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Takahashi S, Peluso MJ, Hakim J, Turcios K, Janson O, Routledge I, Busch MP, Hoh R, Tai V, Kelly JD, Martin JN, Deeks SG, Henrich TJ, Greenhouse B, Rodríguez-Barraquer I. SARS-CoV-2 Serology Across Scales: A Framework for Unbiased Estimation of Cumulative Incidence Incorporating Antibody Kinetics and Epidemic Recency. Am J Epidemiol 2023; 192:1562-1575. [PMID: 37119030 PMCID: PMC10472487 DOI: 10.1093/aje/kwad106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/29/2022] [Accepted: 04/24/2023] [Indexed: 04/30/2023] Open
Abstract
Serosurveys are a key resource for measuring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) population exposure. A growing body of evidence suggests that asymptomatic and mild infections (together making up over 95% of all infections) are associated with lower antibody titers than severe infections. Antibody levels also peak a few weeks after infection and decay gradually. We developed a statistical approach to produce estimates of cumulative incidence from raw seroprevalence survey results that account for these sources of spectrum bias. We incorporate data on antibody responses on multiple assays from a postinfection longitudinal cohort, along with epidemic time series to account for the timing of a serosurvey relative to how recently individuals may have been infected. We applied this method to produce estimates of cumulative incidence from 5 large-scale SARS-CoV-2 serosurveys across different settings and study designs. We identified substantial differences between raw seroprevalence and cumulative incidence of over 2-fold in the results of some surveys, and we provide a tool for practitioners to generate cumulative incidence estimates with preset or custom parameter values. While unprecedented efforts have been launched to generate SARS-CoV-2 seroprevalence estimates over this past year, interpretation of results from these studies requires properly accounting for both population-level epidemiologic context and individual-level immune dynamics.
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Affiliation(s)
- Saki Takahashi
- Correspondence to Dr. Saki Takahashi, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 (e-mail: )
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2
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Routledge I, Takahashi S, Epstein A, Hakim J, Janson O, Turcios K, Vinden J, Risos JT, Baniqued MR, Pham L, Di Germanio C, Busch M, Kushel M, Greenhouse B, Rodríguez-Barraquer I. Using sero-epidemiology to monitor disparities in vaccination and infection with SARS-CoV-2. Nat Commun 2022; 13:2451. [PMID: 35508478 PMCID: PMC9068757 DOI: 10.1038/s41467-022-30051-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/07/2022] [Indexed: 01/02/2023] Open
Abstract
As SARS-CoV-2 continues to spread and vaccines are rolled-out, the "double burden" of disparities in exposure and vaccination intersect to determine patterns of infection, immunity, and mortality. Serology provides a unique opportunity to measure prior infection and vaccination simultaneously. Leveraging algorithmically-selected residual sera from two hospital networks in the city of San Francisco, cross-sectional samples from 1,014 individuals from February 4-17, 2021 were each tested on two assays (Ortho Clinical Diagnostics VITROS Anti-SARS-CoV-2 and Roche Elecsys Anti-SARS-CoV-2), capturing the first year of the epidemic and early roll-out of vaccination. We estimated, using Bayesian estimation of infection and vaccination, that infection risk of Hispanic/Latinx residents was five times greater than of White residents aged 18-64 (95% Credible Interval (CrI): 3.2-10.3), and that White residents over 65 were twice as likely to be vaccinated as Black/African American residents (95% CrI: 1.1-4.6). We found that socioeconomically-deprived zipcodes had higher infection probabilities and lower vaccination coverage than wealthier zipcodes. While vaccination has created a 'light at the end of the tunnel' for this pandemic, ongoing challenges in achieving and maintaining equity must also be considered.
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Affiliation(s)
- Isobel Routledge
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Saki Takahashi
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Adrienne Epstein
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jill Hakim
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Owen Janson
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Keirstinne Turcios
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jo Vinden
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Infectious Disease and Immunity Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - John Tomas Risos
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Rose Baniqued
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lori Pham
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Michael Busch
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Margot Kushel
- Center for Vulnerable Populations, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, San Francisco, CA, USA
| | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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3
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Routledge I, Takahashi S, Epstein A, Hakim J, Janson O, Turcios K, Vinden J, Risos JT, Baniqued MR, Pham L, Di Germanio C, Busch M, Kushel M, Greenhouse B, Rodríguez-Barraquer I. Using sero-epidemiology to monitor disparities in vaccination and infection with SARS-CoV-2. medRxiv 2021:2021.10.06.21264573. [PMID: 34642695 PMCID: PMC8509086 DOI: 10.1101/2021.10.06.21264573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND As COVID-19 vaccines continue to be rolled-out, the "double burden" of health disparities in both exposure to infection and vaccination coverage intersect to determine the current and future patterns of infection, immunity, and mortality. Serology provides a unique opportunity to measure biomarkers of infection and vaccination simultaneously, and to relate these metrics to demographic and geographic factors. METHODS Leveraging algorithmically selected residual serum samples from two hospital networks in San Francisco, we sampled 1014 individuals during February 2021, capturing transmission during the first 11 months of the epidemic and the early roll out of vaccination. These samples were tested using two serologic assays: one detecting antibodies elicited by infection, and not by vaccines, and one detecting antibodies elicited by both infection and vaccination. We used Bayesian statistical models to estimate the proportion of the population that was naturally infected and the proportion protected due to vaccination. FINDINGS We estimated that the risk of prior infection of Latinx residents was 5.3 (95% CI: 3.2 - 10.3) times greater than the risk of white residents aged 18-64 and that white San Francisco residents over the age of 65 were twice as likely (2.0, 95% CI: 1.1 - 4.6) to be vaccinated as Black residents. We also found socioeconomically deprived zipcodes in the city had high probabilities of natural infections and lower vaccination coverage than wealthier zipcodes. INTERPRETATION Using a platform we created for SARS-CoV-2 serologic data collection in San Francisco, we characterized and quantified the stark disparities in infection rates and vaccine coverage by demographic groups over the first year of the pandemic. While the arrival of the SARS-CoV-2 vaccine has created a 'light at the end of the tunnel' for this pandemic, ongoing challenges in achieving and maintaining equity must also be considered. FUNDING NIH, NIGMS, Schmidt Science Fellows in partnership with the Rhodes Trust and the Chan Zuckerberg Biohub.
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Affiliation(s)
- Isobel Routledge
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Saki Takahashi
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Adrienne Epstein
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jill Hakim
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Owen Janson
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Keirstinne Turcios
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jo Vinden
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
- Infectious Disease and Immunity Graduate Group, University of California Berkeley, Berkeley, California, USA
| | - John Tomas Risos
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Margaret Rose Baniqued
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Lori Pham
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | | | - Michael Busch
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
- Vitalant Research Institute, San Francisco, California, USA
| | - Margot Kushel
- Center for Vulnerable Populations, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, San Francisco, California, USA
| | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
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4
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Takahashi S, Peluso MJ, Hakim J, Turcios K, Janson O, Routledge I, Busch MP, Hoh R, Tai V, Kelly JD, Martin JN, Deeks SG, Henrich TJ, Greenhouse B, Rodríguez-Barraquer I. SARS-CoV-2 serology across scales: a framework for unbiased seroprevalence estimation incorporating antibody kinetics and epidemic recency. medRxiv 2021:2021.09.09.21263139. [PMID: 34545373 PMCID: PMC8452112 DOI: 10.1101/2021.09.09.21263139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Serosurveys are a key resource for measuring SARS-CoV-2 cumulative incidence. A growing body of evidence suggests that asymptomatic and mild infections (together making up over 95% of all infections) are associated with lower antibody titers than severe infections. Antibody levels also peak a few weeks after infection and decay gradually. We developed a statistical approach to produce adjusted estimates of seroprevalence from raw serosurvey results that account for these sources of spectrum bias. We incorporate data on antibody responses on multiple assays from a post-infection longitudinal cohort, along with epidemic time series to account for the timing of a serosurvey relative to how recently individuals may have been infected. We applied this method to produce adjusted seroprevalence estimates from five large-scale SARS-CoV-2 serosurveys across different settings and study designs. We identify substantial differences between reported and adjusted estimates of over two-fold in the results of some surveys, and provide a tool for practitioners to generate adjusted estimates with pre-set or custom parameter values. While unprecedented efforts have been launched to generate SARS-CoV-2 seroprevalence estimates over this past year, interpretation of results from these studies requires properly accounting for both population-level epidemiologic context and individual-level immune dynamics.
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Affiliation(s)
- Saki Takahashi
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
| | - Michael J. Peluso
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
| | - Jill Hakim
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
| | - Keirstinne Turcios
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
| | - Owen Janson
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
| | - Isobel Routledge
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
| | - Michael P. Busch
- Department of Laboratory Medicine, University of California, San Francisco, USA
- Vitalant Research Institute, San Francisco, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
| | - Viva Tai
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
- Institute for Global Health Sciences, University of California, San Francisco, USA
- F.I. Proctor Foundation, University of California, San Francisco, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, USA
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Peluso MJ, Deitchman AN, Torres L, Iyer NS, Munter SE, Nixon CC, Donatelli J, Thanh C, Takahashi S, Hakim J, Turcios K, Janson O, Hoh R, Tai V, Hernandez Y, Fehrman EA, Spinelli MA, Gandhi M, Trinh L, Wrin T, Petropoulos CJ, Aweeka FT, Rodriguez-Barraquer I, Kelly JD, Martin JN, Deeks SG, Greenhouse B, Rutishauser RL, Henrich TJ. Long-term SARS-CoV-2-specific immune and inflammatory responses in individuals recovering from COVID-19 with and without post-acute symptoms. Cell Rep 2021; 36:109518. [PMID: 34358460 PMCID: PMC8342976 DOI: 10.1016/j.celrep.2021.109518] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/14/2021] [Accepted: 07/21/2021] [Indexed: 12/26/2022] Open
Abstract
We describe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell responses, soluble markers of inflammation, and antibody levels and neutralization capacity longitudinally in 70 individuals with PCR-confirmed SARS-CoV-2 infection. Participants represent a spectrum of illness and recovery, including some with persistent viral shedding in saliva and many experiencing post-acute sequelae of SARS-CoV-2 infection (PASC). T cell responses remain stable for up to 9 months. Whereas the magnitude of early CD4+ T cell immune responses correlates with severity of initial infection, pre-existing lung disease is independently associated with higher long-term SARS-CoV-2-specific CD8+ T cell responses. Among participants with PASC 4 months following coronavirus disease 2019 (COVID-19) symptom onset, we observe a lower frequency of CD8+ T cells expressing CD107a, a marker of degranulation, in response to Nucleocapsid (N) peptide pool stimulation, and a more rapid decline in the frequency of N-specific interferon-γ-producing CD8+ T cells. Neutralizing antibody levels strongly correlate with SARS-CoV-2-specific CD4+ T cell responses.
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Affiliation(s)
- Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amelia N Deitchman
- Department of Clinical Pharmacy, University of California, San Francisco, CA, USA
| | - Leonel Torres
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nikita S Iyer
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher C Nixon
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Donatelli
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cassandra Thanh
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Saki Takahashi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jill Hakim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Keirstinne Turcios
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Owen Janson
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Viva Tai
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yanel Hernandez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Emily A Fehrman
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew A Spinelli
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lan Trinh
- Monogram Biosciences, Inc., South San Francisco, CA, USA
| | - Terri Wrin
- Monogram Biosciences, Inc., South San Francisco, CA, USA
| | | | - Francesca T Aweeka
- Department of Clinical Pharmacy, University of California, San Francisco, CA, USA
| | - Isabel Rodriguez-Barraquer
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
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6
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Elledge SK, Zhou XX, Byrnes JR, Martinko AJ, Lui I, Pance K, Lim SA, Glasgow JE, Glasgow AA, Turcios K, Iyer NS, Torres L, Peluso MJ, Henrich TJ, Wang TT, Tato CM, Leung KK, Greenhouse B, Wells JA. Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection. Nat Biotechnol 2021. [PMID: 33767397 DOI: 10.1038/s41587-41021-00878-41588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Current serology tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies mainly take the form of enzyme-linked immunosorbent assays, chemiluminescent microparticle immunoassays or lateral flow assays, which are either laborious, expensive or lacking sufficient sensitivity and scalability. Here we present the development and validation of a rapid, low-cost, solution-based assay to detect antibodies in serum, plasma, whole blood and to a lesser extent saliva, using rationally designed split luciferase antibody biosensors. This new assay, which generates quantitative results in 30 min, substantially reduces the complexity and improves the scalability of coronavirus disease 2019 (COVID-19) antibody tests. This assay is well-suited for point-of-care, broad population testing, and applications in low-resource settings, for monitoring host humoral responses to vaccination or viral infection.
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Affiliation(s)
- Susanna K Elledge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | | | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Katarina Pance
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Shion A Lim
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Jeff E Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Anum A Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Keirstinne Turcios
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
| | - Nikita S Iyer
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
| | - Leonel Torres
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
| | - Taia T Wang
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Departments of Medicine and of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Bryan Greenhouse
- Division of Experimental Medicine, University of California, San Francisco, San Francisco CA, USA
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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7
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Peluso MJ, Takahashi S, Hakim J, Kelly JD, Torres L, Iyer NS, Turcios K, Janson O, Munter SE, Thanh C, Donatelli J, Nixon CC, Hoh R, Tai V, Fehrman EA, Hernandez Y, Spinelli MA, Gandhi M, Palafox MA, Vallari A, Rodgers MA, Prostko J, Hackett J, Trinh L, Wrin T, Petropoulos CJ, Chiu CY, Norris PJ, DiGermanio C, Stone M, Busch MP, Elledge SK, Zhou XX, Wells JA, Shu A, Kurtz TW, Pak JE, Wu W, Burbelo PD, Cohen JI, Rutishauser RL, Martin JN, Deeks SG, Henrich TJ, Rodriguez-Barraquer I, Greenhouse B. SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay. Sci Adv 2021; 7:eabh3409. [PMID: 34330709 PMCID: PMC8324059 DOI: 10.1126/sciadv.abh3409] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/16/2021] [Indexed: 05/02/2023]
Abstract
Interpretation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serosurveillance studies is limited by poorly defined performance of antibody assays over time in individuals with different clinical presentations. We measured antibody responses in plasma samples from 128 individuals over 160 days using 14 assays. We found a consistent and strong effect of disease severity on antibody magnitude, driven by fever, cough, hospitalization, and oxygen requirement. Responses to spike protein versus nucleocapsid had consistently higher correlation with neutralization. Assays varied substantially in sensitivity during early convalescence and time to seroreversion. Variability was dramatic for individuals with mild infection, who had consistently lower antibody titers, with sensitivities at 6 months ranging from 33 to 98% for commercial assays. Thus, the ability to detect previous infection by SARS-CoV-2 is highly dependent on infection severity, timing, and the assay used. These findings have important implications for the design and interpretation of SARS-CoV-2 serosurveillance studies.
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Affiliation(s)
- Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Saki Takahashi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jill Hakim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Leonel Torres
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nikita S Iyer
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Keirstinne Turcios
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Owen Janson
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cassandra Thanh
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Donatelli
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher C Nixon
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Viva Tai
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Emily A Fehrman
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yanel Hernandez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew A Spinelli
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | - Lan Trinh
- Monogram Biosciences Inc., South San Francisco, CA, USA
| | - Terri Wrin
- Monogram Biosciences Inc., South San Francisco, CA, USA
| | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | | | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
| | - Michael P Busch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Susanna K Elledge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Albert Shu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Theodore W Kurtz
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rachel L Rutishauser
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Isabel Rodriguez-Barraquer
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
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8
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Peluso MJ, Takahashi S, Hakim J, Kelly JD, Torres L, Iyer NS, Turcios K, Janson O, Munter SE, Thanh C, Nixon CC, Hoh R, Tai V, Fehrman EA, Hernandez Y, Spinelli MA, Gandhi M, Palafox MA, Vallari A, Rodgers MA, Prostko J, Hackett J, Trinh L, Wrin T, Petroplolous CJ, Chiu CY, Norris PJ, DiGermanio C, Stone M, Busch MP, Elledge SK, Zhou XX, Wells JA, Shu A, Kurtz TW, Pak JE, Wu W, Burbelo PD, Cohen JI, Rutishauser RL, Martin JN, Deeks SG, Henrich TJ, Rodriguez-Barraquer I, Greenhouse B. SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay. medRxiv 2021:2021.03.03.21251639. [PMID: 33688675 PMCID: PMC7941652 DOI: 10.1101/2021.03.03.21251639] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Serosurveillance studies are critical for estimating SARS-CoV-2 transmission and immunity, but interpretation of results is currently limited by poorly defined variability in the performance of antibody assays to detect seroreactivity over time in individuals with different clinical presentations. We measured longitudinal antibody responses to SARS-CoV-2 in plasma samples from a diverse cohort of 128 individuals over 160 days using 14 binding and neutralization assays. For all assays, we found a consistent and strong effect of disease severity on antibody magnitude, with fever, cough, hospitalization, and oxygen requirement explaining much of this variation. We found that binding assays measuring responses to spike protein had consistently higher correlation with neutralization than those measuring responses to nucleocapsid, regardless of assay format and sample timing. However, assays varied substantially with respect to sensitivity during early convalescence and in time to seroreversion. Variations in sensitivity and durability were particularly dramatic for individuals with mild infection, who had consistently lower antibody titers and represent the majority of the infected population, with sensitivities often differing substantially from reported test characteristics (e.g., amongst commercial assays, sensitivity at 6 months ranged from 33% for ARCHITECT IgG to 98% for VITROS Total Ig). Thus, the ability to detect previous infection by SARS-CoV-2 is highly dependent on the severity of the initial infection, timing relative to infection, and the assay used. These findings have important implications for the design and interpretation of SARS-CoV-2 serosurveillance studies.
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Affiliation(s)
- Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Saki Takahashi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Jill Hakim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Leonel Torres
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Nikita S Iyer
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Keirstinne Turcios
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Owen Janson
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Cassandra Thanh
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Christopher C Nixon
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Viva Tai
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Emily A Fehrman
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Yanel Hernandez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Matthew A Spinelli
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | | | | | | | | | | | - Lan Trinh
- Monogram Biosciences, Inc., South San Francisco, CA, USA
| | - Terri Wrin
- Monogram Biosciences, Inc., South San Francisco, CA, USA
| | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, USA
- Division of Infectious Diseases, University of California, San Francisco, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, USA
| | | | | | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
| | - Michael P Busch
- Department of Laboratory Medicine, University of California, San Francisco, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Susanna K Elledge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
| | - Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, USA
| | - Albert Shu
- Department of Laboratory Medicine, University of California, San Francisco, USA
| | - Theodore W Kurtz
- Department of Laboratory Medicine, University of California, San Francisco, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, USA
| | - Peter D Burbelo
- National Institute of Dental Research, National Institutes of Health, Bethesda, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, USA
| | | | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
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9
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Peluso MJ, Deitchman AN, Torres L, Iyer NS, Nixon CC, Munter SE, Donatelli J, Thanh C, Takahashi S, Hakim J, Turcios K, Janson O, Hoh R, Tai V, Hernandez Y, Fehrman E, Spinelli MA, Gandhi M, Trinh L, Wrin T, Petropoulos CJ, Aweeka FT, Rodriguez-Barraquer I, Kelly JD, Martin JN, Deeks SG, Greenhouse B, Rutishauser RL, Henrich TJ. Long-Term SARS-CoV-2-Specific Immune and Inflammatory Responses Across a Clinically Diverse Cohort of Individuals Recovering from COVID-19. medRxiv 2021. [PMID: 33688685 PMCID: PMC7941662 DOI: 10.1101/2021.02.26.21252308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A detailed understanding of long-term SARS-CoV-2-specific T cell responses and their relationship to humoral immunity and markers of inflammation in diverse groups of individuals representing the spectrum of COVID-19 illness and recovery is urgently needed. Data are also lacking as to whether and how adaptive immune and inflammatory responses differ in individuals that experience persistent symptomatic sequelae months following acute infection compared to those with complete, rapid recovery. We measured SARS-CoV-2-specific T cell responses, soluble markers of inflammation, and antibody levels and neutralization capacity longitudinally up to 9 months following infection in a diverse group of 70 individuals with PCR-confirmed SARS-CoV-2 infection. The participants had varying degrees of initial disease severity and were enrolled in the northern California Long-term Impact of Infection with Novel Coronavirus (LIINC) cohort. Adaptive T cell responses remained remarkably stable in all participants across disease severity during the entire study interval. Whereas the magnitude of the early CD4+ T cell immune response is determined by the severity of initial infection (participants requiring hospitalization or intensive care), pre-existing lung disease was significantly associated with higher long-term SARS-CoV2-specific CD8+ T cell responses, independent of initial disease severity or age. Neutralizing antibody levels were strongly correlated with SARS-CoV-2-specific CD4+ T but not CD8+ T cell responses. Importantly, we did not identify substantial differences in long-term virus-specific T cell or antibody responses between participants with and without COVID-19-related symptoms that persist months after initial infection.
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Affiliation(s)
- Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Amelia N Deitchman
- Department of Clinical Pharmacy, University of California, San Francisco, USA
| | - Leonel Torres
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA.,Division of Experimental Medicine, University of California, San Francisco, USA
| | - Nikita S Iyer
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Christopher C Nixon
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Joanna Donatelli
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Cassandra Thanh
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Saki Takahashi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Jill Hakim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Keirstinne Turcios
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Owen Janson
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Viva Tai
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Yanel Hernandez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Emily Fehrman
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Matthew A Spinelli
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Lan Trinh
- Monogram Biosciences, Inc., South San Francisco, USA
| | - Terri Wrin
- Monogram Biosciences, Inc., South San Francisco, USA
| | | | - Francesca T Aweeka
- Department of Clinical Pharmacy, University of California, San Francisco, USA
| | - Isabel Rodriguez-Barraquer
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA.,Division of Experimental Medicine, University of California, San Francisco, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA.,Division of Experimental Medicine, University of California, San Francisco, USA
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10
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Routledge I, Epstein A, Takahashi S, Janson O, Hakim J, Duarte E, Turcios K, Vinden J, Sujishi K, Rangel J, Coh M, Besana L, Ho WK, Oon CY, Ong CM, Yun C, Lynch K, Wu AHB, Wu W, Karlon W, Thornborrow E, Peluso MJ, Henrich TJ, Pak JE, Briggs J, Greenhouse B, Rodriguez-Barraquer I. Citywide serosurveillance of the initial SARS-CoV-2 outbreak in San Francisco. Res Sq 2021:rs.3.rs-180966. [PMID: 33564754 PMCID: PMC7872360 DOI: 10.21203/rs.3.rs-180966/v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Serosurveillance provides a unique opportunity to quantify the proportion of the population that has been exposed to pathogens. Here, we developed and piloted Serosurveillance for Continuous, ActionabLe Epidemiologic Intelligence of Transmission (SCALE-IT), a platform through which we systematically tested remnant samples from routine blood draws in two major hospital networks in San Francisco for SARS-CoV-2 antibodies during the early months of the pandemic. Importantly, SCALE-IT allows for algorithmic sample selection and rich data on covariates by leveraging electronic medical record data. We estimated overall seroprevalence at 4.2%, corresponding to a case ascertainment rate of only 4.9%, and identified important heterogeneities by neighborhood, homelessness status, and race/ethnicity. Neighborhood seroprevalence estimates from SCALE-IT were comparable to local community-based surveys, while providing results encompassing the entire city that have been previously unavailable. Leveraging this hybrid serosurveillance approach has strong potential for application beyond this local context and for diseases other than SARS-CoV-2.
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11
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Appa A, Takahashi S, Rodriguez-Barraquer I, Chamie G, Sawyer A, Duarte E, Hakim J, Turcios K, Vinden J, Janson O, Manglik A, Peluso MJ, Deeks SG, Henrich TJ, Torres L, Rodgers M, Hackett J, Chiu C, Havlir D, Greenhouse B. Universal Polymerase Chain Reaction and Antibody Testing Demonstrate Little to No Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in a Rural Community. Open Forum Infect Dis 2021; 8:ofaa531. [PMID: 34109255 PMCID: PMC7665736 DOI: 10.1093/ofid/ofaa531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/27/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Limited systematic surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the early months of the US epidemic curtailed accurate appraisal of transmission intensity. Our objective was to perform case detection of an entire rural community to quantify SARS-CoV-2 transmission using polymerase chain reaction (PCR) and antibody testing. METHODS We conducted a cross-sectional survey of SARS-CoV-2 infection in the rural town of Bolinas, California (population 1620), 4 weeks after shelter-in-place orders. Participants were tested between April 20 and 24, 2020. Prevalence by PCR and seroprevalence from 2 forms of antibody testing were performed in parallel (Abbott ARCHITECT immunoglobulin [Ig]G and in-house IgG enzyme-linked immunosorbent assay). RESULTS Of 1891 participants, 1312 were confirmed Bolinas residents (>80% community ascertainment). Zero participants were PCR positive. Assuming 80% sensitivity, it would have been unlikely to observe these results (P < .05) if there were >3 active infections in the community. Based on antibody results, estimated prevalence of prior infection was 0.16% (95% credible interval [CrI], 0.02%-0.46%). The positive predictive value (PPV) of a positive result on both tests was 99.11% (95% CrI, 95.75%-99.94%), compared with PPV 44.19%-63.32% (95% CrI, 3.25%-98.64%) if 1 test was utilized. CONCLUSIONS Four weeks after shelter-in-place, SARS-CoV-2 infection in a rural Northern California community was extremely rare. In this low-prevalence setting, use of 2 antibody tests increased seroprevalence estimate precision. This was one of the first community-wide studies to successfully implement synchronous PCR and antibody testing, particularly in a rural setting. Widespread testing remains an underpinning of effective disease control in conjunction with consistent uptake of public health measures.
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Affiliation(s)
- Ayesha Appa
- University of California San Francisco, San Francisco, California, USA
| | - Saki Takahashi
- University of California San Francisco, San Francisco, California, USA
| | | | - Gabriel Chamie
- University of California San Francisco, San Francisco, California, USA
| | - Aenor Sawyer
- University of California San Francisco, San Francisco, California, USA
| | - Elias Duarte
- University of California San Francisco, San Francisco, California, USA
| | - Jill Hakim
- University of California San Francisco, San Francisco, California, USA
| | | | - Joanna Vinden
- University of California Berkeley, Berkeley, California, USA
| | - Owen Janson
- University of California San Francisco, San Francisco, California, USA
| | - Aashish Manglik
- University of California San Francisco, San Francisco, California, USA
| | - Michael J Peluso
- University of California San Francisco, San Francisco, California, USA
| | - Steven G Deeks
- University of California San Francisco, San Francisco, California, USA
| | - Timothy J Henrich
- University of California San Francisco, San Francisco, California, USA
| | - Leonel Torres
- University of California San Francisco, San Francisco, California, USA
| | | | | | - Charles Chiu
- University of California San Francisco, San Francisco, California, USA
| | - Diane Havlir
- University of California San Francisco, San Francisco, California, USA
| | - Bryan Greenhouse
- University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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12
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Elledge SK, Zhou XX, Byrnes JR, Martinko AJ, Lui I, Pance K, Lim SA, Glasgow JE, Glasgow AA, Turcios K, Iyer N, Torres L, Peluso MJ, Henrich TJ, Wang TT, Tato CM, Leung KK, Greenhouse B, Wells JA. Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection. medRxiv 2020:2020.08.17.20176925. [PMID: 32839788 PMCID: PMC7444307 DOI: 10.1101/2020.08.17.20176925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Current serology tests for SARS-CoV-2 antibodies mainly take the form of enzyme-linked immunosorbent assays or lateral flow assays, with the former being laborious and the latter being expensive and often lacking sufficient sensitivity and scalability. Here we present the development and validation of a rapid, low-cost solution-based assay to detect antibodies in serum, plasma, whole blood, and saliva, using rationally designed split luciferase antibody biosensors (spLUC). This new assay, which generates quantitative results in as short as 5 minutes, substantially reduces the complexity and improves the scalability of COVID-19 antibody tests for point-of-care and broad population testing.
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Affiliation(s)
- Susanna K. Elledge
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Xin X. Zhou
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - James R. Byrnes
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | | | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Katarina Pance
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Shion A. Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Jeff E. Glasgow
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Anum A. Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Keirstinne Turcios
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Nikita Iyer
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Leonel Torres
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Michael J. Peluso
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Timothy J. Henrich
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
| | - Taia T. Wang
- Chan Zuckerberg Biohub, San Francisco, California, 94158, USA
- Departments of Medicine and of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | | | - Kevin K. Leung
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158, USA
- Chan Zuckerberg Biohub, San Francisco, California, 94158, USA
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
- Chan Zuckerberg Biohub, San Francisco, California, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, 94158, USA
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13
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Appa A, Takahashi S, Rodriguez-Barraquer I, Chamie G, Sawyer A, Consortium CLIAHUB, Duarte E, Hakim J, Turcios K, Vinden J, Janson O, Manglik A, Peluso MJ, Deeks SG, Henrich TJ, Torres L, Rodgers M, Hackett J, Chiu C, Havlir D, Greenhouse B. Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community. medRxiv 2020:2020.08.15.20175786. [PMID: 32839781 PMCID: PMC7444294 DOI: 10.1101/2020.08.15.20175786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The absence of systematic surveillance for SARS-CoV-2 has curtailed accurate appraisal of transmission intensity. Our objective was to perform case detection of an entire rural community to quantify SARS-CoV-2 transmission using PCR and antibody testing. METHODS We conducted a cross-sectional survey of the prevalence and cumulative incidence of SARS-CoV-2 infection in the rural town of Bolinas, California (population 1,620), four weeks following shelter-in-place orders. Residents and county essential workers were tested between April 20th-24th, 2020. Prevalence by PCR and seroprevalence combining data from two forms of antibody testing were performed in parallel (Abbott ARCHITECT IgG to nucleocapsid protein and in-house IgG ELISA to the receptor binding domain). RESULTS Of 1,891 participants, 1,312 were confirmed Bolinas residents (>80% community ascertainment). Zero participants were PCR positive. Assuming 80% sensitivity, it would have been unlikely to observe these results (p<0.05) if there were >3 active infections in the community. Based on antibody results, estimated prevalence of prior infection was 0.16% (95% CrI: 0.02%, 0.46%). Seroprevalence estimates using only one of the two tests would have been higher, with greater uncertainty. The positive predictive value (PPV) of a positive result on both tests was 99.11% (95% CrI: 95.75%, 99.94%), compared to PPV 44.19%-63.32% (95% CrI range 3.25%-98.64%) if only one test was utilized. CONCLUSIONS Four weeks following shelter-in-place, active and prior SARS-CoV-2 infection in a rural Northern California community was extremely rare. In this low prevalence setting, use of two antibody tests increased the PPV and precision of seroprevalence estimates.
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Affiliation(s)
- Ayesha Appa
- University Of California San Francisco, San Francisco, CA, USA
| | - Saki Takahashi
- University Of California San Francisco, San Francisco, CA, USA
| | | | - Gabriel Chamie
- University Of California San Francisco, San Francisco, CA, USA
| | - Aenor Sawyer
- University Of California San Francisco, San Francisco, CA, USA
| | - CLIAHUB Consortium
- University Of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Elias Duarte
- University Of California San Francisco, San Francisco, CA, USA
| | - Jill Hakim
- University Of California San Francisco, San Francisco, CA, USA
| | | | - Joanna Vinden
- University of California Berkeley, Berkeley, CA, USA
| | - Owen Janson
- University Of California San Francisco, San Francisco, CA, USA
| | - Aashish Manglik
- University Of California San Francisco, San Francisco, CA, USA
| | | | - Steven G. Deeks
- University Of California San Francisco, San Francisco, CA, USA
| | | | - Leonel Torres
- University Of California San Francisco, San Francisco, CA, USA
| | | | | | - Charles Chiu
- University Of California San Francisco, San Francisco, CA, USA
| | - Diane Havlir
- University Of California San Francisco, San Francisco, CA, USA
| | - Bryan Greenhouse
- University Of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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