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1. US National Institutes of Health Prioritization of SARS-CoV-2 Variants

Author

Sam Turner, Arghavan Alisoltani, Debbie Bratt, Liel Cohen-Lavi, Bethany L. Dearlove, Christian Drosten, Will M. Fischer, Ron A.M. Fouchier, Ana Silvia Gonzalez-Reiche, Lukasz Jaroszewski, Zain Khalil, Eric LeGresley, Marc Johnson, Terry C. Jones, Barbara Mühlemann, David O’Connor, Mayya Sedova, Maulik Shukla, James Theiler, Zachary S. Wallace, Hyejin Yoon, Yun Zhang, Harm van Bakel, Marciela M. Degrace, Elodie Ghedin, Adam Godzik, Tomer Hertz, Bette Korber, Jacob Lemieux, Anna M. Niewiadomska, Diane J. Post, Morgane Rolland, Richard Scheuermann, and Derek J. Smith

Subjects
COVID-19, 2019 novel coronavirus disease, coronavirus disease, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, viruses, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

Since late 2020, SARS-CoV-2 variants have regularly emerged with competitive and phenotypic differences from previously circulating strains, sometimes with the potential to escape from immunity produced by prior exposure and infection. The Early Detection group is one of the constituent groups of the US National Institutes of Health National Institute of Allergy and Infectious Diseases SARS-CoV-2 Assessment of Viral Evolution program. The group uses bioinformatic methods to monitor the emergence, spread, and potential phenotypic properties of emerging and circulating strains to identify the most relevant variants for experimental groups within the program to phenotypically characterize. Since April 2021, the group has prioritized variants monthly. Prioritization successes include rapidly identifying most major variants of SARS-CoV-2 and providing experimental groups within the National Institutes of Health program easy access to regularly updated information on the recent evolution and epidemiology of SARS-CoV-2 that can be used to guide phenotypic investigations.

Published
2023
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2. Defining the risk of SARS-CoV-2 variants on immune protection

Author

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 van 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, Mehul S. Suthar, Ghedin, Elodie [0000-0002-1515-725X], Frieman, Matthew B [0000-0003-0107-0775], Krammer, Florian [0000-0003-4121-776X], Grifoni, Alba [0000-0002-2209-5966], Alter, Galit [0000-0002-7680-9215], Amara, Rama R [0000-0002-6309-6797], Baric, Ralph S [0000-0001-6827-8701], Barouch, Dan H [0000-0001-5127-4659], Bloom, Jesse D [0000-0003-1267-3408], Bloyet, Louis-Marie [0000-0002-5648-3190], Boon, Adrianus CM [0000-0002-4700-8224], Bratt, Debbie L [0000-0002-5822-5558], Buchser, William J [0000-0002-6675-6359], Cohen-Lavi, Liel [0000-0001-6909-4779], Dearlove, Bethany L [0000-0003-3653-4592], Drosten, Christian [0000-0001-7923-0519], Edara, Venkata-Viswanadh [0000-0001-9321-7839], Ellebedy, Ali [0000-0002-6129-2532], Fabrizio, Thomas P [0000-0002-8960-0728], Fouchier, Ron AM [0000-0001-8095-2869], García-Sastre, Adolfo [0000-0002-6551-1827], Godzik, Adam [0000-0002-2425-852X], Gonzalez-Reiche, Ana Silvia [0000-0003-3583-4497], Gordon, Aubree [0000-0002-9352-7877], Haagmans, Bart L [0000-0001-6221-2015], Ho, David D [0000-0003-1627-149X], Holbrook, Michael R [0000-0002-0824-2667], Huang, Yaoxing [0000-0001-6270-1644], James, Sarah L [0000-0002-6969-1167], Johnson, Robert M [0000-0002-1976-7688], Jones, Terry C [0000-0003-1120-9531], Joshi, Astha [0000-0003-4914-8228], Kawaoka, Yoshihiro [0000-0001-5061-8296], Kercher, Lisa [0000-0001-6300-0452], Koopmans, Marion PG [0000-0002-5204-2312], Korber, Bette [0000-0002-2026-5757], LeGresley, Eric B [0000-0002-5286-5693], Liebeskind, Mariel J [0000-0003-4595-0651], Liu, Zhuoming [0000-0001-8198-0976], Logue, James P [0000-0002-7410-9741], Luo, Yang [0000-0003-3277-8792], McDermott, Adrian B [0000-0003-0616-9117], Meliopoulos, Victoria A [0000-0003-1442-9177], Menachery, Vineet D [0000-0001-8803-7606], Munster, Vincent J [0000-0002-2288-3196], Nair, Manoj S [0000-0002-5994-3957], Netzl, Antonia [0000-0001-8034-2382], Pekosz, Andrew [0000-0003-3248-1761], Perlman, Stanley [0000-0003-4213-2354], Rockx, Barry [0000-0003-2463-027X], Rolland, Morgane [0000-0003-3650-8490], Rothlauf, Paul W [0000-0002-0941-4467], Scheuermann, Richard H [0000-0003-1355-892X], Schotsaert, Michael [0000-0003-3156-3132], Schultz-Cherry, Stacey [0000-0002-2021-727X], Seder, Robert A [0000-0003-3133-0849], Shabman, Reed S [0000-0003-3272-3484], Shi, Pei-Yong [0000-0001-5553-1616], Simon, Viviana [0000-0002-6416-5096], Thackray, Larissa B [0000-0002-9380-6569], Thomas, Paul G [0000-0001-7955-0256], Trifkovic, Sanja [0000-0002-0710-9514], Türeli, Sina [0000-0001-7342-9295], van Bakel, Harm [0000-0002-1376-6916], VanBlargan, Laura A [0000-0002-8922-8946], Vincent, Leah R [0000-0001-9262-1813], Wallace, Zachary S [0000-0003-0237-501X], Wang, Pengfei [0000-0003-2454-7652], Weaver, Scott C [0000-0001-8016-8556], Webby, Richard J [0000-0002-4397-7132], Weiss, Carol D [0000-0002-9965-1289], Wentworth, David E [0000-0002-5190-980X], Weston, Stuart M [0000-0001-9840-2953], Whelan, Sean PJ [0000-0003-1564-8590], Whitener, Bradley M [0000-0001-6652-0701], Xie, Xuping [0000-0003-0918-016X], Yoon, Hyejin [0000-0002-3344-9096], Hertz, Tomer [0000-0002-0561-1578], Smith, Derek J [0000-0002-2393-1890], Diamond, Michael S [0000-0002-8791-3165], Post, Diane J [0000-0003-3890-9116], Suthar, Mehul S [0000-0002-2686-8380], and Apollo - University of Cambridge Repository

Subjects
Multidisciplinary, COVID-19 Vaccines, Pharmacogenomic Variants, Virulence, SARS-CoV-2, COVID-19, Biological Evolution, Article, United States, SDG 3 - Good Health and Well-being, National Institute of Allergy and Infectious Diseases (U.S.), Animals, Humans, Pandemics
Abstract

The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced following 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 (NIAID) within the National Institutes of Health (NIH) established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) program. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants potentially impacting transmission, virulence, and resistance to convalescent and vaccine-induced immunity. The SAVE program serves as a critical data-generating component of the United States 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 pivotal findings facilitated by this collaborative approach and identify future challenges. This program serves as a template for the response against rapidly evolving pandemic pathogens by monitoring viral evolution in the human population to identify variants that could erode the effectiveness of countermeasures.

Published
2022

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