401
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Olsen RJ, Christensen PA, Long SW, Subedi S, Hodjat P, Olson R, Nguyen M, Davis JJ, Yerramilli P, Saavedra MO, Pruitt L, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Finkelstein IJ, Gollihar J, Musser JM. Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:1754-1773. [PMID: 34303698 PMCID: PMC8299152 DOI: 10.1016/j.ajpath.2021.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022]
Abstract
Certain genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of substantial concern because they may be more transmissible or detrimentally alter the pandemic course and disease features in individual patients. SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist health care system diagnosed from January 1 through May 31, 2021 are reported here. Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63% to 90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non-B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants [eg, B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1] also increased rapidly, although the magnitude was less than that in B.1.1.7. Twenty-two patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants had a high rate of hospitalization. Breakthrough cases (n = 207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many not currently designated variants of interest or concern. In the aggregate, this study delineates the trajectory of SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston, TX, and heralds the arrival of B.1.617 variants in the metroplex.
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Affiliation(s)
- Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Parsa Hodjat
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Robert Olson
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Matthew O Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Combat Capabilities Development Command (CCDC) Army Research Laboratory-South, University of Texas, Austin, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York.
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402
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Dong J, Zost SJ, Greaney AJ, Starr TN, Dingens AS, Chen EC, Chen RE, Case JB, Sutton RE, Gilchuk P, Rodriguez J, Armstrong E, Gainza C, Nargi RS, Binshtein E, Xie X, Zhang X, Shi PY, Logue J, Weston S, McGrath ME, Frieman MB, Brady T, Tuffy KM, Bright H, Loo YM, McTamney PM, Esser MT, Carnahan RH, Diamond MS, Bloom JD, Crowe JE. Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nat Microbiol 2021; 6:1233-1244. [PMID: 34548634 PMCID: PMC8543371 DOI: 10.1038/s41564-021-00972-2] [Citation(s) in RCA: 187] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
Understanding the molecular basis for immune recognition of SARS-CoV-2 spike glycoprotein antigenic sites will inform the development of improved therapeutics. We determined the structures of two human monoclonal antibodies-AZD8895 and AZD1061-which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor-binding domain (RBD) of SARS-CoV-2 to define the genetic and structural basis of neutralization. AZD8895 forms an 'aromatic cage' at the heavy/light chain interface using germ line-encoded residues in complementarity-determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals. AZD1061 has an unusually long LCDR1; the HCDR3 makes interactions with the opposite face of the RBD from that of AZD8895. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the crucial binding residues of both antibodies and identified positions of concern with regards to virus escape from antibody-mediated neutralization. Both AZD8895 and AZD1061 have strong neutralizing activity against SARS-CoV-2 and variants of concern with antigenic substitutions in the RBD. We conclude that germ line-encoded antibody features enable recognition of the SARS-CoV-2 spike RBD and demonstrate the utility of the cocktail AZD7442 in neutralizing emerging variant viruses.
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MESH Headings
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antigenic Variation
- Binding Sites
- COVID-19/immunology
- COVID-19/virology
- Complementarity Determining Regions/chemistry
- Complementarity Determining Regions/genetics
- Humans
- Mutation
- Protein Domains
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Jinhui Dong
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Allison J Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Adam S Dingens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elaine C Chen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel E Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jessica Rodriguez
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Erica Armstrong
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher Gainza
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rachel S Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xuping Xie
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Xianwen Zhang
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - James Logue
- Department of Microbiology and Immunology, The University of Maryland, College Park, MD, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, The University of Maryland, College Park, MD, USA
| | - Marisa E McGrath
- Department of Microbiology and Immunology, The University of Maryland, College Park, MD, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, The University of Maryland, College Park, MD, USA
| | - Tyler Brady
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | - Kevin M Tuffy
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | - Helen Bright
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | - Yueh-Ming Loo
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | | | - Mark T Esser
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
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403
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Prévost J, Richard J, Gasser R, Ding S, Fage C, Anand SP, Adam D, Gupta Vergara N, Tauzin A, Benlarbi M, Gong SY, Goyette G, Privé A, Moreira S, Charest H, Roger M, Mothes W, Pazgier M, Brochiero E, Boivin G, Abrams CF, Schön A, Finzi A. Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. J Biol Chem 2021; 297:101151. [PMID: 34478710 PMCID: PMC8406544 DOI: 10.1016/j.jbc.2021.101151] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 12/29/2022] Open
Abstract
The seasonal nature of outbreaks of respiratory viral infections with increased transmission during low temperatures has been well established. Accordingly, temperature has been suggested to play a role on the viability and transmissibility of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The receptor-binding domain (RBD) of the Spike glycoprotein is known to bind to its host receptor angiotensin-converting enzyme 2 (ACE2) to initiate viral fusion. Using biochemical, biophysical, and functional assays to dissect the effect of temperature on the receptor-Spike interaction, we observed a significant and stepwise increase in RBD-ACE2 affinity at low temperatures, resulting in slower dissociation kinetics. This translated into enhanced interaction of the full Spike glycoprotein with the ACE2 receptor and higher viral attachment at low temperatures. Interestingly, the RBD N501Y mutation, present in emerging variants of concern (VOCs) that are fueling the pandemic worldwide (including the B.1.1.7 (α) lineage), bypassed this requirement. This data suggests that the acquisition of N501Y reflects an adaptation to warmer climates, a hypothesis that remains to be tested.
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Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada
| | - Clément Fage
- Centre de Recherche du CHU de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Damien Adam
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Médicine, Université de Montréal, Montréal, Quebec, Canada
| | - Natasha Gupta Vergara
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada
| | - Shang Yu Gong
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Guillaume Goyette
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada
| | - Anik Privé
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada
| | - Sandrine Moreira
- Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Hugues Charest
- Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Michel Roger
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada; Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Emmanuelle Brochiero
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Médicine, Université de Montréal, Montréal, Quebec, Canada
| | - Guy Boivin
- Centre de Recherche du CHU de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Cameron F Abrams
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada; Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.
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404
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Dudas G, Hong SL, Potter BI, Calvignac-Spencer S, Niatou-Singa FS, Tombolomako TB, Fuh-Neba T, Vickos U, Ulrich M, Leendertz FH, Khan K, Huber C, Watts A, Olendraitė I, Snijder J, Wijnant KN, Bonvin AMJJ, Martres P, Behillil S, Ayouba A, Maidadi MF, Djomsi DM, Godwe C, Butel C, Šimaitis A, Gabrielaitė M, Katėnaitė M, Norvilas R, Raugaitė L, Koyaweda GW, Kandou JK, Jonikas R, Nasvytienė I, Žemeckienė Ž, Gečys D, Tamušauskaitė K, Norkienė M, Vasiliūnaitė E, Žiogienė D, Timinskas A, Šukys M, Šarauskas M, Alzbutas G, Aziza AA, Lusamaki EK, Cigolo JCM, Mawete FM, Lofiko EL, Kingebeni PM, Tamfum JJM, Belizaire MRD, Essomba RG, Assoumou MCO, Mboringong AB, Dieng AB, Juozapaitė D, Hosch S, Obama J, Ayekaba MO, Naumovas D, Pautienius A, Rafaï CD, Vitkauskienė A, Ugenskienė R, Gedvilaitė A, Čereškevičius D, Lesauskaitė V, Žemaitis L, Griškevičius L, Baele G. Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Nat Commun 2021; 12:5769. [PMID: 34599175 PMCID: PMC8486757 DOI: 10.1038/s41467-021-26055-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.
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Affiliation(s)
- Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Barney I Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
- Viral Evolution, Robert Koch Institute, 13353, Berlin, Germany
| | - Frédéric S Niatou-Singa
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Thais B Tombolomako
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Terence Fuh-Neba
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Ulrich Vickos
- Infectious and Tropical Diseases Unit, Department of medicine, Amitié Hospital, Bangui, Central African Republic
- Academic Department of Pediatrics, Clinical immunology and vaccinology, Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Markus Ulrich
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
| | - Kamran Khan
- BlueDot, Toronto, ON, M5J 1A7, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, M5B 1A6, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, M5S 3H2, Canada
| | | | | | - Ingrida Olendraitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Lab, CB2 2QQ, Cambridge, UK
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Kim N Wijnant
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Pascale Martres
- Microbiology, Centre Hospitalier René Dubos, Cergy Pontoise, France
| | - Sylvie Behillil
- Molecular Genetics of RNA viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Ahidjo Ayouba
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France
| | - Martin Foudi Maidadi
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Dowbiss Meta Djomsi
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Celestin Godwe
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Christelle Butel
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France
| | - Aistis Šimaitis
- The Office of the Government of the Republic of Lithuania, Vilnius, Lithuania
| | | | - Monika Katėnaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Rimvydas Norvilas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Department of Experimental, Preventive and Clinical Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Ligita Raugaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Giscard Wilfried Koyaweda
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Jephté Kaleb Kandou
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Rimvydas Jonikas
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Inga Nasvytienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Živilė Žemeckienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Dovydas Gečys
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Kamilė Tamušauskaitė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Milda Norkienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Emilija Vasiliūnaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Danguolė Žiogienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Albertas Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Marius Šukys
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Mantas Šarauskas
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Gediminas Alzbutas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Adrienne Amuri Aziza
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Eddy Kinganda Lusamaki
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Jean-Claude Makangara Cigolo
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Francisca Muyembe Mawete
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Emmanuel Lokilo Lofiko
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
| | - Placide Mbala Kingebeni
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe Tamfum
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | | | - René Ghislain Essomba
- National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Marie Claire Okomo Assoumou
- National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Alle Baba Dieng
- World Health Organization, Cameroon Office, Yaoundé, Cameroon
| | - Dovilė Juozapaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Justino Obama
- Ministry of Health and Social Welfare, Malabo, Equatorial Guinea
| | | | - Daniel Naumovas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Arnoldas Pautienius
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Clotaire Donatien Rafaï
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Astra Vitkauskienė
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rasa Ugenskienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alma Gedvilaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Darius Čereškevičius
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vaiva Lesauskaitė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Lukas Žemaitis
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
- National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Laimonas Griškevičius
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
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405
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Ameratunga R, Longhurst H, Steele R, Lehnert K, Leung E, Brooks AES, Woon ST. Common Variable Immunodeficiency Disorders, T-Cell Responses to SARS-CoV-2 Vaccines, and the Risk of Chronic COVID-19. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2021; 9:3575-3583. [PMID: 34182162 PMCID: PMC8230758 DOI: 10.1016/j.jaip.2021.06.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/13/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022]
Abstract
COVID-19 has had a calamitous effect on the global community. Despite intense study, the immunologic response to the infection is only partially understood. In addition to older age and ethnicity, patients with comorbidities including obesity, diabetes, hypertension, coronary artery disease, malignancy, renal, and pulmonary disease may experience severe outcomes. Some patients with primary immunodeficiency (PID) and secondary immunodeficiency also appear to be at increased risk from COVID-19. In addition to vulnerability to SARS-CoV-2, patients with PIDs often have chronic pulmonary disease and may not respond to vaccines, which exacerbates their long-term risk. Patients with common variable immunodeficiency disorders, the most frequent symptomatic PID in adults and children, have a spectrum of B- and T-cell defects. It may be possible to stratify their risk for severe COVID-19 based on age, ethnicity, the severity of the T-cell defect, and the presence of other comorbidities. Patients with common variable immunodeficiency disorders and other immunodeficiencies are at risk for Chronic COVID-19, a dangerous stalemate between a suboptimal immune response and SARS-CoV-2. Intra-host viral evolution could result in the rapid emergence of vaccine-resistant mutants and variants of high consequence; it is a public health emergency. Vaccination and prevention of Chronic COVID-19 in immunodeficient patients is therefore of the utmost priority. Having a reliable diagnostic assay for T-cell immunity to SARS-CoV-2 is critical for evaluating responses to vaccines in these patients. New treatments for SARS-CoV-2 such as NZACE2-Pātari are likely to be particularly beneficial for immunodeficient patients, especially those who fail to mount a robust T-cell response to COVID-19 vaccines.
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Affiliation(s)
- Rohan Ameratunga
- Department of Clinical Immunology, Auckland Hospital, Auckland, New Zealand; Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
| | - Hilary Longhurst
- Department of Clinical Immunology, Auckland Hospital, Auckland, New Zealand; Department of Medicine, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Richard Steele
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand; Department of Respiratory Medicine, Wellington Hospital, Wellington, New Zealand
| | - Klaus Lehnert
- Centre for Brain Research, School of Biological Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Anna E S Brooks
- Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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406
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Krsak M, Harry BL, Palmer BE, Franco-Paredes C. Postinfectious Immunity After COVID-19 and Vaccination Against SARS-CoV-2. Viral Immunol 2021; 34:504-509. [PMID: 34227891 DOI: 10.1089/vim.2021.0054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Early results suggest that SARS-CoV-2 vaccines are highly effective for the prevention of COVID-19. Unfortunately, until we can safely, rapidly, and affordably vaccinate enough people to achieve collective immunity, we cannot afford to disregard the benefits of naturally acquired immunity in those, whose prior documented infections have already run their course. As long as the vaccine manufacturing, supply, or administration are limited in capacity, vaccination of individuals with naturally acquired immunity at the expense of others without any immune protection is inherently inequitable, and violates the principle of justice in biomedical ethics. Any preventable disease acquired during the period of such unnecessary delay in vaccination should not be overlooked, as it may and will result in some additional morbidity, mortality, related hospitalizations, and expense. Low vaccine production capacity complicated by inefficiencies in vaccine administration suggests, that vaccinating preferentially those without any prior protection will result in fewer natural infections more rapidly.
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Affiliation(s)
- Martin Krsak
- Divisions of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Brian L Harry
- Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Brent E Palmer
- Divisions of Allergy and Clinical Immunology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Carlos Franco-Paredes
- Divisions of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Hospital Infantil de México, Federico Gomez, México City, Mexico
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407
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Knight AC, Montgomery SA, Fletcher CA, Baxter VK. Mouse Models for the Study of SARS-CoV-2 Infection. Comp Med 2021; 71:383-397. [PMID: 34610856 PMCID: PMC8594264 DOI: 10.30802/aalas-cm-21-000031] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/19/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023]
Abstract
Mice are an invaluable resource for studying virus-induced disease. They are a small, genetically modifiable animal for which a large arsenal of genetic and immunologic tools is available for evaluation of pathogenesis and potential vaccines and therapeutics. SARS-CoV-2, the betacoronavirus responsible for the COVID-19 pandemic, does not naturally replicate in wild-type mice, due to structural differences between human and mouse ACE2, the primary receptor for SARS-CoV-2 entry into cells. However, several mouse strains have been developed that allow for SARS-CoV-2 replication and clinical disease. Two broad strategies have primarily been deployed for developing mouse strains susceptible to COVID-19-like disease: adding in the human ACE2 gene and adapting the virus to the mouse ACE2 receptor. Both approaches result in mice that develop several of the clinical and pathologic hallmarks of COVID-19, including acute respiratory distress syndrome and acute lung injury. In this review, we describe key acute pulmonary and extrapulmonary pathologic changes seen in COVID-19 patients that mouse models of SARS-CoV-2 infection ideally replicate, the essential development of mouse models for the study of Severe Acute Respiratory Syndrome and Middle Eastern Respiratory Syndrome and the basis of many of the models of COVID-19, and key clinical and pathologic features of currently available mouse models of SARS-CoV-2 infection.
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Key Words
- aav, adeno-associated virus
- ace2, angiotensin-converting enzyme 2
- ali, acute lung injury
- ards, acute respiratory distress syndrome
- covid-19, coronavirus disease 19
- dad, diffuse alveolar damage
- dpi, days postinfection
- dpp4, dipeptidyl peptidase 4
- hace2, human angiotensin-converting enzyme 2
- mace2, mouse angiotensin-converting enzyme 2
- mers, middle eastern respiratory syndrome
- mers-cov, middle eastern respiratory syndrome coronavirus
- sars, severe acute respiratory syndrome
- sars-cov, severe acute respiratory syndrome coronavirus
- sars-cov-2, severe acute respiratory syndrome coronavirus 2
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Affiliation(s)
- Audrey C Knight
- Department of Pathology and Laboratory Medicine
- Institute for Global Health and Infectious Diseases, and
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Craig A Fletcher
- Department of Pathology and Laboratory Medicine
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Victoria K Baxter
- Department of Pathology and Laboratory Medicine
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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408
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Lennerstrand J, Palanisamy N. Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Viruses 2021; 13:1974. [PMID: 34696404 PMCID: PMC8538289 DOI: 10.3390/v13101974] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Several vaccines with varying efficacies have been developed and are currently administered globally to minimize the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite having an RNA-dependent RNA polymerase with a proofreading activity, new variants of SARS-CoV-2 are on the rise periodically. Some of the mutations in these variants, especially mutations on the spike protein, aid the virus in transmission, infectivity and host immune evasion. Further, these mutations also reduce the effectiveness of some of the current vaccines and monoclonal antibodies (mAbs). In the present study, using the available 984,769 SARS-CoV-2 nucleotide sequences on the NCBI database from the end of 2019 till 28 July 2021, we have estimated the global prevalence of so-called 'adaptive mutations' and 'mutations identified in the prolonged infections', in the receptor-binding domain (RBD) of the spike (S) protein. Irrespective of the geographical region, in the case of the adaptive mutations, N501Y (48.38%) was found to be the dominant mutation followed by L452R (17.52%), T478K (14.31%), E484K (4.69%), S477N (3.29%), K417T (1.64%), N439K (0.7%) and S494P (0.7%). Other mutations were found to be less prevalent (less than 0.7%). Since the last two months, there has been a massive increase of L452R and T478K mutations (delta variant) in certain areas. In the case of prolonged infections' mutations (long-term SARS-CoV-2 infections), V483A (0.009%) was found to be dominant followed by Q493R (0.009%), while other mutations were found in less than 0.007% of the studied sequences. The data obtained in this study will aid in the development of better infection control policies, thereby curbing the spread of this virus.
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Affiliation(s)
- Johan Lennerstrand
- Department of Medical Sciences, Section of Clinical Microbiology, Uppsala University, 751 85 Uppsala, Sweden;
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409
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Fast SARS-CoV-2 Variant Detection Using Snapback Primer High-Resolution Melting. Diagnostics (Basel) 2021; 11:diagnostics11101788. [PMID: 34679489 PMCID: PMC8534650 DOI: 10.3390/diagnostics11101788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/28/2022] Open
Abstract
SARS-CoV-2, the virus responsible for COVID-19, emerged in late 2019 and has since spread throughout the world, infecting over 200 million people. The fast spread of SARS-CoV-2 showcased the need for rapid and sensitive testing methodologies to help track the disease. Over the past 18 months, numerous SARS-CoV-2 variants have emerged. Many of these variants are suggested to be more transmissible as well as less responsive to neutralization by vaccine-induced antibodies. Viral whole-genome sequencing is the current standard for tracking these variants. However, whole-genome sequencing is costly and the technology and expertise are limited to larger reference laboratories. Here, we present the feasibility of a fast, inexpensive methodology using snapback primer-based high-resolution melting to test for >20 high-consequence SARS-CoV-2 spike mutations. This assay can distinguish between multiple variant lineages and be completed in roughly 2 h for less than $10 per sample.
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410
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Hirotsu Y, Omata M. SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community. INFECTION GENETICS AND EVOLUTION 2021; 95:105088. [PMID: 34560289 PMCID: PMC8454025 DOI: 10.1016/j.meegid.2021.105088] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/09/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022]
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan. Methods We performed the whole genome sequencing using SARS-CoV-2 positive samples collected from February 2020 to the end of June 2021. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages. Results We successfully obtained 325 viral genome sequences and the number of analyzed samples accounted for 15.4% of the total 2109 COVID-19 patients identified in our district. We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta). These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April 2021. Conclusion We clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI.
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Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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411
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Long S. SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives. Viruses 2021; 13:1923. [PMID: 34696353 PMCID: PMC8539008 DOI: 10.3390/v13101923] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2, the etiologic agent at the root of the ongoing COVID-19 pandemic, harbors a large RNA genome from which a tiered ensemble of subgenomic RNAs (sgRNAs) is generated. Comprehensive definition and investigation of these RNA products are important for understanding SARS-CoV-2 pathogenesis. This review summarizes the recent progress on SARS-CoV-2 sgRNA identification, characterization, and application as a viral replication marker. The significance of these findings and potential future research areas of interest are discussed.
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Affiliation(s)
- Samuel Long
- Independent Researcher, Clarksburg, MD 20871, USA
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412
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Thye AYK, Law JWF, Pusparajah P, Letchumanan V, Chan KG, Lee LH. Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis. Biomedicines 2021; 9:1303. [PMID: 34680420 PMCID: PMC8533361 DOI: 10.3390/biomedicines9101303] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 09/18/2021] [Indexed: 12/12/2022] Open
Abstract
The worldwide battle against the SARS-CoV-2 virus rages on, with millions infected and many innocent lives lost. The causative organism, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a beta coronavirus that belongs to the Coronaviridae family. Many clinically significant variants have emerged, as the virus's genome is prone to various mutations, leading to antigenic drift and resulting in evasion of host immune recognition. The current variants of concern (VOCs) include B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), and P.1 (Gamma). The emerging variants contain various important mutations on the spike protein, leading to deleterious consequences, such as immune invasion and vaccine escape. These adverse effects result in increased transmissibility, morbidity, and mortality and the evasion of detection by existing or currently available diagnostic tests, potentially delaying diagnosis and treatment. This review discusses the key mutations present in the VOC strains and provides insights into how these mutations allow for greater transmissibility and immune evasion than the progenitor strain. Continuous monitoring and surveillance of VOC strains play a vital role in preventing and controlling the virus's spread.
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Affiliation(s)
- Angel Yun-Kuan Thye
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
| | - Jodi Woan-Fei Law
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
| | - Priyia Pusparajah
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
| | - Vengadesh Letchumanan
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang 212013, China
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
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413
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Liu Z, Xu W, Chen Z, Fu W, Zhan W, Gao Y, Zhou J, Zhou Y, Wu J, Wang Q, Zhang X, Hao A, Wu W, Zhang Q, Li Y, Fan K, Chen R, Jiang Q, Mayer CT, Schoofs T, Xie Y, Jiang S, Wen Y, Yuan Z, Wang K, Lu L, Sun L, Wang Q. An ultrapotent pan-β-coronavirus lineage B (β-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope. Protein Cell 2021; 13:655-675. [PMID: 34554412 PMCID: PMC8458794 DOI: 10.1007/s13238-021-00871-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/02/2021] [Indexed: 01/09/2023] Open
Abstract
New threats posed by the emerging circulating variants of SARS-CoV-2 highlight the need to find conserved neutralizing epitopes for therapeutic antibodies and efficient vaccine design. Here, we identified a receptor-binding domain (RBD)-binding antibody, XG014, which potently neutralizes β-coronavirus lineage B (β-CoV-B), including SARS-CoV-2, its circulating variants, SARS-CoV and bat SARSr-CoV WIV1. Interestingly, antibody family members competing with XG014 binding show reduced levels of cross-reactivity and induce antibody-dependent SARS-CoV-2 spike (S) protein-mediated cell-cell fusion, suggesting a unique mode of recognition by XG014. Structural analyses reveal that XG014 recognizes a conserved epitope outside the ACE2 binding site and completely locks RBD in the non-functional "down" conformation, while its family member XG005 directly competes with ACE2 binding and position the RBD "up". Single administration of XG014 is effective in protection against and therapy of SARS-CoV-2 infection in vivo. Our findings suggest the potential to develop XG014 as pan-β-CoV-B therapeutics and the importance of the XG014 conserved antigenic epitope for designing broadly protective vaccines against β-CoV-B and newly emerging SARS-CoV-2 variants of concern.
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Affiliation(s)
- Zezhong Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhenguo Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wangjun Fu
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wuqiang Zhan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yidan Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jie Zhou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yunjiao Zhou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jianbo Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiang Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Aihua Hao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wei Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qianqian Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yaming Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Kaiyue Fan
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruihong Chen
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiaochu Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Christian T Mayer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yumei Wen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Kang Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Lei Sun
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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414
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Skidmore PT, Kaelin EA, Holland LA, Maqsood R, Wu LI, Mellor NJ, Blain JM, Harris V, LaBaer J, Murugan V, Lim ES. Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. Emerg Infect Dis 2021; 27:2718-2720. [PMID: 34545803 PMCID: PMC8462350 DOI: 10.3201/eid2710.211189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genomic surveillance can provide early insights into new circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. While conducting genomic surveillance (1,663 cases) from December 2020–April 2021 in Arizona, USA, we detected an emergent E484K-harboring variant, B.1.243.1. This finding demonstrates the importance of real-time SARS-CoV-2 surveillance to better inform public health responses.
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415
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Upadhyay V, Lucas A, Panja S, Miyauchi R, Mallela KMG. Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. J Biol Chem 2021; 297:101208. [PMID: 34543625 PMCID: PMC8445900 DOI: 10.1016/j.jbc.2021.101208] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023] Open
Abstract
Emergence of new severe acute respiratory syndrome coronavirus 2 variants has raised concerns related to the effectiveness of vaccines and antibody therapeutics developed against the unmutated wildtype virus. Here, we examined the effect of the 12 most commonly occurring mutations in the receptor-binding domain of the spike protein on its expression, stability, activity, and antibody escape potential. Stability was measured using thermal denaturation, and the activity and antibody escape potential were measured using isothermal titration calorimetry in terms of binding to the human angiotensin-converting enzyme 2 and to neutralizing human antibody CC12.1, respectively. Our results show that mutants differ in their expression levels. Of the eight best-expressed mutants, two (N501Y and K417T/E484K/N501Y) showed stronger affinity to angiotensin-converting enzyme 2 compared with the wildtype, whereas four (Y453F, S477N, T478I, and S494P) had similar affinity and two (K417N and E484K) had weaker affinity than the wildtype. Compared with the wildtype, four mutants (K417N, Y453F, N501Y, and K417T/E484K/N501Y) had weaker affinity for the CC12.1 antibody, whereas two (S477N and S494P) had similar affinity, and two (T478I and E484K) had stronger affinity than the wildtype. Mutants also differ in their thermal stability, with the two least stable mutants showing reduced expression. Taken together, these results indicate that multiple factors contribute toward the natural selection of variants, and all these factors need to be considered to understand the evolution of the virus. In addition, since not all variants can escape a given neutralizing antibody, antibodies to treat new variants can be chosen based on the specific mutations in that variant.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alexandra Lucas
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sudipta Panja
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ryuki Miyauchi
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Krishna M G Mallela
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
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416
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Ye F, Lin X, Chen Z, Yang F, Lin S, Yang J, Chen H, Sun H, Wang L, Wen A, Zhang X, Dai Y, Cao Y, Yang J, Shen G, Yang L, Li J, Wang Z, Wang W, Wei X, Lu G. S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis. Signal Transduct Target Ther 2021; 6:343. [PMID: 34531369 PMCID: PMC8444507 DOI: 10.1038/s41392-021-00756-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 recognizes, via its spike receptor-binding domain (S-RBD), human angiotensin-converting enzyme 2 (ACE2) to initiate infection. Ecto-domain protein of ACE2 can therefore function as a decoy. Here we show that mutations of S19W, T27W, and N330Y in ACE2 could individually enhance SARS-CoV-2 S-RBD binding. Y330 could be synergistically combined with either W19 or W27, whereas W19 and W27 are mutually unbeneficial. The structures of SARS-CoV-2 S-RBD bound to the ACE2 mutants reveal that the enhanced binding is mainly contributed by the van der Waals interactions mediated by the aromatic side-chains from W19, W27, and Y330. While Y330 and W19/W27 are distantly located and devoid of any steric interference, W19 and W27 are shown to orient their side-chains toward each other and to cause steric conflicts, explaining their incompatibility. Finally, using pseudotyped SARS-CoV-2 viruses, we demonstrate that these residue substitutions are associated with dramatically improved entry-inhibition efficacy toward both wild-type and antibody-resistant viruses. Taken together, our biochemical and structural data have delineated the basis for the elevated S-RBD binding associated with S19W, T27W, and N330Y mutations in ACE2, paving the way for potential application of these mutants in clinical treatment of COVID-19.
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Affiliation(s)
- Fei Ye
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xi Lin
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zimin Chen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fanli Yang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sheng Lin
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Yang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hua Chen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Honglu Sun
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lingling Wang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ao Wen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xindan Zhang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yushan Dai
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Cao
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingyun Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guobo Shen
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiong Li
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhenling Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wei Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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417
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Ortega-Rivera O, Shin MD, Chen A, Beiss V, Moreno-Gonzalez MA, Lopez-Ramirez MA, Reynoso M, Wang H, Hurst BL, Wang J, Pokorski JK, Steinmetz NF. Trivalent Subunit Vaccine Candidates for COVID-19 and Their Delivery Devices. J Am Chem Soc 2021; 143:14748-14765. [PMID: 34490778 PMCID: PMC8442557 DOI: 10.1021/jacs.1c06600] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Indexed: 02/06/2023]
Abstract
The COVID-19 pandemic highlights the need for platform technologies enabling rapid development of vaccines for emerging viral diseases. The current vaccines target the SARS-CoV-2 spike (S) protein and thus far have shown tremendous efficacy. However, the need for cold-chain distribution, a prime-boost administration schedule, and the emergence of variants of concern (VOCs) call for diligence in novel SARS-CoV-2 vaccine approaches. We studied 13 peptide epitopes from SARS-CoV-2 and identified three neutralizing epitopes that are highly conserved among the VOCs. Monovalent and trivalent COVID-19 vaccine candidates were formulated by chemical conjugation of the peptide epitopes to cowpea mosaic virus (CPMV) nanoparticles and virus-like particles (VLPs) derived from bacteriophage Qβ. Efficacy of this approach was validated first using soluble vaccine candidates as solo or trivalent mixtures and subcutaneous prime-boost injection. The high thermal stability of our vaccine candidates allowed for formulation into single-dose injectable slow-release polymer implants, manufactured by melt extrusion, as well as microneedle (MN) patches, obtained through casting into micromolds, for prime-boost self-administration. Immunization of mice yielded high titers of antibodies against the target epitope and S protein, and data confirms that antibodies block receptor binding and neutralize SARS-CoV and SARS-CoV-2 against infection of human cells. We present a nanotechnology vaccine platform that is stable outside the cold-chain and can be formulated into delivery devices enabling single administration or self-administration. CPMV or Qβ VLPs could be stockpiled, and epitopes exchanged to target new mutants or emergent diseases as the need arises.
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Affiliation(s)
- Oscar
A. Ortega-Rivera
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
| | - Matthew D. Shin
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
| | - Angela Chen
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
| | - Veronique Beiss
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
| | - Miguel A. Moreno-Gonzalez
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
| | - Miguel A. Lopez-Ramirez
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
| | - Maria Reynoso
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
- Institute
for Antiviral Research, Utah State University, Logan, Utah 84322, United States
| | - Hong Wang
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
| | - Brett L. Hurst
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
- Institute
for Antiviral Research, Utah State University, Logan, Utah 84322, United States
| | - Joseph Wang
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
| | - Jonathan K. Pokorski
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
| | - Nicole F. Steinmetz
- Department
of NanoEngineering, Center for Nano-ImmunoEngineering, Institute for Materials
Discovery and Design, Department of Bioengineering, Department of Radiology, and Moores Cancer Center, University of California−San Diego, La Jolla, California 92039, United States
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418
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Kirkham AM, Monaghan M, Bailey AJM, Shorr R, Lalu MM, Fergusson DA, Allan DS. Mesenchymal stromal cells as a therapeutic intervention for COVID-19: a living systematic review and meta-analysis protocol. Syst Rev 2021; 10:249. [PMID: 34526123 PMCID: PMC8441251 DOI: 10.1186/s13643-021-01803-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mesenchymal stromal cells (MSCs) have significant immunomodulatory and tissue repair capabilities, mediated partly by conditioned media or through secreted extracellular vesicles (MSC-EVs). Infection with SARS-CoV-2 can cause mild to life-threatening illness due to activated immune responses that may be dampened by MSCs or their secretome. Many clinical studies of MSCs have been launched since the beginning of the global pandemic, however, few have been completed and most lack power to assess efficacy. Repeated systematic searches and meta-analyses are needed to understand, in real time, the extent of potential benefit in different patient populations as the evidence emerges. METHODS This living systematic review will be maintained to provide up-to-date information as the pandemic evolves. A systematic literature search of Embase, MEDLINE, and Cochrane Central Register of Controlled Trials databases will be performed. All clinical studies (e.g., randomized, pseudorandomized and non-randomized controlled trials, uncontrolled trials, and case series) employing MSCs or their secretome as a therapeutic intervention for COVID-19 will be included. Patients must have confirmed SARS-CoV-2 infection. Study screening and data extraction will be performed in duplicate. Information concerning interventions, patient populations, methods of MSC isolation and characterization, primary and secondary clinical and/or laboratory outcomes, and adverse events will be extracted. Key clinical outcomes will be pooled through random-effects meta-analysis to determine the efficacy of MSCs and their secreted products for COVID-19. DISCUSSION Our systematic review and subsequent updates will inform the scientific, medical, and health policy communities as the pandemic evolves to guide decisions on the appropriate use of MSC-related products to treat COVID-19. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD 42021225431.
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Affiliation(s)
- Aidan M Kirkham
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, Canada.,Clinical Epidemiology, Ottawa Hospital Research Institute, 501 Smyth Rd, Box 704, Ottawa, ON, K1H 8L6, Canada
| | - Madeline Monaghan
- Clinical Epidemiology, Ottawa Hospital Research Institute, 501 Smyth Rd, Box 704, Ottawa, ON, K1H 8L6, Canada
| | - Adrian J M Bailey
- Clinical Epidemiology, Ottawa Hospital Research Institute, 501 Smyth Rd, Box 704, Ottawa, ON, K1H 8L6, Canada.,School of Medicine, University of Ottawa, Ottawa, Canada
| | - Risa Shorr
- Medical Information and Learning Services, The Ottawa Hospital, Ottawa, Canada
| | - Manoj M Lalu
- Clinical Epidemiology, Ottawa Hospital Research Institute, 501 Smyth Rd, Box 704, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada.,Regenerative Medicine, Ottawa Hospital Research Institute, 501 Smyth Rdx, Box 704, Ottawa, ON, K1H 8L6, Canada.,Department of Anesthesiology and Pain Medicine, The Ottawa Hospital, Ottawa, Canada
| | - Dean A Fergusson
- Clinical Epidemiology, Ottawa Hospital Research Institute, 501 Smyth Rd, Box 704, Ottawa, ON, K1H 8L6, Canada.,School of Public Health and Epidemiology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Department of Medicine, The Ottawa Hospital, Ottawa, Canada
| | - David S Allan
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, Canada. .,Clinical Epidemiology, Ottawa Hospital Research Institute, 501 Smyth Rd, Box 704, Ottawa, ON, K1H 8L6, Canada. .,Regenerative Medicine, Ottawa Hospital Research Institute, 501 Smyth Rdx, Box 704, Ottawa, ON, K1H 8L6, Canada. .,Department of Medicine, The Ottawa Hospital, Ottawa, Canada.
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419
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Schmitz AJ, Turner JS, Liu Z, Zhou JQ, Aziati ID, Chen RE, Joshi A, Bricker TL, Darling TL, Adelsberg DC, Altomare CG, Alsoussi WB, Case JB, VanBlargan LA, Lei T, Thapa M, Amanat F, Jeevan T, Fabrizio T, O'Halloran JA, Shi PY, Presti RM, Webby RJ, Krammer F, Whelan SPJ, Bajic G, Diamond MS, Boon ACM, Ellebedy AH. A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Immunity 2021; 54:2159-2166.e6. [PMID: 34464596 PMCID: PMC8367776 DOI: 10.1016/j.immuni.2021.08.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/04/2021] [Accepted: 08/11/2021] [Indexed: 11/22/2022]
Abstract
The emergence of SARS-CoV-2 antigenic variants with increased transmissibility is a public health threat. Some variants show substantial resistance to neutralization by SARS-CoV-2 infection- or vaccination-induced antibodies. Here, we analyzed receptor binding domain-binding monoclonal antibodies derived from SARS-CoV-2 mRNA vaccine-elicited germinal center B cells for neutralizing activity against the WA1/2020 D614G SARS-CoV-2 strain and variants of concern. Of five monoclonal antibodies that potently neutralized the WA1/2020 D614G strain, all retained neutralizing capacity against the B.1.617.2 variant, four also neutralized the B.1.1.7 variant, and only one, 2C08, also neutralized the B.1.351 and B.1.1.28 variants. 2C08 reduced lung viral load and morbidity in hamsters challenged with the WA1/2020 D614G, B.1.351, or B.1.617.2 strains. Clonal analysis identified 2C08-like public clonotypes among B cells responding to SARS-CoV-2 infection or vaccination in 41 out of 181 individuals. Thus, 2C08-like antibodies can be induced by SARS-CoV-2 vaccines and mitigate resistance by circulating variants of concern.
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Affiliation(s)
- Aaron J Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jackson S Turner
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Julian Q Zhou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ishmael D Aziati
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Astha Joshi
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Traci L Bricker
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Tamarand L Darling
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel C Adelsberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clara G Altomare
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wafaa B Alsoussi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Tingting Lei
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mahima Thapa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Trushar Jeevan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Thomas Fabrizio
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jane A O'Halloran
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rachel M Presti
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard J Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Adrianus C M Boon
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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420
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Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation. BIOLOGY 2021; 10:biology10090880. [PMID: 34571756 PMCID: PMC8470537 DOI: 10.3390/biology10090880] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/28/2021] [Accepted: 09/02/2021] [Indexed: 12/23/2022]
Abstract
Since the beginning of the coronavirus 19 (COVID-19) pandemic in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving through the acquisition of genomic mutations, leading to the emergence of multiple variants of concern (VOCs) and variants of interest (VOIs). Currently, four VOCs (Alpha, Beta, Delta, and Gamma) and seven VOIs (Epsilon, Zeta, Eta, Theta, Iota, Kappa, and Lambda) of SARS-CoV-2 have been identified in worldwide circulation. Here, we investigated the interactions of the receptor-binding domain (RBD) of five SARS-CoV-2 variants with the human angiotensin-converting enzyme 2 (hACE2) receptor in host cells, to determine the extent of molecular divergence and the impact of mutation, using protein-protein docking and dynamics simulation approaches. Along with the wild-type (WT) SARS-CoV-2, this study included the Brazilian (BR/lineage P.1/Gamma), Indian (IN/lineage B.1.617/Delta), South African (SA/lineage B.1.351/Beta), United Kingdom (UK/lineage B.1.1.7/Alpha), and United States (US/lineage B.1.429/Epsilon) variants. The protein-protein docking and dynamics simulation studies revealed that these point mutations considerably affected the structural behavior of the spike (S) protein compared to the WT, which also affected the binding of RBD with hACE2 at the respective sites. Additional experimental studies are required to determine whether these effects have an influence on drug-S protein binding and its potential therapeutic effect.
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421
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Pan X, Shi J, Hu X, Wu Y, Zeng L, Yao Y, Shang W, Liu K, Gao G, Guo W, Peng Y, Chen S, Gao X, Peng C, Rao J, Zhao J, Gong C, Zhou H, Lu Y, Wang Z, Hu X, Cong W, Fang L, Yan Y, Zhang J, Xiong H, Yi J, Yuan Z, Zhou P, Shan C, Xiao G. RBD-homodimer, a COVID-19 subunit vaccine candidate, elicits immunogenicity and protection in rodents and nonhuman primates. Cell Discov 2021; 7:82. [PMID: 34493710 PMCID: PMC8423076 DOI: 10.1038/s41421-021-00320-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/08/2021] [Indexed: 12/14/2022] Open
Abstract
The pandemic of COVID-19 caused by SARS-CoV-2 has raised a new challenges to the scientific and industrious fields after over 1-year spread across different countries. The ultimate approach to end the pandemic is the timely application of vaccines to achieve herd immunity. Here, a novel SARS-CoV-2 receptor-binding domain (RBD) homodimer was developed as a SARS-CoV-2 vaccine candidate. Formulated with aluminum adjuvant, RBD dimer elicited strong immune response in both rodents and non-human primates, and protected mice from SARS-CoV-2 challenge with significantly reducing viral load and alleviating pathological injury in the lung. In the non-human primates, the vaccine could prevent majority of the animals from SARS-CoV-2 infection in the respiratory tract and reduce lung damage. In addition, antibodies elicited by this vaccine candidate showed cross-neutralization activities to SARS-CoV-2 variants. Furthermore, with our expression system, we provided a high-yield RBD homodimer vaccine without additional biosafety or special transport device supports. Thus, it may serve as a safe, effective, and low-cost SARS-CoV-2 vaccine candidate.
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Affiliation(s)
- Xiaoyan Pan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of the Chinese Academy of Sciences, Beijing, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jian Shi
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Xue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yan Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Liang Zeng
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Yanfeng Yao
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Kunpeng Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Ge Gao
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Weiwei Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yun Peng
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Shaohong Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiaoxiao Gao
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Cheng Peng
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Juhong Rao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jiaxuan Zhao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Cheng Gong
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Hui Zhou
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Yudong Lu
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Zili Wang
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Xiliang Hu
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - WenJuan Cong
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Lijuan Fang
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | | | - Jing Zhang
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Hui Xiong
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Jizu Yi
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China
| | - Zhiming Yuan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
| | - Pengfei Zhou
- Wuhan YZY Biopharma Co., Ltd., Wuhan, Hubei, China.
| | - Chao Shan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
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422
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Makdasi E, Zvi A, Alcalay R, Noy-Porat T, Peretz E, Mechaly A, Levy Y, Epstein E, Chitlaru T, Tennenhouse A, Aftalion M, Gur D, Paran N, Tamir H, Zimhony O, Weiss S, Mandelboim M, Mendelson E, Zuckerman N, Nemet I, Kliker L, Yitzhaki S, Shapira SC, Israely T, Fleishman SJ, Mazor O, Rosenfeld R. The neutralization potency of anti-SARS-CoV-2 therapeutic human monoclonal antibodies is retained against viral variants. Cell Rep 2021; 36:109679. [PMID: 34464610 PMCID: PMC8379094 DOI: 10.1016/j.celrep.2021.109679] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/01/2021] [Accepted: 08/17/2021] [Indexed: 12/14/2022] Open
Abstract
A wide range of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing monoclonal antibodies (mAbs) have been reported, most of which target the spike glycoprotein. Therapeutic implementation of these antibodies has been challenged by emerging SARS-CoV-2 variants harboring mutated spike versions. Consequently, re-assessment of previously identified mAbs is of high priority. Four previously selected mAbs targeting non-overlapping epitopes are now evaluated for binding potency to mutated RBD versions, reported to mediate escape from antibody neutralization. In vitro neutralization potencies of these mAbs, and two NTD-specific mAbs, are evaluated against two frequent SARS-CoV-2 variants of concern, the B.1.1.7 Alpha and the B.1.351 Beta. Furthermore, we demonstrate therapeutic potential of three selected mAbs by treatment of K18-human angiotensin-converting enzyme 2 (hACE2) transgenic mice 2 days post-infection with each virus variant. Thus, despite the accumulation of spike mutations, the highly potent MD65 and BL6 mAbs retain their ability to bind the prevalent viral mutants, effectively protecting against B.1.1.7 and B.1.351 variants.
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Affiliation(s)
- Efi Makdasi
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Anat Zvi
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Ron Alcalay
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Tal Noy-Porat
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Eldar Peretz
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Adva Mechaly
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Yinon Levy
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Eyal Epstein
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Theodor Chitlaru
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Ariel Tennenhouse
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600001, Israel
| | - Moshe Aftalion
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - David Gur
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Nir Paran
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Hadas Tamir
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Oren Zimhony
- Infectious Diseases Unit, Kaplan Medical Center, Rehovot, Israel, affiliated to the School of Medicine, Hebrew University and Hadassah, Jerusalem, Israel
| | - Shay Weiss
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Michal Mandelboim
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ella Mendelson
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Neta Zuckerman
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Ital Nemet
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Limor Kliker
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Shmuel Yitzhaki
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Shmuel C Shapira
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Tomer Israely
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600001, Israel
| | - Ohad Mazor
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel.
| | - Ronit Rosenfeld
- Israel Institute for Biological Research, Ness-Ziona 7410001, Israel.
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423
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Jabłońska K, Aballéa S, Toumi M. The real-life impact of vaccination on COVID-19 mortality in Europe and Israel. Public Health 2021; 198:230-237. [PMID: 34482101 PMCID: PMC8413007 DOI: 10.1016/j.puhe.2021.07.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/14/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVES This study aimed at estimating the real-life impact of vaccination on COVID-19 mortality, with adjustment for SARS-CoV-2 variants spread and other factors across Europe and Israel. STUDY DESIGN Time series analysis. METHODS Time series analysis of the daily number of COVID-19 deaths was performed using non-linear Poisson mixed regression models. Variables such as variants' frequency, demographics, climate, health, and mobility characteristics of thirty-two countries between January 2020 and April 2021 were considered as potentially relevant adjustment factors. RESULTS The analysis revealed that vaccination efficacy in terms of protection against deaths was 72%, with a lower reduction of the number of deaths for B.1.1.7 vs non-B.1.1.7 variants (70% and 78%, respectively). Other factors significantly related to mortality were arrivals at airports, mobility change from the prepandemic level, and temperature. CONCLUSIONS Our study confirms a strong effectiveness of COVID-19 vaccination based on real-life public data, although lower than expected from clinical trials. This suggests the absence of indirect protection for non-vaccinated individuals. Results also show that vaccination effectiveness against mortality associated with the B.1.1.7 variant is slightly lower than that with other variants. Lastly, this analysis confirms the role of mobility reduction, within and between countries, as an effective way to reduce COVID-19 mortality and suggests the possibility of seasonal variations in COVID-19 incidence.
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Affiliation(s)
| | - Samuel Aballéa
- Creativ-Ceutical, Westblaak 90, Rotterdam, 3012KM, the Netherlands.
| | - Mondher Toumi
- Faculty of Medicine, Public Health Department, Aix-Marseille University, 27 Boulevard Jean Moulin, Marseille, 13005, France.
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424
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Pinto D, Sauer MM, Czudnochowski N, Low JS, Tortorici MA, Housley MP, Noack J, Walls AC, Bowen JE, Guarino B, Rosen LE, di Iulio J, Jerak J, Kaiser H, Islam S, Jaconi S, Sprugasci N, Culap K, Abdelnabi R, Foo C, Coelmont L, Bartha I, Bianchi S, Silacci-Fregni C, Bassi J, Marzi R, Vetti E, Cassotta A, Ceschi A, Ferrari P, Cippà PE, Giannini O, Ceruti S, Garzoni C, Riva A, Benigni F, Cameroni E, Piccoli L, Pizzuto MS, Smithey M, Hong D, Telenti A, Lempp FA, Neyts J, Havenar-Daughton C, Lanzavecchia A, Sallusto F, Snell G, Virgin HW, Beltramello M, Corti D, Veesler D. Broad betacoronavirus neutralization by a stem helix-specific human antibody. Science 2021; 373:1109-1116. [PMID: 34344823 PMCID: PMC9268357 DOI: 10.1126/science.abj3321] [Citation(s) in RCA: 268] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/29/2021] [Indexed: 12/11/2022]
Abstract
The spillovers of betacoronaviruses in humans and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight the need for broad coronavirus countermeasures. We describe five monoclonal antibodies (mAbs) cross-reacting with the stem helix of multiple betacoronavirus spike glycoproteins isolated from COVID-19 convalescent individuals. Using structural and functional studies, we show that the mAb with the greatest breadth (S2P6) neutralizes pseudotyped viruses from three different subgenera through the inhibition of membrane fusion, and we delineate the molecular basis for its cross-reactivity. S2P6 reduces viral burden in hamsters challenged with SARS-CoV-2 through viral neutralization and Fc-mediated effector functions. Stem helix antibodies are rare, oftentimes of narrow specificity, and can acquire neutralization breadth through somatic mutations. These data provide a framework for structure-guided design of pan-betacoronavirus vaccines eliciting broad protection.
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Affiliation(s)
- Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Maximilian M. Sauer
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | | | - Julia Noack
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Josipa Jerak
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | | | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Lotte Coelmont
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Eneida Vetti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Alessandro Ceschi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, 8091 Zurich, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Pietro E. Cippà
- Department of Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Faculty of Medicine, University of Zurich, 8057 Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
| | - Samuele Ceruti
- Intensive Care Unit, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Agostino Riva
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Matteo S. Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - David Hong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | | | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | | | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA
- UT Southwestern Medical Center, Dallas, TX 75390, USA
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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425
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Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, Di Iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, Bartha I, Housley MP, Lempp FA, Rosen LE, Dellota E, Kaiser H, Montiel-Ruiz M, Zhou J, Addetia A, Guarino B, Culap K, Sprugasci N, Saliba C, Vetti E, Giacchetto-Sasselli I, Fregni CS, Abdelnabi R, Foo SYC, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Virgin HW, Whelan SPJ, Snell G, Bloom JD, Corti D, Veesler D, Pizzuto MS. Broad sarbecovirus neutralization by a human monoclonal antibody. Nature 2021; 597:103-108. [PMID: 34280951 PMCID: PMC9341430 DOI: 10.1038/s41586-021-03817-4] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023]
Abstract
The recent emergence of SARS-CoV-2 variants of concern1-10 and the recurrent spillovers of coronaviruses11,12 into the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here we describe a human monoclonal antibody designated S2X259, which recognizes a highly conserved cryptic epitope of the receptor-binding domain and cross-reacts with spikes from all clades of sarbecovirus. S2X259 broadly neutralizes spike-mediated cell entry of SARS-CoV-2, including variants of concern (B.1.1.7, B.1.351, P.1, and B.1.427/B.1.429), as well as a wide spectrum of human and potentially zoonotic sarbecoviruses through inhibition of angiotensin-converting enzyme 2 (ACE2) binding to the receptor-binding domain. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses an escape profile that is limited to a single substitution, G504D. We show that prophylactic and therapeutic administration of S2X259 protects Syrian hamsters (Mesocricetus auratus) against challenge with the prototypic SARS-CoV-2 and the B.1.351 variant of concern, which suggests that this monoclonal antibody is a promising candidate for the prevention and treatment of emergent variants and zoonotic infections. Our data reveal a key antigenic site that is targeted by broadly neutralizing antibodies and will guide the design of vaccines that are effective against all sarbecoviruses.
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Affiliation(s)
- M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | | | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | - Amin Addetia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Eneida Vetti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | | | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | | | | | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | | | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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426
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Starr TN, Czudnochowski N, Liu Z, Zatta F, Park YJ, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, Tortorici MA, Walls AC, Wojcechowskyj JA, De Marco A, Rosen LE, Zhou J, Montiel-Ruiz M, Kaiser H, Dillen JR, Tucker H, Bassi J, Silacci-Fregni C, Housley MP, di Iulio J, Lombardo G, Agostini M, Sprugasci N, Culap K, Jaconi S, Meury M, Dellota E, Abdelnabi R, Foo SYC, Cameroni E, Stumpf S, Croll TI, Nix JC, Havenar-Daughton C, Piccoli L, Benigni F, Neyts J, Telenti A, Lempp FA, Pizzuto MS, Chodera JD, Hebner CM, Virgin HW, Whelan SPJ, Veesler D, Corti D, Bloom JD, Snell G. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature 2021; 597:97-102. [PMID: 34261126 PMCID: PMC9282883 DOI: 10.1038/s41586-021-03807-6] [Citation(s) in RCA: 321] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape1-3, have activity against diverse sarbecoviruses4-7, and be highly protective through viral neutralization8-11 and effector functions12,13. Understanding how these properties relate to each other and vary across epitopes would aid the development of therapeutic antibodies and guide vaccine design. Here we comprehensively characterize escape, breadth and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD). Despite a trade-off between in vitro neutralization potency and breadth of sarbecovirus binding, we identify neutralizing antibodies with exceptional sarbecovirus breadth and a corresponding resistance to SARS-CoV-2 escape. One of these antibodies, S2H97, binds with high affinity across all sarbecovirus clades to a cryptic epitope and prophylactically protects hamsters from viral challenge. Antibodies that target the angiotensin-converting enzyme 2 (ACE2) receptor-binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency. Nevertheless, we also characterize a potent RBM antibody (S2E128) with breadth across sarbecoviruses related to SARS-CoV-2 and a high barrier to viral escape. These data highlight principles underlying variation in escape, breadth and potency among antibodies that target the RBD, and identify epitopes and features to prioritize for therapeutic development against the current and potential future pandemics.
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MESH Headings
- Adult
- Aged
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibody Affinity
- Broadly Neutralizing Antibodies/chemistry
- Broadly Neutralizing Antibodies/immunology
- COVID-19/immunology
- COVID-19/virology
- COVID-19 Vaccines/chemistry
- COVID-19 Vaccines/immunology
- Cell Line
- Cricetinae
- Cross Reactions/immunology
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Female
- Humans
- Immune Evasion/genetics
- Immune Evasion/immunology
- Male
- Mesocricetus
- Middle Aged
- Models, Molecular
- SARS-CoV-2/chemistry
- SARS-CoV-2/classification
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vaccinology
- COVID-19 Drug Treatment
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Affiliation(s)
- Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Fabrizia Zatta
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Amin Addetia
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dora Pinto
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Martina Beltramello
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Allison J Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Roberta Marzi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - William G Glass
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ivy Zhang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Adam S Dingens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Anna De Marco
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | | | - Jessica Bassi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Gloria Lombardo
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Nicole Sprugasci
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Katja Culap
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Elisabetta Cameroni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Spencer Stumpf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Luca Piccoli
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | | | | | - Matteo S Pizzuto
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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427
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Yin R, Guest JD, Taherzadeh G, Gowthaman R, Mittra I, Quackenbush J, Pierce BG. Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants. PLoS Comput Biol 2021; 17:e1009380. [PMID: 34491988 PMCID: PMC8448325 DOI: 10.1371/journal.pcbi.1009380] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/17/2021] [Accepted: 08/25/2021] [Indexed: 11/19/2022] Open
Abstract
The SARS-CoV-2 pandemic highlights the need for a detailed molecular understanding of protective antibody responses. This is underscored by the emergence and spread of SARS-CoV-2 variants, including Alpha (B.1.1.7) and Delta (B.1.617.2), some of which appear to be less effectively targeted by current monoclonal antibodies and vaccines. Here we report a high resolution and comprehensive map of antibody recognition of the SARS-CoV-2 spike receptor binding domain (RBD), which is the target of most neutralizing antibodies, using computational structural analysis. With a dataset of nonredundant experimentally determined antibody-RBD structures, we classified antibodies by RBD residue binding determinants using unsupervised clustering. We also identified the energetic and conservation features of epitope residues and assessed the capacity of viral variant mutations to disrupt antibody recognition, revealing sets of antibodies predicted to effectively target recently described viral variants. This detailed structure-based reference of antibody RBD recognition signatures can inform therapeutic and vaccine design strategies.
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Affiliation(s)
- Rui Yin
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Johnathan D. Guest
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Ghazaleh Taherzadeh
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Ipsa Mittra
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Jane Quackenbush
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Brian G. Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
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428
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Szemiel AM, Merits A, Orton RJ, MacLean OA, Pinto RM, Wickenhagen A, Lieber G, Turnbull ML, Wang S, Furnon W, Suarez NM, Mair D, da Silva Filipe A, Willett BJ, Wilson SJ, Patel AH, Thomson EC, Palmarini M, Kohl A, Stewart ME. In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. PLoS Pathog 2021; 17:e1009929. [PMID: 34534263 PMCID: PMC8496873 DOI: 10.1371/journal.ppat.1009929] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 10/07/2021] [Accepted: 08/30/2021] [Indexed: 01/18/2023] Open
Abstract
Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV. Using high throughput sequencing, we identified a single mutation in RNA-dependent RNA polymerase (NSP12) at a residue conserved among all coronaviruses in two independently evolved populations displaying decreased RDV sensitivity. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. Substitution of E802 did not affect viral replication or activity of an alternate nucleoside analogue (EIDD2801) but did affect virus fitness in a competition assay. Analysis of the globally circulating SARS-CoV-2 variants (>800,000 sequences) showed no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we observed an excess of substitutions in spike at corresponding sites identified in the emerging SARS-CoV-2 variants of concern (i.e., H69, E484, N501, H655) indicating that they can arise in vitro in the absence of immune selection. The identification and characterisation of a drug resistant signature within the SARS-CoV-2 genome has implications for clinical management and virus surveillance.
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Affiliation(s)
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Oscar A. MacLean
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Gauthier Lieber
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Matthew L. Turnbull
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sainan Wang
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicolas M. Suarez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Brian J. Willett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Meredith E. Stewart
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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429
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Francino-Urdaniz IM, Steiner PJ, Kirby MB, Zhao F, Haas CM, Barman S, Rhodes ER, Leonard AC, Peng L, Sprenger KG, Jardine JG, Whitehead TA. One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening. Cell Rep 2021; 36:109627. [PMID: 34416153 PMCID: PMC8352667 DOI: 10.1016/j.celrep.2021.109627] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/12/2021] [Accepted: 08/05/2021] [Indexed: 12/23/2022] Open
Abstract
The potential emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) escape mutants is a threat to the efficacy of existing vaccines and neutralizing antibody (nAb) therapies. An understanding of the antibody/S escape mutation landscape is urgently needed to preemptively address this threat. Here we describe a rapid method to identify escape mutants for nAbs targeting the S receptor binding site. We identified escape mutants for five nAbs, including three from the public germline class VH3-53 elicited by natural coronavirus disease 2019 (COVID-19) infection. Escape mutations predominantly mapped to the periphery of the angiotensin-converting enzyme 2 (ACE2) recognition site on the RBD with K417, D420, Y421, F486, and Q493 as notable hotspots. We provide libraries, methods, and software as an openly available community resource to accelerate new therapeutic strategies against SARS-CoV-2.
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Affiliation(s)
- Irene M Francino-Urdaniz
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Monica B Kirby
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Fangzhu Zhao
- The Scripps Research Institute, La Jolla, CA, USA
| | - Cyrus M Haas
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Shawn Barman
- The Scripps Research Institute, La Jolla, CA, USA
| | - Emily R Rhodes
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Alison C Leonard
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | | | - Kayla G Sprenger
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | | | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA.
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430
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Rodríguez-Maldonado AP, Vázquez-Pérez JA, Cedro-Tanda A, Taboada B, Boukadida C, Wong-Arámbula C, Nuñez-García TE, Cruz-Ortiz N, Barrera-Badillo G, Hernández-Rivas L, López-Martínez I, Mendoza-Vargas A, Reyes-Grajeda JP, Alcaraz N, Peñaloza-Figueroa F, Gonzalez-Barrera D, Rangel-DeLeon D, Herrera-Montalvo LA, Mejía-Nepomuceno F, Hernández-Terán A, Mújica-Sánchez M, Becerril-Vargas E, Martínez-Orozco JA, Pérez-Padilla R, Salas-Hernández J, Sanchez-Flores A, Isa P, Matías-Florentino M, Ávila-Ríos S, Muñoz-Medina JE, Grajales-Muñiz C, Salas-Lais AG, Santos Coy-Arechavaleta A, Hidalgo-Miranda A, Arias CF, Ramírez-González JE. Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. Arch Virol 2021; 166:3173-3177. [PMID: 34448936 PMCID: PMC8390838 DOI: 10.1007/s00705-021-05208-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/27/2021] [Indexed: 11/28/2022]
Abstract
SARS-CoV-2 variants emerged in late 2020, and at least three variants of concern (B.1.1.7, B.1.351, and P1) have been reported by WHO. These variants have several substitutions in the spike protein that affect receptor binding; they exhibit increased transmissibility and may be associated with reduced vaccine effectiveness. In the present work, we report the identification of a potential variant of interest, harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.1.1.519, that rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021.
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Affiliation(s)
- Abril Paulina Rodríguez-Maldonado
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | | | | | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | - Claudia Wong-Arámbula
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Tatiana Ernestina Nuñez-García
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Natividad Cruz-Ortiz
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Gisela Barrera-Badillo
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Lucía Hernández-Rivas
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Irma López-Martínez
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | | | | | - Nicolas Alcaraz
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | | | | | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pavel Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | | | | | | | | | | | - Carlos F Arias
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico.
| | - José Ernesto Ramírez-González
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico.
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431
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Zhong H, Liu S, Cao F, Zhao Y, Zhou J, Tang F, Peng Z, Li Y, Xu S, Wang C, Yang G, Li ZQ. Dissecting Tumor Antigens and Immune Subtypes of Glioma to Develop mRNA Vaccine. Front Immunol 2021; 12:709986. [PMID: 34512630 PMCID: PMC8429949 DOI: 10.3389/fimmu.2021.709986] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/28/2021] [Indexed: 01/02/2023] Open
Abstract
Background Nowadays, researchers are leveraging the mRNA-based vaccine technology used to develop personalized immunotherapy for cancer. However, its application against glioma is still in its infancy. In this study, the applicable candidates were excavated for mRNA vaccine treatment in the perspective of immune regulation, and suitable glioma recipients with corresponding immune subtypes were further investigated. Methods The RNA-seq data and clinical information of 702 and 325 patients were recruited from TCGA and CGGA, separately. The genetic alteration profile was visualized and compared by cBioPortal. Then, we explored prognostic outcomes and immune correlations of the selected antigens to validate their clinical relevance. The prognostic index was measured via GEPIA2, and infiltration of antigen-presenting cells (APCs) was calculated and visualized by TIMER. Based on immune-related gene expression, immune subtypes of glioma were identified using consensus clustering analysis. Moreover, the immune landscape was visualized by graph learning-based dimensionality reduction analysis. Results Four glioma antigens, namely ANXA5, FKBP10, MSN, and PYGL, associated with superior prognoses and infiltration of APCs were selected. Three immune subtypes IS1-IS3 were identified, which fundamentally differed in molecular, cellular, and clinical signatures. Patients in subtypes IS2 and IS3 carried immunologically cold phenotypes, whereas those in IS1 carried immunologically hot phenotype. Particularly, patients in subtypes IS3 and IS2 demonstrated better outcomes than that in IS1. Expression profiles of immune checkpoints and immunogenic cell death (ICD) modulators showed a difference among IS1-IS3 tumors. Ultimately, the immune landscape of glioma elucidated considerable heterogeneity not only between individual patients but also within the same immune subtype. Conclusions ANXA5, FKBP10, MSN, and PYGL are identified as potential antigens for anti-glioma mRNA vaccine production, specifically for patients in immune subtypes 2 and 3. In summary, this study may shed new light on the promising approaches of immunotherapy, such as devising mRNA vaccination tailored to applicable glioma recipients.
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Affiliation(s)
- Hua Zhong
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Shuai Liu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Fang Cao
- Department of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yi Zhao
- Department of Medical Genetics, School of Basic Medical Science, Demonstration Center for Experimental Basic Medicine Education, Wuhan University, Wuhan, China
| | - Jianguo Zhou
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Feng Tang
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Yangsheng Li
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Shen Xu
- Department of Neurosurgery, No. 901 Hospital of the Chinese People’s Liberation Army Logistic Support Force, Hefei, China
| | - Chunlin Wang
- Department of Neurosurgery, No. 901 Hospital of the Chinese People’s Liberation Army Logistic Support Force, Hefei, China
| | - Guohua Yang
- Department of Medical Genetics, School of Basic Medical Science, Demonstration Center for Experimental Basic Medicine Education, Wuhan University, Wuhan, China
| | - Zhi-Qiang Li
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
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432
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Ying B, Whitener B, VanBlargan LA, Hassan AO, Shrihari S, Liang CY, Karl CE, Mackin S, Chen RE, Kafai NM, Wilks SH, Smith DJ, Carreño JM, Singh G, Krammer F, Carfi A, Elbashir S, Edwards DK, Thackray LB, Diamond MS. Protective activity of mRNA vaccines against ancestral and variant SARS-CoV-2 strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.25.457693. [PMID: 34462745 PMCID: PMC8404887 DOI: 10.1101/2021.08.25.457693] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although mRNA vaccines prevent COVID-19, variants jeopardize their efficacy as immunity wanes. Here, we assessed the immunogenicity and protective activity of historical (mRNA-1273, designed for Wuhan-1 spike) or modified (mRNA-1273.351, designed for B.1.351 spike) preclinical Moderna mRNA vaccines in 129S2 and K18-hACE2 mice. Immunization with high or low dose formulations of mRNA vaccines induced neutralizing antibodies in serum against ancestral SARS-CoV-2 and several variants, although levels were lower particularly against the B.1.617.2 (Delta) virus. Protection against weight loss and lung pathology was observed with all high-dose vaccines against all viruses. Nonetheless, low-dose formulations of the vaccines, which produced lower magnitude antibody and T cell responses, and serve as a possible model for waning immunity, showed breakthrough lung infection and pneumonia with B.1.617.2. Thus, as levels of immunity induced by mRNA vaccines decline, breakthrough infection and disease likely will occur with some SARS-CoV-2 variants, suggesting a need for additional booster regimens.
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Affiliation(s)
- Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bradley Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ahmed O. Hassan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chieh-Yu Liang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Courtney E. Karl
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine. St. Louis, MO, USA
| | - Samantha Mackin
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Natasha M. Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel H. Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge UK
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge UK
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Larissa B. Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, 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
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433
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Wilhelm A, Toptan T, Pallas C, Wolf T, Goetsch U, Gottschalk R, Vehreschild MJGT, Ciesek S, Widera M. Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Viruses 2021; 13:v13091693. [PMID: 34578275 DOI: 10.1101/2021.08.09.21261704] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/22/2021] [Indexed: 05/24/2023] Open
Abstract
The capacity of convalescent and vaccine-elicited sera and monoclonal antibodies (mAb) to neutralize SARS-CoV-2 variants is currently of high relevance to assess the protection against infections. We performed a cell culture-based neutralization assay focusing on authentic SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.427/B.1.429 (Epsilon), all harboring the spike substitution L452R. We found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. Compared to B.1, Kappa and Delta showed a reduced neutralization by convalescent sera by a factor of 8.00 and 5.33, respectively, which constitutes a 2-fold greater reduction when compared to Epsilon. BNT2b2 and mRNA1273 vaccine-elicited sera were less effective against Kappa, Delta, and Epsilon compared to B.1. No difference was observed between Kappa and Delta towards vaccine-elicited sera, whereas convalescent sera were 1.51-fold less effective against Delta, respectively. Both B.1.617 variants Kappa (+E484Q) and Delta (+T478K) were less susceptible to either casirivimab or imdevimab. In conclusion, in contrast to the parallel circulating Kappa variant, the neutralization efficiency of convalescent and vaccine-elicited sera against Delta was moderately reduced. Delta was resistant to imdevimab, which, however, might be circumvented by combination therapy with casirivimab together.
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Udo Goetsch
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany
| | - Rene Gottschalk
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Branch Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
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434
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Wilhelm A, Toptan T, Pallas C, Wolf T, Goetsch U, Gottschalk R, Vehreschild MJGT, Ciesek S, Widera M. Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Viruses 2021; 13:1693. [PMID: 34578275 PMCID: PMC8473269 DOI: 10.3390/v13091693] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/22/2021] [Indexed: 12/23/2022] Open
Abstract
The capacity of convalescent and vaccine-elicited sera and monoclonal antibodies (mAb) to neutralize SARS-CoV-2 variants is currently of high relevance to assess the protection against infections. We performed a cell culture-based neutralization assay focusing on authentic SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.427/B.1.429 (Epsilon), all harboring the spike substitution L452R. We found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. Compared to B.1, Kappa and Delta showed a reduced neutralization by convalescent sera by a factor of 8.00 and 5.33, respectively, which constitutes a 2-fold greater reduction when compared to Epsilon. BNT2b2 and mRNA1273 vaccine-elicited sera were less effective against Kappa, Delta, and Epsilon compared to B.1. No difference was observed between Kappa and Delta towards vaccine-elicited sera, whereas convalescent sera were 1.51-fold less effective against Delta, respectively. Both B.1.617 variants Kappa (+E484Q) and Delta (+T478K) were less susceptible to either casirivimab or imdevimab. In conclusion, in contrast to the parallel circulating Kappa variant, the neutralization efficiency of convalescent and vaccine-elicited sera against Delta was moderately reduced. Delta was resistant to imdevimab, which, however, might be circumvented by combination therapy with casirivimab together.
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (T.W.); (M.J.G.T.V.)
| | - Udo Goetsch
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany; (U.G.); (R.G.)
| | - Rene Gottschalk
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany; (U.G.); (R.G.)
| | - Maria J. G. T. Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (T.W.); (M.J.G.T.V.)
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Branch Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
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435
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Rotondo JC, Martini F, Maritati M, Mazziotta C, Di Mauro G, Lanzillotti C, Barp N, Gallerani A, Tognon M, Contini C. SARS-CoV-2 Infection: New Molecular, Phylogenetic, and Pathogenetic Insights. Efficacy of Current Vaccines and the Potential Risk of Variants. Viruses 2021; 13:1687. [PMID: 34578269 PMCID: PMC8473168 DOI: 10.3390/v13091687] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly discovered coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic. COVID-19 has rapidly become a public health emergency of international concern. Although remarkable scientific achievements have been reached since the beginning of the pandemic, the knowledge behind this novel coronavirus, in terms of molecular and pathogenic characteristics and zoonotic potential, is still relatively limited. Today, there is a vaccine, or rather several vaccines, which, for the first time in the history of highly contagious infectious diseases that have plagued mankind, has been manufactured in just one year. Currently, four vaccines are licensed by regulatory agencies, and they use RNA or viral vector technologies. The positive effects of the vaccination campaign are being felt in many parts of the world, but the disappearance of this new infection is still far from being a reality, as it is also threatened by the presence of novel SARS-CoV-2 variants that could undermine the effectiveness of the vaccine, hampering the immunization control efforts. Indeed, the current findings indicate that SARS-CoV-2 is adapting to transmission in humans more efficiently, while further divergence from the initial archetype should be considered. In this review, we aimed to provide a collection of the current knowledge regarding the molecular, phylogenetic, and pathogenetic insights into SARS-CoV-2. The most recent findings obtained with respect to the impact of novel emerging SARS-CoV-2 variants as well as the development and implementation of vaccines are highlighted.
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Affiliation(s)
- John Charles Rotondo
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Martina Maritati
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Chiara Mazziotta
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Giulia Di Mauro
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Carmen Lanzillotti
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Nicole Barp
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Altea Gallerani
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Carlo Contini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
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436
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Li D, Sempowski GD, Saunders KO, Acharya P, Haynes BF. SARS-CoV-2 Neutralizing Antibodies for COVID-19 Prevention and Treatment. Annu Rev Med 2021; 73:1-16. [PMID: 34428080 DOI: 10.1146/annurev-med-042420-113838] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Prophylactic and therapeutic drugs are urgently needed to combat coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Over the past year, SARS-CoV-2 neutralizing antibodies have been developed for preventive or therapeutic uses. While neutralizing antibodies target the spike protein, their neutralization potency and breadth vary according to recognition epitopes. Several potent SARS-CoV-2 antibodies have shown degrees of success in preclinical or clinical trials, and the US Food and Drug Administration has issued emergency use authorization for two neutralizing antibody cocktails. Nevertheless, antibody therapy for SARS-CoV-2 still faces potential challenges, including emerging viral variants of concern that have antibody-escape mutations and the potential for antibody-mediated enhancement of infection or inflammation. This review summarizes representative SARS-CoV-2 neutralizing antibodies that have been reported and discusses prospects and challenges for the development of the next generation of COVID-19 preventive or therapeutic antibodies. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Dapeng Li
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Pathology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Surgery, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Surgery, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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437
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He X, Ding L, Cao K, Peng H, Gu C, Li Y, Li D, Dong L, Hong X, Wang X, Fu M, Qiu C, Zhu C, Zhang Z, Song S, Wang C, Jiang Z, Xie Y, Qi Z, Zhao C, Zhao P, Zhang X, Xu J. A human cell-based SARS-CoV-2 vaccine elicits potent neutralizing antibody responses and protects mice from SARS-CoV-2 challenge. Emerg Microbes Infect 2021; 10:1555-1573. [PMID: 34304724 PMCID: PMC8366622 DOI: 10.1080/22221751.2021.1957400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To curb the pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), multiple platforms have been employed toward a safe and highly effective vaccine. Here, we develop a novel cell-based vaccine candidate, namely K562-S, by utilizing human cell K562 as a cellular carrier to display Spike (S) protein of SARS-CoV-2 on the membrane. Analogous to the traditional inactivated vaccine, K562-S cells can be propagated to a large scale by culturing and completely lose their viability after exposure to X-ray irradiation or formalin. We in turn demonstrated high immunogenicity of formalin-inactivated K562-S vaccine in both mouse and non-human primates and its protective efficacy in mice. In mice, immunization with inactivated K562-S vaccines can elicit potent neutralizing antibody (nAb) responses persisting longer than 5 months. We consequently showed in a hACE2 mouse model of SARS-CoV-2 infection that a two-shot vaccination with adjuvanted K562-S rendered greater than 3 log reduction in viral lung load and concomitant ameliorated lung pathology. Of importance, the administration of the same regimen in non-human primates was able to induce a neutralizing antibody titer averaging three-fold higher relative to human convalescent serum. These results together support the promise of K562-based, S-protein-expressing vaccines as a novel vaccination approach against SARS-CoV-2. Importantly, with a powerful capacity to carry external genes for cell-based vectors, this platform could rapidly generate two- and multiple-valent vaccines by incorporating SARS-CoV-2 mutants, SARS-CoV, or MERS-CoV.
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Affiliation(s)
- Xiangchuan He
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Longfei Ding
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Kangli Cao
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Haoran Peng
- Department of Microbiology, Second Military Medical University, Shanghai, People's Republic of China
| | - Chenjian Gu
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yutang Li
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Duoduo Li
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Lanlan Dong
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Xiujing Hong
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Xiangwei Wang
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Meilan Fu
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Chenli Qiu
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Cuisong Zhu
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Ziling Zhang
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Shu Song
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Chenguang Wang
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences & Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, People's Republic of China
| | - Zhengfan Jiang
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences & Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, People's Republic of China
| | - Youhua Xie
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Zhongtian Qi
- Department of Microbiology, Second Military Medical University, Shanghai, People's Republic of China
| | - Chen Zhao
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Ping Zhao
- Department of Microbiology, Second Military Medical University, Shanghai, People's Republic of China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
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438
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Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. INFECTION GENETICS AND EVOLUTION 2021; 95:105038. [PMID: 34403832 PMCID: PMC8364171 DOI: 10.1016/j.meegid.2021.105038] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/21/2021] [Accepted: 08/11/2021] [Indexed: 12/25/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between January and April 2021, were processed for genome sequencing and lineage determination following the nanopore amplicon ARTIC network protocol and PANGOLIN pipeline. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes I95I, Y144T, Y145S and the insertion 146 N in the N-terminal domain, R346K, E484K and N501Y in the Receptor binding Domain (RBD) and P681H in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlantico, Bolivar, Bogotá D.C, and Santander that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage.
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439
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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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440
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Edara VV, Pinsky BA, Suthar MS, Lai L, Davis-Gardner ME, Floyd K, Flowers MW, Wrammert J, Hussaini L, Ciric CR, Bechnak S, Stephens K, Graham BS, Bayat Mokhtari E, Mudvari P, Boritz E, Creanga A, Pegu A, Derrien-Colemyn A, Henry AR, Gagne M, Douek DC, Sahoo MK, Sibai M, Solis D, Webby RJ, Jeevan T, Fabrizio TP. Infection and Vaccine-Induced Neutralizing-Antibody Responses to the SARS-CoV-2 B.1.617 Variants. N Engl J Med 2021; 385:664-666. [PMID: 34233096 PMCID: PMC8279090 DOI: 10.1056/nejmc2107799] [Citation(s) in RCA: 230] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Lilin Lai
- Emory University School of Medicine, Atlanta, GA
| | | | | | | | | | | | | | | | | | - Barney S Graham
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | | | - Prakriti Mudvari
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Eli Boritz
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Adrian Creanga
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Amarendra Pegu
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | | | - Amy R Henry
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Matthew Gagne
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Daniel C Douek
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | | | - Mamdouh Sibai
- Stanford University School of Medicine, Stanford, CA
| | - Daniel Solis
- Stanford University School of Medicine, Stanford, CA
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441
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TMPRSS2 and RNA-Dependent RNA Polymerase Are Effective Targets of Therapeutic Intervention for Treatment of COVID-19 Caused by SARS-CoV-2 Variants (B.1.1.7 and B.1.351). Microbiol Spectr 2021; 9:e0047221. [PMID: 34378968 PMCID: PMC8552736 DOI: 10.1128/spectrum.00472-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a causative agent of the coronavirus disease 2019 (COVID-19) pandemic, and the development of therapeutic interventions is urgently needed. So far, monoclonal antibodies and drug repositioning are the main methods for drug development, and this effort was partially successful. Since the beginning of the COVID-19 pandemic, the emergence of SARS-CoV-2 variants has been reported in many parts of the world, and the main concern is whether the current vaccines and therapeutics are still effective against these variant viruses. Viral entry and viral RNA-dependent RNA polymerase (RdRp) are the main targets of current drug development; therefore, the inhibitory effects of transmembrane serine protease 2 (TMPRSS2) and RdRp inhibitors were compared among the early SARS-CoV-2 isolate (lineage A) and the two recent variants (lineage B.1.1.7 and lineage B.1.351) identified in the United Kingdom and South Africa, respectively. Our in vitro analysis of viral replication showed that the drugs targeting TMPRSS2 and RdRp are equally effective against the two variants of concern. IMPORTANCE The COVID-19 pandemic is causing unprecedented global problems in both public health and human society. While some vaccines and monoclonal antibodies were successfully developed very quickly and are currently being used, numerous variants of the causative SARS-CoV-2 are emerging and threatening the efficacy of vaccines and monoclonal antibodies. In order to respond to this challenge, we assessed antiviral efficacy of small-molecule inhibitors that are being developed for treatment of COVID-19 and found that they are still very effective against the SARS-CoV-2 variants. Since most small-molecule inhibitors target viral or host factors other than the mutated sequence of the viral spike protein, they are expected to be potent control measures against the COVID-19 pandemic.
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442
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SARS-CoV-2 Genomic Sequencing Revealed N501Y and L452R Mutants of S/A Lineage in Tianjin Municipality, China. Virol Sin 2021; 36:1228-1231. [PMID: 34379315 PMCID: PMC8356212 DOI: 10.1007/s12250-021-00432-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/26/2021] [Indexed: 11/29/2022] Open
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443
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Muecksch F, Weisblum Y, Barnes CO, Schmidt F, Schaefer-Babajew D, Wang Z, C Lorenzi JC, Flyak AI, DeLaitsch AT, Huey-Tubman KE, Hou S, Schiffer CA, Gaebler C, Da Silva J, Poston D, Finkin S, Cho A, Cipolla M, Oliveira TY, Millard KG, Ramos V, Gazumyan A, Rutkowska M, Caskey M, Nussenzweig MC, Bjorkman PJ, Hatziioannou T, Bieniasz PD. Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations. Immunity 2021; 54:1853-1868.e7. [PMID: 34331873 PMCID: PMC8323339 DOI: 10.1016/j.immuni.2021.07.008] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/26/2021] [Accepted: 07/12/2021] [Indexed: 12/23/2022]
Abstract
Antibodies elicited by infection accumulate somatic mutations in germinal centers that can increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) Spike receptor-binding domain (RBD)-specific antibodies from 5 individuals shortly after infection and later in convalescence to determine the impact of maturation over months. In addition to increased affinity and neutralization potency, antibody evolution changed the mutational pathways for the acquisition of viral resistance and restricted neutralization escape options. For some antibodies, maturation imposed a requirement for multiple substitutions to enable escape. For certain antibodies, affinity maturation enabled the neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.
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MESH Headings
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibody Affinity/immunology
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Epitopes/chemistry
- Epitopes/immunology
- Host-Pathogen Interactions/immunology
- Humans
- Models, Molecular
- Mutation
- Neutralization Tests
- Protein Binding
- Protein Conformation
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Structure-Activity Relationship
- Virulence/genetics
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Affiliation(s)
- Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Andrew I Flyak
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew T DeLaitsch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Justin Da Silva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Poston
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Magdalena Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute.
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute.
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444
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Duerr R, Dimartino D, Marier C, Zappile P, Wang G, Lighter J, Elbel B, Troxel AB, Heguy A. Dominance of alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City. J Clin Invest 2021; 131:e152702. [PMID: 34375308 DOI: 10.1172/jci152702] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022] Open
Abstract
The efficacy of COVID-19 mRNA vaccines is high, but breakthrough infections still occur. We compared the SARS-CoV-2 genomes of 76 breakthrough cases after full vaccination with BNT162b2 (Pfizer/BioNTech), mRNA-1273 (Moderna), or JNJ-78436735 (Janssen) to unvaccinated controls (February-April 2021) in metropolitan New York, including their phylogenetic relationship, distribution of variants, and full spike mutation profiles. Their median age was 48 years; seven required hospitalization and one died. Most breakthrough infections (57/76) occurred with B.1.1.7 (Alpha) or B.1.526 (Iota). Among the 7 hospitalized cases, 4 were infected with B.1.1.7, including 1 death. Both unmatched and matched statistical analyses considering age, sex, vaccine type, and study month as covariates supported the null hypothesis of equal variant distributions between vaccinated and unvaccinated in chi-squared and McNemar tests (p>0.1) highlighting a high vaccine efficacy against B.1.1.7 and B.1.526. There was no clear association among breakthroughs between type of vaccine received and variant. In the vaccinated group, spike mutations in the N-terminal domain and receptor-binding domain that have been associated with immune evasion were overrepresented. The evolving dynamic of SARS-CoV-2 variants requires broad genomic analyses of breakthrough infections to provide real-life information on immune escape mediated by circulating variants and their spike mutations.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, NYU Langone Health, New York, United States of America
| | - Dacia Dimartino
- Office for Science and Research, NYU Langone Health, New York, United States of America
| | - Christian Marier
- Office for Science and Research, NYU Langone Health, New York, United States of America
| | - Paul Zappile
- Office for Science and Research, NYU Langone Health, New York, United States of America
| | - Guiqing Wang
- Department of Pathology, NYU Langone Health, New York, United States of America
| | - Jennifer Lighter
- Department of Pediatric Infectious Diseases, NYU Langone Health, New York, United States of America
| | - Brian Elbel
- Department of Population Health, NYU Langone Health, New York, United States of America
| | - Andrea B Troxel
- Department of Population Health, NYU Langone Health, New York, United States of America
| | - Adriana Heguy
- NYU Langone Health, New York, United States of America
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445
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Padilla-Rojas C, Jimenez-Vasquez V, Hurtado V, Mestanza O, Molina IS, Barcena L, Morales Ruiz S, Acedo S, Lizarraga W, Bailon H, Cáceres O, Galarza M, Rojas-Serrano N, Vargas-Herrera N, Lope-Pari P, Huayra J, Solari L. Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS-COV-2 lineage in Peru despite circulation of variants of concern. J Med Virol 2021; 93:6845-6849. [PMID: 34370324 PMCID: PMC8427000 DOI: 10.1002/jmv.27261] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 01/06/2023]
Abstract
The pandemic generated by SARS‐Cov‐2 has caused a large number of cases and deaths in the world, but South America has been one of the continents that were most hard hit. The appearance of new variants causes concern because of the possibility that they may evade the protection generated by vaccination campaigns, their greater capacity to be transmitted, or their higher virulence. We analyzed the circulating variants in Peru after improving our Genomic Surveillance program. The results indicate a steep increase of the lambda lineage (C.37) until becoming predominant between January and April 2021, despite the cocirculation of other variants of concern or interest. Lambda lineage deserves close monitoring and could probably become a variant of concern in the near future.
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Affiliation(s)
- Carlos Padilla-Rojas
- Laboratorio de Referencia Nacional de Virus Respiratorios, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Victor Jimenez-Vasquez
- Laboratorio de Referencia Nacional de Virus Respiratorios, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Veronica Hurtado
- Laboratorio de Referencia Nacional de Virus Respiratorios, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Orson Mestanza
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Iris S Molina
- Laboratorio de Referencia Nacional de Virus Respiratorios, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Luis Barcena
- Laboratorio de Referencia Nacional de Virus Respiratorios, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Sandra Morales Ruiz
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Steve Acedo
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Wendy Lizarraga
- Laboratorio de Referencia Nacional de Virus Respiratorios, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Henri Bailon
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Omar Cáceres
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Marco Galarza
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru.,National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Nancy Rojas-Serrano
- National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Natalia Vargas-Herrera
- National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Priscila Lope-Pari
- Laboratorio de Referencia Nacional de Virus Respiratorios, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Joseph Huayra
- Laboratorio de Referencia Nacional de Virus Respiratorios, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
| | - Lely Solari
- National Genomic Surveillance Program for SARS-CoV-2, Centro Nacional de Salud Publica, Instituto Nacional de Salud Peru, Lima, Peru
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446
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McCallum M, Bassi J, De Marco A, Chen A, Walls AC, Di Iulio J, Tortorici MA, Navarro MJ, Silacci-Fregni C, Saliba C, Sprouse KR, Agostini M, Pinto D, Culap K, Bianchi S, Jaconi S, Cameroni E, Bowen JE, Tilles SW, Pizzuto MS, Guastalla SB, Bona G, Pellanda AF, Garzoni C, Van Voorhis WC, Rosen LE, Snell G, Telenti A, Virgin HW, Piccoli L, Corti D, Veesler D. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 2021; 373:648-654. [PMID: 34210893 PMCID: PMC9835956 DOI: 10.1126/science.abi7994] [Citation(s) in RCA: 302] [Impact Index Per Article: 100.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/25/2021] [Indexed: 01/16/2023]
Abstract
A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429), which was originally detected in California, carries spike glycoprotein mutations S13I in the signal peptide, W152C in the N-terminal domain (NTD), and L452R in the receptor-binding domain (RBD). Plasma from individuals vaccinated with a Wuhan-1 isolate-based messenger RNA vaccine or from convalescent individuals exhibited neutralizing titers that were reduced 2- to 3.5-fold against the B.1.427/B.1.429 variant relative to wild-type pseudoviruses. The L452R mutation reduced neutralizing activity in 14 of 34 RBD-specific monoclonal antibodies (mAbs). The S13I and W152C mutations resulted in total loss of neutralization for 10 of 10 NTD-specific mAbs because the NTD antigenic supersite was remodeled by a shift of the signal peptide cleavage site and the formation of a new disulfide bond, as revealed by mass spectrometry and structural studies.
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MESH Headings
- 2019-nCoV Vaccine mRNA-1273
- Amino Acid Substitution
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- BNT162 Vaccine
- COVID-19/immunology
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Cryoelectron Microscopy
- Humans
- Immune Evasion
- Models, Molecular
- Mutation
- Neutralization Tests
- Protein Conformation
- Protein Domains
- Protein Interaction Domains and Motifs
- Protein Subunits/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alex Chen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Mary-Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | - Giovanni Bona
- Clinical Research Unit, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | | | | | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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447
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Li W, Chen Y, Prévost J, Ullah I, Lu M, Gong SY, Tauzin A, Gasser R, Vézina D, Anand SP, Goyette G, Chaterjee D, Ding S, Tolbert WD, Grunst MW, Bo Y, Zhang S, Richard J, Zhou F, Huang RK, Esser L, Zeher A, Côté M, Kumar P, Sodroski J, Xia D, Uchil PD, Pazgier M, Finzi A, Mothes W. Structural Basis and Mode of Action for Two Broadly Neutralizing Antibodies Against SARS-CoV-2 Emerging Variants of Concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.02.454546. [PMID: 34373853 PMCID: PMC8351775 DOI: 10.1101/2021.08.02.454546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Emerging variants of concern for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit more efficiently and partially evade protective immune responses, thus necessitating continued refinement of antibody therapies and immunogen design. Here we elucidate the structural basis and mode of action for two potent SARS-CoV-2 Spike (S) neutralizing monoclonal antibodies CV3-1 and CV3-25 that remained effective against emerging variants of concern in vitro and in vivo. CV3-1 bound to the (485-GFN-487) loop within the receptor-binding domain (RBD) in the "RBD-up" position and triggered potent shedding of the S1 subunit. In contrast, CV3-25 inhibited membrane fusion by binding to an epitope in the stem helix region of the S2 subunit that is highly conserved among β-coronaviruses. Thus, vaccine immunogen designs that incorporate the conserved regions in RBD and stem helix region are candidates to elicit pan-coronavirus protective immune responses.
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Affiliation(s)
- Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Shang Yu Gong
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Dani Vézina
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - William D. Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Michael W. Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Fei Zhou
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rick K. Huang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Esser
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allison Zeher
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
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448
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Chen RE, Winkler ES, Case JB, Aziati ID, Bricker TL, Joshi A, Darling TL, Ying B, Errico JM, Shrihari S, VanBlargan LA, Xie X, Gilchuk P, Zost SJ, Droit L, Liu Z, Stumpf S, Wang D, Handley SA, Stine WB, Shi PY, Davis-Gardner ME, Suthar MS, Knight MG, Andino R, Chiu CY, Ellebedy AH, Fremont DH, Whelan SPJ, Crowe JE, Purcell L, Corti D, Boon ACM, Diamond MS. In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains. Nature 2021; 596:103-108. [PMID: 34153975 PMCID: PMC8349859 DOI: 10.1038/s41586-021-03720-y] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Rapidly emerging SARS-CoV-2 variants jeopardize antibody-based countermeasures. Although cell culture experiments have demonstrated a loss of potency of several anti-spike neutralizing antibodies against variant strains of SARS-CoV-21-3, the in vivo importance of these results remains uncertain. Here we report the in vitro and in vivo activity of a panel of monoclonal antibodies (mAbs), which correspond to many in advanced clinical development by Vir Biotechnology, AbbVie, AstraZeneca, Regeneron and Lilly, against SARS-CoV-2 variant viruses. Although some individual mAbs showed reduced or abrogated neutralizing activity in cell culture against B.1.351, B.1.1.28, B.1.617.1 and B.1.526 viruses with mutations at residue E484 of the spike protein, low prophylactic doses of mAb combinations protected against infection by many variants in K18-hACE2 transgenic mice, 129S2 immunocompetent mice and hamsters, without the emergence of resistance. Exceptions were LY-CoV555 monotherapy and LY-CoV555 and LY-CoV016 combination therapy, both of which lost all protective activity, and the combination of AbbVie 2B04 and 47D11, which showed a partial loss of activity. When administered after infection, higher doses of several mAb cocktails protected in vivo against viruses with a B.1.351 spike gene. Therefore, many-but not all-of the antibody products with Emergency Use Authorization should retain substantial efficacy against the prevailing variant strains of SARS-CoV-2.
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MESH Headings
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/pharmacology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/immunology
- Antibodies, Viral/pharmacology
- Antibodies, Viral/therapeutic use
- COVID-19/genetics
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- Chlorocebus aethiops
- Female
- Humans
- Male
- Mesocricetus/immunology
- Mesocricetus/virology
- Mice
- Mice, Transgenic
- Neutralization Tests
- Post-Exposure Prophylaxis
- Pre-Exposure Prophylaxis
- SARS-CoV-2/drug effects
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Serine Endopeptidases/genetics
- Serine Endopeptidases/metabolism
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vero Cells
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Affiliation(s)
- Rita E Chen
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Emma S Winkler
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Ishmael D Aziati
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Traci L Bricker
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Astha Joshi
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Tamarand L Darling
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Baoling Ying
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - John M Errico
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lindsay Droit
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Spencer Stumpf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | | | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 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
| | - 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
| | - Miguel Garcia Knight
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Adrianus C M Boon
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
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449
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Turner JS, O'Halloran JA, Kalaidina E, Kim W, Schmitz AJ, Zhou JQ, Lei T, Thapa M, Chen RE, Case JB, Amanat F, Rauseo AM, Haile A, Xie X, Klebert MK, Suessen T, Middleton WD, Shi PY, Krammer F, Teefey SA, Diamond MS, Presti RM, Ellebedy AH. SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses. Nature 2021; 596:109-113. [PMID: 34182569 PMCID: PMC8935394 DOI: 10.1038/s41586-021-03738-2] [Citation(s) in RCA: 521] [Impact Index Per Article: 173.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 mRNA-based vaccines are about 95% effective in preventing COVID-191-5. The dynamics of antibody-secreting plasmablasts and germinal centre B cells induced by these vaccines in humans remain unclear. Here we examined antigen-specific B cell responses in peripheral blood (n = 41) and draining lymph nodes in 14 individuals who had received 2 doses of BNT162b2, an mRNA-based vaccine that encodes the full-length SARS-CoV-2 spike (S) gene1. Circulating IgG- and IgA-secreting plasmablasts that target the S protein peaked one week after the second immunization and then declined, becoming undetectable three weeks later. These plasmablast responses preceded maximal levels of serum anti-S binding and neutralizing antibodies to an early circulating SARS-CoV-2 strain as well as emerging variants, especially in individuals who had previously been infected with SARS-CoV-2 (who produced the most robust serological responses). By examining fine needle aspirates of draining axillary lymph nodes, we identified germinal centre B cells that bound S protein in all participants who were sampled after primary immunization. High frequencies of S-binding germinal centre B cells and plasmablasts were sustained in these draining lymph nodes for at least 12 weeks after the booster immunization. S-binding monoclonal antibodies derived from germinal centre B cells predominantly targeted the receptor-binding domain of the S protein, and fewer clones bound to the N-terminal domain or to epitopes shared with the S proteins of the human betacoronaviruses OC43 and HKU1. These latter cross-reactive B cell clones had higher levels of somatic hypermutation as compared to those that recognized only the SARS-CoV-2 S protein, which suggests a memory B cell origin. Our studies demonstrate that SARS-CoV-2 mRNA-based vaccination of humans induces a persistent germinal centre B cell response, which enables the generation of robust humoral immunity.
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Affiliation(s)
- Jackson S Turner
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jane A O'Halloran
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Elizaveta Kalaidina
- Division of Allergy and Immunology, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Aaron J Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Julian Q Zhou
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Tingting Lei
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Mahima Thapa
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriana M Rauseo
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Alem Haile
- Clinical Trials Unit, Washington University School of Medicine, St Louis, MO, USA
| | - Xuping Xie
- University of Texas Medical Branch, Galveston, TX, USA
| | - Michael K Klebert
- Clinical Trials Unit, Washington University School of Medicine, St Louis, MO, USA
| | - Teresa Suessen
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - William D Middleton
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Pei-Yong Shi
- University of Texas Medical Branch, Galveston, TX, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sharlene A Teefey
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel M Presti
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
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450
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Boehm E, Kronig I, Neher RA, Eckerle I, Vetter P, Kaiser L. Novel SARS-CoV-2 variants: the pandemics within the pandemic. Clin Microbiol Infect 2021; 27:1109-1117. [PMID: 34015535 PMCID: PMC8127517 DOI: 10.1016/j.cmi.2021.05.022] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/05/2021] [Accepted: 05/09/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Many new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been termed variants of concern/interest (VOC/I) because of the greater risk they pose due to possible enhanced transmissibility and/or severity, immune escape, diagnostic and/or treatment failure, and reduced vaccine efficacy. AIMS We sought to review the current knowledge of emerging SARS-CoV-2 variants, particularly those deemed VOC/Is: B.1.351, B.1.1.7, and P.1. SOURCES MEDLINE and BioRxiv databases, as well as the grey literature, were searched for reports of SARS-CoV-2 variants since November 2020. Relevant articles and their references were screened. CONTENT Mutations on the spike protein in particular may affect both affinity for the SARS-CoV-2 cell receptor ACEII and antibody binding. These VOC/Is often share similar mutation sets. The N501Y mutation is shared by the three main VOCs: B.1.1.7, first identified in the United Kingdom, P.1, originating from Brazil, and B.1.351, first described in South Africa. This mutation likely increases transmissibility by increasing affinity for ACEII. The B.1.351 and P.1 variants also display the E484K mutation which decreases binding of neutralizing antibodies, leading to partial immune escape; this favours reinfections, and decreases the in vitro efficacy of some antibody therapies or vaccines. Those mutations may also have phenotypical repercussions of greater severity. Furthermore, the accumulation of mutations poses a diagnostic risk (lowered when using multiplex assays), as seen for some assays targeting the S gene. With ongoing surveillance, many new VOC/Is have been identified. The emergence of the E484K mutation independently in different parts of the globe may reflect the adaptation of SARS-CoV-2 to humans against a background of increasing immunity. IMPLICATIONS These VOC/Is are increasing in frequency globally and pose challenges to any herd immunity approach to managing the pandemic. While vaccination is ongoing, vaccine updates may be prudent. The virus continues to adapt to transmission in humans, and further divergence from the initial Wuhan sequences is expected.
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Affiliation(s)
- Erik Boehm
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland.
| | - Ilona Kronig
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Isabella Eckerle
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Pauline Vetter
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Laurent Kaiser
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
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