the rapid developments during this crisis, we have included as many publications as possible, but many of the cited sources have not yet been peer-reviewed, so we urge researchers to further validate results in their own laboratories. We hope that this review can urgently consolidate and disseminate information to aid researchers in designing and implementing optimized COVID-19 testing protocols to increase the availability, accuracy, and speed of widespread COVID-19 testing.", "date": "2020-07", "date_type": "published", "publication": "RNA", "volume": "26", "number": "7", "publisher": "RNA Society", "pagerange": "771-783", "id_number": "CaltechAUTHORS:20210902-234003301", "issn": "1355-8382", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210902-234003301", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "CC34430" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM098218" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007232" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1261/rna.076232.120", "pmcid": "PMC7297120", "primary_object": { "basename": "RNA-2020-Esbin-771-83.pdf", "url": "https://authors.library.caltech.edu/records/hzqf2-3ap31/files/RNA-2020-Esbin-771-83.pdf" }, "related_objects": [ { "basename": "Supplemental_Table_Legends.docx", "url": "https://authors.library.caltech.edu/records/hzqf2-3ap31/files/Supplemental_Table_Legends.docx" }, { "basename": "Supplemental_Table_S1_.xlsx", "url": "https://authors.library.caltech.edu/records/hzqf2-3ap31/files/Supplemental_Table_S1_.xlsx" }, { "basename": "Supplemental_Table_S2_.xlsx", "url": "https://authors.library.caltech.edu/records/hzqf2-3ap31/files/Supplemental_Table_S2_.xlsx" } ], "pub_year": "2020", "author_list": "Esbin, Meagan N.; Whitney, Oscar N.; et al." }, { "id": "https://authors.library.caltech.edu/records/ghdb0-q2822", "eprint_id": 103889, "eprint_status": "archive", "datestamp": "2023-08-22 05:26:03", "lastmod": "2026-03-29 22:09:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Renyi", "name": { "family": "Zhang", "given": "Renyi" }, "orcid": "0000-0001-8708-3862" }, { "id": "Li-Yixin", "name": { "family": "Li", "given": "Yixin" }, "orcid": "0000-0001-7937-7385" }, { "id": "Zhang-Annie-L", "name": { "family": "Zhang", "given": "Annie L." } }, { "id": "Wang-Yuan", "name": { "family": "Wang", "given": "Yuan" }, "orcid": "0000-0001-6657-8401" }, { "id": "Molina-Mario-J", "name": { "family": "Molina", "given": "Mario J." }, "orcid": "0000-0003-2339-3225" } ] }, "title": "Identifying airborne transmission as the dominant route for the spread of COVID-19", "ispublished": "pub", "full_text_status": "public", "keywords": "COVID-19; virus; aerosol; public health; pandemic", "note": "\u00a9 2020 the Author(s). Published by PNAS.\nThis open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).\n\nContributed by Mario J. Molina, May 16, 2020 (sent for review May 14, 2020; reviewed by Manish Shrivastava and Tong Zhu). First published June 11, 2020.\n\nThis work was supported by the Robert A. Welch Foundation (Grant A-1417). A.L.Z. acknowledges the support of a fellowship from the Robert A. Welch Foundation. We are grateful to Fang Zhang for the PM_(2.5) data in Wuhan, China.\n\nData Availability:\nAll data relevant to this research are available in the main text and SI Appendix.\n\nAuthor contributions: R.Z. designed research; R.Z., Y.L., and Y.W. performed research; R.Z., Y.L., Y.W., and M.J.M. analyzed data; and R.Z., A.L.Z., and M.J.M. wrote the paper.\n\nReviewers: M.S., Pacific Northwest National Laboratory; and T.Z., Peking University.\n\nThe authors declare no competing interest.\n\nThis article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2009637117/-/DCSupplemental.\n\nPublished - 14857.full.pdf
Supplemental Material - pnas.2009637117.sapp.pdf
", "abstract": "Various mitigation measures have been implemented to fight the coronavirus disease 2019 (COVID-19) pandemic, including widely adopted social distancing and mandated face covering. However, assessing the effectiveness of those intervention practices hinges on the understanding of virus transmission, which remains uncertain. Here we show that airborne transmission is highly virulent and represents the dominant route to spread the disease. By analyzing the trend and mitigation measures in Wuhan, China, Italy, and New York City, from January 23 to May 9, 2020, we illustrate that the impacts of mitigation measures are discernable from the trends of the pandemic. Our analysis reveals that the difference with and without mandated face covering represents the determinant in shaping the pandemic trends in the three epicenters. This protective measure alone significantly reduced the number of infections, that is, by over 78,000 in Italy from April 6 to May 9 and over 66,000 in New York City from April 17 to May 9. Other mitigation measures, such as social distancing implemented in the United States, are insufficient by themselves in protecting the public. We conclude that wearing of face masks in public corresponds to the most effective means to prevent interhuman transmission, and this inexpensive practice, in conjunction with simultaneous social distancing, quarantine, and contact tracing, represents the most likely fighting opportunity to stop the COVID-19 pandemic. Our work also highlights the fact that sound science is essential in decision-making for the current and future public health pandemics.", "date": "2020-06-30", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "117", "number": "26", "publisher": "National Academy of Sciences", "pagerange": "14857-14863", "id_number": "CaltechAUTHORS:20200612-143721963", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200612-143721963", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Robert A. Welch Foundation", "grant_number": "A-1417" } ] }, "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1073/pnas.2009637117", "pmcid": "PMC7334447", "primary_object": { "basename": "14857.full.pdf", "url": "https://authors.library.caltech.edu/records/ghdb0-q2822/files/14857.full.pdf" }, "related_objects": [ { "basename": "pnas.2009637117.sapp.pdf", "url": "https://authors.library.caltech.edu/records/ghdb0-q2822/files/pnas.2009637117.sapp.pdf" } ], "pub_year": "2020", "author_list": "Zhang, Renyi; Li, Yixin; et al." }, { "id": "https://authors.library.caltech.edu/records/7h5mf-gpg97", "eprint_id": 103519, "eprint_status": "archive", "datestamp": "2023-08-19 21:33:02", "lastmod": "2026-03-29 18:41:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ahmed-M-Arslan", "name": { "family": "Ahmed", "given": "M. Arslan" }, "orcid": "0000-0002-3479-6946" }, { "id": "Behbahani-Amir-H", "name": { "family": "Behbahani", "given": "Amir H." }, "orcid": "0000-0001-5603-6887" }, { "id": "Br\u00fcckner-Adrian-K", "name": { "family": "Br\u00fcckner", "given": "Adrian" }, "orcid": "0000-0002-9184-8562" }, { "id": "Charpentier-Caroline-J", "name": { "family": "Charpentier", "given": "Caroline J." }, "orcid": "0000-0002-7283-0738" }, { "id": "Morais-Livia-H", "name": { "family": "Morais", "given": "Livia H." } }, { "id": "Mallory-Stewart-A", "name": { "family": "Mallory", "given": "Stewart" }, "orcid": "0000-0003-1364-7252" }, { "id": "Pool-Allan-Hermann", "name": { "family": "Pool", "given": "Allan-Hermann" }, "orcid": "0000-0002-0811-9861" } ] }, "title": "The precarious position of postdocs during COVID-19", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2020 American Association for the Advancement of Science.\nThis is an article distributed under the terms of the Science Journals Default License. \n\nCompeting Interests: All authors are board members of the California Institute of Technology (Caltech) Postdoctoral Association (CPA). The views expressed herein do not in any way represent the view of other members of the CPA board, postdoctoral individuals at Caltech, or Caltech.", "abstract": "Postdoctoral researchers play a crucial role in many research groups, serving as mentors, teachers, and leaders as they develop their skills and prepare for scientific careers (1). However, the coronavirus disease 2019 (COVID-19) crisis has put funding and support for postdoc positions at risk, threatening to upend the career paths available to these junior scientists.", "date": "2020-05-29", "date_type": "published", "publication": "Science", "volume": "368", "number": "6494", "publisher": "American Association for the Advancement of Science", "pagerange": "957-958", "id_number": "CaltechAUTHORS:20200528-120127437", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200528-120127437", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1126/science.abc5143", "pub_year": "2020", "author_list": "Ahmed, M. Arslan; Behbahani, Amir H.; et al." }, { "id": "https://authors.library.caltech.edu/records/71zw8-wk483", "eprint_id": 102979, "eprint_status": "archive", "datestamp": "2023-08-22 04:53:56", "lastmod": "2026-03-30 13:50:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Van-Bavel-Jay-J", "name": { "family": "Van Bavel", "given": "Jay J." }, "orcid": "0000-0002-2520-0442" }, { "name": { "family": "Baicker", "given": "Katherine" }, "orcid": "0000-0001-5960-3058" }, { "name": { "family": "Boggio", "given": "Paulo S." }, "orcid": "0000-0002-6109-0447" }, { "name": { "family": "Capraro", "given": "Valerio" } }, { "name": { "family": "Cichocka", "given": "Aleksandra" }, "orcid": "0000-0003-1703-1586" }, { "name": { "family": "Cikara", "given": "Mina" }, "orcid": "0000-0002-6612-4474" }, { "name": { "family": "Crockett", "given": "Molly J." }, "orcid": "0000-0001-8800-410X" }, { "name": { "family": "Crum", "given": "Alia J." } }, { "name": { "family": "Douglas", "given": "Karen M." }, "orcid": "0000-0002-0381-6924" }, { "name": { "family": "Druckman", "given": "James N." } }, { "name": { "family": "Drury", "given": "John" }, "orcid": "0000-0002-7748-5128" }, { "name": { "family": "Dube", "given": "Oeindrila" } }, { "name": { "family": "Ellemers", "given": "Naomi" } }, { "name": { "family": "Finkel", "given": "Eli J." } }, { "name": { "family": "Fowler", "given": "James H." }, "orcid": "0000-0001-7795-1638" }, { "name": { "family": "Gelfand", "given": "Michele" }, "orcid": "0000-0002-9780-9230" }, { "name": { "family": "Han", "given": "Shihui" }, "orcid": "0000-0003-3350-5104" }, { "name": { "family": "Haslam", "given": "S. Alexander" }, "orcid": "0000-0001-9523-7921" }, { "name": { "family": "Jetten", "given": "Jolanda" }, "orcid": "0000-0002-7588-5355" }, { "name": { "family": "Kitayama", "given": "Shinobu" }, "orcid": "0000-0001-9147-7936" }, { "id": "Mobbs-D", "name": { "family": "Mobbs", "given": "Dean" }, "orcid": "0000-0003-1175-3772" }, { "name": { "family": "Napper", "given": "Lucy E." } }, { "name": { "family": "Packer", "given": "Dominic J." }, "orcid": "0000-0001-8420-6548" }, { "name": { "family": "Pennycook", "given": "Gordon" }, "orcid": "0000-0003-1344-6143" }, { "name": { "family": "Peters", "given": "Ellen" }, "orcid": "0000-0003-0702-6169" }, { "name": { "family": "Petty", "given": "Richard E." }, "orcid": "0000-0002-2870-8575" }, { "name": { "family": "Rand", "given": "David G." }, "orcid": "0000-0001-8975-2783" }, { "name": { "family": "Reicher", "given": "Stephen D." } }, { "name": { "family": "Schnall", "given": "Simone" }, "orcid": "0000-0002-4672-7534" }, { "name": { "family": "Shariff", "given": "Azim" }, "orcid": "0000-0003-4444-460X" }, { "name": { "family": "Skitka", "given": "Linda J." } }, { "name": { "family": "Smith", "given": "Sandra Susan" } }, { "name": { "family": "Sunstein", "given": "Cass R." }, "orcid": "0000-0003-4194-3008" }, { "name": { "family": "Tabri", "given": "Nassim" }, "orcid": "0000-0002-7085-9350" }, { "name": { "family": "Tucker", "given": "Joshua A." }, "orcid": "0000-0003-1321-8650" }, { "name": { "family": "van der Linden", "given": "Sander" }, "orcid": "0000-0002-0269-1744" }, { "name": { "family": "van Lange", "given": "Paul" } }, { "name": { "family": "Weeden", "given": "Kim A." }, "orcid": "0000-0002-9975-8457" }, { "name": { "family": "Wohl", "given": "Michael J. A." }, "orcid": "0000-0001-6945-5562" }, { "name": { "family": "Zaki", "given": "Jamil" } }, { "name": { "family": "Zion", "given": "Sean R." }, "orcid": "0000-0002-0802-2066" }, { "name": { "family": "Willer", "given": "Robb" }, "orcid": "0000-0003-3404-6472" } ] }, "title": "Using social and behavioural science to support COVID-19 pandemic response", "ispublished": "pub", "full_text_status": "public", "keywords": "Human behaviour; Immunology; Sociology", "note": "\u00a9 2020 Springer Nature Limited. \n\nReceived 24 March 2020; Accepted 09 April 2020; Published 30 April 2020. \n\nAuthor Contributions: The corresponding authors (J.V.B and R.W.) came up with the idea for the paper, invited authors to collaborate, and wrote and edited the manuscript. All other contributing authors (K.B., P.S.B., V.C., A.C., M.C., M.J.C, A.J.C., K.M.D., J.N.D., J.D., O.D., N.E., E.J.F., J.H.F., M.G., S.H., S.A.H., J.J., S.K., D.M., K.E.N., D.J.P., G.P., E.P., R.E.P., D.G.R., S.D.R., S.S., A.S., L.J.S., S.S.S., C.R.S., N.T., J.A.T., S.V.L., P.A.M.V.L., K.A.W., M.J.A.W., J.Z. and S.R.Z.) wrote and edited the paper and are listed in alphabetical order. We thank J. Rothschild for his help in inserting citations and organizing the list of biographical references. \n\nThe authors declare no competing interests.\n\nSubmitted - 2020-COVID-Manuscript-FINAL.docx
", "abstract": "The COVID-19 pandemic represents a massive global health crisis. Because the crisis requires large-scale behaviour change and places significant psychological burdens on individuals, insights from the social and behavioural sciences can be used to help align human behaviour with the recommendations of epidemiologists and public health experts. Here we discuss evidence from a selection of research topics relevant to pandemics, including work on navigating threats, social and cultural influences on behaviour, science communication, moral decision-making, leadership, and stress and coping. In each section, we note the nature and quality of prior research, including uncertainty and unsettled issues. We identify several insights for effective response to the COVID-19 pandemic and highlight important gaps researchers should move quickly to fill in the coming weeks and months.", "date": "2020-05", "date_type": "published", "publication": "Nature Human Behaviour", "volume": "4", "number": "5", "publisher": "Springer Nature", "pagerange": "460-471", "id_number": "CaltechAUTHORS:20200504-130436917", "issn": "2397-3374", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200504-130436917", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "COVID-19" } ] }, "doi": "10.1038/s41562-020-0884-z", "primary_object": { "basename": "2020-COVID-Manuscript-FINAL.docx", "url": "https://authors.library.caltech.edu/records/71zw8-wk483/files/2020-COVID-Manuscript-FINAL.docx" }, "pub_year": "2020", "author_list": "Van Bavel, Jay J.; Baicker, Katherine; et al." }, { "id": "https://authors.library.caltech.edu/records/rzcf0-hpf84", "eprint_id": 102210, "eprint_status": "archive", "datestamp": "2023-08-19 20:39:45", "lastmod": "2026-03-30 08:20:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bar-On-Yinon-M", "name": { "family": "Bar-On", "given": "Yinon M." }, "orcid": "0000-0001-8477-609X" }, { "id": "Flamholz-Avi", "name": { "family": "Flamholz", "given": "Avi" }, "orcid": "0000-0002-9278-5479" }, { "id": "Phillips-R", "name": { "family": "Phillips", "given": "Rob" }, "orcid": "0000-0003-3082-2809" }, { "id": "Milo-Ron", "name": { "family": "Milo", "given": "Ron" }, "orcid": "0000-0003-1641-2299" } ] }, "title": "SARS-CoV-2 (COVID-19) by the numbers", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Bar-On et al. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: March 27, 2020. Accepted: March 30, 2020. Accepted Manuscript published: March 31, 2020 (version 1). \n\nWe thank Uri Alon, Niv Antonovsky, David Baltimore, Rachel Banks, Arren Bar Even, Naama Barkai, Molly Bassette, Menalu Berihoon, Biana Bernshtein, Pamela Bjorkman, Cecilia Blikstad, Julia Borden, Bill Burkholder, Griffin Chure, Lillian Cohn, Bernadeta Dadonaite, Emmie De wit, Ron Diskin, Ana Duarte, Tal Einav, Avigdor Eldar, Elizabeth Fischer, William Gelbart, Alon Gildoni, Britt Glausinger, Shmuel Gleizer, Dani Gluck, Soichi Hirokawa, Greg Huber, Christina Hueschen, Amit Huppert, Shalev Itzkovitz, Martin Jonikas, Leeat Keren, Gilmor Keshet, Marc Kirschner, Roy Kishony, Amy Kistler, Liad Levi, Sergei Maslov, Adi Millman, Amir Milo, Elad Noor, Gal Ofir, Alan Perelson, Steve Quake, Itai Raveh, Andrew Rennekamp, Tom Roeschinger, Daniel Rokhsar, Alex Rubinsteyn, Gabriel Salmon, Maya Schuldiner, Eran Segal, Ron Sender, Alex Sigal, Maya Shamir, Arik Shams, Mike Springer, Adi Stern, Noam Stern-Ginossar, Lubert Stryer, Dan Tawfik, Boris Veytsman, Aryeh Wides, Tali Wiesel, Anat Yarden, Yossi Yovel, Dudi Zeevi, Mushon Zer Aviv, and Alexander Zlokapa for productive feedback on this manuscript. Figure created using Biorender. \n\nFunding: National Institutes of Health (1R35 GM118043-01 (Maximizing Investigators Research Award)) - Rob Phillips. Charles and Louise Gartner professional chair - Ron Milo. Azrieli Fellow - Yinon M Bar-On. \n\nThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. \n\nThe authors declare that no competing interests exist.\n\nPublished - elife-57309-v3.pdf
", "abstract": "The current SARS-CoV-2 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a story about the numbers. In this snapshot, our aim is to provide a one-stop, curated graphical source for the key numbers that help us understand the virus driving our current global crisis. The discussion is framed around two broad themes: 1) the biology of the virus itself and 2) the characteristics of the infection of a single human host. Our one-page summary provides the key numbers pertaining to SARS-CoV-2, based mostly on peer-reviewed literature. The numbers reported in summary format are substantiated by the annotated references below. Readers are urged to remember that much uncertainty remains and knowledge of this pandemic and the virus driving it is rapidly evolving. In the paragraphs below we provide 'back of the envelope' calculations that exemplify the insights that can be gained from knowing some key numbers and using quantitative logic. These calculations serve to improve our intuition through sanity checks, but do not replace detailed epidemiological analysis.", "date": "2020-03-31", "date_type": "published", "publication": "eLife", "volume": "9", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e57309", "id_number": "CaltechAUTHORS:20200331-215659202", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200331-215659202", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1R35 GM118043-01" }, { "agency": "Charles and Louise Gartner professional chair" }, { "agency": "Azrieli Fellow" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/elife.57309", "pmcid": "PMC7224694", "primary_object": { "basename": "elife-57309-v3.pdf", "url": "https://authors.library.caltech.edu/records/rzcf0-hpf84/files/elife-57309-v3.pdf" }, "pub_year": "2020", "author_list": "Bar-On, Yinon M.; Flamholz, Avi; et al." }, { "id": "https://authors.library.caltech.edu/records/1bdtt-48q26", "eprint_id": 101899, "eprint_status": "archive", "datestamp": "2023-08-19 20:28:02", "lastmod": "2026-03-29 18:31:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Flyak-Andrew-I", "name": { "family": "Flyak", "given": "Andrew I." }, "orcid": "0000-0002-8722-479X" }, { "id": "Ruiz-Stormy-E", "name": { "family": "Ruiz", "given": "Stormy E." }, "orcid": "0000-0003-0892-9626" }, { "id": "Salas-Jordan", "name": { "family": "Salas", "given": "Jordan" } }, { "id": "Rho-Semi", "name": { "family": "Rho", "given": "Semi" } }, { "id": "Bailey-Justin-R", "name": { "family": "Bailey", "given": "Justin R." } }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "An ultralong CDRH2 in HCV neutralizing antibody demonstrates structural plasticity of antibodies against E2 glycoprotein", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Flyak et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: 30 October 2019; Accepted: 02 March 2020; Published: 03 March 2020. \n\nWe thank the Caltech Protein Expression Center (Dr. Jost Vielmetter, director) for help with protein expression and Dr. Anthony West for helpful discussions. Structural studies were assisted by the Caltech Molecular Observatory (Dr. Jens Kaiser, director). This research was supported by the National Institutes of Health grant R01 AI127469 (to JRB and PJB) (content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH) and the Molecular Observatory at Caltech supported by the Gordon and Betty Moore Foundation. AIF was a Cancer Research Institute Irvington Fellow supported by the Cancer Research Institute. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by NIHGMS P41GM103393. \n\nAuthor contributions: Andrew I Flyak, Conceptualization, Data curation, Software, Formal analysis, Supervision, Validation, Investigation, Visualization, Methodology, Writing - original draft, Writing - review and editing; Stormy E Ruiz, Formal analysis, Investigation, Writing - review and editing; Jordan Salas, Semi Rho, Data curation, Formal analysis, Investigation, Writing - review and editing; Justin R Bailey, Supervision, Funding acquisition, Investigation, Writing - review and editing; Pamela J Bjorkman, Conceptualization, Supervision, Funding acquisition, Project administration, Writing - review and editing. \n\nCompeting interests: Pamela J Bjorkman: Reviewing editor, eLife. Andrew I Flyak, Justin R Bailey: AIF and JRB are inventors of International Patent Application, Serial no. PCT/US2019/029315, pertaining to some of the antibodies presented in this article. The other authors declare that no competing interests exist. \n\nData availability: Diffraction data have been deposited in PDB under the accession code 6URH.\n\nPublished - elife-53169-v2.pdf
Supplemental Material - elife-53169-transrepform-v2.pdf
", "abstract": "A vaccine protective against diverse HCV variants is needed to control the HCV epidemic. Structures of E2 complexes with front layer-specific broadly neutralizing antibodies (bNAbs) isolated from HCV-infected individuals, revealed a disulfide bond-containing CDRH3 that adopts straight (individuals who clear infection) or bent (individuals with chronic infection) conformation. To investigate whether a straight versus bent disulfide bond-containing CDRH3 is specific to particular HCV-infected individuals, we solved a crystal structure of the HCV E2 ectodomain in complex with AR3X, a bNAb with an unusually long CDRH2 that was isolated from the chronically-infected individual from whom the bent CDRH3 bNAbs were derived. The structure revealed that AR3X utilizes both its ultralong CDRH2 and a disulfide motif-containing straight CDRH3 to recognize the E2 front layer. These results demonstrate that both the straight and bent CDRH3 classes of HCV bNAb can be elicited in a single individual, revealing a structural plasticity of VH1-69-derived bNAbs.", "date": "2020-03-03", "date_type": "published", "publication": "eLife", "volume": "9", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e53169", "id_number": "CaltechAUTHORS:20200312-143121974", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200312-143121974", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127469" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Cancer Research Institute" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-76SF00515" }, { "agency": "NIH", "grant_number": "P41GM103393" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/elife.53169", "pmcid": "PMC7064334", "primary_object": { "basename": "elife-53169-v2.pdf", "url": "https://authors.library.caltech.edu/records/1bdtt-48q26/files/elife-53169-v2.pdf" }, "related_objects": [ { "basename": "elife-53169-transrepform-v2.pdf", "url": "https://authors.library.caltech.edu/records/1bdtt-48q26/files/elife-53169-transrepform-v2.pdf" } ], "pub_year": "2020", "author_list": "Flyak, Andrew I.; Ruiz, Stormy E.; et al." } ]![ciab686_suppl_supplementary_figure_s1.jpeg](\"/records/9sgp0-wf083/files/ciab686_suppl_supplementary_figure_s1.jpeg?download=1\"){kind=link}
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