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DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Fischer WM, Florence WC, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli S, Turner SA, Vakaki MA, van Bakel H, VanBlargan LA, Vincent LR, Wallace ZS, Wang L, Wang M, Wang P, Wang W, Weaver SC, Webby RJ, Weiss CD, Wentworth DE, Weston SM, Whelan SPJ, Whitener BM, Wilks SH, Xie X, Ying B, Yoon H, Zhou B, Hertz T, Smith DJ, Diamond MS, Post DJ, Suthar MS. Defining the risk of SARS-CoV-2 variants on immune protection. Nature 2022; 605:640-652. [PMID: 35361968 PMCID: PMC9345323 DOI: 10.1038/s41586-022-04690-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [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: 11/25/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022]
Abstract
The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.
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Affiliation(s)
- Marciela M DeGrace
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Elodie Ghedin
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institutes of Health, Rockville, MD, USA
| | - Matthew B Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA
| | - Rama R Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jesse D Bloom
- Fred Hutch Cancer Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Gaston Bonenfant
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Eli A Boritz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Debbie L Bratt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- CAMRIS, Contractor for NIAID, Bethesda, MD, USA
| | - Traci L Bricker
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Liliana Brown
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - William J Buchser
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liel Cohen-Lavi
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Tamarand L Darling
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Meredith E Davis-Gardner
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Bethany L Dearlove
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Han Di
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Meike Dittmann
- Microbiology Department, New York University Grossman School of Medicine, New York, NY, USA
| | - Nicole A Doria-Rose
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Daniel C Douek
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
| | - Venkata-Viswanadh Edara
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ali Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thomas P Fabrizio
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Will M Fischer
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - William C Florence
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | | | - John Franks
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Godzik
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Ana Silvia Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Bart L Haagmans
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Michael R Holbrook
- National Institute of Allergy and Infectious Diseases Integrated Research Facility, Frederick, MD, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sarah L James
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Lukasz Jaroszewski
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Trushar Jeevan
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert M Johnson
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Astha Joshi
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Lisa Kercher
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Bette Korber
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Eilay Koren
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Richard A Koup
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Mariel J Liebeskind
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Brandi Livingston
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - James P Logue
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Adrian B McDermott
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | | | - Victoria A Meliopoulos
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jenny E Munt
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Sijy O'Dell
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Marjorie C Pontelli
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Barry Rockx
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Morgane Rolland
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sinai Sacharen
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | | | - Stephen D Schmidt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert A Seder
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Mayya Sedova
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 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
| | - Reed S Shabman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Maulik Shukla
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Spencer Stumpf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Nancy J Sullivan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - James Theiler
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Samuel A Turner
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Maria A Vakaki
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Leah R Vincent
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Zachary S Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Li Wang
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wei Wang
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Carol D Weiss
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - David E Wentworth
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stuart M Weston
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Baoling Ying
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Bin Zhou
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tomer Hertz
- Department of Microbiology, Immunology and Genetics Faculty of Health Sciences Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Michael S Diamond
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Diane J Post
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Mehul S Suthar
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
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