Defining the risk of SARS-CoV-2 variants on immune protection

DeGrace, Marciela M.; Ghedin, Elodie; Frieman, Matthew B.; Krammer, Florian; Grifoni, Alba; Alisoltani, Arghavan; Alter, Galit; Amara, Rama R.; Baric, Ralph S.; Barouch, Dan H.; Bloom, Jesse D.; Bloyet, Louis-Marie; Bonenfant, Gaston; Boon, Adrianus C. M.; Boritz, Eli A.; Bratt, Debbie L.; Bricker, Traci L.; Brown, Liliana; Buchser, William J.; Carreño, Juan Manuel; Cohen-Lavi, Liel; Darling, Tamarand L.; Davis-Gardner, Meredith E.; Dearlove, Bethany L.; Di, Han; Dittmann, Meike; Doria-Rose, Nicole A.; Douek, Daniel C.; Drosten, Christian; Edara, Venkata-Viswanadh; Ellebedy, Ali; Fabrizio, Thomas P.; Ferrari, Guido; Fischer, Will M.; Florence, William C.; Fouchier, Ron A. M.; Franks, John; García-Sastre, Adolfo; Godzik, Adam; Gonzalez-Reiche, Ana Silvia; Gordon, Aubree; Haagmans, Bart L.; Halfmann, Peter J.; Ho, David D.; Holbrook, Michael R.; Huang, Yaoxing; James, Sarah L.; Jaroszewski, Lukasz; Jeevan, Trushar; Johnson, Robert M.; Jones, Terry C.; Joshi, Astha; Kawaoka, Yoshihiro; Kercher, Lisa; Koopmans, Marion P. G.; Korber, Bette; Koren, Eilay; Koup, Richard A.; LeGresley, Eric B.; Lemieux, Jacob E.; Liebeskind, Mariel J.; Liu, Zhuoming; Livingston, Brandi; Logue, James P.; Luo, Yang; McDermott, Adrian B.; McElrath, Margaret J.; Meliopoulos, Victoria A.; Menachery, Vineet D.; Montefiori, David C.; Mühlemann, Barbara; Munster, Vincent J.; Munt, Jenny E.; Nair, Manoj S.; Netzl, Antonia; Niewiadomska, Anna M.; O’Dell, Sijy; Pekosz, Andrew; Perlman, Stanley; Pontelli, Marjorie C.; Rockx, Barry; Rolland, Morgane; Rothlauf, Paul W.; Sacharen, Sinai; Scheuermann, Richard H.; Schmidt, Stephen D.; Schotsaert, Michael; Schultz-Cherry, Stacey; Seder, Robert A.; Sedova, Mayya; Sette, Alessandro; Shabman, Reed S.; Shen, Xiaoying; Shi, Pei-Yong; Shukla, Maulik; Simon, Viviana; Stumpf, Spencer; Sullivan, Nancy J.; Thackray, Larissa B.; Theiler, James; Thomas, Paul G.; Trifkovic, Sanja; Türeli, Sina; Turner, Samuel A.; Vakaki, Maria A.; Bakel, Harm; VanBlargan, Laura A.; Vincent, Leah R.; Wallace, Zachary S.; Wang, Li; Wang, Maple; Wang, Pengfei; Wang, Wei; Weaver, Scott C.; Webby, Richard J.; Weiss, Carol D.; Wentworth, David E.; Weston, Stuart M.; Whelan, Sean P. J.; Whitener, Bradley M.; Wilks, Samuel H.; Xie, Xuping; Ying, Baoling; Yoon, Hyejin; Zhou, Bin; Hertz, Tomer; Smith, Derek J.; Diamond, Michael S.; Post, Diane J.; Suthar, Mehul S.

Defining the risk of SARS-CoV-2 variants on immune protection

Marciela M. DeGrace, Elodie Ghedin, Matthew B. Frieman, Florian Krammer (), Alba Grifoni, Arghavan Alisoltani, Galit Alter, Rama R. Amara, Ralph S. Baric, Dan H. Barouch, Jesse D. Bloom, Louis-Marie Bloyet, Gaston Bonenfant, Adrianus C. M. Boon, Eli A. Boritz, Debbie L. Bratt, Traci L. Bricker, Liliana Brown, William J. Buchser, Juan Manuel Carreño, Liel Cohen-Lavi, Tamarand L. Darling, Meredith E. Davis-Gardner, Bethany L. Dearlove, Han Di, Meike Dittmann, Nicole A. Doria-Rose, Daniel C. Douek, Christian Drosten, Venkata-Viswanadh Edara, Ali Ellebedy, Thomas P. Fabrizio, Guido Ferrari, Will M. Fischer, William C. Florence, Ron A. M. Fouchier, John Franks, Adolfo García-Sastre, Adam Godzik, Ana Silvia Gonzalez-Reiche, Aubree Gordon, Bart L. Haagmans, Peter J. Halfmann, David D. Ho, Michael R. Holbrook, Yaoxing Huang, Sarah L. James, Lukasz Jaroszewski, Trushar Jeevan, Robert M. Johnson, Terry C. Jones, Astha Joshi, Yoshihiro Kawaoka, Lisa Kercher, Marion P. G. Koopmans, Bette Korber, Eilay Koren, Richard A. Koup, Eric B. LeGresley, Jacob E. Lemieux, Mariel J. Liebeskind, Zhuoming Liu, Brandi Livingston, James P. Logue, Yang Luo, Adrian B. McDermott, Margaret J. McElrath, Victoria A. Meliopoulos, Vineet D. Menachery, David C. Montefiori, Barbara Mühlemann, Vincent J. Munster, Jenny E. Munt, Manoj S. Nair, Antonia Netzl, Anna M. Niewiadomska, Sijy O’Dell, Andrew Pekosz, Stanley Perlman, Marjorie C. Pontelli, Barry Rockx, Morgane Rolland, Paul W. Rothlauf, Sinai Sacharen, Richard H. Scheuermann, Stephen D. Schmidt, Michael Schotsaert, Stacey Schultz-Cherry, Robert A. Seder, Mayya Sedova, Alessandro Sette, Reed S. Shabman, Xiaoying Shen, Pei-Yong Shi, Maulik Shukla, Viviana Simon, Spencer Stumpf, Nancy J. Sullivan, Larissa B. Thackray, James Theiler, Paul G. Thomas, Sanja Trifkovic, Sina Türeli, Samuel A. Turner, Maria A. Vakaki, Harm Bakel, Laura A. VanBlargan, Leah R. Vincent, Zachary S. Wallace, Li Wang, Maple Wang, Pengfei Wang, Wei Wang, Scott C. Weaver, Richard J. Webby, Carol D. Weiss, David E. Wentworth, Stuart M. Weston, Sean P. J. Whelan, Bradley M. Whitener, Samuel H. Wilks, Xuping Xie, Baoling Ying, Hyejin Yoon, Bin Zhou, Tomer Hertz (), Derek J. Smith (), Michael S. Diamond (), Diane J. Post () and Mehul S. Suthar ()
Additional contact information
Marciela M. DeGrace: National Institutes of Health
Elodie Ghedin: National Institutes of Health
Matthew B. Frieman: The University of Maryland School of Medicine
Florian Krammer: Icahn School of Medicine at Mount Sinai
Alba Grifoni: La Jolla Institute for Immunology
Arghavan Alisoltani: University of California Riverside School of Medicine
Galit Alter: Ragon Institute of MGH, MIT, and Harvard
Rama R. Amara: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University School of Medicine
Ralph S. Baric: University of North Carolina at Chapel Hill
Dan H. Barouch: Beth Israel Deaconess Medical Center
Jesse D. Bloom: Howard Hughes Medical Institute
Louis-Marie Bloyet: Washington University School of Medicine
Gaston Bonenfant: CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention
Adrianus C. M. Boon: Washington University in St Louis
Eli A. Boritz: National Institutes of Health
Debbie L. Bratt: National Institutes of Health
Traci L. Bricker: Washington University in St Louis
Liliana Brown: National Institutes of Health
William J. Buchser: Washington University School of Medicine
Juan Manuel Carreño: Icahn School of Medicine at Mount Sinai
Liel Cohen-Lavi: Ben-Gurion University of the Negev
Tamarand L. Darling: Washington University in St Louis
Meredith E. Davis-Gardner: Emory Vaccine Center, Emory University School of Medicine
Bethany L. Dearlove: US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research
Han Di: CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention
Meike Dittmann: New York University Grossman School of Medicine
Nicole A. Doria-Rose: National Institutes of Health
Daniel C. Douek: National Institutes of Health
Christian Drosten: Charité–Universitätsmedizin and German Center for Infection Research (DZIF)
Venkata-Viswanadh Edara: Emory Vaccine Center, Emory University School of Medicine
Ali Ellebedy: Washington University School of Medicine
Thomas P. Fabrizio: St Jude Children’s Research Hospital
Guido Ferrari: Duke University Medical Center
Will M. Fischer: New Mexico Consortium
William C. Florence: National Institutes of Health
Ron A. M. Fouchier: Erasmus MC
John Franks: St Jude Children’s Research Hospital
Adolfo García-Sastre: Icahn School of Medicine at Mount Sinai
Adam Godzik: University of California Riverside School of Medicine
Ana Silvia Gonzalez-Reiche: Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai
Aubree Gordon: University of Michigan
Bart L. Haagmans: Erasmus MC
Peter J. Halfmann: University of Wisconsin
David D. Ho: Columbia University Vagelos College of Physicians and Surgeons
Michael R. Holbrook: National Institute of Allergy and Infectious Diseases Integrated Research Facility
Yaoxing Huang: Columbia University Vagelos College of Physicians and Surgeons
Sarah L. James: University of Cambridge
Lukasz Jaroszewski: University of California Riverside School of Medicine
Trushar Jeevan: St Jude Children’s Research Hospital
Robert M. Johnson: The University of Maryland School of Medicine
Terry C. Jones: Charité–Universitätsmedizin and German Center for Infection Research (DZIF)
Astha Joshi: Washington University in St Louis
Yoshihiro Kawaoka: University of Wisconsin
Lisa Kercher: St Jude Children’s Research Hospital
Marion P. G. Koopmans: Erasmus MC
Bette Korber: New Mexico Consortium
Eilay Koren: Ben-Gurion University of the Negev
Richard A. Koup: National Institutes of Health
Eric B. LeGresley: University of Cambridge
Jacob E. Lemieux: Broad Institute of MIT and Harvard
Mariel J. Liebeskind: Washington University School of Medicine
Zhuoming Liu: Washington University School of Medicine
Brandi Livingston: St Jude Children’s Research Hospital
James P. Logue: The University of Maryland School of Medicine
Yang Luo: Columbia University Vagelos College of Physicians and Surgeons
Adrian B. McDermott: National Institutes of Health
Margaret J. McElrath: Fred Hutchinson Cancer Research Center
Victoria A. Meliopoulos: St Jude Children’s Research Hospital
Vineet D. Menachery: University of Texas Medical Branch
David C. Montefiori: Duke University Medical Center
Barbara Mühlemann: Charité–Universitätsmedizin and German Center for Infection Research (DZIF)
Vincent J. Munster: National Institute of Allergy and Infectious Diseases, National Institutes of Health
Jenny E. Munt: University of North Carolina at Chapel Hill
Manoj S. Nair: Columbia University Vagelos College of Physicians and Surgeons
Antonia Netzl: University of Cambridge
Anna M. Niewiadomska: J. Craig Venter Institute
Sijy O’Dell: National Institutes of Health
Andrew Pekosz: Johns Hopkins Bloomberg School of Public Health
Stanley Perlman: University of Iowa
Marjorie C. Pontelli: Washington University School of Medicine
Barry Rockx: Erasmus MC
Morgane Rolland: US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research
Paul W. Rothlauf: Washington University School of Medicine
Sinai Sacharen: Ben-Gurion University of the Negev
Richard H. Scheuermann: J. Craig Venter Institute
Stephen D. Schmidt: National Institutes of Health
Michael Schotsaert: Icahn School of Medicine at Mount Sinai
Stacey Schultz-Cherry: St Jude Children’s Research Hospital
Robert A. Seder: National Institutes of Health
Mayya Sedova: University of California Riverside School of Medicine
Alessandro Sette: La Jolla Institute for Immunology
Reed S. Shabman: National Institutes of Health
Xiaoying Shen: Duke University Medical Center
Pei-Yong Shi: The University of Texas Medical Branch
Maulik Shukla: University of Chicago
Viviana Simon: Icahn School of Medicine at Mount Sinai
Spencer Stumpf: Washington University School of Medicine
Nancy J. Sullivan: National Institutes of Health
Larissa B. Thackray: Washington University in St Louis
James Theiler: New Mexico Consortium
Paul G. Thomas: St Jude Children’s Research Hospital
Sanja Trifkovic: St Jude Children’s Research Hospital
Sina Türeli: University of Cambridge
Samuel A. Turner: University of Cambridge
Maria A. Vakaki: Washington University School of Medicine
Harm Bakel: Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai
Laura A. VanBlargan: Washington University in St Louis
Leah R. Vincent: National Institutes of Health
Zachary S. Wallace: J. Craig Venter Institute
Li Wang: CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention
Maple Wang: Columbia University Vagelos College of Physicians and Surgeons
Pengfei Wang: Columbia University Vagelos College of Physicians and Surgeons
Wei Wang: US Food and Drug Administration
Scott C. Weaver: University of Texas Medical Branch
Richard J. Webby: St Jude Children’s Research Hospital
Carol D. Weiss: US Food and Drug Administration
David E. Wentworth: CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention
Stuart M. Weston: The University of Maryland School of Medicine
Sean P. J. Whelan: Washington University School of Medicine
Bradley M. Whitener: Washington University in St Louis
Samuel H. Wilks: University of Cambridge
Xuping Xie: The University of Texas Medical Branch
Baoling Ying: Washington University in St Louis
Hyejin Yoon: New Mexico Consortium
Bin Zhou: CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention
Tomer Hertz: Immunology and Genetics Faculty of Health Sciences Ben-Gurion University of the Negev
Derek J. Smith: University of Cambridge
Michael S. Diamond: Washington University in St Louis
Diane J. Post: National Institutes of Health
Mehul S. Suthar: Emory Vaccine Center, Emory University School of Medicine

Nature, 2022, vol. 605, issue 7911, 640-652

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41586-022-04690-5

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