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Garg R, Liu Q, Van Kessel J, Asavajaru A, Uhlemann EM, Joessel M, Hamonic G, Khatooni Z, Kroeker A, Lew J, Scruten E, Pennington P, Deck W, Prysliak T, Nickol M, Apel F, Courant T, Kelvin AA, Van Kessel A, Collin N, Gerdts V, Köster W, Falzarano D, Racine T, Banerjee A. Efficacy of a stable broadly protective subunit vaccine platform against SARS-CoV-2 variants of concern. Vaccine 2024:S0264-410X(24)00586-3. [PMID: 38769033 DOI: 10.1016/j.vaccine.2024.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024]
Abstract
The emergence and ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for rapid vaccine development platforms that can be updated to counteract emerging variants of currently circulating and future emerging coronaviruses. Here we report the development of a "train model" subunit vaccine platform that contains a SARS-CoV-2 Wuhan S1 protein (the "engine") linked to a series of flexible receptor binding domains (RBDs; the "cars") derived from SARS-CoV-2 variants of concern (VOCs). We demonstrate that these linked subunit vaccines when combined with Sepivac SWE™, a squalene in water emulsion (SWE) adjuvant, are immunogenic in Syrian hamsters and subsequently provide protection from infection with SARS-CoV-2 VOCs Omicron (BA.1), Delta, and Beta. Importantly, the bivalent and trivalent vaccine candidates offered protection against some heterologous SARS-CoV-2 VOCs that were not included in the vaccine design, demonstrating the potential for broad protection against a range of different VOCs. Furthermore, these formulated vaccine candidates were stable at 2-8 °C for up to 13 months post-formulation, highlighting their utility in low-resource settings. Indeed, our vaccine platform will enable the development of safe and broadly protective vaccines against emerging betacoronaviruses that pose a significant health risk for humans and agricultural animals.
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Affiliation(s)
- Ravendra Garg
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Qiang Liu
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada
| | - Jill Van Kessel
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Akarin Asavajaru
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Eva-Maria Uhlemann
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Morgane Joessel
- Vaccine Formulation Institute (VFI), Plan-Les-Ouates, Switzerland
| | - Glenn Hamonic
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Zahed Khatooni
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Andrea Kroeker
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Erin Scruten
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Paul Pennington
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - William Deck
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Tracy Prysliak
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Michaela Nickol
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Falko Apel
- Vaccine Formulation Institute (VFI), Plan-Les-Ouates, Switzerland
| | - Thomas Courant
- Vaccine Formulation Institute (VFI), Plan-Les-Ouates, Switzerland
| | - Alyson A Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Andrew Van Kessel
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Nicolas Collin
- Vaccine Formulation Institute (VFI), Plan-Les-Ouates, Switzerland
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Wolfgang Köster
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Trina Racine
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada.
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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So M, Goldberg SA, Lu S, Garcia-Knight M, Davidson MC, Tassetto M, Murray VW, Anglin K, Pineda-Ramirez J, Chen JY, Rugart PR, Richardson ET, Briggs-Hagen M, Midgley CM, Andino R, Seitzman GD, Gonzales J, Peluso MJ, Martin JN, Kelly JD. Prevalence, Patterns, and Predictors of SARS-CoV-2 RNA and Culturable Virus in Tears of a Case-Ascertained Household Cohort. Am J Ophthalmol 2024; 265:48-53. [PMID: 38663502 DOI: 10.1016/j.ajo.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/30/2024] [Accepted: 04/14/2024] [Indexed: 05/20/2024]
Abstract
PURPOSE To investigate the prevalence, patterns, and predictors of SARS-CoV-2 RNA and culturable virus in tears of a case-ascertained household cohort. DESIGN Prospective, longitudinal case-ascertained household cohort identified through convenience sampling. METHODS This analysis was restricted to individuals who were non-hospitalized, symptomatic, and tested positive for SARS-CoV-2 by nasal RT-PCR. Tears and anterior nasal biospecimens were serially collected throughout the acute period. Tears specimens were collected by the study staff using Schirmer test strips, and nasal specimens were self-collected. For both, SARS-CoV-2 RNA was quantified using qRT-PCR, and culturable virus was detected using presence of cytopathic effect (CPE) in tissue culture; positive CPE was confirmed by a qRT-PCR step. A series of cross-sectional unadjusted analyses were performed investigating the relationship between different sociodemographic determinants and biological factors associated with tears RNA positivity. RESULTS Among the 83 SARS-CoV-2 infected participants, 10 (12%) had at least one RNA-positive tears specimen. Amongst these 10, 5 (50%) had concurrent presence of culturable virus, at a median of 7 days postsymptom onset (IQR: 4-7 days) (absolute range: 4-8 days). CONCLUSIONS In this longitudinal cohort, we found evidence of culturable virus in the tears of a small proportion of nonhospitalized SARS-CoV-2 infected individuals. Current public health infection precautions do not account for transmission via tears, so these findings may improve our understanding of potential sources of SARS-CoV-2 transmission and contribute to developing future guidelines.
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Affiliation(s)
- Matthew So
- Institute for Global Health Sciences (M.S, S.A.G, S.L, K.A, J.P.-R, J.Y.C, J.D.K), University of California, San Francisco, California, USA
| | - Sarah A Goldberg
- Institute for Global Health Sciences (M.S, S.A.G, S.L, K.A, J.P.-R, J.Y.C, J.D.K), University of California, San Francisco, California, USA; Department of Epidemiology and Biostatistics (S.A.G, S.L, P.R.R, J.N.M, J.D.K), University of California, San Francisco, San Francisco, California, USA
| | - Scott Lu
- Institute for Global Health Sciences (M.S, S.A.G, S.L, K.A, J.P.-R, J.Y.C, J.D.K), University of California, San Francisco, California, USA; Department of Epidemiology and Biostatistics (S.A.G, S.L, P.R.R, J.N.M, J.D.K), University of California, San Francisco, San Francisco, California, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology (M.G.-K, M.T), University of California, San Francisco, San Francisco, California, USA
| | - Michelle C Davidson
- School of Medicine (M.C.D), University of California, San Francisco, San Francisco, California, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology (M.G.-K, M.T), University of California, San Francisco, San Francisco, California, USA
| | - Victoria Wong Murray
- School of Medicine (V.W.M), Cooper Medical School of Rowan University, Camden, New Jersey, USA
| | - Khamal Anglin
- Institute for Global Health Sciences (M.S, S.A.G, S.L, K.A, J.P.-R, J.Y.C, J.D.K), University of California, San Francisco, California, USA
| | - Jesus Pineda-Ramirez
- Institute for Global Health Sciences (M.S, S.A.G, S.L, K.A, J.P.-R, J.Y.C, J.D.K), University of California, San Francisco, California, USA
| | - Jessica Y Chen
- Institute for Global Health Sciences (M.S, S.A.G, S.L, K.A, J.P.-R, J.Y.C, J.D.K), University of California, San Francisco, California, USA
| | - Paulina R Rugart
- Department of Epidemiology and Biostatistics (S.A.G, S.L, P.R.R, J.N.M, J.D.K), University of California, San Francisco, San Francisco, California, USA
| | - Eugene T Richardson
- Department of Global Health and Social Medicine (E.T.R), Harvard Medical School, Boston, Massachusetts, USA; Division of Infectious Diseases (E.T.R), Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Melissa Briggs-Hagen
- Coronavirus and Other Respiratory Viruses Division (M.B.H, C.M.M), National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claire M Midgley
- Coronavirus and Other Respiratory Viruses Division (M.B.H, C.M.M), National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Raul Andino
- Department of Microbiology and Immunology (M.G.-K, M.T), University of California, San Francisco, San Francisco, California, USA
| | - Gerami D Seitzman
- F.I. Proctor Foundation (G.D.S, J.G, J.D.K), University of California, San Francisco, San Francisco, California, USA; Department of Ophthalmology (G.D.S, J.G), University of California, San Francisco, California, USA
| | - John Gonzales
- F.I. Proctor Foundation (G.D.S, J.G, J.D.K), University of California, San Francisco, San Francisco, California, USA; Department of Ophthalmology (G.D.S, J.G), University of California, San Francisco, California, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine (M.J.P), Zuckerberg San Francisco General Hospital, San Francisco, California, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics (S.A.G, S.L, P.R.R, J.N.M, J.D.K), University of California, San Francisco, San Francisco, California, USA
| | - John Daniel Kelly
- Institute for Global Health Sciences (M.S, S.A.G, S.L, K.A, J.P.-R, J.Y.C, J.D.K), University of California, San Francisco, California, USA; Department of Epidemiology and Biostatistics (S.A.G, S.L, P.R.R, J.N.M, J.D.K), University of California, San Francisco, San Francisco, California, USA; F.I. Proctor Foundation (G.D.S, J.G, J.D.K), University of California, San Francisco, San Francisco, California, USA; Division of Hospital Medicine (J.D.K), San Francisco Veterans Affairs Medical Center, San Francisco, California, USA.
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3
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Holm RH, Rempala GA, Choi B, Brick JM, Amraotkar AR, Keith RJ, Rouchka EC, Chariker JH, Palmer KE, Smith T, Bhatnagar A. Dynamic SARS-CoV-2 surveillance model combining seroprevalence and wastewater concentrations for post-vaccine disease burden estimates. COMMUNICATIONS MEDICINE 2024; 4:70. [PMID: 38594350 PMCID: PMC11004132 DOI: 10.1038/s43856-024-00494-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Despite wide scale assessments, it remains unclear how large-scale severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination affected the wastewater concentration of the virus or the overall disease burden as measured by hospitalization rates. METHODS We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and linked vaccination and hospitalization data, from April 2021-August 2021 in Jefferson County, Kentucky (USA). Our susceptible ( S ), vaccinated ( V ), variant-specific infected (I 1 andI 2 ), recovered ( R ), and seropositive ( T ) model ( S V I 2 R T ) tracked prevalence longitudinally. This was related to wastewater concentration. RESULTS Here we show the 64% county vaccination rate translate into about a 61% decrease in SARS-CoV-2 incidence. The estimated effect of SARS-CoV-2 Delta variant emergence is a 24-fold increase of infection counts, which correspond to an over 9-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration have the strongest correlation (r = 0.95) at 1 week lag. CONCLUSIONS Our study underscores the importance of continuing environmental surveillance post-vaccine and provides a proof-of-concept for environmental epidemiology monitoring of infectious disease for future pandemic preparedness.
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Grants
- P20 GM103436 NIGMS NIH HHS
- This study was supported by Centers for Disease Control and Prevention (75D30121C10273), Louisville Metro Government, James Graham Brown Foundation, Owsley Brown II Family Foundation, Welch Family, Jewish Heritage Fund for Excellence, the National Institutes of Health, (P20GM103436), the Rockefeller Foundation, the National Sciences Foundation (DMS-2027001), and the Basic Science Research Program National Research Foundation of Korea (NRF) (RS-2023-00245056).
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Affiliation(s)
- Rochelle H Holm
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Grzegorz A Rempala
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
| | - Boseung Choi
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
- Division of Big Data Science, Korea University, Sejong, South Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon, South Korea
| | | | - Alok R Amraotkar
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Rachel J Keith
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
| | - Julia H Chariker
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
| | - Kenneth E Palmer
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, 40202, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA.
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Leung C, Su L, Taylor L, Oliveira EA, Simões E Silva AC. Effectiveness of oseltamivir in reducing COVID-19-related in-hospital deaths: A pharmacoepidemiological study. Int J Antimicrob Agents 2024; 63:107111. [PMID: 38354825 DOI: 10.1016/j.ijantimicag.2024.107111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/22/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Oseltamivir is a low-cost antiviral agent that could support or complement treatment of COVID-19. This study assessed whether oseltamivir is effective in reducing COVID-19-related mortality. METHODS This retrospective cohort study evaluated real-world data from a nationwide database of hospitalisation due to severe acute respiratory syndrome in Brazil. Propensity score matching was used to mimic a randomised controlled trial with 'oseltamivir' and 'no antivirals at all' as the intervention and control groups, respectively. RESULTS A total of 21 480 and 268 486 patients admitted between February 2020 and January 2023 were included in the intervention and control groups, respectively. After matching, the odds ratio (OR) for death was 0.901 (95% confidence interval [CI] 0.873-0.930). The OR (95% CI) for death in patients who were admitted to the ICU, and on non-invasive or invasive ventilation was 0.868 (0.821-0.917), 0.935 (0.893-0.980), and 0.883 (0.814-0.958), respectively. CONCLUSIONS Overall, the use of oseltamivir was associated with an attributable risk reduction of 2.50% (95% CI 1.77-3.29). Similar results were observed in patients who were admitted to the ICU, and on non-invasive or invasive ventilation. Oseltamivir is a low-cost potential antiviral treatment for COVID-19.
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Affiliation(s)
- Char Leung
- Department of Population Health Sciences, University of Leicester, Leicester, UK.
| | - Li Su
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Lucy Taylor
- Leicester Medical School, University of Leicester, Leicester, UK
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5
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Oordt-Speets AM, Spinardi JR, Mendoza CF, Yang J, del Carmen Morales G, Kyaw MH. Duration of SARS-CoV-2 shedding: A systematic review. J Glob Health 2024; 14:05005. [PMID: 38547496 PMCID: PMC10978056 DOI: 10.7189/jogh.14.05005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
Abstract
Background Positive viral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cultures indicate shedding of infectious virus and corresponding transmission risk of coronavirus disease 2019 (COVID-19). The research question of this systematic review was: Is there a discernible pattern in the timing of SARS-CoV-2 virus isolation, and what is the proportion of positive and negative results for isolation of SARS-CoV-2 virus with viral culture relative to the onset of clinical symptoms or the day of diagnosis, as indicated by longitudinal studies? Methods We systematically searched PubMed and Embase from inception to 16 February 2023 for English-language studies with serial viral culture testing within symptomatic or asymptomatic SARS-CoV-2 infected persons during the post-vaccination period. Outcomes of interest were the daily culture status per study and the overall daily culture positivity rate of SARS-CoV-2. We critically appraised the selected studies using the Newcastle-Ottawa quality assessment scale. Results We included 14 viral shedding studies in this systematic review. Positive viral SARS-CoV-2 cultures were detected in samples ranging from 4 days before to 18 days after symptom onset. The daily culture SARS-CoV-2 positivity rate since symptom onset or diagnosis showed a steep decline between day 5 and 9, starting with a peak ranging from 44% to 50% on days -1 to 5, decreasing to 28% on day 7 and 11% on day 9, and finally ranging between 0% and 8% on days 10-17. Conclusions Viral shedding peaked within 5 days since symptom onset or diagnosis and the culture positivity rate rapidly declined hereafter. This systematic review provides an overview of current evidence on the daily SARS-CoV-2 culture positivity rates during the post-vaccination period. These findings could be used to estimate the effectiveness of public health control measures, including treatment and preventive strategies, to reduce the spread of COVID-19.
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Affiliation(s)
| | - Julia R Spinardi
- Vaccine Medical Affairs, Emerging Markets, Pfizer Inc., Itapevi, Brazil
| | | | - Jingyan Yang
- Global Value and Access, Pfizer Inc., New York, USA
| | | | - Moe H Kyaw
- Vaccine Scientific Affairs, Emerging Markets, Pfizer Inc., New York, USA
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6
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Overton CE, Abbey R, Baird T, Christie R, Daniel O, Day J, Gittins M, Jones O, Paton R, Tang M, Ward T, Wilkinson J, Woodrow-Hill C, Aldridge T, Chen Y. Identifying employee, workplace and population characteristics associated with COVID-19 outbreaks in the workplace: a population-based study. Occup Environ Med 2024; 81:92-100. [PMID: 38191477 DOI: 10.1136/oemed-2023-109032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/15/2023] [Indexed: 01/10/2024]
Abstract
OBJECTIVES To identify risk factors that contribute to outbreaks of COVID-19 in the workplace and quantify their effect on outbreak risk. METHODS We identified outbreaks of COVID-19 cases in the workplace and investigated the characteristics of the individuals, the workplaces, the areas they work and the mode of commute to work, through data linkages based on Middle Layer Super Output Areas in England between 20 June 2021 and 20 February 2022. We estimated population-level associations between potential risk factors and workplace outbreaks, adjusting for plausible confounders identified using a directed acyclic graph. RESULTS For most industries, increased physical proximity in the workplace was associated with increased risk of COVID-19 outbreaks, while increased vaccination was associated with reduced risk. Employee demographic risk factors varied across industry, but for the majority of industries, a higher proportion of black/African/Caribbean ethnicities and living in deprived areas, was associated with increased outbreak risk. A higher proportion of employees in the 60-64 age group was associated with reduced outbreak risk. There were significant associations between gender, work commute modes and staff contract type with outbreak risk, but these were highly variable across industries. CONCLUSIONS This study has used novel national data linkages to identify potential risk factors of workplace COVID-19 outbreaks, including possible protective effects of vaccination and increased physical distance at work. The same methodological approach can be applied to wider occupational and environmental health research.
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Affiliation(s)
- Christopher E Overton
- UK Health Security Agency, London, UK
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
| | | | - Tarrion Baird
- UK Health Security Agency, London, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | - Julie Day
- UK Health Security Agency, London, UK
| | - Matthew Gittins
- Centre for Biostatistics, The University of Manchester, Manchester, UK
| | | | | | | | - Tom Ward
- UK Health Security Agency, London, UK
| | - Jack Wilkinson
- Centre for Biostatistics, The University of Manchester, Manchester, UK
| | | | | | - Yiqun Chen
- Science Division, Health and Safety Executive, Buxton, UK
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7
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Prelog M, Jeske SD, Asam C, Fuchs A, Wieser A, Gall C, Wytopil M, Mueller-Schmucker SM, Beileke S, Goekkaya M, Kling E, Geldmacher C, Rubio-Acero R, Plank M, Christa C, Willmann A, Vu M, Einhauser S, Weps M, Lampl BMJ, Almanzar G, Kousha K, Schwägerl V, Liebl B, Weber B, Drescher J, Scheidt J, Gefeller O, Messmann H, Protzer U, Liese J, Hoelscher M, Wagner R, Überla K, Steininger P. Clinical and immunological benefits of full primary COVID-19 vaccination in individuals with SARS-CoV-2 breakthrough infections: A prospective cohort study in non-hospitalized adults. J Clin Virol 2024; 170:105622. [PMID: 38091664 DOI: 10.1016/j.jcv.2023.105622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/23/2023] [Accepted: 11/26/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND SARS-CoV-2 variants of concern (VOC) may result in breakthrough infections (BTIs) in vaccinated individuals. The aim of this study was to investigate the effects of full primary (two-dose) COVID-19 vaccination with wild-type-based SARS-CoV-2 vaccines on symptoms and immunogenicity of SARS-CoV-2 VOC BTIs. METHODS In a longitudinal multicenter controlled cohort study in Bavaria, Germany, COVID-19 vaccinated and unvaccinated non-hospitalized individuals were prospectively enrolled within 14 days of a PCR-confirmed SARS-CoV-2 infection. Individuals were visited weekly up to 4 times, performing a structured record of medical data and viral load assessment. SARS-CoV-2-specific antibody response was characterized by anti-spike-(S)- and anti-nucleocapsid-(N)-antibody concentrations, anti-S-IgG avidity and neutralization capacity. RESULTS A total of 300 individuals (212 BTIs, 88 non-BTIs) were included with VOC Alpha or Delta SARS-CoV-2 infections. Full primary COVID-19 vaccination provided a significant effectiveness against five symptoms (relative risk reduction): fever (33 %), cough (21 %), dysgeusia (22 %), dizziness (52 %) and nausea/vomiting (48 %). Full primary vaccinated individuals showed significantly higher 50 % inhibitory concentration (IC50) values against the infecting VOC compared to unvaccinated individuals at week 1 (269 vs. 56, respectively), and weeks 5-7 (1,917 vs. 932, respectively) with significantly higher relative anti-S-IgG avidity (78% vs. 27 % at week 4, respectively). CONCLUSIONS Full primary COVID-19 vaccination reduced symptom frequencies in non-hospitalized individuals with BTIs and elicited a more rapid and longer lasting neutralization capacity against the infecting VOC compared to unvaccinated individuals. These results support the recommendation to offer at least full primary vaccination to all adults to reduce disease severity caused by immune escape-variants.
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Affiliation(s)
- Martina Prelog
- Pediatric Rheumatology / Special Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Samuel D Jeske
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Claudia Asam
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Andre Fuchs
- Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital of Augsburg, Augsburg, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Christine Gall
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Monika Wytopil
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sandra M Mueller-Schmucker
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stephanie Beileke
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mehmet Goekkaya
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Institute of Environmental Medicine Helmholtz Zentrum München, German Research Center for Environmental Health, Augsburg, Germany
| | - Elisabeth Kling
- Institute of Laboratory Medicine and Microbiology University Hospital Augsburg, Augsburg, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Michael Plank
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Catharina Christa
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Annika Willmann
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Martin Vu
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Sebastian Einhauser
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Manuela Weps
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Benedikt M J Lampl
- Regensburg Department of Public Health, Division of Infection Control and Prevention, Regensburg, Germany; Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Giovanni Almanzar
- Pediatric Rheumatology / Special Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Kimia Kousha
- Pediatric Rheumatology / Special Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Valeria Schwägerl
- Pediatric Infectious Diseases, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Bernhard Liebl
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - Beatrix Weber
- Institute for Information Systems, University of Applied Sciences Hof, Hof, Germany
| | | | - Jörg Scheidt
- Institute for Information Systems, University of Applied Sciences Hof, Hof, Germany
| | - Olaf Gefeller
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Helmut Messmann
- Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital of Augsburg, Augsburg, Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany; Institute of Virology, Helmholtz Munich, Munich, Germany, and German Center for Infection Research, Munich partner site
| | - Johannes Liese
- Pediatric Infectious Diseases, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ralf Wagner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany; Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Klaus Überla
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Philipp Steininger
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
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8
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Choudhry S, Rowland TAJ, McClelland K, Renz E, Iyanger N, Chow JY, Aiano F, Ladhani SN, Jeffery-Smith A, Andrews NJ, Zambon M. Protection from infection and reinfection due to the Omicron BA.1 variant in care homes. Front Immunol 2023; 14:1186134. [PMID: 37936695 PMCID: PMC10627010 DOI: 10.3389/fimmu.2023.1186134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/26/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction Following the emergence of SARS-CoV-2 in 2020, care homes were disproportionately impacted by high mortality and morbidity of vulnerable elderly residents. Non-pharmaceutical interventions (NPIs) and improved infection control measures together with vaccination campaigns have since improved outcomes of infection. We studied the utility of past infection status, recent vaccination and anti-S antibody titres as possible correlates of protection against a newly emergent Omicron variant infection. Methods Prospective longitudinal surveillance of nine sentinel London care homes from April 2020 onwards found that all experienced COVID-19 outbreaks due to Omicron (BA.1) during December 2021 and January 2022, despite extensive prior SARS-CoV-2 exposure and high COVID-19 vaccination rates, including booster vaccines (>70% residents, >40% staff). Results Detailed investigation showed that 46% (133/288) of Omicron BA.1 infections were SARS-CoV-2 reinfections. Two and three COVID-19 vaccine doses were protective against Omicron infection within 2-9 weeks of vaccination, though protection waned from 10 weeks post-vaccination. Prior infection provided additional protection in vaccinated individuals, approximately halving the risk of SARS-CoV-2 infection. Discussion Anti-S antibody titre showed a dose-dependent protective effect but did not fully account for the protection provided by vaccination or past infection, indicating that other mechanisms of protection are also involved.
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Affiliation(s)
- Saher Choudhry
- Virus Reference Department, UK Health Security Agency, London, United Kingdom
| | | | - Kamil McClelland
- Virus Reference Department, UK Health Security Agency, London, United Kingdom
| | - Erik Renz
- Virus Reference Department, UK Health Security Agency, London, United Kingdom
| | - Nalini Iyanger
- London Coronavirus Response Centre, UK Health Security Agency, London, United Kingdom
| | - J Yimmy Chow
- London Coronavirus Response Centre, UK Health Security Agency, London, United Kingdom
| | - Felicity Aiano
- Immunisations and Countermeasures Division, UK Health Security Agency, London, United Kingdom
| | - Shamez N. Ladhani
- Immunisations and Countermeasures Division, UK Health Security Agency, London, United Kingdom
| | - Anna Jeffery-Smith
- Virus Reference Department, UK Health Security Agency, London, United Kingdom
| | - Nick J. Andrews
- Statistics, Modelling and Economics Unit, UK Health Security Agency, London, United Kingdom
| | - Maria Zambon
- Virus Reference Department, UK Health Security Agency, London, United Kingdom
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9
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Painter MM, Johnston TS, Lundgreen KA, Santos JJS, Qin JS, Goel RR, Apostolidis SA, Mathew D, Fulmer B, Williams JC, McKeague ML, Pattekar A, Goode A, Nasta S, Baxter AE, Giles JR, Skelly AN, Felley LE, McLaughlin M, Weaver J, Kuthuru O, Dougherty J, Adamski S, Long S, Kee M, Clendenin C, da Silva Antunes R, Grifoni A, Weiskopf D, Sette A, Huang AC, Rader DJ, Hensley SE, Bates P, Greenplate AR, Wherry EJ. Prior vaccination promotes early activation of memory T cells and enhances immune responses during SARS-CoV-2 breakthrough infection. Nat Immunol 2023; 24:1711-1724. [PMID: 37735592 DOI: 10.1038/s41590-023-01613-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/07/2023] [Indexed: 09/23/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of vaccinated individuals is increasingly common but rarely results in severe disease, likely due to the enhanced potency and accelerated kinetics of memory immune responses. However, there have been few opportunities to rigorously study early recall responses during human viral infection. To better understand human immune memory and identify potential mediators of lasting vaccine efficacy, we used high-dimensional flow cytometry and SARS-CoV-2 antigen probes to examine immune responses in longitudinal samples from vaccinated individuals infected during the Omicron wave. These studies revealed heightened spike-specific responses during infection of vaccinated compared to unvaccinated individuals. Spike-specific cluster of differentiation (CD)4 T cells and plasmablasts expanded and CD8 T cells were robustly activated during the first week. In contrast, memory B cell activation, neutralizing antibody production and primary responses to nonspike antigens occurred during the second week. Collectively, these data demonstrate the functionality of vaccine-primed immune memory and highlight memory T cells as rapid responders during SARS-CoV-2 infection.
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Affiliation(s)
- Mark M Painter
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Timothy S Johnston
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Kendall A Lundgreen
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Jefferson J S Santos
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Juliana S Qin
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Rishi R Goel
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Bria Fulmer
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Justine C Williams
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Michelle L McKeague
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ajinkya Pattekar
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ahmad Goode
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sean Nasta
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy E Baxter
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Josephine R Giles
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ashwin N Skelly
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura E Felley
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Maura McLaughlin
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Joellen Weaver
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Oliva Kuthuru
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeanette Dougherty
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sharon Adamski
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sherea Long
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Macy Kee
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Cynthia Clendenin
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Alexander C Huang
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn Medicine Biobank, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott E Hensley
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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10
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Ferrantelli F, Manfredi F, Chiozzini C, Leone P, Pugliese K, Spada M, Di Virgilio A, Giovannelli A, Valeri M, Cara A, Michelini Z, Andreotti M, Federico M. SARS-CoV-2-Specific CD8 + T-Cells in Blood but Not in the Lungs of Vaccinated K18-hACE2 Mice after Infection. Vaccines (Basel) 2023; 11:1433. [PMID: 37766110 PMCID: PMC10535545 DOI: 10.3390/vaccines11091433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 enters the host by infecting nasal ciliated cells. Then, the virus can spread towards the oropharyngeal cavity and the pulmonary tissues. The antiviral adaptive immunity is promptly induced in response to the virus's detection, with virus-specific T-lymphocytes appearing before antiviral antibodies. Both the breadth and potency of antiviral CD8+ T-cell immunity have a key role in containing viral spread and disease severity. Current anti-SARS-CoV-2 vaccines do not impede the virus's replication in the upper respiratory tract, and there is consensus on the fact that the best potency of the antiviral immune response in both blood and the upper respiratory tract can be reached upon infection in vaccinees (i.e., breakthrough infection). However, whether the antiviral CD8+ T-cells developing in response to the breakthrough infection in the upper respiratory tract diffuse to the lungs is also still largely unknown. To fill the gap, we checked the CD8+ T-cell immunity elicited after infection of K18-hACE2 transgenic mice both at 3 weeks and 3 months after anti-spike vaccination. Virus-specific CD8+ T-cell immunity was monitored in both blood and the lungs before and after infection. By investigating the de novo generation of the CD8+ T-cells specific for SARS-CoV-2 viral proteins, we found that both membrane (M) and/or nucleocapsid (N)-specific CD8+ T-cells were induced at comparable levels in the blood of both unvaccinated and vaccinated mice. Conversely, N-specific CD8+ T-cells were readily found in the lungs of the control mice but were either rare or absent in those of vaccinated mice. These results support the idea that the hybrid cell immunity developing after asymptomatic/mild breakthrough infection strengthens the antiviral cell immunity in the lungs only marginally, implying that the direct exposition of viral antigens is required for the induction of an efficient antiviral cell immunity in the lungs.
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Affiliation(s)
- Flavia Ferrantelli
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Francesco Manfredi
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Chiara Chiozzini
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Patrizia Leone
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Katherina Pugliese
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Massimo Spada
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (A.D.V.); (A.G.); (M.V.)
| | - Antonio Di Virgilio
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (A.D.V.); (A.G.); (M.V.)
| | - Andrea Giovannelli
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (A.D.V.); (A.G.); (M.V.)
| | - Mauro Valeri
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (A.D.V.); (A.G.); (M.V.)
| | - Andrea Cara
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Zuleika Michelini
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Mauro Andreotti
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Maurizio Federico
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
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11
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Arts PJ, Kelly JD, Midgley CM, Anglin K, Lu S, Abedi GR, Andino R, Bakker KM, Banman B, Boehm AB, Briggs-Hagen M, Brouwer AF, Davidson MC, Eisenberg MC, Garcia-Knight M, Knight S, Peluso MJ, Pineda-Ramirez J, Diaz Sanchez R, Saydah S, Tassetto M, Martin JN, Wigginton KR. Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage. mSphere 2023; 8:e0013223. [PMID: 37338211 PMCID: PMC10506459 DOI: 10.1128/msphere.00132-23] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 06/21/2023] Open
Abstract
Wastewater-based epidemiology (WBE) emerged during the coronavirus disease 2019 (COVID-19) pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden. The lack of high-resolution fecal shedding data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) limits our ability to link WBE measurements to disease burden. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as for the commonly used fecal indicators pepper mild mottle virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2-infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding. Of the individuals that provided at least three stool samples spanning more than 14 days, 77% had one or more samples that tested positive for SARS-CoV-2 RNA. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall. CrAssphage DNA was detected in at least one sample from 80% (38/48) of individuals and was detected in 48% (179/371) of all samples. The geometric mean concentrations of PMMoV and crAssphage in stool across all individuals were 8.7 × 104 and 1.4 × 104 gene copies/milligram-dry weight, respectively, and crAssphage shedding was more consistent for individuals than PMMoV shedding. These results provide us with a missing link needed to connect laboratory WBE results with mechanistic models, and this will aid in more accurate estimates of COVID-19 burden in sewersheds. Additionally, the PMMoV and crAssphage data are critical for evaluating their utility as fecal strength normalizing measures and for source-tracking applications. IMPORTANCE This research represents a critical step in the advancement of wastewater monitoring for public health. To date, mechanistic materials balance modeling of wastewater-based epidemiology has relied on SARS-CoV-2 fecal shedding estimates from small-scale clinical reports or meta-analyses of research using a wide range of analytical methodologies. Additionally, previous SARS-CoV-2 fecal shedding data have not contained sufficient methodological information for building accurate materials balance models. Like SARS-CoV-2, fecal shedding of PMMoV and crAssphage has been understudied to date. The data presented here provide externally valid and longitudinal fecal shedding data for SARS-CoV-2, PMMoV, and crAssphage which can be directly applied to WBE models and ultimately increase the utility of WBE.
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Affiliation(s)
- Peter J. Arts
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Division of Hospital Medicine, UCSF, San Francisco, California, USA
- F.I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Claire M. Midgley
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Glen R. Abedi
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Raul Andino
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
| | - Kevin M. Bakker
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Bryon Banman
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandria B. Boehm
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California, USA
| | - Melissa Briggs-Hagen
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrew F. Brouwer
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marisa C. Eisenberg
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Sterling Knight
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael J. Peluso
- Division of HIV, Infectious Disease, and Global Medicine, UCSF, San Francisco, California, USA
| | - Jesus Pineda-Ramirez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Ruth Diaz Sanchez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Sharon Saydah
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
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12
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Goldberg SA, Lu S, Garcia-Knight M, Davidson MC, Tassetto M, Anglin K, Pineda-Ramirez J, Chen JY, Rugart PR, Mathur S, Forman CA, Donohue KC, Abedi GR, Saydah S, Briggs-Hagen M, Midgley CM, Andino R, Peluso MJ, Glidden DV, Martin JN, Kelly JD. Viral Determinants of Acute COVID-19 Symptoms in a Nonhospitalized Adult Population in the Pre-Omicron Era. Open Forum Infect Dis 2023; 10:ofad396. [PMID: 37636517 PMCID: PMC10456204 DOI: 10.1093/ofid/ofad396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/20/2023] [Indexed: 08/29/2023] Open
Abstract
Background The influence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA level and presence of infectious virus on symptom occurrence is poorly understood, particularly among nonhospitalized individuals. Methods The study included 85 nonhospitalized, symptomatic adults, who were enrolled from September 2020 to November 2021. Data from a longitudinal cohort studied over 28 days was used to analyze the association of individual symptoms with SARS-CoV-2 viral RNA load, or the presence or level of infectious (culturable) virus. Presence of infectious virus and viral RNA load were assessed daily, depending on specimen availability, and amount of infectious virus was assessed on the day of maximum RNA load. Participants were surveyed for the start and end dates of 31 symptoms at enrollment and at days 9, 14, 21, and 28; daily symptom presence was determined analytically. We describe symptoms and investigate their possible association with viral determinants through a series of single or pooled (multiple days across acute period) cross-sectional analyses. Results There was an association between viral RNA load and the same-day presence of many individual symptoms. Additionally, individuals with infectious virus were more than three times as likely to have a concurrent fever than individuals without infectious virus, and more than two times as likely to have concurrent myalgia, chills, headache, or sore throat. Conclusions We found evidence to support the association of viral RNA load and infectious virus on some, but not all symptoms. Fever was most strongly associated with the presence of infectious virus; this may support the potential for symptom-based isolation guidance for COVID-19.
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Affiliation(s)
- Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Michelle C Davidson
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Khamal Anglin
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Jesus Pineda-Ramirez
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Y Chen
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Paulina R Rugart
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Sujata Mathur
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Carrie A Forman
- College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
| | - Kevin C Donohue
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Glen R Abedi
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sharon Saydah
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa Briggs-Hagen
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claire M Midgley
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, San Francisco, California, USA
| | - David V Glidden
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, California, USA
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco, California, USA
- Division of Hospital Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
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13
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Deyoe JE, Kelly JD, Grijalva CG, Bonenfant G, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Hagen MB, Saydah S, Abedi GR, Goldberg SA, Tassetto M, Zhang A, Donohue KC, Davidson MC, Sanchez RD, Djomaleu M, Mathur S, Shak JR, Deeks SG, Peluso MJ, Chiu CY, Zhu Y, Halasa NB, Chappell JD, Mellis A, Reed C, Andino R, Martin JN, Zhou B, Talbot HK, Midgley CM, Rolfes MA. Association of Culturable-Virus Detection and Household Transmission of SARS-CoV-2, California and Tennessee, 2020-2022. J Infect Dis 2023; 227:1343-1347. [PMID: 36705269 PMCID: PMC10266938 DOI: 10.1093/infdis/jiad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/27/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
From 2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) household transmission studies (enrolling April 2020 to January 2022) with rapid enrollment and specimen collection for 14 days, 61% (43/70) of primary cases had culturable virus detected ≥6 days post-onset. Risk of secondary infection among household contacts tended to be greater when primary cases had culturable virus detected after onset. Regardless of duration of culturable virus, most secondary infections (70%, 28/40) had serial intervals <6 days, suggesting early transmission. These data examine viral culture as a proxy for infectiousness, reaffirm the need for rapid control measures after infection, and highlight the potential for prolonged infectiousness (≥6 days) in many individuals.
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Affiliation(s)
- Jessica E Deyoe
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- San Francisco VA Medical Center, San Francisco, California, USA
- F.I. Proctor Foundation, University of California, San Francisco, California, USA
| | | | - Gaston Bonenfant
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Jesus Pineda-Ramirez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | | | - Sharon Saydah
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Glen R Abedi
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Amethyst Zhang
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Kevin C Donohue
- School of Medicine, University of California, San Francisco, California, USA
| | - Michelle C Davidson
- School of Medicine, University of California, San Francisco, California, USA
| | - Ruth Diaz Sanchez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Manuella Djomaleu
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Sujata Mathur
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Joshua R Shak
- San Francisco VA Medical Center, San Francisco, California, USA
- School of Medicine, University of California, San Francisco, California, USA
| | - Steven G Deeks
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, California, USA
| | - Michael J Peluso
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, California, USA
| | - Charles Y Chiu
- Division of Infectious Diseases, University of California, San Francisco, California, USA
| | - Yuwei Zhu
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | | | - Alexandra Mellis
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Carrie Reed
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Bin Zhou
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - H Keipp Talbot
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Claire M Midgley
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa A Rolfes
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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14
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Pearson J, Wessler T, Chen A, Boucher RC, Freeman R, Lai SK, Pickles R, Forest MG. Modeling identifies variability in SARS-CoV-2 uptake and eclipse phase by infected cells as principal drivers of extreme variability in nasal viral load in the 48 h post infection. J Theor Biol 2023; 565:111470. [PMID: 36965846 PMCID: PMC10033495 DOI: 10.1016/j.jtbi.2023.111470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/25/2023]
Abstract
The SARS-CoV-2 coronavirus continues to evolve with scores of mutations of the spike, membrane, envelope, and nucleocapsid structural proteins that impact pathogenesis. Infection data from nasal swabs, nasal PCR assays, upper respiratory samples, ex vivo cell cultures and nasal epithelial organoids reveal extreme variabilities in SARS-CoV-2 RNA titers within and between the variants. Some variabilities are naturally prone to clinical testing protocols and experimental controls. Here we focus on nasal viral load sensitivity arising from the timing of sample collection relative to onset of infection and from heterogeneity in the kinetics of cellular infection, uptake, replication, and shedding of viral RNA copies. The sources of between-variant variability are likely due to SARS-CoV-2 structural protein mutations, whereas within-variant population variability is likely due to heterogeneity in cellular response to that particular variant. With the physiologically faithful, agent-based mechanistic model of inhaled exposure and infection from (Chen et al., 2022), we perform statistical sensitivity analyses of the progression of nasal viral titers in the first 0-48 h post infection, focusing on three kinetic mechanisms. Model simulations reveal shorter latency times of infected cells (including cellular uptake, viral RNA replication, until the onset of viral RNA shedding) exponentially accelerate nasal viral load. Further, the rate of infectious RNA copies shed per day has a proportional influence on nasal viral load. Finally, there is a very weak, negative correlation of viral load with the probability of infection per virus-cell encounter, the model proxy for spike-receptor binding affinity.
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Affiliation(s)
- Jason Pearson
- Department of Mathematics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy Wessler
- Department of Mathematics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alex Chen
- Department of Mathematics, California State University-Dominguez Hills, Carson, CA 90747, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel K Lai
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27606, USA; Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Raymond Pickles
- Marsico Lung Institute, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Gregory Forest
- Department of Mathematics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Department of Applied Physical Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27606, USA.
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15
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Corchis-Scott R, Geng Q, Al Riahi AM, Labak A, Podadera A, Ng KKS, Porter LA, Tong Y, Dixon JC, Menard SL, Seth R, McKay RM. Actionable wastewater surveillance: application to a university residence hall during the transition between Delta and Omicron resurgences of COVID-19. Front Public Health 2023; 11:1139423. [PMID: 37265515 PMCID: PMC10230041 DOI: 10.3389/fpubh.2023.1139423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Wastewater surveillance has gained traction during the COVID-19 pandemic as an effective and non-biased means to track community infection. While most surveillance relies on samples collected at municipal wastewater treatment plants, surveillance is more actionable when samples are collected "upstream" where mitigation of transmission is tractable. This report describes the results of wastewater surveillance for SARS-CoV-2 at residence halls on a university campus aimed at preventing outbreak escalation by mitigating community spread. Another goal was to estimate fecal shedding rates of SARS-CoV-2 in a non-clinical setting. Passive sampling devices were deployed in sewer laterals originating from residence halls at a frequency of twice weekly during fall 2021 as the Delta variant of concern continued to circulate across North America. A positive detection as part of routine sampling in late November 2021 triggered daily monitoring and further isolated the signal to a single wing of one residence hall. Detection of SARS-CoV-2 within the wastewater over a period of 3 consecutive days led to a coordinated rapid antigen testing campaign targeting the residence hall occupants and the identification and isolation of infected individuals. With knowledge of the number of individuals testing positive for COVID-19, fecal shedding rates were estimated to range from 3.70 log10 gc ‧ g feces-1 to 5.94 log10 gc ‧ g feces-1. These results reinforce the efficacy of wastewater surveillance as an early indicator of infection in congregate living settings. Detections can trigger public health measures ranging from enhanced communications to targeted coordinated testing and quarantine.
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Affiliation(s)
- Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Abdul Monem Al Riahi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Amr Labak
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ana Podadera
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Lisa A. Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Jess C. Dixon
- Department of Kinesiology, University of Windsor, Windsor, ON, Canada
| | | | - Rajesh Seth
- Civil and Environmental Engineering, University of Windsor, Windsor, ON, Canada
| | - R. Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
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16
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Anastasiou OE, Le-Trilling VTK, Trilling M. A simple algorithm based on initial Ct values predicts the duration to SARS-CoV-2 negativity and allows more efficient test-to-release and return-to-work schedules. Diagn Microbiol Infect Dis 2023; 106:115949. [PMID: 37087843 PMCID: PMC10060011 DOI: 10.1016/j.diagmicrobio.2023.115949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
Especially during global pandemics but also in the context of epidemic waves, the capacity for diagnostic quantitative reverse transcription-polymerase chain reactions (qRT-PCRs) rapidly becomes a limiting factor. The aim of the study was to optimize retesting regimens for test-to-release from isolation and return-to-work applications. For this purpose, we investigated the association between Ct values at the first diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the period until test negativity was reached, or at least until the Ct value exceeded 30, which is considered to indicate the transition to a non-infectious state. We included results from the testing of respiratory material samples for the detection of SARS-CoV-2 RNA, tested from March 1, 2020 to January 31, 2022. Lower initial Ct values were associated with longer periods of SARS-CoV-2 RNA positivity. Starting with Ct values of <20, 20 to 24.99, 25 to 29.99, 30 to 34.99, and ≥35, it took median intervals of 20 (interval: 14-25), 16 (interval: 10-21), 12 (interval: 7-16), 7 (interval: 5-14), and 5 (interval: 2-7) days, respectively, until the person tested negative. Accordingly, a Ct threshold of 30 was surpassed after 13 (interval: 8-19), 9 (interval: 6-14), 7 (interval: 6-11), 6 (interval: 4-10), and 3 (interval: 1-6) days, respectively, in individuals with aforementioned start Ct values. Furthermore, the time to negativity was longer for adults versus children, wild-type SARS-CoV-2 variant versus other variants of concern, and in patients who were treated in the intensive care units. Based on these data, we propose an adjusted retesting strategy according to the initial Ct value in order to optimize available PCR resources.
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Affiliation(s)
- Olympia E Anastasiou
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Duisburg-Essen, NRW, Germany.
| | - Vu Thuy Khanh Le-Trilling
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Duisburg-Essen, NRW, Germany
| | - Mirko Trilling
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Duisburg-Essen, NRW, Germany
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17
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Abstract
SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed.
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Affiliation(s)
- Olha Puhach
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
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18
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Koutsakos M, Reynaldi A, Lee WS, Nguyen J, Amarasena T, Taiaroa G, Kinsella P, Liew KC, Tran T, Kent HE, Tan HX, Rowntree LC, Nguyen THO, Thomas PG, Kedzierska K, Petersen J, Rossjohn J, Williamson DA, Khoury D, Davenport MP, Kent SJ, Wheatley AK, Juno JA. SARS-CoV-2 breakthrough infection induces rapid memory and de novo T cell responses. Immunity 2023; 56:879-892.e4. [PMID: 36958334 PMCID: PMC9970913 DOI: 10.1016/j.immuni.2023.02.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/26/2023] [Accepted: 02/24/2023] [Indexed: 03/24/2023]
Abstract
Although the protective role of neutralizing antibodies against COVID-19 is well established, questions remain about the relative importance of cellular immunity. Using 6 pMHC multimers in a cohort with early and frequent sampling, we define the phenotype and kinetics of recalled and primary T cell responses following Delta or Omicron breakthrough infection in previously vaccinated individuals. Recall of spike-specific CD4+ T cells was rapid, with cellular proliferation and extensive activation evident as early as 1 day post symptom onset. Similarly, spike-specific CD8+ T cells were rapidly activated but showed variable degrees of expansion. The frequency of activated SARS-CoV-2-specific CD8+ T cells at baseline and peak inversely correlated with peak SARS-CoV-2 RNA levels in nasal swabs and accelerated viral clearance. Our study demonstrates that a rapid and extensive recall of memory T cell populations occurs early after breakthrough infection and suggests that CD8+ T cells contribute to the control of viral replication in breakthrough SARS-CoV-2 infections.
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Affiliation(s)
- Marios Koutsakos
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Arnold Reynaldi
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Julie Nguyen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thakshila Amarasena
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - George Taiaroa
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Paul Kinsella
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kwee Chin Liew
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Helen E Kent
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Jan Petersen
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - David Khoury
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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19
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Painter MM, Johnston TS, Lundgreen KA, Santos JJS, Qin JS, Goel RR, Apostolidis SA, Mathew D, Fulmer B, Williams JC, McKeague ML, Pattekar A, Goode A, Nasta S, Baxter AE, Giles JR, Skelly AN, Felley LE, McLaughlin M, Weaver J, Kuthuru O, Dougherty J, Adamski S, Long S, Kee M, Clendenin C, da Silva Antunes R, Grifoni A, Weiskopf D, Sette A, Huang AC, Rader DJ, Hensley SE, Bates P, Greenplate AR, Wherry EJ. Prior vaccination enhances immune responses during SARS-CoV-2 breakthrough infection with early activation of memory T cells followed by production of potent neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.05.527215. [PMID: 36798171 PMCID: PMC9934532 DOI: 10.1101/2023.02.05.527215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
SARS-CoV-2 infection of vaccinated individuals is increasingly common but rarely results in severe disease, likely due to the enhanced potency and accelerated kinetics of memory immune responses. However, there have been few opportunities to rigorously study early recall responses during human viral infection. To better understand human immune memory and identify potential mediators of lasting vaccine efficacy, we used high-dimensional flow cytometry and SARS-CoV-2 antigen probes to examine immune responses in longitudinal samples from vaccinated individuals infected during the Omicron wave. These studies revealed heightened Spike-specific responses during infection of vaccinated compared to unvaccinated individuals. Spike-specific CD4 T cells and plasmablasts expanded and CD8 T cells were robustly activated during the first week. In contrast, memory B cell activation, neutralizing antibody production, and primary responses to non-Spike antigens occurred during the second week. Collectively, these data demonstrate the functionality of vaccine-primed immune memory and highlight memory T cells as rapid responders during SARS-CoV-2 infection.
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Affiliation(s)
- Mark M Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Timothy S Johnston
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kendall A Lundgreen
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Jefferson J S Santos
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Juliana S Qin
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Rishi R Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Bria Fulmer
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Justine C Williams
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Michelle L McKeague
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ajinkya Pattekar
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ahmad Goode
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sean Nasta
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Amy E Baxter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Josephine R Giles
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ashwin N Skelly
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Laura E Felley
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Maura McLaughlin
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Joellen Weaver
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oliva Kuthuru
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Jeanette Dougherty
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sharon Adamski
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sherea Long
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Macy Kee
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Cynthia Clendenin
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Alexander C Huang
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott E Hensley
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
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20
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Nielsen SS, Alvarez J, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Velarde A, Viltrop A, Winckler C, Adlhoch C, Aznar I, Baldinelli F, Boklund A, Broglia A, Gerhards N, Mur L, Nannapaneni P, Ståhl K. SARS-CoV-2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control. EFSA J 2023; 21:e07822. [PMID: 36860662 PMCID: PMC9968901 DOI: 10.2903/j.efsa.2023.7822] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit SARS-CoV-2 are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse and white-tailed deer. Among farmed animals, American mink have the highest likelihood to become infected from humans or animals and further transmit SARS-CoV-2. In the EU, 44 outbreaks were reported in 2021 in mink farms in seven MSs, while only six in 2022 in two MSs, thus representing a decreasing trend. The introduction of SARS-CoV-2 into mink farms is usually via infected humans; this can be controlled by systematically testing people entering farms and adequate biosecurity. The current most appropriate monitoring approach for mink is the outbreak confirmation based on suspicion, testing dead or clinically sick animals in case of increased mortality or positive farm personnel and the genomic surveillance of virus variants. The genomic analysis of SARS-CoV-2 showed mink-specific clusters with a potential to spill back into the human population. Among companion animals, cats, ferrets and hamsters are those at highest risk of SARS-CoV-2 infection, which most likely originates from an infected human, and which has no or very low impact on virus circulation in the human population. Among wild animals (including zoo animals), mostly carnivores, great apes and white-tailed deer have been reported to be naturally infected by SARS-CoV-2. In the EU, no cases of infected wildlife have been reported so far. Proper disposal of human waste is advised to reduce the risks of spill-over of SARS-CoV-2 to wildlife. Furthermore, contact with wildlife, especially if sick or dead, should be minimised. No specific monitoring for wildlife is recommended apart from testing hunter-harvested animals with clinical signs or found-dead. Bats should be monitored as a natural host of many coronaviruses.
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21
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Mathur S, Davidson MC, Anglin K, Lu S, Goldberg SA, Garcia-Knight M, Tassetto M, Zhang A, Romero M, Pineda-Ramirez J, Diaz-Sanchez R, Rugart P, Chen JY, Donohue K, Shak JR, Chenna A, Winslow JW, Petropoulos CJ, Yee BC, Lambert J, Glidden DV, Rutherford GW, Deeks SG, Peluso MJ, Andino R, Martin JN, Kelly JD. Evaluation of Severe Acute Respiratory Syndrome Coronavirus 2 Nucleocapsid Antigen in the Blood as a Diagnostic Test for Infection and Infectious Viral Shedding. Open Forum Infect Dis 2022; 9:ofac563. [PMID: 36381627 PMCID: PMC9620332 DOI: 10.1093/ofid/ofac563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022] Open
Abstract
Background SARS-CoV-2 nucleocapsid antigen can be detected in plasma, but little is known about its performance as a diagnostic test for acute SARS-CoV-2 infection or infectious viral shedding among nonhospitalized individuals. Methods We used data generated from anterior nasal and blood samples collected in a longitudinal household cohort of SARS-CoV-2 cases and contacts. Participants were classified as true positives if polymerase chain reaction (PCR) positive for SARS-CoV-2 and as true negatives if PCR negative and seronegative. Infectious viral shedding was determined by the cytopathic effect from viral culture. Stratified by 7 days after symptom onset, we constructed receiver operating characteristic (ROC) curves to describe optimized accuracy (Youden index), optimized sensitivity, and specificity. Results Of 80 participants, 58 (73%) were true positives while 22 (27%) were true negatives. Using the manufacturer's cutoff of 1.25 pg/mL for evaluating infection, sensitivity was higher from 0 to 7 days (77.6% [95% confidence interval {CI}, 64%-88.2%]) than from 8 to 14 days (43.2% [95% CI, 31.1%-54.5%]) after symptom onset; specificity was unchanged at 100% (95% CI, 88.1%-100%). This test had higher sensitivity (100% [95% CI, 88.4%-100%]) and lower specificity (65% [95% CI, 40.8%-84.6%]) for infectious viral shedding as compared with infection, particularly within the first week of symptom onset. Although the presence of N-antigen correlated with infectious viral shedding (r = 0.63; P < .01), sensitivity still declined over time. Additional cutoffs from ROC curves were identified to optimize sensitivity and specificity. Conclusions We found that this SARS-CoV-2 N-antigen test was highly sensitive for detecting early but not late infectious viral shedding, making it a viable screening test for community-dwelling individuals to inform isolation practices.
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Affiliation(s)
- Sujata Mathur
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Michelle C Davidson
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
- School of Medicine, University of California, San Francisco, California, USA
| | - Khamal Anglin
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Amethyst Zhang
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Mariela Romero
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Jesus Pineda-Ramirez
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Ruth Diaz-Sanchez
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Paulina Rugart
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Jessica Y Chen
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Kevin Donohue
- School of Medicine, University of California, San Francisco, California, USA
| | - Joshua R Shak
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
| | - Ahmed Chenna
- Labcorp-Monogram Biosciences, South San Francisco, California, USA
| | - John W Winslow
- Labcorp-Monogram Biosciences, South San Francisco, California, USA
| | | | - Brandon C Yee
- Labcorp-Monogram Biosciences, South San Francisco, California, USA
| | | | - David V Glidden
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - George W Rutherford
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Steven G Deeks
- Division of HIV, Infectious Disease, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA
| | - Michael J Peluso
- Division of HIV, Infectious Disease, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
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