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1. Imprinted antibody responses against SARS-CoV-2 Omicron sublineages

Author

Young-Jun Park, Dora Pinto, Alexandra C. Walls, Zhuoming Liu, Anna De Marco, Fabio Benigni, Fabrizia Zatta, Chiara Silacci-Fregni, Jessica Bassi, Kaitlin R. Sprouse, Amin Addetia, John E. Bowen, Cameron Stewart, Martina Giurdanella, Christian Saliba, Barbara Guarino, Michael A. Schmid, Nicholas M. Franko, Jennifer K. Logue, Ha V. Dang, Kevin Hauser, Julia di Iulio, William Rivera, Gretja Schnell, Anushka Rajesh, Jiayi Zhou, Nisar Farhat, Hannah Kaiser, Martin Montiel-Ruiz, Julia Noack, Florian A. Lempp, Javier Janer, Rana Abdelnabi, Piet Maes, Paolo Ferrari, Alessandro Ceschi, Olivier Giannini, Guilherme Dias de Melo, Lauriane Kergoat, Hervé Bourhy, Johan Neyts, Leah Soriaga, Lisa A. Purcell, Gyorgy Snell, Sean P. J. Whelan, Antonio Lanzavecchia, Herbert W. Virgin, Luca Piccoli, Helen Y. Chu, Matteo Samuele Pizzuto, Davide Corti, David Veesler, University of Washington [Seattle], Humabs BioMed SA, Washington University School of Medicine [Saint Louis, MO], Vir Biotechnology Inc [San Francisco], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Università della Svizzera italiana = University of Italian Switzerland (USI), Lugano Regional Hospital [Lugano], University of New South Wales [Sydney] (UNSW), University hospital of Zurich [Zurich], Bellinzona Regional Hospital [Bellinzona], Lyssavirus, épidémiologie et neuropathologie - Lyssavirus Epidemiology and Neuropathology, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), University of Texas Southwestern Medical Center [Dallas], and This study was supported by the National Institute of Allergy and Infectious Diseases (DP1AI158186 and HHSN272201700059C to D.V.), a Pew Biomedical Scholars Award (D.V.), an Investigators in the Pathogenesis of Infectious Disease Awards from the Burroughs Wellcome Fund (D.V.), Fast Grants (D.V.), the University of Washington Arnold and Mabel Beckman cryoEM center and the National Institute of Health grant S10OD032290 (to D.V.). S.P.J.W. supported be NIH grant AI163019. D.V. is an Investigator of the Howard Hughes Medical Institute. O.G. is funded by the Swiss Kidney Foundation.

Subjects
Multidisciplinary, SARS-CoV-2, COVID-19, Antibodies, Viral, Antibodies, Neutralizing, Article, Memory B Cells, Neutralization Tests, Antibody Formation, Spike Glycoprotein, Coronavirus, Humans, [SDV.IMM]Life Sciences [q-bio]/Immunology, Immunologic Memory, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Immune Evasion
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant-neutralizing antibody that is a strong candidate for clinical development. ispartof: SCIENCE vol:378 issue:6620 pages:619-+ ispartof: location:United States status: published

Published
2022
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2. Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology

Author

Herbert W. Virgin, David K. Hong, Alessandra Franzetti Pellanda, John E. Bowen, Alessandro Ceschi, Andrea Minola, M. Alejandra Tortorici, Agostino Riva, Colin Havenar-Daughton, G. Snell, Paolo Ferrari, Nicole Sprugasci, Oliver J. Acton, Sneha V. Gupta, Luca Piccoli, Anna De Marco, Enos Bernasconi, Alexandra C. Walls, David Veesler, Nadine Czudnochowski, Antonio Lanzavecchia, Blanca Fernandez Rodriguez, Emiliano Albanese, Katja Fink, Barbara Guarino, Alessia Peter, Giovanni Piumatti, Stefano Jaconi, Maciej Tarkowski, Davide Corti, Christian Garzoni, Elisabetta Cameroni, Jessica Bassi, Laura E. Rosen, Chiara Silacci-Fregni, Valentino Lepori, Federica Sallusto, Dora Pinto, Federico Mele, Megan Smithey, Fabrizia Zatta, Feng Jin, Jay C. Nix, Sandra Jovic, Martina Beltramello, Matteo Samuele Pizzuto, Young-Jun Park, Maira Biggiogero, Luigia Elzi, Giorgia Lo Presti, Humabs BioMed SA, University of Washington [Seattle], Vir Biotechnology [San Francisco], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Università della Svizzera italiana = University of Italian Switzerland (USI), Clinica Luganese Moncucco [Lugano], Luigi Sacco University Hospital [Milan], Vir Biotechnology Inc [San Francisco], University hospital of Zurich [Zurich], Ospedale Civico and Ospedale Italiano [Lugano], Ospedale Regionale Bellinzona e Valli and Ospedale Regionale [Locarno], University of New South Wales [Sydney] (UNSW), and Institute for Research in Biomedicine

Subjects
Antibodies, Viral, Medical and Health Sciences, Immunoglobulin G, Epitope, Antigen-Antibody Reactions, Epitopes, 0302 clinical medicine, Monoclonal, Viral, Neutralizing, Lung, 0303 health sciences, biology, Antibodies, Monoclonal, Biological Sciences, Spike Glycoprotein, 3. Good health, Infectious Diseases, Spike Glycoprotein, Coronavirus, Pneumonia & Influenza, Angiotensin-Converting Enzyme 2, Antibody, Coronavirus Infections, Infection, Protein Binding, Protein Structure, coronaviruses, Pneumonia, Viral, Immunodominance, Peptidyl-Dipeptidase A, Molecular Dynamics Simulation, Article, General Biochemistry, Genetics and Molecular Biology, Antibodies, effector functions, Affinity maturation, Quaternary, Vaccine Related, 03 medical and health sciences, Betacoronavirus, Antigen, Protein Domains, Clinical Research, Biodefense, Humans, Avidity, neutralizing antibodies, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Protein Structure, Quaternary, Pandemics, 030304 developmental biology, Binding Sites, SARS-CoV-2, Prevention, COVID-19, Pneumonia, Antibodies, Neutralizing, Virology, immunity, Immunoglobulin A, Coronavirus, Kinetics, Epitope mapping, Emerging Infectious Diseases, Good Health and Well Being, Immunoglobulin M, biology.protein, Immunization, 030217 neurology & neurosurgery, Epitope Mapping, Developmental Biology
Abstract

Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics., Graphical Abstract, Highlights • SARS-CoV-2 RBD is immunodominant and accounts for 90% of serum neutralizing activity • RBD antibodies decline with a half-life of ∼50 days, but their avidity increases • Structural definition of a SARS-CoV-2 RBD antigenic map using monoclonal antibodies • ACE2-binding site dominates SARS-CoV-2 polyclonal neutralizing antibody responses, Serological analyses of ∼650 SARS-CoV-2-exposed individuals show that 90% of the serum or plasma neutralizing activity targets the virus receptor-binding domain, with structural insights revealing how distinct types of neutralizing antibodies targeting the ACE2-binding site dominate the immune response against SARS-CoV-2 spike.

Published
2020
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3. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody

Author

Anna De Marco, Michael S. Diamond, Herbert W. Virgin, M. Alejandra Tortorici, Fabrizia Zatta, Katja Culap, Siro Bianchi, Stefano Jaconi, Martina Beltramello, Colin Havenar-Daughton, Amalio Telenti, David Veesler, Antonio Lanzavecchia, Davide Corti, Barbara Guarino, Dora Pinto, Gyorgy Snell, James Brett Case, Alessia Peter, Rita E. Chen, Elisabetta Cameroni, Katja Fink, Young-Jun Park, Roberto Spreafico, Alexandra C. Walls, Humabs BioMed SA, Department of Biochemistry [Washington ], University of Washington [Seattle], Virologie Structurale - Structural Virology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Vir Biotechnology Inc [San Francisco], Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), Scuola Universitaria Professionale della Svizzera italiana, and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]

Subjects
Models, Molecular, 0301 basic medicine, viruses, [SDV]Life Sciences [q-bio], Antibodies, Viral, Severe Acute Respiratory Syndrome, medicine.disease_cause, Epitope, Neutralization, 0302 clinical medicine, Chlorocebus aethiops, skin and connective tissue diseases, Coronavirus, B-Lymphocytes, Multidisciplinary, biology, Antibodies, Monoclonal, virus diseases, Entry into host, 3. Good health, Killer Cells, Natural, Severe acute respiratory syndrome-related coronavirus, Spike Glycoprotein, Coronavirus, Monoclonal, Epitopes, B-Lymphocyte, Angiotensin-Converting Enzyme 2, Antibody, Coronavirus Infections, medicine.drug_class, Pneumonia, Viral, Cross Reactions, Peptidyl-Dipeptidase A, Monoclonal antibody, Betacoronavirus, Immunoglobulin Fab Fragments, 03 medical and health sciences, Neutralization Tests, medicine, Animals, Humans, Pandemics, Vero Cells, Immune Evasion, SARS-CoV-2, Cryoelectron Microscopy, fungi, Antibody-Dependent Cell Cytotoxicity, COVID-19, biology.organism_classification, Antibodies, Neutralizing, Virology, body regions, HEK293 Cells, 030104 developmental biology, biology.protein, Immunologic Memory, 030217 neurology & neurosurgery
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerged coronavirus that is responsible for the current pandemic of coronavirus disease 2019 (COVID-19), which has resulted in more than 3.7 million infections and 260,000 deaths as of 6 May 20201,2. Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe several monoclonal antibodies that target the S glycoprotein of SARS-CoV-2, which we identified from memory B cells of an individual who was infected with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. One antibody (named S309) potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2, by engaging the receptor-binding domain of the S glycoprotein. Using cryo-electron microscopy and binding assays, we show that S309 recognizes an epitope containing a glycan that is conserved within the Sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails that include S309 in combination with other antibodies that we identified further enhanced SARS-CoV-2 neutralization, and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and antibody cocktails containing S309 for prophylaxis in individuals at a high risk of exposure or as a post-exposure therapy to limit or treat severe disease.

Published
2020
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