1
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Turcinovic J, Kuhfeldt K, Sullivan M, Landaverde L, Platt JT, Alekseyev YO, Doucette-Stamm L, Hamer DH, Klapperich C, Landsberg HE, Connor JH. Transmission Dynamics and Rare Clustered Transmission Within an Urban University Population Before Widespread Vaccination. J Infect Dis 2024; 229:485-492. [PMID: 37856283 DOI: 10.1093/infdis/jiad397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Universities returned to in-person learning in 2021 while SARS-CoV-2 spread remained high. At the time, it was not clear whether in-person learning would be a source of disease spread. METHODS We combined surveillance testing, universal contact tracing, and viral genome sequencing to quantify introductions and identify likely on-campus spread. RESULTS Ninety-one percent of viral genotypes occurred once, indicating no follow-on transmission. Less than 5% of introductions resulted in >3 cases, with 2 notable exceptions of 40 and 47 cases. Both partially overlapped with outbreaks defined by contact tracing. In both cases, viral genomics eliminated over half the epidemiologically linked cases but added an equivalent or greater number of individuals to the transmission cluster. CONCLUSIONS Public health interventions prevented within-university transmission for most SARS-CoV-2 introductions, with only 2 major outbreaks being identified January to May 2021. The genetically linked cases overlap with outbreaks identified by contact tracing; however, they persisted in the university population for fewer days and rounds of transmission than estimated via contact tracing. This underscores the effectiveness of test-trace-isolate strategies in controlling undetected spread of emerging respiratory infectious diseases. These approaches limit follow-on transmission in both outside-in and internal transmission conditions.
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Affiliation(s)
- Jacquelyn Turcinovic
- Department of Virology, Immunology, and Microbiology, Chobanian & Avedisian School of Medicine
- National Emerging Infectious Diseases Laboratories
- Program in Bioinformatics
| | | | | | - Lena Landaverde
- Department of Biomedical Engineering
- Precision Diagnostics Center
- BU Clinical Testing Laboratory, Research Department
| | | | | | | | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratories
- Precision Diagnostics Center
- Department of Global Health, School of Public Health
- Section of Infectious Disease, Department of Medicine, Chobanian & Avedisian School of Medicine
- Center for Emerging Infectious Disease Policy and Research, Boston University, Massachusetts
| | - Catherine Klapperich
- Department of Biomedical Engineering
- Precision Diagnostics Center
- BU Clinical Testing Laboratory, Research Department
| | | | - John H Connor
- Department of Virology, Immunology, and Microbiology, Chobanian & Avedisian School of Medicine
- National Emerging Infectious Diseases Laboratories
- Program in Bioinformatics
- Center for Emerging Infectious Disease Policy and Research, Boston University, Massachusetts
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2
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Hauser B, Sangesland M, Lam EC, St Denis KJ, Sheehan ML, Vu ML, Cheng AH, Sordilla S, Lamson DT, Almawi AW, Balazs AB, Lingwood D, Schmidt AG. Heterologous Sarbecovirus Receptor Binding Domains as Scaffolds for SARS-CoV-2 Receptor Binding Motif Presentation. ACS Infect Dis 2024; 10:553-561. [PMID: 38281136 PMCID: PMC10862550 DOI: 10.1021/acsinfecdis.3c00483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/30/2024]
Abstract
Structure-guided rational immunogen design can generate optimized immunogens that elicit a desired humoral response. Design strategies often center on targeting conserved sites on viral glycoproteins that will ultimately confer potent neutralization. For SARS-CoV-2 (SARS-2), the surface-exposed spike glycoprotein includes a broadly conserved portion, the receptor binding motif (RBM), that is required to engage the host cellular receptor, ACE2. Expanding humoral responses to this site may result in a more potent neutralizing antibody response against diverse sarbecoviruses. Here, we used a "resurfacing" approach and iterative design cycles to graft the SARS-2 RBM onto heterologous sarbecovirus scaffolds. The scaffolds were selected to vary the antigenic distance relative to SARS-2 to potentially focus responses to RBM. Multimerized versions of these immunogens elicited broad neutralization against sarbecoviruses in the context of preexisting SARS-2 immunity. These validated engineering approaches can help inform future immunogen design efforts for sarbecoviruses and are generally applicable to other viruses.
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Affiliation(s)
- Blake
M. Hauser
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Maya Sangesland
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Evan C. Lam
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Kerri J. St Denis
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Maegan L. Sheehan
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Mya L. Vu
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Agnes H. Cheng
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Sophia Sordilla
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Dana Thornlow Lamson
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ahmad W. Almawi
- Center
for Molecular Interactions, Department of Biological Chemistry and
Molecular Pharmacology, Harvard Medical
School, Boston, Massachusetts 02115, United States
| | - Alejandro B. Balazs
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Daniel Lingwood
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Aaron G. Schmidt
- Ragon
Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
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3
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Kolson DL. Can immunological imprinting drive neurological dysfunction in long COVID? Brain 2023; 146:3960-3962. [PMID: 37681523 PMCID: PMC11004940 DOI: 10.1093/brain/awad307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023] Open
Abstract
This scientific commentary refers to ‘Neurologic sequelae of COVID-19 are determined by immunologic imprinting from previous coronaviruses’ by Spatola et al. (https://doi.org/10.1093/brain/awad155).
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Affiliation(s)
- Dennis L Kolson
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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4
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Spatola M, Nziza N, Jung W, Deng Y, Yuan D, Dinoto A, Bozzetti S, Chiodega V, Ferrari S, Lauffenburger DA, Mariotto S, Alter G. Neurologic sequelae of COVID-19 are determined by immunologic imprinting from previous coronaviruses. Brain 2023; 146:4292-4305. [PMID: 37161609 PMCID: PMC11004923 DOI: 10.1093/brain/awad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/28/2023] [Accepted: 04/10/2023] [Indexed: 05/11/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health emergency. Although SARS-CoV-2 is primarily a respiratory pathogen, extra-respiratory organs, including the CNS, can also be affected. Neurologic symptoms have been observed not only during acute SARS-CoV-2 infection, but also at distance from respiratory disease, also known as long-COVID or neurological post-acute sequelae of COVID-19 (neuroPASC). The pathogenesis of neuroPASC is not well understood, but hypotheses include SARS-CoV-2-induced immune dysfunctions, hormonal dysregulations and persistence of SARS-CoV-2 reservoirs. In this prospective cohort study, we used a high throughput systems serology approach to dissect the humoral response to SARS-CoV-2 (and other common coronaviruses: 229E, HKU1, NL63 and OC43) in the serum and CSF from 112 infected individuals who developed (n = 18) or did not develop (n = 94) neuroPASC. Unique SARS-CoV-2 humoral profiles were observed in the CSF of neuroPASC compared with serum responses. All antibody isotypes (IgG, IgM, IgA) and subclasses (IgA1-2, IgG1-4) were detected in serum, whereas CSF was characterized by focused IgG1 (and absence of IgM). These data argue in favour of compartmentalized brain-specific responses against SARS-CoV-2 through selective transfer of antibodies from the serum to the CSF across the blood-brain barrier, rather than intrathecal synthesis, where more diversity in antibody classes/subclasses would be expected. Compared to individuals who did not develop post-acute complications following infection, individuals with neuroPASC had similar demographic features (median age 65 versus 66.5 years, respectively, P = 0.55; females 33% versus 44%, P = 0.52) but exhibited attenuated systemic antibody responses against SARS-CoV-2, characterized by decreased capacity to activate antibody-dependent complement deposition (ADCD), NK cell activation (ADNKA) and to bind Fcγ receptors. However, surprisingly, neuroPASC individuals showed significantly expanded antibody responses to other common coronaviruses, including 229E, HKU1, NL63 and OC43. This biased humoral activation across coronaviruses was particularly enriched in neuroPASC individuals with poor outcome, suggesting an 'original antigenic sin' (or immunologic imprinting), where pre-existing immune responses against related viruses shape the response to the current infection, as a key prognostic marker of neuroPASC disease. Overall, these findings point to a pathogenic role for compromised anti-SARS-CoV-2 responses in the CSF, likely resulting in incomplete virus clearance from the brain and persistent neuroinflammation, in the development of post-acute neurologic complications of SARS-CoV-2 infection.
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Affiliation(s)
- Marianna Spatola
- Ragon Institute of MGH, MIT and Harvard Medical School, Cambridge, MA 02139, USA
| | - Nadège Nziza
- Ragon Institute of MGH, MIT and Harvard Medical School, Cambridge, MA 02139, USA
| | - Wonyeong Jung
- Ragon Institute of MGH, MIT and Harvard Medical School, Cambridge, MA 02139, USA
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yixiang Deng
- Ragon Institute of MGH, MIT and Harvard Medical School, Cambridge, MA 02139, USA
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dansu Yuan
- Ragon Institute of MGH, MIT and Harvard Medical School, Cambridge, MA 02139, USA
| | - Alessandro Dinoto
- Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, 37131 Verona, Italy
| | - Silvia Bozzetti
- Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, 37131 Verona, Italy
| | - Vanessa Chiodega
- Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, 37131 Verona, Italy
- Department of Neurology/Stroke Unit, San Maurizio Hospital, 39100 Bolzano, Italy
| | - Sergio Ferrari
- Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, 37131 Verona, Italy
| | | | - Sara Mariotto
- Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, 37131 Verona, Italy
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard Medical School, Cambridge, MA 02139, USA
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5
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Miller J, Hachmann NP, Collier ARY, Lasrado N, Mazurek CR, Patio RC, Powers O, Surve N, Theiler J, Korber B, Barouch DH. Substantial Neutralization Escape by SARS-CoV-2 Omicron Variants BQ.1.1 and XBB.1. N Engl J Med 2023; 388:662-664. [PMID: 36652339 PMCID: PMC9878581 DOI: 10.1056/nejmc2214314] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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6
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Duvallet C, Wu F, McElroy KA, Imakaev M, Endo N, Xiao A, Zhang J, Floyd-O’Sullivan R, Powell MM, Mendola S, Wilson ST, Cruz F, Melman T, Sathyanarayana CL, Olesen SW, Erickson TB, Ghaeli N, Chai P, Alm EJ, Matus M. Nationwide Trends in COVID-19 Cases and SARS-CoV-2 RNA Wastewater Concentrations in the United States. ACS ES T Water 2022; 2:1899-1909. [PMID: 36380771 PMCID: PMC9092192 DOI: 10.1021/acsestwater.1c00434] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Wastewater-based epidemiology has emerged as a promising technology for population-level surveillance of COVID-19. In this study, we present results of a large nationwide SARS-CoV-2 wastewater monitoring system in the United States. We profile 55 locations with at least six months of sampling from April 2020 to May 2021. These locations represent more than 12 million individuals across 19 states. Samples were collected approximately weekly by wastewater treatment utilities as part of a regular wastewater surveillance service and analyzed for SARS-CoV-2 RNA concentrations. SARS-CoV-2 RNA concentrations were normalized to pepper mild mottle virus, an indicator of fecal matter in wastewater. We show that wastewater data reflect temporal and geographic trends in clinical COVID-19 cases and investigate the impact of normalization on correlations with case data within and across locations. We also provide key lessons learned from our broad-scale implementation of wastewater-based epidemiology, which can be used to inform wastewater-based epidemiology approaches for future emerging diseases. This work demonstrates that wastewater surveillance is a feasible approach for nationwide population-level monitoring of COVID-19 disease. With an evolving epidemic and effective vaccines against SARS-CoV-2, wastewater-based epidemiology can serve as a passive surveillance approach for detecting changing dynamics or resurgences of the virus.
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Affiliation(s)
- Claire Duvallet
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Fuqing Wu
- Center
for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT
Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Kyle A. McElroy
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Maxim Imakaev
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Noriko Endo
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Amy Xiao
- Center
for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT
Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Jianbo Zhang
- Center
for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT
Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
| | | | - Morgan M. Powell
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Samuel Mendola
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Shane T. Wilson
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Francis Cruz
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Tamar Melman
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | | | - Scott W. Olesen
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Timothy B. Erickson
- Department
of Emergency Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Division
of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Harvard
Humanitarian Initiative, Cambridge, Massachusetts 02138, United States
| | - Newsha Ghaeli
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Peter Chai
- Division
of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- The
Fenway Institute, Boston, Massachusetts 02215, United States
- The
Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Eric J. Alm
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
- Center
for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT
Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Mariana Matus
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
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7
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Nguyen LH, Anyane-Yeboa A, Klaser K, Merino J, Drew DA, Ma W, Mehta RS, Kim DY, Warner ET, Joshi AD, Graham MS, Sudre CH, Thompson EJ, May A, Hu C, Jørgensen S, Selvachandran S, Berry SE, David SP, Martinez ME, Figueiredo JC, Murray AM, Sanders AR, Koenen KC, Wolf J, Ourselin S, Spector TD, Steves CJ, Chan AT. The mental health burden of racial and ethnic minorities during the COVID-19 pandemic. PLoS One 2022; 17:e0271661. [PMID: 35947543 PMCID: PMC9365178 DOI: 10.1371/journal.pone.0271661] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Racial/ethnic minorities have been disproportionately impacted by COVID-19. The effects of COVID-19 on the long-term mental health of minorities remains unclear. To evaluate differences in odds of screening positive for depression and anxiety among various racial and ethnic groups during the latter phase of the COVID-19 pandemic, we performed a cross-sectional analysis of 691,473 participants nested within the prospective smartphone-based COVID Symptom Study in the United States (U.S.) and United Kingdom (U.K). from February 23, 2021 to June 9, 2021. In the U.S. (n=57,187), compared to White participants, the multivariable odds ratios (ORs) for screening positive for depression were 1·16 (95% CI: 1·02 to 1·31) for Black, 1·23 (1·11 to 1·36) for Hispanic, and 1·15 (1·02 to 1·30) for Asian participants, and 1·34 (1·13 to 1·59) for participants reporting more than one race/other even after accounting for personal factors such as prior history of a mental health disorder, COVID-19 infection status, and surrounding lockdown stringency. Rates of screening positive for anxiety were comparable. In the U.K. (n=643,286), racial/ethnic minorities had similarly elevated rates of positive screening for depression and anxiety. These disparities were not fully explained by changes in leisure time activities. Racial/ethnic minorities bore a disproportionate mental health burden during the COVID-19 pandemic. These differences will need to be considered as health care systems transition from prioritizing infection control to mitigating long-term consequences.
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Affiliation(s)
- Long H. Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Adjoa Anyane-Yeboa
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Jordi Merino
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - David A. Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Wenjie Ma
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Raaj S. Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Daniel Y. Kim
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Erica T. Warner
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Amit D. Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Mark S. Graham
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Carole H. Sudre
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Ellen J. Thompson
- Harvard/MGH Center on Genomics, Vulnerable Populations, and Health Disparities, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | | | | | | | | | - Sarah E. Berry
- Department of Nutritional Sciences, King’s College London, London, United Kingdom
| | - Sean P. David
- Department of Family Medicine, University of Chicago, Evanston, IL, United States of America
| | - Maria Elena Martinez
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, United States of America
- Department of Family Medicine and Public Health, University of California at San Diego, La Jolla, CA, United States of America
| | - Jane C. Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Anne M. Murray
- Division of Geriatrics, Department of Medicine, Hennepin Healthcare, University of Minnesota, Minneapolis, MN, United States of America
- Berman Center for Outcomes and Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare, Minneapolis, MN, United States of America
| | - Alan R. Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL, United States of America
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, United States of America
| | - Karestan C. Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | | | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Claire J. Steves
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health,
Boston, MA, United States of America
- Massachusetts Consortium on Pathogen Readiness, Cambridge, MA, United States of America
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8
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Banday AR, Stanifer ML, Florez-Vargas O, Onabajo OO, Papenberg BW, Zahoor MA, Mirabello L, Ring TJ, Lee CH, Albert PS, Andreakos E, Arons E, Barsh G, Biesecker LG, Boyle DL, Brahier MS, Burnett-Hartman A, Carrington M, Chang E, Choe PG, Chisholm RL, Colli LM, Dalgard CL, Dude CM, Edberg J, Erdmann N, Feigelson HS, Fonseca BA, Firestein GS, Gehring AJ, Guo C, Ho M, Holland S, Hutchinson AA, Im H, Irby L, Ison MG, Joseph NT, Kim HB, Kreitman RJ, Korf BR, Lipkin SM, Mahgoub SM, Mohammed I, Paschoalini GL, Pacheco JA, Peluso MJ, Rader DJ, Redden DT, Ritchie MD, Rosenblum B, Ross ME, Anna HPS, Savage SA, Sharma S, Siouti E, Smith AK, Triantafyllia V, Vargas JM, Vargas JD, Verma A, Vij V, Wesemann DR, Yeager M, Yu X, Zhang Y, Boulant S, Chanock SJ, Feld JJ, Prokunina-Olsson L. Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries. Nat Genet 2022; 54:1103-1116. [PMID: 35835913 PMCID: PMC9355882 DOI: 10.1038/s41588-022-01113-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 05/26/2022] [Indexed: 12/22/2022]
Abstract
The chr12q24.13 locus encoding OAS1-OAS3 antiviral proteins has been associated with coronavirus disease 2019 (COVID-19) susceptibility. Here, we report genetic, functional and clinical insights into this locus in relation to COVID-19 severity. In our analysis of patients of European (n = 2,249) and African (n = 835) ancestries with hospitalized versus nonhospitalized COVID-19, the risk of hospitalized disease was associated with a common OAS1 haplotype, which was also associated with reduced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance in a clinical trial with pegIFN-λ1. Bioinformatic analyses and in vitro studies reveal the functional contribution of two associated OAS1 exonic variants comprising the risk haplotype. Derived human-specific alleles rs10774671-A and rs1131454 -A decrease OAS1 protein abundance through allele-specific regulation of splicing and nonsense-mediated decay (NMD). We conclude that decreased OAS1 expression due to a common haplotype contributes to COVID-19 severity. Our results provide insight into molecular mechanisms through which early treatment with interferons could accelerate SARS-CoV-2 clearance and mitigate against severe COVID-19.
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Affiliation(s)
- A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Olusegun O Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Brenen W Papenberg
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Muhammad A Zahoor
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Timothy J Ring
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Chia-Han Lee
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Paul S Albert
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Evgeny Arons
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Greg Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - David L Boyle
- Altman Clinical & Translational Research Institute, UC San Diego Health Sciences, San Diego, CA, USA
| | - Mark S Brahier
- Georgetown University School of Medicine, Washington, DC, USA
| | | | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Euijin Chang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leandro M Colli
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Clifton L Dalgard
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Carolynn M Dude
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeff Edberg
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nathan Erdmann
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Benedito A Fonseca
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Gary S Firestein
- Altman Clinical & Translational Research Institute, UC San Diego Health Sciences, San Diego, CA, USA
| | - Adam J Gehring
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Cuncai Guo
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle Ho
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Steven Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hogune Im
- Genome Opinion, Inc., Seoul, Republic of Korea
| | - Les'Shon Irby
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Naima T Joseph
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Robert J Kreitman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven M Lipkin
- Department of Medicine and Program in Mendelian Genetics, Weill Cornell Medicine, New York, NY, USA
| | - Siham M Mahgoub
- Department of Medicine, Infectious Diseases Division, Howard University Hospital, Howard University College of Medicine, Washington, DC, USA
| | - Iman Mohammed
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Guilherme L Paschoalini
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, CA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David T Redden
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brooke Rosenblum
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Hanaisa P Sant Anna
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, National Human Genome Center, Howard University College of Medicine, Washington, DC, USA
| | - Eleni Siouti
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Vasiliki Triantafyllia
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Joselin M Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jose D Vargas
- Veterans Affairs Medical Center, Washington, DC, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vibha Vij
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jordan J Feld
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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9
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Obermeyer F, Jankowiak M, Barkas N, Schaffner SF, Pyle JD, Yurkovetskiy L, Bosso M, Park DJ, Babadi M, MacInnis BL, Luban J, Sabeti PC, Lemieux JE. Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness. Science 2022; 376:1327-1332. [PMID: 35608456 PMCID: PMC9161372 DOI: 10.1126/science.abm1208] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Repeated emergence of SARS-CoV-2 variants with increased fitness underscores the value of rapid detection and characterization of new lineages. We have developed PyR0, a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR0 to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR0 forecasts growth of new lineages from their mutational profile, ranks the fitness of lineages as new sequences become available, and prioritizes mutations of biological and public health concern for functional characterization.
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10
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He X, Aid M, Chandrashekar A, Yu J, McMahan K, Wegmann F, Jacob-Dolan C, Maron JS, Atyeo C, Wan H, Sellers D, Liu J, Lifton M, Gardner S, Bondzie EA, Barrett J, Ahmad K, Anioke T, Yalley-Ogunro J, Muench J, Goode A, Andersen H, Lewis MG, Alter G, Schuitemaker H, Zahn R, Barouch DH. A homologous or variant booster vaccine after Ad26.COV2.S immunization enhances SARS-CoV-2-specific immune responses in rhesus macaques. Sci Transl Med 2022; 14:eabm4996. [PMID: 35191769 PMCID: PMC9802654 DOI: 10.1126/scitranslmed.abm4996] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/11/2022] [Indexed: 01/12/2023]
Abstract
Ad26.COV2.S has demonstrated durability and clinical efficacy against symptomatic COVID-19 in humans. In this study, we report the correlates of durability of humoral and cellular immune responses in 20 rhesus macaques immunized with single-shot Ad26.COV2.S and the immunogenicity of a booster shot at 8 to 10 months after the initial immunization. Ad26.COV2.S elicited durable binding and neutralizing antibodies as well as memory B cells and long-lived bone marrow plasma cells. Innate immune responses and bone marrow plasma cell responses correlated with durable antibody responses. After Ad26.COV2.S boost immunization, binding and neutralizing antibody responses against multiple SARS-CoV-2 variants increased 31- to 69-fold and 23- to 43-fold, respectively, compared with preboost concentrations. Antigen-specific B cell and T cell responses also increased substantially after the boost immunization. Boosting with a modified Ad26.COV2.S.351 vaccine expressing the SARS-CoV-2 spike protein from the beta variant led to largely comparable responses with slightly higher beta- and omicron-specific humoral immune responses. These data demonstrate that a late boost with Ad26.COV2.S or Ad26.COV2.S.351 resulted in a marked increase in humoral and cellular immune responses that were highly cross-reactive across multiple SARS-CoV-2 variants in rhesus macaques.
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Affiliation(s)
- Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Malika Aid
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Frank Wegmann
- Janssen Vaccines and Prevention, Leiden, Netherlands
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Jenny S. Maron
- Harvard Medical School, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Caroline Atyeo
- Harvard Medical School, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Daniel Sellers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Michelle Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Sarah Gardner
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Esther A. Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kunza Ahmad
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | | | | | | | | | - Galit Alter
- Harvard Medical School, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hanneke Schuitemaker
- Janssen Vaccines and Prevention, Leiden, Netherlands
- Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Roland Zahn
- Janssen Vaccines and Prevention, Leiden, Netherlands
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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11
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Finch E, Lowe R, Fischinger S, de St Aubin M, Siddiqui SM, Dayal D, Loesche MA, Rhee J, Beger S, Hu Y, Gluck MJ, Mormann B, Hasdianda MA, Musk ER, Alter G, Menon AS, Nilles EJ, Kucharski AJ. SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort. PLoS Biol 2022; 20:e3001531. [PMID: 35143473 PMCID: PMC8865659 DOI: 10.1371/journal.pbio.3001531] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 02/23/2022] [Accepted: 01/07/2022] [Indexed: 11/28/2022] Open
Abstract
Identifying the potential for SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort of 4,411 United States employees in 4 states between April 2020 and February 2021. We conducted a multivariable logistic regression investigating the association between baseline serological status and subsequent PCR test result in order to calculate an odds ratio for reinfection. We estimated an odds ratio for reinfection ranging from 0.14 (95% CI: 0.019 to 0.63) to 0.28 (95% CI: 0.05 to 1.1), implying that the presence of SARS-CoV-2 antibodies at baseline is associated with around 72% to 86% reduced odds of a subsequent PCR positive test based on our point estimates. This suggests that primary infection with SARS-CoV-2 provides protection against reinfection in the majority of individuals, at least over a 6-month time period. We also highlight 2 major sources of bias and uncertainty to be considered when estimating the relative risk of reinfection, confounders and the choice of baseline time point, and show how to account for both in reinfection analysis. Identifying the potential for SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. Analysis of a seroepidemiological cohort suggests that primary infection with SARS-CoV-2 protects against reinfection in the majority of individuals, at least over a six month period.
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Affiliation(s)
- Emilie Finch
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Institut für HIV Forschung, Universität Duisburg-Essen, Duisburg, Germany
| | - Michael de St Aubin
- Harvard Humanitarian Initiative, Cambridge, Massachusetts, United States of America
| | - Sameed M. Siddiqui
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Diana Dayal
- Space Exploration Technologies Corp, Hawthorne, California, United States of America
| | - Michael A. Loesche
- Space Exploration Technologies Corp, Hawthorne, California, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Justin Rhee
- Space Exploration Technologies Corp, Hawthorne, California, United States of America
| | - Samuel Beger
- Space Exploration Technologies Corp, Hawthorne, California, United States of America
| | - Yiyuan Hu
- Space Exploration Technologies Corp, Hawthorne, California, United States of America
| | - Matthew J. Gluck
- Space Exploration Technologies Corp, Hawthorne, California, United States of America
| | - Benjamin Mormann
- Space Exploration Technologies Corp, Hawthorne, California, United States of America
| | | | - Elon R. Musk
- Space Exploration Technologies Corp, Hawthorne, California, United States of America
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Anil S. Menon
- Space Exploration Technologies Corp, Hawthorne, California, United States of America
| | - Eric J. Nilles
- Harvard Humanitarian Initiative, Cambridge, Massachusetts, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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12
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Nabel KG, Clark SA, Shankar S, Pan J, Clark LE, Yang P, Coscia A, McKay LGA, Varnum HH, Brusic V, Tolan NV, Zhou G, Desjardins M, Turbett SE, Kanjilal S, Sherman AC, Dighe A, LaRocque RC, Ryan ET, Tylek C, Cohen-Solal JF, Darcy AT, Tavella D, Clabbers A, Fan Y, Griffiths A, Correia IR, Seagal J, Baden LR, Charles RC, Abraham J. Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain. Science 2022; 375:eabl6251. [PMID: 34855508 PMCID: PMC9127715 DOI: 10.1126/science.abl6251] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- BNT162 Vaccine/immunology
- Betacoronavirus/immunology
- COVID-19/immunology
- COVID-19/virology
- Cross Reactions
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Epitopes
- Evolution, Molecular
- Humans
- Immune Evasion
- Models, Molecular
- Mutation
- Polysaccharides/analysis
- Protein Binding
- Protein Domains
- Receptors, Coronavirus/chemistry
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Viral Pseudotyping
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Affiliation(s)
- Katherine G. Nabel
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah A. Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sundaresh Shankar
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Junhua Pan
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lars E. Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Pan Yang
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Adrian Coscia
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay G. A. McKay
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Haley H. Varnum
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Vesna Brusic
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole V. Tolan
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Guohai Zhou
- Center for Clinical Investigation, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Michaël Desjardins
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Centre Hospitalier de l’Université de Montréal, Montreal QC H2X 0C1, Canada
| | - Sarah E. Turbett
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sanjat Kanjilal
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Amy C. Sherman
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anand Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Edward T. Ryan
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Casey Tylek
- AbbVie Bioresearch Center, Worcester, MA 01605, USA
| | | | | | | | | | - Yao Fan
- AbbVie Bioresearch Center, Worcester, MA 01605, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Jane Seagal
- AbbVie Bioresearch Center, Worcester, MA 01605, USA
| | - Lindsey R. Baden
- Center for Clinical Investigation, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Richelle C. Charles
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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13
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Collier ARY, Yu J, McMahan K, Liu J, Chandrashekar A, Maron JS, Atyeo C, Martinez DR, Ansel JL, Aguayo R, Rowe M, Jacob-Dolan C, Sellers D, Barrett J, Ahmad K, Anioke T, VanWyk H, Gardner S, Powers O, Bondzie EA, Wan H, Baric RS, Alter G, Hacker MR, Barouch DH. Differential Kinetics of Immune Responses Elicited by Covid-19 Vaccines. N Engl J Med 2021; 385:2010-2012. [PMID: 34648703 PMCID: PMC8531985 DOI: 10.1056/nejmc2115596] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Jingyou Yu
- Beth Israel Deaconess Medical Center, Boston, MA
| | | | - Jinyan Liu
- Beth Israel Deaconess Medical Center, Boston, MA
| | | | - Jenny S Maron
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | | | - Kunza Ahmad
- Beth Israel Deaconess Medical Center, Boston, MA
| | - Tochi Anioke
- Beth Israel Deaconess Medical Center, Boston, MA
| | - Haley VanWyk
- Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | | | - Huahua Wan
- Beth Israel Deaconess Medical Center, Boston, MA
| | - Ralph S Baric
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
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14
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Zhang J, Cai Y, Xiao T, Lu J, Peng H, Sterling SM, Walsh RM, Rits-Volloch S, Zhu H, Woosley AN, Yang W, Sliz P, Chen B. Structural impact on SARS-CoV-2 spike protein by D614G substitution. Science 2021; 372:525-530. [PMID: 33727252 PMCID: PMC8139424 DOI: 10.1126/science.abf2303] [Citation(s) in RCA: 267] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/10/2021] [Indexed: 12/14/2022]
Abstract
Substitution for aspartic acid (D) by glycine (G) at position 614 in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appears to facilitate rapid viral spread. The G614 strain and its recent variants are now the dominant circulating forms. Here, we report cryo-electron microscopy structures of a full-length G614 S trimer, which adopts three distinct prefusion conformations that differ primarily by the position of one receptor-binding domain. A loop disordered in the D614 S trimer wedges between domains within a protomer in the G614 spike. This added interaction appears to prevent premature dissociation of the G614 trimer-effectively increasing the number of functional spikes and enhancing infectivity-and to modulate structural rearrangements for membrane fusion. These findings extend our understanding of viral entry and suggest an improved immunogen for vaccine development.
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Affiliation(s)
- Jun Zhang
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Yongfei Cai
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Tianshu Xiao
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jianming Lu
- Codex BioSolutions, Inc., Gaithersburg, MD 20879, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sarah M Sterling
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Richard M Walsh
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sophia Rits-Volloch
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA 02115, USA
| | - Alec N Woosley
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA 02115, USA
| | - Wei Yang
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA 02115, USA
| | - Piotr Sliz
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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15
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Yu J, Tostanoski LH, Peter L, Mercado NB, McMahan K, Mahrokhian SH, Nkolola JP, Liu J, Li Z, Chandrashekar A, Martinez DR, Loos C, Atyeo C, Fischinger S, Burke JS, Slein MD, Chen Y, Zuiani A, Lelis FJN, Travers M, Habibi S, Pessaint L, Van Ry A, Blade K, Brown R, Cook A, Finneyfrock B, Dodson A, Teow E, Velasco J, Zahn R, Wegmann F, Bondzie EA, Dagotto G, Gebre MS, He X, Jacob-Dolan C, Kirilova M, Kordana N, Lin Z, Maxfield LF, Nampanya F, Nityanandam R, Ventura JD, Wan H, Cai Y, Chen B, Schmidt AG, Wesemann DR, Baric RS, Alter G, Andersen H, Lewis MG, Barouch DH. DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science 2020; 369:806-811. [PMID: 32434945 PMCID: PMC7243363 DOI: 10.1126/science.abc6284] [Citation(s) in RCA: 817] [Impact Index Per Article: 204.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/16/2020] [Indexed: 12/22/2022]
Abstract
The global coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made the development of a vaccine a top biomedical priority. In this study, we developed a series of DNA vaccine candidates expressing different forms of the SARS-CoV-2 spike (S) protein and evaluated them in 35 rhesus macaques. Vaccinated animals developed humoral and cellular immune responses, including neutralizing antibody titers at levels comparable to those found in convalescent humans and macaques infected with SARS-CoV-2. After vaccination, all animals were challenged with SARS-CoV-2, and the vaccine encoding the full-length S protein resulted in >3.1 and >3.7 log10 reductions in median viral loads in bronchoalveolar lavage and nasal mucosa, respectively, as compared with viral loads in sham controls. Vaccine-elicited neutralizing antibody titers correlated with protective efficacy, suggesting an immune correlate of protection. These data demonstrate vaccine protection against SARS-CoV-2 in nonhuman primates.
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MESH Headings
- Adjuvants, Immunologic
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Betacoronavirus/immunology
- Betacoronavirus/physiology
- Bronchoalveolar Lavage Fluid/virology
- COVID-19
- COVID-19 Vaccines
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Disease Models, Animal
- Female
- Humans
- Immunity, Cellular
- Immunity, Humoral
- Immunization, Secondary
- Immunogenicity, Vaccine
- Immunologic Memory
- Macaca mulatta
- Male
- Mutant Proteins/chemistry
- Mutant Proteins/immunology
- Nasal Mucosa/virology
- Pandemics/prevention & control
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- Protein Domains
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vaccination
- Vaccines, DNA/administration & dosage
- Vaccines, DNA/immunology
- Viral Load
- Viral Vaccines/administration & dosage
- Viral Vaccines/immunology
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Affiliation(s)
- Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lisa H Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lauren Peter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Shant H Mahrokhian
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Zhenfeng Li
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - John S Burke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Matthew D Slein
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Yuezhou Chen
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adam Zuiani
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Felipe J N Lelis
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Meghan Travers
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shaghayegh Habibi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | - Roland Zahn
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Frank Wegmann
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Esther A Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Gabriel Dagotto
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Makda S Gebre
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Marinela Kirilova
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Nicole Kordana
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Zijin Lin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lori F Maxfield
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ramya Nityanandam
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - John D Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | - Bing Chen
- Children's Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
| | - Duane R Wesemann
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
| | | | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
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