[ { "id": "authors:act7x-zp783", "collection": "authors", "collection_id": "act7x-zp783", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230323-420614000.1", "type": "monograph", "title": "Index Cases First Identified by Nasal-Swab Rapid COVID-19 Tests Had More Transmission to Household Contacts Than Cases Identified by Other Test Types", "author": [ { "family_name": "Ji", "given_name": "Jenny", "orcid": "0000-0002-7901-5605", "clpid": "Ji-Jenny" }, { "family_name": "Winnett", "given_name": "Alexander Viloria", "orcid": "0000-0002-7338-5605", "clpid": "Winnett-Alexander-Viloria" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663", "clpid": "Shelby-Natasha" }, { "family_name": "Reyes", "given_name": "Jessica A.", "orcid": "0000-0002-5507-7633", "clpid": "Reyes-Jessica-A" }, { "family_name": "Schlenker", "given_name": "Noah W.", "orcid": "0000-0002-8581-4403", "clpid": "Schlenker-Noah-W" }, { "family_name": "Davich", "given_name": "Hannah", "orcid": "0000-0001-6880-3086", "clpid": "Davich-Hannah" }, { "family_name": "Caldera", "given_name": "Saharai", "orcid": "0000-0001-5057-9186", "clpid": "Caldera-Saharai" }, { "family_name": "Tognazzini", "given_name": "Colten", "orcid": "0000-0002-2754-3588", "clpid": "Tognazzini-Colten" }, { "family_name": "Goh", "given_name": "Ying-Ying", "orcid": "0000-0001-5136-7214", "clpid": "Goh-Ying-Ying" }, { "family_name": "Feaster", "given_name": "Matt", "orcid": "0000-0001-9966-2845", "clpid": "Feaster-Matthew" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "Importance. At-home rapid COVID-19 tests utilize nasal-swab specimens and require high viral loads to reliably give positive results. Longitudinal studies from the onset of infection have found infectious virus can present in oral specimens days before nasal. Detection and initiation of infection-control practices may therefore be delayed when nasal-swab rapid tests are used, resulting in greater exposure and transmission to contacts. \n\nObjective. We assessed whether index cases first identified by rapid nasal-swab COVID-19 tests had more transmission to household contacts than index cases who used other test types (tests with higher analytical sensitivity but longer turnaround times, and/or that utilize non-nasal specimen types). \n\nDesign. In this observational cohort study, members of households with a recent COVID-19 case were screened for infection at least daily by RT-qPCR on one or more self-collected upper-respiratory specimen types. Participants reported demographic/medical information (including COVID-19 testing), symptom and exposure information, and household infection-control practices. A two-level random intercept model was used to assess the association between the infection outcome of household contacts and each covariable (household size, race/ethnicity, age, vaccination status, viral variant, infection-control practices, and whether a rapid nasal-swab test was used to initially identify the household index case). \n\nSetting. Southern California, September 2020\u2014June 2021 and November 2021\u2014March 2022. \n\nParticipants. Cohort of 370 individuals from 85 households. \n\nMain Outcome(s) and Measure(s)Transmission was quantified by adjusted secondary attack rates (aSAR) and adjusted odds ratios (aOR). \n\nResults. An aSAR of 53.6% (95% CI 38.8\u201368.3%) was observed among households where the index case first tested positive by a rapid nasal-swab COVID-19 test, which was significantly higher than the aSAR for households where the index case utilized another test type (27.2% 95% CI 19.5\u2013 35.0%,P=0.003 pairwise comparisons of predictive margins). We observed an aOR of 4.90 (95% CI 1.65\u201314.56) for transmission to household contacts when a nasal-swab rapid test was used to identify the index case, compared to other test types. \n\nConclusions and Relevance. Use of nasal-swab rapid COVID-19 tests for initial detection of infection and initiation of infection control may not limit transmission as well as other test types. \n\nKey Points: \nQuestion: Does identification of index cases by rapid nasal-swab tests limit household transmission of SARS-CoV-2 as well as other test types? \n\nFinding. Significantly higher adjusted secondary attack rates and adjusted odds ratios for transmission were observed in households where the index case used a nasal rapid COVID-19 test for initial detection versus other test types.\n\nMeaning. The use of nasal-swab rapid COVID-19 tests for initial detection of infection and initiation of infection control may not limit transmission as well as other test types.", "doi": "10.1101/2023.03.09.23286855", "publication_date": "2023-03-10" }, { "id": "authors:x0cjg-kxg25", "collection": "authors", "collection_id": "x0cjg-kxg25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220720-917093000", "type": "monograph", "title": "Why Daily SARS-CoV-2 Nasal Rapid Antigen Testing Poorly Detects Infected and Infectious Individuals", "author": [ { "family_name": "Winnett", "given_name": "Alexander Viloria", "orcid": "0000-0002-7338-5605", "clpid": "Winnett-Alexander-Viloria" }, { "family_name": "Akana", "given_name": "Reid", "orcid": "0000-0003-4422-587X", "clpid": "Akana-Reid" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663", "clpid": "Shelby-Natasha" }, { "family_name": "Davich", "given_name": "Hannah", "orcid": "0000-0001-6880-3086", "clpid": "Davich-Hannah" }, { "family_name": "Caldera", "given_name": "Saharai", "orcid": "0000-0001-5057-9186", "clpid": "Caldera-Saharai" }, { "family_name": "Yamada", "given_name": "Taikun", "clpid": "Yamada-Taikun" }, { "family_name": "Reyna", "given_name": "John Raymond B.", "clpid": "Reyna-John-Raymond-B" }, { "family_name": "Romano", "given_name": "Anna E.", "orcid": "0000-0002-7148-0668", "clpid": "Romano-Anne-E" }, { "family_name": "Carter", "given_name": "Alyssa M.", "orcid": "0000-0002-2776-9421", "clpid": "Carter-Alyssa-M" }, { "family_name": "Kim", "given_name": "Mi Kyung", "clpid": "Kim-Mi-Kyung" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Tognazzini", "given_name": "Colten", "orcid": "0000-0002-2754-3588", "clpid": "Tognazzini-Colten" }, { "family_name": "Feaster", "given_name": "Matthew", "orcid": "0000-0001-9966-2845", "clpid": "Feaster-Matthew" }, { "family_name": "Goh", "given_name": "Ying-Ying", "orcid": "0000-0001-5136-7214", "clpid": "Goh-Ying-Ying" }, { "family_name": "Chew", "given_name": "Yap Ching", "orcid": "0000-0002-1686-6541", "clpid": "Chew-Yap-Ching" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "Background. 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 timepoint. We hypothesized these differences may hinder low-analytical-sensitivity assays (including antigen rapid diagnostic tests, Ag-RDTs) using a single specimen type (e.g., ANS) from reliably detecting infected and infectious individuals. \n\nMethods. We evaluated a daily at-home ANS Ag-RDT (Quidel QuickVue) in a cross-sectional analysis of 228 individuals and in a longitudinal analysis (throughout infection) of 17 individuals enrolled early in the course of infection. Ag-RDT results were compared to RT-qPCR results and high, presumably infectious viral loads (in each, or any, specimen type). \n\nResults. The ANS Ag-RDT correctly detected only 44% of timepoints from infected individuals on cross-sectional analysis, and in this population had an inferred limit of detection of 7.6 \u00d7 10\u2076 copies/mL. From the longitudinal cohort, daily Ag-RDT clinical sensitivity was very low (<3%) during the early, pre-infectious period of the infection. Further, the Ag-RDT detected \u226463% of presumably infectious timepoints. 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. \n\nConclusion. Nasal Ag-RDTs, even when used daily, can miss individuals infected with the Omicron variant and even those presumably infectious. Evaluations of Ag-RDT detection of infected or infectious individuals should be compared with a composite (multi-specimen) infection status to correctly assess performance. \n\nKey points. Nasal-swab rapid antigen tests have low analytical sensitivity and the sampling of only the nasal cavity hinders their ability to detect infected individuals, including those with high and presumably infectious viral loads in throat or saliva specimens.", "doi": "10.1101/2022.07.13.22277513", "publication_date": "2022-07-15" }, { "id": "authors:vtef0-x7037", "collection": "authors", "collection_id": "vtef0-x7037", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220720-917402000", "type": "monograph", "title": "Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods", "author": [ { "family_name": "Winnett", "given_name": "Alexander Viloria", "orcid": "0000-0002-7338-5605", "clpid": "Winnett-Alexander-V" }, { "family_name": "Akana", "given_name": "Reid", "orcid": "0000-0003-4422-587X", "clpid": "Akana-Reid" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663", "clpid": "Shelby-Natasha" }, { "family_name": "Davich", "given_name": "Hannah", "orcid": "0000-0001-6880-3086", "clpid": "Davich-Hannah" }, { "family_name": "Caldera", "given_name": "Saharai", "orcid": "0000-0001-5057-9186", "clpid": "Caldera-Saharai" }, { "family_name": "Yamada", "given_name": "Taikun", "clpid": "Yamada-Taikun" }, { "family_name": "Reyna", "given_name": "John Raymond B.", "clpid": "Reyna-John-Raymond-B" }, { "family_name": "Romano", "given_name": "Anna E.", "orcid": "0000-0002-7148-0668", "clpid": "Romano-Anne-E" }, { "family_name": "Carter", "given_name": "Alyssa M.", "orcid": "0000-0002-2776-9421", "clpid": "Carter-Alyssa-M" }, { "family_name": "Kim", "given_name": "Mi Kyung", "clpid": "Kim-Mi-Kyung" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Tognazzini", "given_name": "Colten", "orcid": "0000-0002-2754-3588", "clpid": "Tognazzini-Colten" }, { "family_name": "Feaster", "given_name": "Matthew", "orcid": "0000-0001-9966-2845", "clpid": "Feaster-Matthew" }, { "family_name": "Goh", "given_name": "Ying-Ying", "orcid": "0000-0001-5136-7214", "clpid": "Goh-Ying-Ying" }, { "family_name": "Chew", "given_name": "Yap Ching", "orcid": "0000-0002-1686-6541", "clpid": "Chew-Yap-Ching" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "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-host 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 up to 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-nasal swab, and assays with high analytical sensitivity, were inferred to have significantly better clinical sensitivity to detect presumed pre-infectious and infectious individuals.", "doi": "10.1101/2022.07.13.22277113", "publication_date": "2022-07-15" }, { "id": "authors:p6mn1-gs660", "collection": "authors", "collection_id": "p6mn1-gs660", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220706-965018000", "type": "monograph", "title": "Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa", "author": [ { "family_name": "Poceviciute", "given_name": "Roberta", "orcid": "0000-0002-6649-2170", "clpid": "Poceviciute-Roberta" }, { "family_name": "Bogatyrev", "given_name": "Said R.", "orcid": "0000-0003-0486-9451", "clpid": "Bogatyrev-Said-R" }, { "family_name": "Romano", "given_name": "Anna E.", "orcid": "0000-0002-7148-0668", "clpid": "Romano-Anne-E" }, { "family_name": "Dilmore", "given_name": "Amanda H.", "orcid": "0000-0001-6493-7116", "clpid": "Dilmore-Amanda-H" }, { "family_name": "Mondrag\u00f3n-Palomino", "given_name": "Octavio", "orcid": "0000-0003-1129-4932", "clpid": "Mondrag\u00f3n-Palomino-Octavio" }, { "family_name": "Takko", "given_name": "Heli", "orcid": "0000-0003-2544-409X", "clpid": "Takko-Heli" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "The small intestine (SI) is the primary site of nutrient absorption, so its large surface area lacks the thick protective mucus that is characteristic of the large intestine. Because the SI epithelium is relatively exposed, any microbes that colonize the thin mucosa of the SI may exert a substantial effect on the host. Thus far, potential bacterial colonization of the SI mucosa has only been documented in disease states, suggesting mucosal colonization is a rare occurrence, likely requiring multiple perturbations.ResultsHere, we tested whether we could induce bacterial association with jejunum mucosa by a combination of malnutrition and oral co-gavage with a specific bacterial cocktail (E. coli and Bacteroides spp.) that has previously induced environmental enteropathy in mouse models. To overcome the current limitations in imaging and allow definite determination of whether bacterial colonization of the SI mucosa is occurring, we optimized our previously developed whole-tissue three-dimensional (3D) imaging tools with third-generation hybridization chain reaction (HCR v3.0) probes. Only in mice that were malnourished and gavaged with the bacterial cocktail did we detect dense bacterial clusters surrounding intestinal villi suggestive of colonization. Healthy mice gavaged with bacteria and malnourished mice not gavaged with bacteria showed no evidence of mucosal colonization. Furthermore, in malnourished mice gavaged with bacteria we detected villus loss, which may represent one possible consequence that bacterial colonization of the SI mucosa has on the host.ConclusionsOur results suggest that dense bacterial colonization of jejunum mucosa is possible in the presence of multiple perturbations and that villus loss may be one possible consequence to such colonization. Furthermore, our results demonstrate the utility of whole-tissue 3D imaging tools. Although 2D imaging of thin sections may have failed to detect and capture the full spatial complexity of such rare events, whole-tissue 3D imaging tools enabled their detection over large areas of intestinal mucosa and visualization of their spatial complexity in 3D.", "doi": "10.1101/2022.06.17.496478", "publication_date": "2022-06-21" }, { "id": "authors:wkjh4-6nf06", "collection": "authors", "collection_id": "wkjh4-6nf06", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220307-188444000", "type": "monograph", "title": "Morning SARS-CoV-2 testing yields better detection of infection due to higher viral loads in saliva and nasal swabs upon waking", "author": [ { "family_name": "Winnett", "given_name": "Alexander Viloria", "orcid": "0000-0002-7338-5605", "clpid": "Winnett-Alexander-Viloria" }, { "family_name": "Porter", "given_name": "Michael K.", "orcid": "0000-0002-0777-7563", "clpid": "Porter-Michael-K" }, { "family_name": "Romano", "given_name": "Anna E.", "orcid": "0000-0003-1871-1727", "clpid": "Romano-Anna-E" }, { "family_name": "Savela", "given_name": "Emily S.", "orcid": "0000-0001-9614-4276", "clpid": "Savela-Emily-S" }, { "family_name": "Akana", "given_name": "Reid", "orcid": "0000-0003-4422-587X", "clpid": "Akana-Reid" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663", "clpid": "Shelby-Natasha" }, { "family_name": "Reyes", "given_name": "Jessica A.", "orcid": "0000-0002-5507-7633", "clpid": "Reyes-Jessica-A" }, { "family_name": "Schlenker", "given_name": "Noah W.", "orcid": "0000-0002-8581-4403", "clpid": "Schlenker-Noah-W" }, { "family_name": "Cooper", "given_name": "Matthew M.", "orcid": "0000-0002-5868-5159", "clpid": "Cooper-Matthew-M" }, { "family_name": "Carter", "given_name": "Alyssa M.", "orcid": "0000-0002-2776-9421", "clpid": "Carter-Alyssa-M" }, { "family_name": "Ji", "given_name": "Jenny", "orcid": "0000-0002-7901-5605", "clpid": "Ji-Jenny" }, { "family_name": "Barlow", "given_name": "Jacob T.", "orcid": "0000-0002-1842-4835", "clpid": "Barlow-Jacob-T" }, { "family_name": "Tognazzini", "given_name": "Colten", "orcid": "0000-0002-2754-3588", "clpid": "Tognazzini-Colten" }, { "family_name": "Feaster", "given_name": "Matthew", "orcid": "0000-0001-9966-2845", "clpid": "Feaster-Matthew" }, { "family_name": "Goh", "given_name": "Ying-Ying", "orcid": "0000-0001-5136-7214", "clpid": "Goh-Ying-Ying" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "Background. The analytical sensitivities of SARS-CoV-2 diagnostic tests span 6 orders of magnitude. Optimizing sample-collection methods to achieve the most reliable detection for a given sensitivity would increase the effectiveness of testing and minimize COVID-19 outbreaks. \n\nMethods. From September 2020 to April 2021 we performed a household-transmission study in which participants self-collected samples every morning and evening throughout acute SARS-CoV-2 infection. Seventy mildly symptomatic participants collected saliva and, of those, 29 also collected nasal-swab samples. Viral load was quantified in 1194 saliva and 661 nasal-swab samples using a high-analytical-sensitivity RT-qPCR assay (LOD, 1,000 SARS-CoV-2 RNA copies/mL).\n\nFindings. Viral loads in both saliva and nasal-swab samples were significantly higher in morning-collected samples than evening-collected samples after symptom onset. We used these quantitative measurements to infer which diagnostic tests would have detected infection (based on sample type and test analytical sensitivity). We find 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, which would likely have missed infections if sampling in the evening. \n\nInterpretation. Collecting samples 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. The phenomenon of higher viral loads in the morning may also have implications related to when transmission is more likely to occur. \n\nFunding. Bill & Melinda Gates Foundation, Ronald and Maxine Linde Center for New Initiatives (Caltech), Jacobs Institute for Molecular Engineering for Medicine (Caltech)\n\nRESEARCH IN CONTEXT. Evidence before this studyReliable COVID-19 diagnostic testing is critical to reducing transmission of SARS-CoV-2 and reducing cases of severe or fatal disease, particularly in areas with limited vaccine access or uptake. Saliva and anterior-nares nasal swabs are common sample types; however, different diagnostic tests using these sample types have a range of analytical sensitivities spanning 6 orders of magnitude, with limits of detection (LODs) between 102 and 108 genomic copy equivalents of SARS-CoV-2 RNA (copies) per mL of sample. Due to limitations in clinical laboratory capacity, many low-resource settings rely on COVID-19 tests that fall on the moderate (LODs of 104 to 105 copies/mL) to lower (LODs of 105 to 108 copies/mL) end of this spectrum of analytical sensitivity. Alterations in sample collection methods, including time of sample collection, may improve the performance of these diagnostics.Added value of this studyThis study quantifies viral loads from saliva and nasal-swab samples that were longitudinally self-collected by symptomatic patients in the morning immediately after waking and in the evening just prior to sleeping throughout the course of acute SARS-CoV-2 infection. The study cohort was composed of mildly or moderately symptomatic individuals (outpatients). This analysis demonstrates significantly higher viral loads in samples collected in the morning, relative to those collected in the evening. When using moderate to lower analytical sensitivity test methods, these loads are inferred to result in significantly better detection of infected individuals in the morning. \n\nImplications of available evidence. These findings suggest that samples collected in the morning immediately after waking will better detect SARS-CoV-2 infection in symptomatic individuals tested by moderate to lower analytical sensitivity COVID-19 diagnostic tests (LODs at or above 104 viral copies per mL of sample), such as many rapid antigen tests currently available.", "doi": "10.1101/2022.03.02.22271724", "publication_date": "2022-03-04" }, { "id": "authors:800n3-aga64", "collection": "authors", "collection_id": "800n3-aga64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211015-222210959", "type": "monograph", "title": "3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa", "author": [ { "family_name": "Mondrag\u00f3n-Palomino", "given_name": "Octavio", "orcid": "0000-0003-1129-4932", "clpid": "Mondrag\u00f3n-Palomino-Octavio" }, { "family_name": "Poceviciute", "given_name": "Roberta", "orcid": "0000-0002-6649-2170", "clpid": "Poceviciute-Roberta" }, { "family_name": "Lignell", "given_name": "Antti", "orcid": "0000-0001-7664-5583", "clpid": "Lignell-Antti" }, { "family_name": "Griffiths", "given_name": "Jessica A.", "orcid": "0000-0002-5586-1567", "clpid": "Griffiths-Jessica-A" }, { "family_name": "Takko", "given_name": "Heli", "orcid": "0000-0003-2544-409X", "clpid": "Takko-Heli" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "Improving our understanding of host-microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the 3D spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 days after recovery when overall bacterial loads returned to pre-antibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern was resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that bacterial taxa are distributed differently within crypts, with Lactobacilli laying closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.", "doi": "10.1101/2021.10.07.463215", "publication_date": "2021-10-09" }, { "id": "authors:ze84b-v1782", "collection": "authors", "collection_id": "ze84b-v1782", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201211-113537700", "type": "monograph", "title": "SARS-CoV-2 Viral Load in Saliva Rises Gradually and to Moderate Levels in Some Humans", "author": [ { "family_name": "Winnett", "given_name": "Alexander", "orcid": "0000-0002-7338-5605", "clpid": "Winnett-Alexander" }, { "family_name": "Cooper", "given_name": "Matthew M.", "orcid": "0000-0002-5868-5159", "clpid": "Cooper-Matthew-M" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663", "clpid": "Shelby-Natasha" }, { "family_name": "Romano", "given_name": "Anna E.", "orcid": "0000-0003-1871-1727", "clpid": "Romano-Anna-E" }, { "family_name": "Reyes", "given_name": "Jessica A.", "orcid": "0000-0002-5507-7633", "clpid": "Reyes-Jessica-A" }, { "family_name": "Ji", "given_name": "Jenny", "orcid": "0000-0002-7901-5605", "clpid": "Ji-Jenny" }, { "family_name": "Porter", "given_name": "Michael K.", "orcid": "0000-0002-0777-7563", "clpid": "Porter-Michael-K" }, { "family_name": "Savela", "given_name": "Emily S.", "orcid": "0000-0001-9614-4276", "clpid": "Savela-Emily-S" }, { "family_name": "Barlow", "given_name": "Jacob T.", "orcid": "0000-0002-1842-4835", "clpid": "Barlow-Jacob-T" }, { "family_name": "Akana", "given_name": "Reid", "orcid": "0000-0003-4422-587X", "clpid": "Akana-Reid" }, { "family_name": "Tognazzini", "given_name": "Colten", "orcid": "0000-0002-2754-3588", "clpid": "Tognazzini-Colten" }, { "family_name": "Feaster", "given_name": "Matthew", "orcid": "0000-0001-9966-2845", "clpid": "Feaster-Matthew" }, { "family_name": "Goh", "given_name": "Ying-Ying", "orcid": "0000-0001-5136-7214", "clpid": "Goh-Ying-Ying" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "Transmission of SARS-CoV-2 in community settings often occurs before symptom onset, therefore testing strategies that can reliably detect people in the early phase of infection are urgently needed. Early detection of SARS-CoV-2 infection is especially critical to protect vulnerable populations who require frequent interactions with caretakers. Rapid COVID-19 tests have been proposed as an attractive strategy for surveillance, however a limitation of most rapid tests is their low sensitivity. Low-sensitivity tests are comparable to high sensitivity tests in detecting early infections when two assumptions are met: (1) viral load rises quickly (within hours) after infection and (2) viral load reaches and sustains high levels (>10\u2075 - 10\u2076 RNA copies/mL). However, there are no human data testing these assumptions. In this study, we document a case of presymptomatic household transmission from a healthy college student to his brother and father. Participants prospectively provided twice-daily saliva samples. Samples were analyzed by RT-qPCR and RT-ddPCR and we measured the complete viral load profiles throughout the course of infection of the brother and father. This study provides evidence that in at least some human cases of SARS-CoV-2, viral load rises slowly (over days, not hours) and not to such high levels to be detectable reliably by any low-sensitivity test. Additional viral load profiles from different samples types across a broad demographic must be obtained to describe the early phase of infection and determine which testing strategies will be most effective for identifying SARS-CoV-2 infection before transmission can occur.", "doi": "10.1101/2020.12.09.20239467", "pmcid": "PMC7743094", "publication_date": "2020-12-11" }, { "id": "authors:msp7x-hgx37", "collection": "authors", "collection_id": "msp7x-hgx37", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200519-071416134", "type": "monograph", "title": "Commercial stocks of SARS-CoV-2 RNA may report low concentration values, leading to artificially increased apparent sensitivity of diagnostic assays", "author": [ { "family_name": "Jue", "given_name": "Erik", "orcid": "0000-0001-7585-3794", "clpid": "Jue-Erik" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "In response to the rapidly evolving COVID-19 pandemic, the U.S. Food and Drug Administration (FDA) has rapidly issued 49 emergency use authorizations (EUAs) for SARS-CoV-2 in vitro diagnostic test-kits. A critical metric in the performance evaluation for a diagnostic test kit is the analytical sensitivity, which is measured by the limit of detection (LOD). Commercial RNA stocks with known titers are used to determine LOD. We identified a problem with the titer reported for the commercial stocks when examining the analytical sensitivity of the reverse transcription quantitative PCR (RT-qPCR) protocol that is recommended by the Centers for Disease Control and Prevention (CDC) using plasmid DNA from Integrated DNA Technologies (IDT), synthetic RNA from BEI Resources (BEI), and extracted genomic RNA from BEI. We detected 3/3 positives for reactions containing synthetic RNA at a concentration of 0.1 copies/reaction (based on the supplier's label concentration). The apparent better-than-single-molecule performance is a statistically highly unlikely event, indicating a potential inaccuracy in the supplier's quantification of the stock material. Using an ultrasensitive and precise assay, reverse transcription digital PCR (RT-dPCR), we independently quantified concentrations of commercial SARS-CoV-2 plasmid DNA and SARS-CoV-2 RNA stocks. For plasmid DNA, the actual concentration measured by RT-dPCR was 11% of the nominal label concentration. For synthetic RNA, the actual concentration measured by RT-dPCR for one lot was 770% of the label concentration and for a different lot was 57% of the label concentration. For genomic RNA, the concentration measured by RT-dPCR for one lot was 240% of the label concentration and for a different lot it was 300% of the label concentration. This SARS-CoV-2 genomic RNA from BEI Resources has been used in at least 11 approved FDA Emergency Use Authorizations as of April 27, 2020. Such deviations of reported RNA or DNA stock concentrations from true concentrations can result in inaccurate quantification and calculation of LOD. Precise and accurate reporting of DNA and RNA stock concentrations by commercial suppliers will enable accurate quantification of assay performance, which is urgently needed to improve evaluation of different assays by diagnostic developers and regulatory bodies.", "doi": "10.1101/2020.04.28.20077602", "publication_date": "2020-05-04" }, { "id": "authors:25pjj-0yh40", "collection": "authors", "collection_id": "25pjj-0yh40", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200303-084602692", "type": "monograph", "title": "Metabolic multi-stability and hysteresis in a model aerobe-anaerobe microbiome community", "author": [ { "family_name": "Khazaei", "given_name": "Tahmineh", "orcid": "0000-0002-4743-2383", "clpid": "Khazaei-T" }, { "family_name": "Williams", "given_name": "Rory L.", "orcid": "0000-0003-2605-5790", "clpid": "Williams-Rory-L" }, { "family_name": "Bogatyrev", "given_name": "Said R.", "orcid": "0000-0003-0486-9451", "clpid": "Bogatyrev-S-R" }, { "family_name": "Doyle", "given_name": "John C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Henry", "given_name": "Christopher S.", "orcid": "0000-0001-8058-9123", "clpid": "Henry-C-S" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "Changes in the composition of the human microbiome are associated with health and disease. Some microbiome states persist in seemingly unfavorable conditions, e.g., the proliferation of aerobe-anaerobe communities in oxygen-exposed environments in wounds or small intestinal bacterial overgrowth. However, it remains unclear how different stable microbiome states can exist under the same conditions, or why some states persist under seemingly unfavorable conditions. Here, using two microbes relevant to the human microbiome, we combine genome-scale mathematical modeling, bioreactor experiments, transcriptomics, and dynamical systems theory, to show that multi-stability and hysteresis (MSH) is a mechanism that can describe the shift from an aerobe-dominated state to a resilient, paradoxically persistent aerobe-anaerobe state. We examine the impact of changing oxygen and nutrient regimes and identify factors, including changes in metabolism and gene expression, that lead to MSH. When analyzing the transitions between the two states in this system, the familiar conceptual connection between causation and correlation is broken and MSH must be used to interpret the dynamics. Using MSH to analyze microbiome dynamics will improve our conceptual understanding of the stability of microbiome states and the transitions among microbiome states.", "doi": "10.1101/2020.02.28.968941", "publication_date": "2020-02-29" }, { "id": "authors:d9gp6-r3c07", "collection": "authors", "collection_id": "d9gp6-r3c07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200123-094353991", "type": "monograph", "title": "Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding", "author": [ { "family_name": "Bogatyrev", "given_name": "Said R.", "orcid": "0000-0003-0486-9451", "clpid": "Bogatyrev-S-R" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "Current methods for detecting, accurately quantifying, and profiling complex microbial communities based on the microbial 16S rRNA marker genes are limited by a number of factors, including inconsistent extraction of microbial nucleic acids, amplification interference from contaminants and host DNA, different coverage of PCR primers utilized for quantification and sequencing, and potentially biases in PCR amplification rates among microbial taxa during amplicon barcoding. Here, we describe a single-step method that enables the quantification of microbial 16S rRNA gene DNA copies with wide dynamic range and broad microbial diversity, and simultaneous amplicon barcoding for quantitative 16S rRNA gene amplicon profiling of microbiota. The method is suitable for a variety of sample types and is robust in samples with low microbial abundance, including samples containing high levels of host mammalian DNA, as is common in human clinical samples. We demonstrate that our modification to the Earth Microbiome Project (EMP) V4 16S rRNA gene primers expands their microbial coverage while dramatically reducing non-specific mammalian mitochondrial DNA amplification, thus achieving wide dynamic range in microbial quantification and broad coverage for capturing high microbial diversity in samples with or without high host DNA background. The approach relies only on broadly available hardware (real-time PCR instruments) and standard reagents utilized for conventional 16S rRNA gene amplicon library preparation both of which make it amenable for immediate and widespread adoption. Simultaneous 16S rRNA gene DNA copy quantification and amplicon barcoding for multiplexed next-generation sequencing from the same analyzed sample, performed in a combined workflow, reduces the amount of sample needed and reduces time and reagent costs. Additionally, we demonstrate that using our modified 16S rRNA gene primers in a digital PCR (dPCR) format enables precise and exact microbial quantification in samples with very high host DNA background levels without the need for quantification standards. Potential future applications of this approach include: (1) quantitative microbiome profiling in human and animal microbiome research; (2) detection of monoinfections and profiling of polymicrobial infections in tissues, stool, and bodily fluids in human and veterinary medicine; (3) environmental sample analyses (e.g., soil and water); and (4) broad-coverage detection of microbial food contamination in products high in mammalian DNA, such as meat products. We predict that utilization of this approach primarily for quantitative microbiome profiling will be invaluable to microbiome studies, which have historically been limited to analysis of relative abundances of microbes.", "doi": "10.1101/2020.01.22.914705", "publication_date": "2020-01-22" } ]