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Martinez J, Subbarao Malireddi RK, Lu Q, Cunha LD, Pelletier S, Gingras S, Orchard R, Guan JL, Tan H, Peng J, Kanneganti TD, Virgin HW, Green DR. Retraction Note: Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins. Nat Cell Biol 2024; 26:660. [PMID: 38438803 PMCID: PMC11036535 DOI: 10.1038/s41556-024-01383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Affiliation(s)
- Jennifer Martinez
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Immunity, Inflammation, and Disease Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | | | - Qun Lu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Larissa Dias Cunha
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stephane Pelletier
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Embryonic Stem Cell Laboratory, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sebastien Gingras
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Embryonic Stem Cell Laboratory, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert Orchard
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Haiyan Tan
- St Jude Proteomics Facility, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Junmin Peng
- St Jude Proteomics Facility, St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Departments of Structural Biology and Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Douglas R Green
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
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2
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Feng S, McNehlan ME, Kinsella RL, Sur Chowdhury C, Chavez SM, Naik SK, McKee SR, Van Winkle JA, Dubey N, Samuels A, Swain A, Cui X, Hendrix SV, Woodson R, Kreamalmeyer D, Smirnov A, Artyomov MN, Virgin HW, Wang YT, Stallings CL. Autophagy promotes efficient T cell responses to restrict high-dose Mycobacterium tuberculosis infection in mice. Nat Microbiol 2024; 9:684-697. [PMID: 38413834 DOI: 10.1038/s41564-024-01608-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Although autophagy sequesters Mycobacterium tuberculosis (Mtb) in in vitro cultured macrophages, loss of autophagy in macrophages in vivo does not result in susceptibility to a standard low-dose Mtb infection until late during infection, leaving open questions regarding the protective role of autophagy during Mtb infection. Here we report that loss of autophagy in lung macrophages and dendritic cells results in acute susceptibility of mice to high-dose Mtb infection, a model mimicking active tuberculosis. Rather than observing a role for autophagy in controlling Mtb replication in macrophages, we find that autophagy suppresses macrophage responses to Mtb that otherwise result in accumulation of myeloid-derived suppressor cells and subsequent defects in T cell responses. Our finding that the pathogen-plus-susceptibility gene interaction is dependent on dose has important implications both for understanding how Mtb infections in humans lead to a spectrum of outcomes and for the potential use of autophagy modulators in clinical medicine.
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Affiliation(s)
- Siwei Feng
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Michael E McNehlan
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel L Kinsella
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Chanchal Sur Chowdhury
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Sthefany M Chavez
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Sumanta K Naik
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel R McKee
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacob A Van Winkle
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Neha Dubey
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Samuels
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyan Cui
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Skyler V Hendrix
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Reilly Woodson
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Darren Kreamalmeyer
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Asya Smirnov
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ya-Ting Wang
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA.
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi, China.
| | - Christina L Stallings
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA.
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3
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McAllaster MR, Bhushan J, Balce DR, Orvedahl A, Park A, Hwang S, Sullender ME, Sibley LD, Virgin HW. Autophagy gene-dependent intracellular immunity triggered by interferon-γ. mBio 2023; 14:e0233223. [PMID: 37905813 PMCID: PMC10746157 DOI: 10.1128/mbio.02332-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 11/02/2023] Open
Abstract
Genes required for the lysosomal degradation pathway of autophagy play key roles in topologically distinct and physiologically important cellular processes. Some functions of ATG genes are independent of their role in degradative autophagy. One of the first described of these ATG gene-dependent, but degradative autophagy independent, processes is the requirement for a subset of ATG genes in interferon-γ (IFNγ)-induced inhibition of norovirus and Toxoplasma gondii replication. Herein, we identified additional genes that are required for, or that negatively regulate, this innate immune effector pathway. Enzymes in the UFMylation pathway negatively regulated IFNγ-induced inhibition of norovirus replication via effects of Ern1. IFNγ-induced inhibition of norovirus replication required Gate-16 (also termed GabarapL2), Wipi2b, Atg9a, Cul3, and Klhl9 but not Becn1 (encoding Beclin 1), Atg14, Uvrag, or Sqstm1. The phosphatidylinositol-3-phosphate and ATG16L1-binding domains of WIPI2B, as well as the ATG5-binding domain of ATG16L1, were required for IFNγ-induced inhibition of norovirus replication. Other members of the Cul3, Atg8, and Wipi2 gene families were not required, demonstrating exquisite specificity within these gene families for participation in IFNγ action. The generality of some aspects of this mechanism was demonstrated by a role for GATE-16 and WIPI2 in IFNγ-induced control of Toxoplasma gondii infection in human cells. These studies further delineate the genes and mechanisms of an ATG gene-dependent programmable form of cytokine-induced innate intracellular immunity. IMPORTANCE Interferon-γ (IFNγ) is a critical mediator of cell-intrinsic immunity to intracellular pathogens. Understanding the complex cellular mechanisms supporting robust interferon-γ-induced host defenses could aid in developing new therapeutics to treat infections. Here, we examined the impact of autophagy genes in the interferon-γ-induced host response. We demonstrate that genes within the autophagy pathway including Wipi2, Atg9, and Gate-16, as well as ubiquitin ligase complex genes Cul3 and Klhl9 are required for IFNγ-induced inhibition of murine norovirus (norovirus hereinafter) replication in mouse cells. WIPI2 and GATE-16 were also required for IFNγ-mediated restriction of parasite growth within the Toxoplasma gondii parasitophorous vacuole in human cells. Furthermore, we found that perturbation of UFMylation pathway components led to more robust IFNγ-induced inhibition of norovirus via regulation of endoplasmic reticulum (ER) stress. Enhancing or inhibiting these dynamic cellular components could serve as a strategy to control intracellular pathogens and maintain an effective immune response.
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Affiliation(s)
- Michael R. McAllaster
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Vir Biotechnology, San Francisco, California, USA
| | - Jaya Bhushan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dale R. Balce
- Vir Biotechnology, San Francisco, California, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Anthony Orvedahl
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Arnold Park
- Vir Biotechnology, San Francisco, California, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Meagan E. Sullender
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Herbert W. Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
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4
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Momont C, Dang HV, Zatta F, Hauser K, Wang C, di Iulio J, Minola A, Czudnochowski N, De Marco A, Branch K, Donermeyer D, Vyas S, Chen A, Ferri E, Guarino B, Powell AE, Spreafico R, Croll TI, Belnap DM, Schmid MA, Timothy Schaiff W, Miller JL, Cameroni E, Telenti A, Virgin HW, Rosen LE, Purcell LA, Lanzavecchia A, Snell G, Corti D, Pizzuto MS. How a Potent Anti-neuraminidase Monoclonal Antibody Navigates Recent Immune-evasive Influenza Strains: A Structural Study by Single-particle CryoEM. Microsc Microanal 2023; 29:927. [PMID: 37613467 DOI: 10.1093/micmic/ozad067.459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | | | - Andrea Minola
- 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, USA
| | | | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - David M Belnap
- School of Biological Sciences and Department of Biochemistry, University of Utah, Salt Lake City, Utah, USA
| | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | | | | | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
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5
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Momont C, Dang HV, Zatta F, Hauser K, Wang C, di Iulio J, Minola A, Czudnochowski N, De Marco A, Branch K, Donermeyer D, Vyas S, Chen A, Ferri E, Guarino B, Powell AE, Spreafico R, Yim SS, Balce DR, Bartha I, Meury M, Croll TI, Belnap DM, Schmid MA, Schaiff WT, Miller JL, Cameroni E, Telenti A, Virgin HW, Rosen LE, Purcell LA, Lanzavecchia A, Snell G, Corti D, Pizzuto MS. Author Correction: A pan-influenza antibody inhibiting neuraminidase via receptor mimicry. Nature 2023:10.1038/s41586-023-06385-x. [PMID: 37407829 DOI: 10.1038/s41586-023-06385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Affiliation(s)
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Andrea Minola
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Alex Chen
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | | | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - David M Belnap
- School of Biological Sciences, Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
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6
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Momont C, Dang HV, Zatta F, Hauser K, Wang C, di Iulio J, Minola A, Czudnochowski N, De Marco A, Branch K, Donermeyer D, Vyas S, Chen A, Ferri E, Guarino B, Powell AE, Spreafico R, Yim SS, Balce DR, Bartha I, Meury M, Croll TI, Belnap DM, Schmid MA, Schaiff WT, Miller JL, Cameroni E, Telenti A, Virgin HW, Rosen LE, Purcell LA, Lanzavecchia A, Snell G, Corti D, Pizzuto MS. A pan-influenza antibody inhibiting neuraminidase via receptor mimicry. Nature 2023:10.1038/s41586-023-06136-y. [PMID: 37258672 DOI: 10.1038/s41586-023-06136-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/26/2023] [Indexed: 06/02/2023]
Abstract
Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies predominantly to the highly variable head region of haemagglutinin and their effectiveness is limited by viral drift1 and suboptimal immune responses2. Here we describe a neuraminidase-targeting monoclonal antibody, FNI9, that potently inhibits the enzymatic activity of all group 1 and group 2 IAVs, as well as Victoria/2/87-like, Yamagata/16/88-like and ancestral IBVs. FNI9 broadly neutralizes seasonal IAVs and IBVs, including the immune-evading H3N2 strains bearing an N-glycan at position 245, and shows synergistic activity when combined with anti-haemagglutinin stem-directed antibodies. Structural analysis reveals that D107 in the FNI9 heavy chain complementarity-determinant region 3 mimics the interaction of the sialic acid carboxyl group with the three highly conserved arginine residues (R118, R292 and R371) of the neuraminidase catalytic site. FNI9 demonstrates potent prophylactic activity against lethal IAV and IBV infections in mice. The unprecedented breadth and potency of the FNI9 monoclonal antibody supports its development for the prevention of influenza illness by seasonal and pandemic viruses.
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Affiliation(s)
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Andrea Minola
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Alex Chen
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | | | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - David M Belnap
- School of Biological Sciences, Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
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7
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Gupta R, Purcell LA, Corti D, Virgin HW. Pandemic preparedness strategies must go beyond vaccines. Sci Transl Med 2023; 15:eadd3055. [PMID: 37018420 DOI: 10.1126/scitranslmed.add3055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Monoclonal antibodies can fill a critical gap to help stop the next infectious disease outbreak from becoming the next pandemic.
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Affiliation(s)
- Rajesh Gupta
- Rajesh Gupta is at Vir Biotechnology, San Francisco, CA, USA.
- Lisa A. Purcell is at Vir Biotechnology, San Francisco, CA, USA
- Davide Corti is at Humabs Biomed SA (a Vir Biotechnology subsidiary), Bellinzona, Switzerland
- Herbert W. Virgin is at Altos Labs, Redwood City, CA, and is an adjunct professor at Washington University School of Medicine, St. Louis, MO, USA, and the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lisa A Purcell
- Rajesh Gupta is at Vir Biotechnology, San Francisco, CA, USA.
- Lisa A. Purcell is at Vir Biotechnology, San Francisco, CA, USA
- Davide Corti is at Humabs Biomed SA (a Vir Biotechnology subsidiary), Bellinzona, Switzerland
- Herbert W. Virgin is at Altos Labs, Redwood City, CA, and is an adjunct professor at Washington University School of Medicine, St. Louis, MO, USA, and the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Davide Corti
- Rajesh Gupta is at Vir Biotechnology, San Francisco, CA, USA.
- Lisa A. Purcell is at Vir Biotechnology, San Francisco, CA, USA
- Davide Corti is at Humabs Biomed SA (a Vir Biotechnology subsidiary), Bellinzona, Switzerland
- Herbert W. Virgin is at Altos Labs, Redwood City, CA, and is an adjunct professor at Washington University School of Medicine, St. Louis, MO, USA, and the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Herbert W Virgin
- Rajesh Gupta is at Vir Biotechnology, San Francisco, CA, USA.
- Lisa A. Purcell is at Vir Biotechnology, San Francisco, CA, USA
- Davide Corti is at Humabs Biomed SA (a Vir Biotechnology subsidiary), Bellinzona, Switzerland
- Herbert W. Virgin is at Altos Labs, Redwood City, CA, and is an adjunct professor at Washington University School of Medicine, St. Louis, MO, USA, and the University of Texas Southwestern Medical Center, Dallas, TX, USA
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8
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Marzi R, Bassi J, Silacci-Fregni C, Bartha I, Muoio F, Culap K, Sprugasci N, Lombardo G, Saliba C, Cameroni E, Cassotta A, Low JS, Walls AC, McCallum M, Tortorici MA, Bowen JE, Dellota EA, Dillen JR, Czudnochowski N, Pertusini L, Terrot T, Lepori V, Tarkowski M, Riva A, Biggiogero M, Franzetti-Pellanda A, Garzoni C, Ferrari P, Ceschi A, Giannini O, Havenar-Daughton C, Telenti A, Arvin A, Virgin HW, Sallusto F, Veesler D, Lanzavecchia A, Corti D, Piccoli L. Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape. iScience 2023; 26:105726. [PMID: 36507220 PMCID: PMC9721160 DOI: 10.1016/j.isci.2022.105726] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/21/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Memory B cells (MBCs) generate rapid antibody responses upon secondary encounter with a pathogen. Here, we investigated the kinetics, avidity, and cross-reactivity of serum antibodies and MBCs in 155 SARS-CoV-2 infected and vaccinated individuals over a 16-month time frame. SARS-CoV-2-specific MBCs and serum antibodies reached steady-state titers with comparable kinetics in infected and vaccinated individuals. Whereas MBCs of infected individuals targeted both prefusion and postfusion Spike (S), most vaccine-elicited MBCs were specific for prefusion S, consistent with the use of prefusion-stabilized S in mRNA vaccines. Furthermore, a large fraction of MBCs recognizing postfusion S cross-reacted with human betacoronaviruses. The avidity of MBC-derived and serum antibodies increased over time resulting in enhanced resilience to viral escape by SARS-CoV-2 variants, including Omicron BA.1 and BA.2 sublineages, albeit only partially for BA.4 and BA.5 sublineages. Overall, the maturation of high-affinity and broadly reactive MBCs provides the basis for effective recall responses to future SARS-CoV-2 variants.
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Affiliation(s)
- Roberta Marzi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Jessica Bassi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Istvan Bartha
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Francesco Muoio
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Katja Culap
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Gloria Lombardo
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Christian Saliba
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | | | - Laura Pertusini
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Tatiana Terrot
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Maciej Tarkowski
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Milan, Italy
| | - Agostino Riva
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Milan, Italy
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milan, Italy
| | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco, Lugano, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Paolo Ferrari
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Alessandro Ceschi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | | | | | - Ann Arvin
- Vir Biotechnology, San Francisco, CA, 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
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
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9
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Park YJ, Pinto D, Walls AC, Liu Z, De Marco A, Benigni F, Zatta F, Silacci-Fregni C, Bassi J, Sprouse KR, Addetia A, Bowen JE, Stewart C, Giurdanella M, Saliba C, Guarino B, Schmid MA, Franko NM, Logue JK, Dang HV, Hauser K, di Iulio J, Rivera W, Schnell G, Rajesh A, Zhou J, Farhat N, Kaiser H, Montiel-Ruiz M, Noack J, Lempp FA, Janer J, Abdelnabi R, Maes P, Ferrari P, Ceschi A, Giannini O, de Melo GD, Kergoat L, Bourhy H, Neyts J, Soriaga L, Purcell LA, Snell G, Whelan SPJ, Lanzavecchia A, Virgin HW, Piccoli L, Chu HY, Pizzuto MS, Corti D, Veesler D. Imprinted antibody responses against SARS-CoV-2 Omicron sublineages. Science 2022; 378:619-627. [PMID: 36264829 DOI: 10.1126/science.adc9127] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Dora Pinto
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anna De Marco
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Jessica Bassi
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Christian Saliba
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Michael A Schmid
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicholas M Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jennifer K Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | | | | | - Javier Janer
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Guilherme Dias de Melo
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | | | | | | | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 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
| | - Luca Piccoli
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | | | - Davide Corti
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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10
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Park YJ, Pinto D, Walls AC, Liu Z, De Marco A, Benigni F, Zatta F, Silacci-Fregni C, Bassi J, Sprouse KR, Addetia A, Bowen JE, Stewart C, Giurdanella M, Saliba C, Guarino B, Schmid MA, Franko NM, Logue JK, Dang HV, Hauser K, di Iulio J, Rivera W, Schnell G, Rajesh A, Zhou J, Farhat N, Kaiser H, Montiel-Ruiz M, Noack J, Lempp FA, Janer J, Abdelnabi R, Maes P, Ferrari P, Ceschi A, Giannini O, de Melo GD, Kergoat L, Bourhy H, Neyts J, Soriaga L, Purcell LA, Snell G, Whelan SPJ, Lanzavecchia A, Virgin HW, Piccoli L, Chu HY, Pizzuto MS, Corti D, Veesler D. Imprinted antibody responses against SARS-CoV-2 Omicron sublineages. Science 2022. [PMID: 36264829 DOI: 10.1101/2022.05.08.491108v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Dora Pinto
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anna De Marco
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Jessica Bassi
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Christian Saliba
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Michael A Schmid
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicholas M Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jennifer K Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | | | | | - Javier Janer
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Guilherme Dias de Melo
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | | | | | | | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 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
| | - Luca Piccoli
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | | | - Davide Corti
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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11
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Marzi R, Bassi J, Silacci-Fregni C, Bartha I, Muoio F, Culap K, Sprugasci N, Lombardo G, Saliba C, Cameroni E, Cassotta A, Low JS, Walls AC, McCallum M, Tortorici MA, Bowen JE, Dellota EA, Dillen JR, Czudnochowski N, Pertusini L, Terrot T, Lepori V, Tarkowski M, Riva A, Biggiogero M, Pellanda AF, Garzoni C, Ferrari P, Ceschi A, Giannini O, Havenar-Daughton C, Telenti A, Arvin A, Virgin HW, Sallusto F, Veesler D, Lanzavecchia A, Corti D, Piccoli L. Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape. bioRxiv 2022:2022.09.30.509852. [PMID: 36203553 PMCID: PMC9536037 DOI: 10.1101/2022.09.30.509852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Memory B cells (MBCs) generate rapid antibody responses upon secondary encounter with a pathogen. Here, we investigated the kinetics, avidity and cross-reactivity of serum antibodies and MBCs in 155 SARS-CoV-2 infected and vaccinated individuals over a 16-month timeframe. SARS-CoV-2-specific MBCs and serum antibodies reached steady-state titers with comparable kinetics in infected and vaccinated individuals. Whereas MBCs of infected individuals targeted both pre- and postfusion Spike (S), most vaccine-elicited MBCs were specific for prefusion S, consistent with the use of prefusion-stabilized S in mRNA vaccines. Furthermore, a large fraction of MBCs recognizing postfusion S cross-reacted with human betacoronaviruses. The avidity of MBC-derived and serum antibodies increased over time resulting in enhanced resilience to viral escape by SARS-CoV-2 variants, including Omicron BA.1 and BA.2 sub-lineages, albeit only partially for BA.4 and BA.5 sublineages. Overall, the maturation of high-affinity and broadly-reactive MBCs provides the basis for effective recall responses to future SARS-CoV-2 variants.
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Affiliation(s)
- Roberta Marzi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Jessica Bassi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Istvan Bartha
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Francesco Muoio
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Katja Culap
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Gloria Lombardo
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Christian Saliba
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | | | - Josh R Dillen
- Vir Biotechnology, San Francisco, CA, United States of America
| | | | - Laura Pertusini
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Tatiana Terrot
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Maciej Tarkowski
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milan, Italy
| | - Agostino Riva
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milan, Italy
| | - Maira Biggiogero
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Paolo Ferrari
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, Australia
| | - Alessandro Ceschi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Science of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | | | - Amalio Telenti
- Vir Biotechnology, San Francisco, CA, United States of America
| | - Ann Arvin
- Vir Biotechnology, San Francisco, CA, United States of America
| | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, United States of America
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | | | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
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12
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Park YJ, Pinto D, Walls AC, Liu Z, Marco AD, Benigni F, Zatta F, Silacci-Fregni C, Bassi J, Sprouse KR, Addetia A, Bowen JE, Stewart C, Giurdanella M, Saliba C, Guarino B, Schmid MA, Franko N, Logue J, Dang HV, Hauser K, Iulio JD, Rivera W, Schnell G, Rajesh A, Zhou J, Farhat N, Kaiser H, Montiel-Ruiz M, Noack J, Lempp FA, Janer J, Abdelnabi R, Maes P, Ferrari P, Ceschi A, Giannini O, de Melo GD, Kergoat L, Bourhy H, Neyts J, Soriaga L, Purcell LA, Snell G, Whelan SPJ, Lanzavecchia A, Virgin HW, Piccoli L, Chu H, Pizzuto MS, Corti D, Veesler D. Imprinted antibody responses against SARS-CoV-2 Omicron sublineages. bioRxiv 2022:2022.05.08.491108. [PMID: 35677069 PMCID: PMC9176643 DOI: 10.1101/2022.05.08.491108] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
SARS-CoV-2 Omicron sublineages carry distinct spike mutations and represent an antigenic shift resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters result in potent plasma neutralizing activity against Omicron BA.1 and BA.2 and that breakthrough infections, but not vaccination-only, induce neutralizing activity 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 and BA.2 receptor-binding domains whereas Omicron primary infections elicit B cells of narrow specificity. While most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant antibody, that is unaffected by any Omicron lineage spike mutations and is a strong candidate for clinical development.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Martina Giurdanella
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicholas Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Jennifer Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | | | | | - Julia Noack
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Javier Janer
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rana Abdelnabi
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Piet Maes
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Guilherme Dias de Melo
- Institut Pasteur, Université de Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, F-75015, France
| | - Lauriane Kergoat
- Institut Pasteur, Université de Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, F-75015, France
| | - Hervé Bourhy
- Institut Pasteur, Université de Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, F-75015, France
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | | | | | | | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA 94158, 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
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Helen Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | | | - 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
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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13
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Maher MC, Soriaga LB, Gupta A, Chen YP, di Iulio J, Ledoux S, Smithey MJ, Cathcart AL, McKusick K, Sun D, Aldinger M, Alexander E, Purcell L, Ding X, Peppercorn A, Austin D, Mogalian E, Yeh WW, Shapiro AE, Corti D, Virgin HW, Pang PS, Telenti A. Antibody therapy reverses biological signatures of COVID-19 progression. Cell Rep Med 2022; 3:100721. [PMID: 35977462 PMCID: PMC9380250 DOI: 10.1016/j.xcrm.2022.100721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/21/2022] [Accepted: 07/20/2022] [Indexed: 01/19/2023]
Abstract
Understanding who is at risk of progression to severe coronavirus disease 2019 (COVID-19) is key to clinical decision making and effective treatment. We study correlates of disease severity in the COMET-ICE clinical trial that randomized 1:1 to placebo or to sotrovimab, a monoclonal antibody for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (ClinicalTrials.gov04545060). Laboratory parameters identify study participants at greater risk of severe disease, including a high neutrophil-to-lymphocyte ratio (NLR), a negative SARS-CoV-2 serologic test, and whole-blood transcriptome profiles. Sotrovimab treatment is associated with normalization of NLR and the transcriptomic profile and with a decrease of viral RNA in nasopharyngeal samples. Transcriptomics provides the most sensitive detection of participants who would go on to be hospitalized or die. To facilitate timely measurement, we identify a 10-gene signature with similar predictive accuracy. We identify markers of risk for disease progression and demonstrate that normalization of these parameters occurs with antibody treatment of established infection.
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Affiliation(s)
- M. Cyrus Maher
- Vir Biotechnology, San Francisco, CA, USA,Corresponding author
| | | | - Anil Gupta
- Albion Finch Medical, William Osler Health Centre, Toronto, ON, Canada
| | | | | | | | | | | | | | - David Sun
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | - Xiao Ding
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | | | - Adrienne E. Shapiro
- Departments of Global Health and Medicine, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, CA, USA,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Amalio Telenti
- Vir Biotechnology, San Francisco, CA, USA,Corresponding author
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14
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Collier DA, De Marco A, Ferreira IATM, Meng B, Datir RP, Walls AC, Kemp SA, Bassi J, Pinto D, Silacci-Fregni C, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A, Elmer A, Kingston N, Graves B, McCoy LE, Smith KGC, Bradley JR, Temperton N, Ceron-Gutierrez L, Barcenas-Morales G, Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D, Gupta RK. Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature 2022; 608:E24. [PMID: 35864232 PMCID: PMC9302219 DOI: 10.1038/s41586-022-05103-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dami A Collier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Matteo S Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Agostino Riva
- Division of Infectious Diseases, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | | | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Bioresource, Cambridge, UK
| | | | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
- Laboratorio de Inmunologia, UNAM, Cuautitlán, Mexico
| | - William Harvey
- Institute of Biodiversity, University of Glasgow, Glasgow, UK
| | | | | | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Mark Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- University of KwaZulu Natal, Durban, South Africa.
- Africa Health Research Institute, Durban, South Africa.
- Department of Infectious Diseases, Cambridge University Hospitals NHS Trust, Cambridge, UK.
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15
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Case JB, Mackin S, Errico JM, Chong Z, Madden EA, Whitener B, Guarino B, Schmid MA, Rosenthal K, Ren K, Dang HV, Snell G, Jung A, Droit L, Handley SA, Halfmann PJ, Kawaoka Y, Crowe JE, Fremont DH, Virgin HW, Loo YM, Esser MT, Purcell LA, Corti D, Diamond MS. Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains. Nat Commun 2022; 13:3824. [PMID: 35780162 PMCID: PMC9250508 DOI: 10.1038/s41467-022-31615-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/24/2022] [Indexed: 11/09/2022] Open
Abstract
Omicron variant strains encode large numbers of changes in the spike protein compared to historical SARS-CoV-2 isolates. Although in vitro studies have suggested that several monoclonal antibody therapies lose neutralizing activity against Omicron variants, the effects in vivo remain largely unknown. Here, we report on the protective efficacy against three SARS-CoV-2 Omicron lineage strains (BA.1, BA.1.1, and BA.2) of two monoclonal antibody therapeutics (S309 [Vir Biotechnology] monotherapy and AZD7442 [AstraZeneca] combination), which correspond to ones used to treat or prevent SARS-CoV-2 infections in humans. Despite losses in neutralization potency in cell culture, S309 or AZD7442 treatments reduced BA.1, BA.1.1, and BA.2 lung infection in susceptible mice that express human ACE2 (K18-hACE2) in prophylactic and therapeutic settings. Correlation analyses between in vitro neutralizing activity and reductions in viral burden in K18-hACE2 or human FcγR transgenic mice suggest that S309 and AZD7442 have different mechanisms of protection against Omicron variants, with S309 utilizing Fc effector function interactions and AZD7442 acting principally by direct neutralization. Our data in mice demonstrate the resilience of S309 and AZD7442 mAbs against emerging SARS-CoV-2 variant strains and provide insight into the relationship between loss of antibody neutralization potency and retained protection in vivo. SARS-CoV-2 variants of concern are less susceptible to therapeutic neutralizing antibodies, given mutations in the surface glycoprotein S. Here, Case et al. show that therapeutic antibodies S309 and AZD7442 reduce lung infection with SARSCoV-2 Omicron lineages in humanized mouse model despite the loss of neutralizing potency in vitro.
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Affiliation(s)
- James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha Mackin
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhenlu Chong
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily A Madden
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bradley Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Barbara Guarino
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Michael A Schmid
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Kim Rosenthal
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Kuishu Ren
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Ana Jung
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - 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
| | - Daved H Fremont
- 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.,Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Herbert W Virgin
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.,Vir Biotechnology, San Francisco, CA, USA.,University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yueh-Ming Loo
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Mark T Esser
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. .,Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA. .,Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO, USA.
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16
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McCallum M, Czudnochowski N, Rosen LE, Zepeda SK, Bowen JE, Walls AC, Hauser K, Joshi A, Stewart C, Dillen JR, Powell AE, Croll TI, Nix J, Virgin HW, Corti D, Snell G, Veesler D. Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement. Science 2022; 375:864-868. [PMID: 35076256 PMCID: PMC9427005 DOI: 10.1126/science.abn8652] [Citation(s) in RCA: 306] [Impact Index Per Article: 153.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and x-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus.
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MESH Headings
- Amino Acid Substitution
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antigenic Drift and Shift
- Broadly Neutralizing Antibodies/chemistry
- Broadly Neutralizing Antibodies/immunology
- Broadly Neutralizing Antibodies/metabolism
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Humans
- Immune Evasion
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation
- Protein Domains/genetics
- Protein Interaction Domains and Motifs/genetics
- Receptors, Coronavirus/chemistry
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/physiology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | | | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Tristan I. Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jay Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis MO 63110
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas TX 75390
| | - 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
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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17
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Maher MC, Bartha I, Weaver S, di Iulio J, Ferri E, Soriaga L, Lempp FA, Hie BL, Bryson B, Berger B, Robertson DL, Snell G, Corti D, Virgin HW, Kosakovsky Pond SL, Telenti A. Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Sci Transl Med 2022; 14:eabk3445. [PMID: 35014856 PMCID: PMC8939770 DOI: 10.1126/scitranslmed.abk3445] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/06/2022] [Indexed: 12/17/2022]
Abstract
SARS-CoV-2 evolution threatens vaccine- and natural infection-derived immunity as well as the efficacy of therapeutic antibodies. To improve public health preparedness, we sought to predict which existing amino acid mutations in SARS-CoV-2 might contribute to future variants of concern. We tested the predictive value of features comprising epidemiology, evolution, immunology, and neural network-based protein sequence modeling, and identified primary biological drivers of SARS-CoV-2 intra-pandemic evolution. We found evidence that ACE2-mediated transmissibility and resistance to population-level host immunity has waxed and waned as a primary driver of SARS-CoV-2 evolution over time. We retroactively identified with high accuracy (area under the receiver operator characteristic curve, AUROC=0.92-0.97) mutations that will spread, at up to four months in advance, across different phases of the pandemic. The behavior of the model was consistent with a plausible causal structure wherein epidemiological covariates combine the effects of diverse and shifting drivers of viral fitness. We applied our model to forecast mutations that will spread in the future and characterize how these mutations affect the binding of therapeutic antibodies. These findings demonstrate that it is possible to forecast the driver mutations that could appear in emerging SARS-CoV-2 variants of concern. We validate this result against Omicron, showing elevated predictive scores for its component mutations prior to emergence, and rapid score increase across daily forecasts during emergence. This modeling approach may be applied to any rapidly evolving pathogens with sufficiently dense genomic surveillance data, such as influenza, and unknown future pandemic viruses.
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Affiliation(s)
| | - Istvan Bartha
- Vir Biotechnology, San Francisco, California 94158, USA
| | - Steven Weaver
- Department of Biology Institute for Genomics and Evolutionary Medicine Temple University, Philadelphia, PA 19122
| | | | - Elena Ferri
- Vir Biotechnology, San Francisco, California 94158, USA
| | - Leah Soriaga
- Vir Biotechnology, San Francisco, California 94158, USA
| | | | - Brian L. Hie
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Bryan Bryson
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bonnie Berger
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Computer Science and Artificial Intelligence Laboratory. Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow GS1 1QH, UK
| | - Gyorgy Snell
- Vir Biotechnology, San Francisco, California 94158, USA
| | - Davide Corti
- Vir Biotechnology, San Francisco, California 94158, USA
| | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, California 94158, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sergei L. Kosakovsky Pond
- Department of Biology Institute for Genomics and Evolutionary Medicine Temple University, Philadelphia, PA 19122
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18
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Cameroni E, Bowen JE, Rosen LE, Saliba C, Zepeda SK, Culap K, Pinto D, VanBlargan LA, De Marco A, di Iulio J, Zatta F, Kaiser H, Noack J, Farhat N, Czudnochowski N, Havenar-Daughton C, Sprouse KR, Dillen JR, Powell AE, Chen A, Maher C, Yin L, Sun D, Soriaga L, Bassi J, Silacci-Fregni C, Gustafsson C, Franko NM, Logue J, Iqbal NT, Mazzitelli I, Geffner J, Grifantini R, Chu H, Gori A, Riva A, Giannini O, Ceschi A, Ferrari P, Cippà PE, Franzetti-Pellanda A, Garzoni C, Halfmann PJ, Kawaoka Y, Hebner C, Purcell LA, Piccoli L, Pizzuto MS, Walls AC, Diamond MS, Telenti A, Virgin HW, Lanzavecchia A, Snell G, Veesler D, Corti D. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. Nature 2022. [PMID: 35016195 DOI: 10.1101/2021.12.12.472269v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The recently emerged SARS-CoV-2 Omicron variant encodes 37 amino acid substitutions in the spike protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody-based therapeutics. Here we show that the Omicron RBD binds to human ACE2 with enhanced affinity, relative to the Wuhan-Hu-1 RBD, and binds to mouse ACE2. Marked reductions in neutralizing activity were observed against Omicron compared to the ancestral pseudovirus in plasma from convalescent individuals and from individuals who had been vaccinated against SARS-CoV-2, but this loss was less pronounced after a third dose of vaccine. Most monoclonal antibodies that are directed against the receptor-binding motif lost in vitro neutralizing activity against Omicron, with only 3 out of 29 monoclonal antibodies retaining unaltered potency, including the ACE2-mimicking S2K146 antibody1. Furthermore, a fraction of broadly neutralizing sarbecovirus monoclonal antibodies neutralized Omicron through recognition of antigenic sites outside the receptor-binding motif, including sotrovimab2, S2X2593 and S2H974. The magnitude of Omicron-mediated immune evasion marks a major antigenic shift in SARS-CoV-2. Broadly neutralizing monoclonal antibodies that recognize RBD epitopes that are conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.
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MESH Headings
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigenic Drift and Shift/genetics
- Antigenic Drift and Shift/immunology
- Broadly Neutralizing Antibodies/immunology
- COVID-19 Vaccines/immunology
- Cell Line
- Convalescence
- Epitopes, B-Lymphocyte/immunology
- Humans
- Immune Evasion
- Mice
- Neutralization Tests
- 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
- Spike Glycoprotein, Coronavirus/metabolism
- Vesiculovirus/genetics
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Affiliation(s)
- Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Laura A VanBlargan
- Department of Medicine, Washington University of School of Medicine, St Louis, MO, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | - Alex Chen
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Li Yin
- Vir Biotechnology, San Francisco, CA, USA
| | - David Sun
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Nicholas M Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jenni Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Ignacio Mazzitelli
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jorge Geffner
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Helen Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Andrea Gori
- Infectious Disease Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Agostino Riva
- Department of Biomedical and Clinical Sciences 'L.Sacco' (DIBIC), Università di Milano, Milan, Italy
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Pietro E Cippà
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | | | | | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Michael S Diamond
- Department of Medicine, Washington University of 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
| | | | - 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
| | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
- National Institute of Molecular Genetics, Milan, Italy
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
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19
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Park YJ, De Marco A, Starr TN, Liu Z, Pinto D, Walls AC, Zatta F, Zepeda SK, Bowen JE, Sprouse KR, Joshi A, Giurdanella M, Guarino B, Noack J, Abdelnabi R, Foo SYC, Rosen LE, Lempp FA, Benigni F, Snell G, Neyts J, Whelan SPJ, Virgin HW, Bloom JD, Corti D, Pizzuto MS, Veesler D. Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry. Science 2022; 375:449-454. [PMID: 34990214 PMCID: PMC9400459 DOI: 10.1126/science.abm8143] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/22/2021] [Indexed: 01/16/2023]
Abstract
Understanding broadly neutralizing sarbecovirus antibody responses is key to developing countermeasures against SARS-CoV-2 variants and future zoonotic sarbecoviruses. We describe the isolation and characterization of a human monoclonal antibody, designated S2K146, that broadly neutralizes viruses belonging to SARS-CoV- and SARS-CoV-2-related sarbecovirus clades which use ACE2 as an entry receptor. Structural and functional studies show that most of the virus residues that directly bind S2K146 are also involved in binding to ACE2. This allows the antibody to potently inhibit receptor attachment. S2K146 protects against SARS-CoV-2 Beta challenge in hamsters and viral passaging experiments reveal a high barrier for emergence of escape mutants, making it a good candidate for clinical development. The conserved ACE2-binding residues present a site of vulnerability that might be leveraged for developing vaccines eliciting broad sarbecovirus immunity.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antibody Affinity
- Betacoronavirus/immunology
- Broadly Neutralizing Antibodies/chemistry
- Broadly Neutralizing Antibodies/immunology
- Broadly Neutralizing Antibodies/metabolism
- Broadly Neutralizing Antibodies/therapeutic use
- COVID-19/immunology
- COVID-19/therapy
- Cross Reactions
- Cryoelectron Microscopy
- Epitopes
- Humans
- Immune Evasion
- Mesocricetus
- Models, Molecular
- Molecular Mimicry
- Mutation
- Protein Conformation
- Protein Domains
- Receptors, Coronavirus/chemistry
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Tyler N. Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Martina Giurdanella
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Julia Noack
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Rana Abdelnabi
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | | | | | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jesse D. Bloom
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - 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
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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20
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Cameroni E, Bowen JE, Rosen LE, Saliba C, Zepeda SK, Culap K, Pinto D, VanBlargan LA, De Marco A, di Iulio J, Zatta F, Kaiser H, Noack J, Farhat N, Czudnochowski N, Havenar-Daughton C, Sprouse KR, Dillen JR, Powell AE, Chen A, Maher C, Yin L, Sun D, Soriaga L, Bassi J, Silacci-Fregni C, Gustafsson C, Franko NM, Logue J, Iqbal NT, Mazzitelli I, Geffner J, Grifantini R, Chu H, Gori A, Riva A, Giannini O, Ceschi A, Ferrari P, Cippà PE, Franzetti-Pellanda A, Garzoni C, Halfmann PJ, Kawaoka Y, Hebner C, Purcell LA, Piccoli L, Pizzuto MS, Walls AC, Diamond MS, Telenti A, Virgin HW, Lanzavecchia A, Snell G, Veesler D, Corti D. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. Nature 2021. [DOI: 10.1038/d41586-021-03825-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Cameroni E, Saliba C, Bowen JE, Rosen LE, Culap K, Pinto D, VanBlargan LA, De Marco A, Zepeda SK, Iulio JD, Zatta F, Kaiser H, Noack J, Farhat N, Czudnochowski N, Havenar-Daughton C, Sprouse KR, Dillen JR, Powell AE, Chen A, Maher C, Yin L, Sun D, Soriaga L, Bassi J, Silacci-Fregni C, Gustafsson C, Franko NM, Logue J, Iqbal NT, Mazzitelli I, Geffner J, Grifantini R, Chu H, Gori A, Riva A, Giannini O, Ceschi A, Ferrari P, Cippà P, Franzetti-Pellanda A, Garzoni C, Halfmann PJ, Kawaoka Y, Hebner C, Purcell LA, Piccoli L, Pizzuto MS, Walls AC, Diamond MS, Telenti A, Virgin HW, Lanzavecchia A, Veesler D, Snell G, Corti D. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. bioRxiv 2021:2021.12.12.472269. [PMID: 34931194 PMCID: PMC8687478 DOI: 10.1101/2021.12.12.472269] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The recently emerged SARS-CoV-2 Omicron variant harbors 37 amino acid substitutions in the spike (S) protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody therapeutics. Here, we show that the Omicron RBD binds to human ACE2 with enhanced affinity relative to the Wuhan-Hu-1 RBD and acquires binding to mouse ACE2. Severe reductions of plasma neutralizing activity were observed against Omicron compared to the ancestral pseudovirus for vaccinated and convalescent individuals. Most (26 out of 29) receptor-binding motif (RBM)-directed monoclonal antibodies (mAbs) lost in vitro neutralizing activity against Omicron, with only three mAbs, including the ACE2-mimicking S2K146 mAb 1 , retaining unaltered potency. Furthermore, a fraction of broadly neutralizing sarbecovirus mAbs recognizing antigenic sites outside the RBM, including sotrovimab 2 , S2X259 3 and S2H97 4 , neutralized Omicron. The magnitude of Omicron-mediated immune evasion and the acquisition of binding to mouse ACE2 mark a major SARS-CoV-2 mutational shift. Broadly neutralizing sarbecovirus mAbs recognizing epitopes conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.
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22
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Park YJ, De Marco A, Starr TN, Liu Z, Pinto D, Walls AC, Zatta F, Zepeda SK, Bowen J, Sprouse KS, Joshi A, Giurdanella M, Guarino B, Noack J, Abdelnabi R, Foo SYC, Lempp FA, Benigni F, Snell G, Neyts J, Whelan SPJ, Virgin HW, Bloom JD, Corti D, Pizzuto MS, Veesler D. Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry. bioRxiv 2021:2021.10.13.464254. [PMID: 34671770 PMCID: PMC8528076 DOI: 10.1101/2021.10.13.464254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Understanding broadly neutralizing sarbecovirus antibody responses is key to developing countermeasures effective against SARS-CoV-2 variants and future spillovers of other sarbecoviruses. Here we describe the isolation and characterization of a human monoclonal antibody, designated S2K146, broadly neutralizing viruses belonging to all three sarbecovirus clades known to utilize ACE2 as entry receptor and protecting therapeutically against SARS-CoV-2 beta challenge in hamsters. Structural and functional studies show that most of the S2K146 epitope residues are shared with the ACE2 binding site and that the antibody inhibits receptor attachment competitively. Viral passaging experiments underscore an unusually high barrier for emergence of escape mutants making it an ideal candidate for clinical development. These findings unveil a key site of vulnerability for the development of a next generation of vaccines eliciting broad sarbecovirus immunity.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin S Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Martina Giurdanella
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Barbara Guarino
- 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, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | - Sean PJ Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109
| | - 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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23
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Ganaie SS, Schwarz MM, McMillen CM, Price DA, Feng AX, Albe JR, Wang W, Miersch S, Orvedahl A, Cole AR, Sentmanat MF, Mishra N, Boyles DA, Koenig ZT, Kujawa MR, Demers MA, Hoehl RM, Moyle AB, Wagner ND, Stubbs SH, Cardarelli L, Teyra J, McElroy A, Gross ML, Whelan SPJ, Doench J, Cui X, Brett TJ, Sidhu SS, Virgin HW, Egawa T, Leung DW, Amarasinghe GK, Hartman AL. Lrp1 is a host entry factor for Rift Valley fever virus. Cell 2021; 184:5163-5178.e24. [PMID: 34559985 DOI: 10.1016/j.cell.2021.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/29/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022]
Abstract
Rift Valley fever virus (RVFV) is a zoonotic pathogen with pandemic potential. RVFV entry is mediated by the viral glycoprotein (Gn), but host entry factors remain poorly defined. Our genome-wide CRISPR screen identified low-density lipoprotein receptor-related protein 1 (mouse Lrp1/human LRP1), heat shock protein (Grp94), and receptor-associated protein (RAP) as critical host factors for RVFV infection. RVFV Gn directly binds to specific Lrp1 clusters and is glycosylation independent. Exogenous addition of murine RAP domain 3 (mRAPD3) and anti-Lrp1 antibodies neutralizes RVFV infection in taxonomically diverse cell lines. Mice treated with mRAPD3 and infected with pathogenic RVFV are protected from disease and death. A mutant mRAPD3 that binds Lrp1 weakly failed to protect from RVFV infection. Together, these data support Lrp1 as a host entry factor for RVFV infection and define a new target to limit RVFV infections.
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Affiliation(s)
- Safder S Ganaie
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Madeline M Schwarz
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cynthia M McMillen
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Price
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Annie X Feng
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Joseph R Albe
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wenjie Wang
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Shane Miersch
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Anthony Orvedahl
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Aidan R Cole
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Monica F Sentmanat
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Nawneet Mishra
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Devin A Boyles
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zachary T Koenig
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael R Kujawa
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew A Demers
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan M Hoehl
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Sarah H Stubbs
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Lia Cardarelli
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Anita McElroy
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pediatrics, Division of Pediatric Infectious Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - John Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoxia Cui
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Tom J Brett
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Current address: Vir Biotechnology, San Francisco, CA, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Amy L Hartman
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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24
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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: 233] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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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: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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26
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Lempp FA, Soriaga LB, Montiel-Ruiz M, Benigni F, Noack J, Park YJ, Bianchi S, Walls AC, Bowen JE, Zhou J, Kaiser H, Joshi A, Agostini M, Meury M, Dellota E, Jaconi S, Cameroni E, Martinez-Picado J, Vergara-Alert J, Izquierdo-Useros N, Virgin HW, Lanzavecchia A, Veesler D, Purcell LA, Telenti A, Corti D. Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies. Nature 2021; 598:342-347. [PMID: 34464958 DOI: 10.1038/s41586-021-03925-1] [Citation(s) in RCA: 189] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 infection-which involves both cell attachment and membrane fusion-relies on the angiotensin-converting enzyme 2 (ACE2) receptor, which is paradoxically found at low levels in the respiratory tract1-3, suggesting that there may be additional mechanisms facilitating infection. Here we show that C-type lectin receptors, DC-SIGN, L-SIGN and the sialic acid-binding immunoglobulin-like lectin 1 (SIGLEC1) function as attachment receptors by enhancing ACE2-mediated infection and modulating the neutralizing activity of different classes of spike-specific antibodies. Antibodies to the amino-terminal domain or to the conserved site at the base of the receptor-binding domain, while poorly neutralizing infection of ACE2-overexpressing cells, effectively block lectin-facilitated infection. Conversely, antibodies to the receptor binding motif, while potently neutralizing infection of ACE2-overexpressing cells, poorly neutralize infection of cells expressing DC-SIGN or L-SIGN and trigger fusogenic rearrangement of the spike, promoting cell-to-cell fusion. Collectively, these findings identify a lectin-dependent pathway that enhances ACE2-dependent infection by SARS-CoV-2 and reveal distinct mechanisms of neutralization by different classes of spike-specific antibodies.
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Affiliation(s)
| | | | | | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | | | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Júlia Vergara-Alert
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Bellaterra (Cerdanyola del Vallès), Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA.,Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
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27
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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: 293] [Impact Index Per Article: 97.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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28
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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: 293] [Impact Index Per Article: 97.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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Telenti A, Arvin A, Corey L, Corti D, Diamond MS, García-Sastre A, Garry RF, Holmes EC, Pang PS, Virgin HW. After the pandemic: perspectives on the future trajectory of COVID-19. Nature 2021; 596:495-504. [PMID: 34237771 DOI: 10.1038/s41586-021-03792-w] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
There is a realistic expectation that the global effort in vaccination will bring the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) under control. Nonetheless, uncertainties remain about the type of long-term association that the virus will establish with the human population and, in particular, whether coronavirus disease 2019 (COVID-19) will become an endemic disease. Although the trajectory is difficult to predict, the conditions, concepts and variables that influence this transition can be anticipated. Persistence of SARS-CoV-2 as an endemic virus, perhaps with seasonal epidemic peaks, may be fuelled by pockets of susceptible individuals and waning immunity after infection or vaccination, changes in the virus through antigenic drift that diminish protection and re-entries from zoonotic reservoirs. Here we review relevant observations from previous epidemics and discuss the potential evolution of SARS-CoV-2 as it adapts during persistent transmission in the presence of a level of population immunity. Lack of effective surveillance or adequate response could enable the emergence of new epidemic or pandemic patterns from an endemic infection of SARS-CoV-2. There are key pieces of data that are urgently needed in order to make good decisions; we outline these and propose a way forward.
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Affiliation(s)
- Amalio Telenti
- Vir Biotechnology, San Francisco, CA, USA. .,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.
| | - Ann Arvin
- Vir Biotechnology, San Francisco, CA, USA.
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - 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.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| | | | - 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.
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30
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Collier DA, De Marco A, Ferreira IATM, Meng B, Datir RP, Walls AC, Kemp SA, Bassi J, Pinto D, Silacci-Fregni C, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A, Elmer A, Kingston N, Graves B, McCoy LE, Smith KGC, Bradley JR, Temperton N, Ceron-Gutierrez L, Barcenas-Morales G, Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D, Gupta RK. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature 2021; 593:136-141. [PMID: 33706364 DOI: 10.1038/s41586-021-03412-7] [Citation(s) in RCA: 494] [Impact Index Per Article: 164.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/01/2021] [Indexed: 02/02/2023]
Abstract
Transmission of SARS-CoV-2 is uncontrolled in many parts of the world; control is compounded in some areas by the higher transmission potential of the B.1.1.7 variant1, which has now been reported in 94 countries. It is unclear whether the response of the virus to vaccines against SARS-CoV-2 on the basis of the prototypic strain will be affected by the mutations found in B.1.1.7. Here we assess the immune responses of individuals after vaccination with the mRNA-based vaccine BNT162b22. We measured neutralizing antibody responses after the first and second immunizations using pseudoviruses that expressed the wild-type spike protein or a mutated spike protein that contained the eight amino acid changes found in the B.1.1.7 variant. The sera from individuals who received the vaccine exhibited a broad range of neutralizing titres against the wild-type pseudoviruses that were modestly reduced against the B.1.1.7 variant. This reduction was also evident in sera from some patients who had recovered from COVID-19. Decreased neutralization of the B.1.1.7 variant was also observed for monoclonal antibodies that target the N-terminal domain (9 out of 10) and the receptor-binding motif (5 out of 31), but not for monoclonal antibodies that recognize the receptor-binding domain that bind outside the receptor-binding motif. Introduction of the mutation that encodes the E484K substitution in the B.1.1.7 background to reflect a newly emerged variant of concern (VOC 202102/02) led to a more-substantial loss of neutralizing activity by vaccine-elicited antibodies and monoclonal antibodies (19 out of 31) compared with the loss of neutralizing activity conferred by the mutations in B.1.1.7 alone. The emergence of the E484K substitution in a B.1.1.7 background represents a threat to the efficacy of the BNT162b2 vaccine.
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MESH Headings
- Aged
- Aged, 80 and over
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/isolation & purification
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- COVID-19/immunology
- COVID-19/metabolism
- COVID-19/therapy
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Female
- HEK293 Cells
- Humans
- Immune Evasion/genetics
- Immune Evasion/immunology
- Immunization, Passive
- Male
- Middle Aged
- Models, Molecular
- Mutation
- Neutralization Tests
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/immunology
- COVID-19 Serotherapy
- mRNA Vaccines
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Affiliation(s)
- Dami A Collier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Matteo S Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Agostino Riva
- Division of Infectious Diseases, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | | | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Bioresource, Cambridge, UK
| | | | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
- Laboratorio de Inmunologia, UNAM, Cuautitlán, Mexico
| | - William Harvey
- Institute of Biodiversity, University of Glasgow, Glasgow, UK
| | | | | | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Mark Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- University of KwaZulu Natal, Durban, South Africa.
- Africa Health Research Institute, Durban, South Africa.
- Department of Infectious Diseases, Cambridge University Hospitals NHS Trust, Cambridge, UK.
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31
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McCallum M, De Marco A, Lempp FA, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Foo SYC, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell 2021; 184:2332-2347.e16. [PMID: 33761326 PMCID: PMC7962585 DOI: 10.1016/j.cell.2021.03.028] [Citation(s) in RCA: 601] [Impact Index Per Article: 200.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/17/2021] [Accepted: 03/09/2021] [Indexed: 01/05/2023]
Abstract
The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351, and P.1 lineages, harbor frequent mutations within the NTD supersite, suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alex Chen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Samantha Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - 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
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Agostino Riva
- III Division of Infectious Diseases, Luigi Sacco Hospital, University of Milan, 20157 Milan, Italy
| | | | | | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - 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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32
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Starr TN, Czudnochowski N, Zatta F, Park YJ, Liu Z, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, Wojcechowskyj JA, De Marco A, Rosen LE, Zhou J, Montiel-Ruiz M, Kaiser H, Tucker H, Housley MP, di Iulio J, Lombardo G, Agostini M, Sprugasci N, Culap K, Jaconi S, Meury M, Dellota E, Cameroni E, Croll TI, Nix JC, Havenar-Daughton C, Telenti A, Lempp FA, Pizzuto MS, Chodera JD, Hebner CM, Whelan SP, Virgin HW, Veesler D, Corti D, Bloom JD, Snell G. Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape. bioRxiv 2021:2021.04.06.438709. [PMID: 33851154 PMCID: PMC8043444 DOI: 10.1101/2021.04.06.438709] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An ideal anti-SARS-CoV-2 antibody would resist viral escape 1-3 , have activity against diverse SARS-related coronaviruses 4-7 , and be highly protective through viral neutralization 8-11 and effector functions 12,13 . Understanding how these properties relate to each other and vary across epitopes would aid development of antibody therapeutics 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), including S309 4 , the parental antibody of the late-stage clinical antibody VIR-7831. We observe a tradeoff between SARS-CoV-2 in vitro neutralization potency and breadth of binding across SARS-related coronaviruses. Nevertheless, we identify several neutralizing antibodies with exceptional breadth and resistance to escape, including a new antibody (S2H97) that binds with high affinity to all SARS-related coronavirus clades via a unique RBD epitope centered on residue E516. S2H97 and other escape-resistant antibodies have high binding affinity and target functionally constrained RBD residues. We find that antibodies targeting the ACE2 receptor binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency, but we identify one potent RBM antibody (S2E12) with breadth across sarbecoviruses closely related to SARS-CoV-2 and with a high barrier to viral escape. These data highlight functional diversity among antibodies targeting the RBD and identify epitopes and features to prioritize for antibody and vaccine development against the current and potential future pandemics.
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Affiliation(s)
- Tyler N. Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Fabrizia Zatta
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amin Addetia
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Dora Pinto
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Martina Beltramello
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Allison J. Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Roberta Marzi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - William G. Glass
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ivy Zhang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Adam S. Dingens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Anna De Marco
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | | | | | | | | | - Gloria Lombardo
- 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
| | - 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
| | - Tristan I. Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | | | - Matteo S. Pizzuto
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Jesse D. Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
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33
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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, Silacci Fregni C, Abdelnabi R, Caroline Foo SY, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Snell G, Virgin HW, Whelan SP, Bloom JD, Corti D, Veesler D, Pizzuto MS. Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody. bioRxiv 2021:2021.04.07.438818. [PMID: 33851169 PMCID: PMC8043460 DOI: 10.1101/2021.04.07.438818] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent emergence of SARS-CoV-2 variants of concern (VOC) and the recurrent spillovers of coronaviruses in 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 (mAb), designated S2X259, recognizing a highly conserved cryptic receptor-binding domain (RBD) epitope and cross-reacting with spikes from all sarbecovirus clades. S2X259 broadly neutralizes spike-mediated entry of SARS-CoV-2 including the B.1.1.7, B.1.351, P.1 and B.1.427/B.1.429 VOC, as well as a wide spectrum of human and zoonotic sarbecoviruses through inhibition of ACE2 binding to the RBD. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses a remarkably high barrier to the emergence of resistance mutants. We show that prophylactic administration of S2X259 protects Syrian hamsters against challenges with the prototypic SARS-CoV-2 and the B.1.351 variant, suggesting this mAb is a promising candidate for the prevention and treatment of emergent VOC and zoonotic infections. Our data unveil a key antigenic site targeted by broadly-neutralizing antibodies and will guide the design of pan-sarbecovirus vaccines.
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Affiliation(s)
- M. Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, 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 98109, USA
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Amin Addetia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Eneida Vetti
- 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, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | - Michael A. Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - 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
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | | | | | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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34
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Chen RE, Zhang X, Case JB, Winkler ES, Liu Y, VanBlargan LA, Liu J, Errico JM, Xie X, Suryadevara N, Gilchuk P, Zost SJ, Tahan S, Droit L, Turner JS, Kim W, Schmitz AJ, Thapa M, Wang D, Boon ACM, Presti RM, O'Halloran JA, Kim AHJ, Deepak P, Pinto D, Fremont DH, Crowe JE, Corti D, Virgin HW, Ellebedy AH, Shi PY, Diamond MS. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat Med 2021; 27:717-726. [PMID: 33664494 PMCID: PMC8058618 DOI: 10.1038/s41591-021-01294-w] [Citation(s) in RCA: 689] [Impact Index Per Article: 229.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global COVID-19 pandemic. Rapidly spreading SARS-CoV-2 variants may jeopardize newly introduced antibody and vaccine countermeasures. Here, using monoclonal antibodies (mAbs), animal immune sera, human convalescent sera and human sera from recipients of the BNT162b2 mRNA vaccine, we report the impact on antibody neutralization of a panel of authentic SARS-CoV-2 variants including a B.1.1.7 isolate, chimeric strains with South African or Brazilian spike genes and isogenic recombinant viral variants. Many highly neutralizing mAbs engaging the receptor-binding domain or N-terminal domain and most convalescent sera and mRNA vaccine-induced immune sera showed reduced inhibitory activity against viruses containing an E484K spike mutation. As antibodies binding to spike receptor-binding domain and N-terminal domain demonstrate diminished neutralization potency in vitro against some emerging variants, updated mAb cocktails targeting highly conserved regions, enhancement of mAb potency or adjustments to the spike sequences of vaccines may be needed to prevent loss of protection in vivo.
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Affiliation(s)
- Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - James Brett Case
- Department of Medicine, 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 & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jianying Liu
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - John M Errico
- Department of Pathology & Immunology, 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
| | - Stephen Tahan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lindsay Droit
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jackson S Turner
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Wooseob Kim
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Aaron J Schmitz
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mahima Thapa
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel M Presti
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jane A O'Halloran
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Alfred H J Kim
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Parakkal Deepak
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Dora Pinto
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Departments of Pediatrics and Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Herbert W Virgin
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Vir Biotechnology, San Francisco, CA, USA
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ali H Ellebedy
- 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.
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
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35
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Thomson EC, Rosen LE, Shepherd JG, Spreafico R, da Silva Filipe A, Wojcechowskyj JA, Davis C, Piccoli L, Pascall DJ, Dillen J, Lytras S, Czudnochowski N, Shah R, Meury M, Jesudason N, De Marco A, Li K, Bassi J, O'Toole A, Pinto D, Colquhoun RM, Culap K, Jackson B, Zatta F, Rambaut A, Jaconi S, Sreenu VB, Nix J, Zhang I, Jarrett RF, Glass WG, Beltramello M, Nomikou K, Pizzuto M, Tong L, Cameroni E, Croll TI, Johnson N, Di Iulio J, Wickenhagen A, Ceschi A, Harbison AM, Mair D, Ferrari P, Smollett K, Sallusto F, Carmichael S, Garzoni C, Nichols J, Galli M, Hughes J, Riva A, Ho A, Schiuma M, Semple MG, Openshaw PJM, Fadda E, Baillie JK, Chodera JD, Rihn SJ, Lycett SJ, Virgin HW, Telenti A, Corti D, Robertson DL, Snell G. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell 2021. [PMID: 33621484 DOI: 10.1101/2020.11.04.355842] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.
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Affiliation(s)
- Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; Department of Clinical Research, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | | | - James G Shepherd
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David J Pascall
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G61 1QH, UK
| | - Josh Dillen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Rajiv Shah
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Natasha Jesudason
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kathy Li
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Aine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Rachel M Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Vattipally B Sreenu
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Jay Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ivy Zhang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Ruth F Jarrett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - William G Glass
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Matteo Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 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
| | - Aoife M Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Paolo Ferrari
- Department of Nephrology, Ospedale Civico Lugano, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland; Prince of Wales Hospital Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland; ETH Institute of Microbiology, ETH Zurich, 8093 Zürich, Switzerland
| | - Stephen Carmichael
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Massimo Galli
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Agostino Riva
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Marco Schiuma
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7BE, UK; Respiratory Medicine, Alder Hey Children's Hospital, Liverpool L12 2AP, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - J Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK; Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh EH16 4SA, UK
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Suzannah J Rihn
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Samantha J Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA; Washington University School of Medicine, Saint Louis, MO 63110, USA
| | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK.
| | - Gyorgy Snell
- Vir Biotechnology, San Francisco, CA 94158, USA.
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36
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Thomson EC, Rosen LE, Shepherd JG, Spreafico R, da Silva Filipe A, Wojcechowskyj JA, Davis C, Piccoli L, Pascall DJ, Dillen J, Lytras S, Czudnochowski N, Shah R, Meury M, Jesudason N, De Marco A, Li K, Bassi J, O'Toole A, Pinto D, Colquhoun RM, Culap K, Jackson B, Zatta F, Rambaut A, Jaconi S, Sreenu VB, Nix J, Zhang I, Jarrett RF, Glass WG, Beltramello M, Nomikou K, Pizzuto M, Tong L, Cameroni E, Croll TI, Johnson N, Di Iulio J, Wickenhagen A, Ceschi A, Harbison AM, Mair D, Ferrari P, Smollett K, Sallusto F, Carmichael S, Garzoni C, Nichols J, Galli M, Hughes J, Riva A, Ho A, Schiuma M, Semple MG, Openshaw PJM, Fadda E, Baillie JK, Chodera JD, Rihn SJ, Lycett SJ, Virgin HW, Telenti A, Corti D, Robertson DL, Snell G. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell 2021; 184:1171-1187.e20. [PMID: 33621484 PMCID: PMC7843029 DOI: 10.1016/j.cell.2021.01.037] [Citation(s) in RCA: 408] [Impact Index Per Article: 136.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/12/2020] [Accepted: 01/22/2021] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.
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Affiliation(s)
- Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; Department of Clinical Research, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | | | - James G Shepherd
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David J Pascall
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G61 1QH, UK
| | - Josh Dillen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Rajiv Shah
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Natasha Jesudason
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kathy Li
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Aine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Rachel M Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Vattipally B Sreenu
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Jay Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ivy Zhang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Ruth F Jarrett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - William G Glass
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Matteo Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 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
| | - Aoife M Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Paolo Ferrari
- Department of Nephrology, Ospedale Civico Lugano, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland; Prince of Wales Hospital Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland; ETH Institute of Microbiology, ETH Zurich, 8093 Zürich, Switzerland
| | - Stephen Carmichael
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Massimo Galli
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Agostino Riva
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Marco Schiuma
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7BE, UK; Respiratory Medicine, Alder Hey Children's Hospital, Liverpool L12 2AP, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - J Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK; Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh EH16 4SA, UK
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Suzannah J Rihn
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Samantha J Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA; Washington University School of Medicine, Saint Louis, MO 63110, USA
| | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK.
| | - Gyorgy Snell
- Vir Biotechnology, San Francisco, CA 94158, USA.
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37
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Collier DA, De Marco A, Ferreira IATM, Meng B, Datir R, Walls AC, Kemp S SA, Bassi J, Pinto D, Fregni CS, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A, Elmer A, Kingston N, Graves B, McCoy LE, Smith KG, Bradley JR, Temperton N, Ceron-Gutierrez L L, Barcenas-Morales G, Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D, Gupta RK. SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. medRxiv 2021:2021.01.19.21249840. [PMID: 33619509 PMCID: PMC7899479 DOI: 10.1101/2021.01.19.21249840] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission is uncontrolled in many parts of the world, compounded in some areas by higher transmission potential of the B1.1.7 variant now seen in 50 countries. It is unclear whether responses to SARS-CoV-2 vaccines based on the prototypic strain will be impacted by mutations found in B.1.1.7. Here we assessed immune responses following vaccination with mRNA-based vaccine BNT162b2. We measured neutralising antibody responses following a single immunization using pseudoviruses expressing the wild-type Spike protein or the 8 amino acid mutations found in the B.1.1.7 spike protein. The vaccine sera exhibited a broad range of neutralising titres against the wild-type pseudoviruses that were modestly reduced against B.1.1.7 variant. This reduction was also evident in sera from some convalescent patients. Decreased B.1.1.7 neutralisation was also observed with monoclonal antibodies targeting the N-terminal domain (9 out of 10), the Receptor Binding Motif (RBM) (5 out of 31), but not in neutralising mAbs binding outside the RBM. Introduction of the E484K mutation in a B.1.1.7 background to reflect newly emerging viruses in the UK led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b.
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Affiliation(s)
- Dami A Collier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Steven A Kemp S
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Katja Culap
- 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
| | | | - Matteo S Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Agostino Riva
- Division of Infectious Diseases, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | | | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Kenneth Gc Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Bioresource, Cambridge, UK
| | | | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, UK
- Laboratorio de Inmunologia, S-Cuautitlán, UNAM, Mexico
| | - William Harvey
- Institute of Biodiversity, University of Glasgow, Glasgow, UK
| | | | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, UK
| | - Mark Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- University of KwaZulu Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Department of Infectious Diseases, Cambridge University Hospitals NHS Trust, Cambridge UK
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38
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Brestoff JR, Wilen CB, Moley JR, Li Y, Zou W, Malvin NP, Rowen MN, Saunders BT, Ma H, Mack MR, Hykes BL, Balce DR, Orvedahl A, Williams JW, Rohatgi N, Wang X, McAllaster MR, Handley SA, Kim BS, Doench JG, Zinselmeyer BH, Diamond MS, Virgin HW, Gelman AE, Teitelbaum SL. Intercellular Mitochondria Transfer to Macrophages Regulates White Adipose Tissue Homeostasis and Is Impaired in Obesity. Cell Metab 2021; 33:270-282.e8. [PMID: 33278339 PMCID: PMC7858234 DOI: 10.1016/j.cmet.2020.11.008] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/03/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Recent studies suggest that mitochondria can be transferred between cells to support the survival of metabolically compromised cells. However, whether intercellular mitochondria transfer occurs in white adipose tissue (WAT) or regulates metabolic homeostasis in vivo remains unknown. We found that macrophages acquire mitochondria from neighboring adipocytes in vivo and that this process defines a transcriptionally distinct macrophage subpopulation. A genome-wide CRISPR-Cas9 knockout screen revealed that mitochondria uptake depends on heparan sulfates (HS). High-fat diet (HFD)-induced obese mice exhibit lower HS levels on WAT macrophages and decreased intercellular mitochondria transfer from adipocytes to macrophages. Deletion of the HS biosynthetic gene Ext1 in myeloid cells decreases mitochondria uptake by WAT macrophages, increases WAT mass, lowers energy expenditure, and exacerbates HFD-induced obesity in vivo. Collectively, this study suggests that adipocytes and macrophages employ intercellular mitochondria transfer as a mechanism of immunometabolic crosstalk that regulates metabolic homeostasis and is impaired in obesity.
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Affiliation(s)
- Jonathan R Brestoff
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Craig B Wilen
- Department of Laboratory Medicine and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - John R Moley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yongjia Li
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wei Zou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole P Malvin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marina N Rowen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian T Saunders
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongming Ma
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Madison R Mack
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barry L Hykes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dale R Balce
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Vir Biotechnology, San Francisco, CA 94158, USA
| | - Anthony Orvedahl
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jesse W Williams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nidhi Rohatgi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyan Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael R McAllaster
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian S Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bernd H Zinselmeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; 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 63110, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Vir Biotechnology, San Francisco, CA 94158, USA; Department of Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew E Gelman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven L Teitelbaum
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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39
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McLellan LK, McAllaster MR, Kim AS, Tóthová Ľ, Olson PD, Pinkner JS, Daugherty AL, Hreha TN, Janetka JW, Fremont DH, Hultgren SJ, Virgin HW, Hunstad DA. A host receptor enables type 1 pilus-mediated pathogenesis of Escherichia coli pyelonephritis. PLoS Pathog 2021; 17:e1009314. [PMID: 33513212 PMCID: PMC7875428 DOI: 10.1371/journal.ppat.1009314] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/10/2021] [Accepted: 01/13/2021] [Indexed: 12/26/2022] Open
Abstract
Type 1 pili have long been considered the major virulence factor enabling colonization of the urinary bladder by uropathogenic Escherichia coli (UPEC). The molecular pathogenesis of pyelonephritis is less well characterized, due to previous limitations in preclinical modeling of kidney infection. Here, we demonstrate in a recently developed mouse model that beyond bladder infection, type 1 pili also are critical for establishment of ascending pyelonephritis. Bacterial mutants lacking the type 1 pilus adhesin (FimH) were unable to establish kidney infection in male C3H/HeN mice. We developed an in vitro model of FimH-dependent UPEC binding to renal collecting duct cells, and performed a CRISPR screen in these cells, identifying desmoglein-2 as a primary renal epithelial receptor for FimH. The mannosylated extracellular domain of human DSG2 bound directly to the lectin domain of FimH in vitro, and introduction of a mutation in the FimH mannose-binding pocket abolished binding to DSG2. In infected C3H/HeN mice, type 1-piliated UPEC and Dsg2 were co-localized within collecting ducts, and administration of mannoside FIM1033, a potent small-molecule inhibitor of FimH, significantly attenuated bacterial loads in pyelonephritis. Our results broaden the biological importance of FimH, specify the first renal FimH receptor, and indicate that FimH-targeted therapeutics will also have application in pyelonephritis. Urinary tract infections (UTIs) are among the most common bacterial infections in humans. While much has been discovered about how E. coli cause bladder infections, less is known about the host-pathogen interactions that underlie kidney infection (pyelonephritis). We employed recently developed mouse models to show that bacterial surface fibers called type 1 pili, which bear the adhesive protein FimH and are known to mediate E. coli binding to bladder epithelium, are also required for ascending kidney infection. We developed a cell-culture model of bacterial binding to renal collecting duct, then performed a screen using the gene-editing tool CRISPR to identify the first known FimH receptor in the kidney. This epithelial cell-surface protein, desmoglein-2, was shown to directly bind FimH, and we localized this binding to specific extracellular domains of DSG2. Further, we showed that mannosides, small-molecule FimH inhibitors currently in development to treat bladder infection, are also effective in experimental kidney infection. Our study reveals a novel host-pathogen interaction during pyelonephritis and demonstrates how this interaction may be therapeutically targeted.
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Affiliation(s)
- Lisa K. McLellan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael R. McAllaster
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Arthur S. Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ľubomíra Tóthová
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patrick D. Olson
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jerome S. Pinkner
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Allyssa L. Daugherty
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Teri N. Hreha
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - James W. Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Daved H. Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Scott J. Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Herbert W. Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - David A. Hunstad
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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40
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McCallum M, Marco AD, Lempp F, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Caroline Foo SY, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. bioRxiv 2021:2021.01.14.426475. [PMID: 33469588 PMCID: PMC7814825 DOI: 10.1101/2021.01.14.426475] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
SARS-CoV-2 entry into host cells is orchestrated by the spike (S) glycoprotein that contains an immunodominant receptor-binding domain (RBD) targeted by the largest fraction of neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge. SARS-CoV-2 variants, including the 501Y.V2 and B.1.1.7 lineages, harbor frequent mutations localized in the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs to protective immunity.
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41
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Tortorici MA, Beltramello M, Lempp FA, Pinto D, Dang HV, Rosen LE, McCallum M, Bowen J, Minola A, Jaconi S, Zatta F, De Marco A, Guarino B, Bianchi S, Lauron EJ, Tucker H, Zhou J, Peter A, Havenar-Daughton C, Wojcechowskyj JA, Case JB, Chen RE, Kaiser H, Montiel-Ruiz M, Meury M, Czudnochowski N, Spreafico R, Dillen J, Ng C, Sprugasci N, Culap K, Benigni F, Abdelnabi R, Foo SYC, Schmid MA, Cameroni E, Riva A, Gabrieli A, Galli M, Pizzuto MS, Neyts J, Diamond MS, Virgin HW, Snell G, Corti D, Fink K, Veesler D. Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms. Science 2020; 370:950-957. [PMID: 32972994 PMCID: PMC7857395 DOI: 10.1126/science.abe3354] [Citation(s) in RCA: 408] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022]
Abstract
Efficient therapeutic options are needed to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has caused more than 922,000 fatalities as of 13 September 2020. We report the isolation and characterization of two ultrapotent SARS-CoV-2 human neutralizing antibodies (S2E12 and S2M11) that protect hamsters against SARS-CoV-2 challenge. Cryo-electron microscopy structures show that S2E12 and S2M11 competitively block angiotensin-converting enzyme 2 (ACE2) attachment and that S2M11 also locks the spike in a closed conformation by recognition of a quaternary epitope spanning two adjacent receptor-binding domains. Antibody cocktails that include S2M11, S2E12, or the previously identified S309 antibody broadly neutralize a panel of circulating SARS-CoV-2 isolates and activate effector functions. Our results pave the way to implement antibody cocktails for prophylaxis or therapy, circumventing or limiting the emergence of viral escape mutants.
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MESH Headings
- Amino Acid Motifs/immunology
- Angiotensin-Converting Enzyme 2
- Animals
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/administration & dosage
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- Betacoronavirus/immunology
- CHO Cells
- COVID-19
- Coronavirus Infections/prevention & control
- Coronavirus Infections/therapy
- Cricetinae
- Cricetulus
- Cryoelectron Microscopy
- HEK293 Cells
- Humans
- Immunodominant Epitopes/chemistry
- Immunodominant Epitopes/immunology
- Microscopy, Electron
- Pandemics/prevention & control
- Peptidyl-Dipeptidase A/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/therapy
- Protein Domains/immunology
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/antagonists & inhibitors
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Martina Beltramello
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Dora Pinto
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Ha V Dang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Andrea Minola
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Anna De Marco
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Siro Bianchi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Alessia Peter
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - James Brett Case
- Departments of Medicine, Molecular Microbiology, Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita E Chen
- Departments of Medicine, Molecular Microbiology, Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | | | - Josh Dillen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Cindy Ng
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Nicole Sprugasci
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Katja Culap
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | - Michael A Schmid
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Agostino Riva
- III Division of Infectious Diseases, Luigi Sacco University Hospital, University of Milan, Italy
| | - Arianna Gabrieli
- III Division of Infectious Diseases, Luigi Sacco University Hospital, University of Milan, Italy
| | - Massimo Galli
- III Division of Infectious Diseases, Luigi Sacco University Hospital, University of Milan, Italy
| | - Matteo S Pizzuto
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA
- Washington University School of Medicine, St. Louis, MO, USA
- UTSouthwestern Medical Center, Dallas, TX, USA
| | | | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Katja Fink
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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42
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Carey KL, Paulus GLC, Wang L, Balce DR, Luo JW, Bergman P, Ferder IC, Kong L, Renaud N, Singh S, Kost-Alimova M, Nyfeler B, Lassen KG, Virgin HW, Xavier RJ. TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41. Cell Rep 2020; 33:108371. [PMID: 33176151 DOI: 10.1016/j.celrep.2020.108371] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 08/18/2020] [Accepted: 10/20/2020] [Indexed: 12/26/2022] Open
Abstract
Transcription factor EB (TFEB) activates lysosomal biogenesis genes in response to environmental cues. Given implications of impaired TFEB signaling and lysosomal dysfunction in metabolic, neurological, and infectious diseases, we aim to systematically identify TFEB-directed circuits by examining transcriptional responses to TFEB subcellular localization and stimulation. We reveal that steady-state nuclear TFEB is sufficient to activate transcription of lysosomal, autophagy, and innate immunity genes, whereas other targets require higher thresholds of stimulation. Furthermore, we identify shared and distinct transcriptional signatures between mTOR inhibition and bacterial autophagy. Using a genome-wide CRISPR library, we find TFEB targets that protect cells from or sensitize cells to lysosomal cell death. BHLHE40 and BHLHE41, genes responsive to high, sustained levels of nuclear TFEB, act in opposition to TFEB upon lysosomal cell death induction. Further investigation identifies genes counter-regulated by TFEB and BHLHE40/41, adding this negative feedback to the current understanding of TFEB regulatory mechanisms.
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Affiliation(s)
- Kimberly L Carey
- Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Geraldine L C Paulus
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lingfei Wang
- Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dale R Balce
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jessica W Luo
- Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Phil Bergman
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Ianina C Ferder
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lingjia Kong
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Nicole Renaud
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maria Kost-Alimova
- Center for the Science of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beat Nyfeler
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Kara G Lassen
- Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ramnik J Xavier
- Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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43
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Bournazos S, Corti D, Virgin HW, Ravetch JV. Fc-optimized antibodies elicit CD8 immunity to viral respiratory infection. Nature 2020; 588:485-490. [PMID: 33032297 PMCID: PMC7672690 DOI: 10.1038/s41586-020-2838-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/02/2020] [Indexed: 02/05/2023]
Abstract
Antibodies against viral pathogens represent promising therapeutic agents for the control of infection, and their antiviral efficacy has been shown to require the coordinated function of both the Fab and Fc domains1. The Fc domain engages a wide spectrum of receptors on discrete cells of the immune system to trigger the clearance of viruses and subsequent killing of infected cells1–4. Here we report that Fc engineering of anti-influenza IgG monoclonal antibodies for selective binding to the activating Fcγ receptor FcγRIIa results in enhanced ability to prevent or treat lethal viral respiratory infection in mice, with increased maturation of dendritic cells and the induction of protective CD8+ T cell responses. These findings highlight the capacity for IgG antibodies to induce protective adaptive immunity to viral infection when they selectively activate a dendritic cell and T cell pathway, with important implications for the development of therapeutic antibodies with improved antiviral efficacy against viral respiratory pathogens. An antibody Fc domain variant with enhanced binding to an activating Fc receptor on dendritic cells promotes the induction of a protective CD8 T cell response.
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Affiliation(s)
- Stylianos Bournazos
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology Inc., Bellinzona, Switzerland
| | | | - Jeffrey V Ravetch
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY, USA.
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Piccoli L, Park YJ, Tortorici MA, Czudnochowski N, Walls AC, Beltramello M, Silacci-Fregni C, Pinto D, Rosen LE, Bowen JE, Acton OJ, Jaconi S, Guarino B, Minola A, Zatta F, Sprugasci N, Bassi J, Peter A, De Marco A, Nix JC, Mele F, Jovic S, Rodriguez BF, Gupta SV, Jin F, Piumatti G, Lo Presti G, Pellanda AF, Biggiogero M, Tarkowski M, Pizzuto MS, Cameroni E, Havenar-Daughton C, Smithey M, Hong D, Lepori V, Albanese E, Ceschi A, Bernasconi E, Elzi L, Ferrari P, Garzoni C, Riva A, Snell G, Sallusto F, Fink K, Virgin HW, Lanzavecchia A, Corti D, Veesler D. Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology. Cell 2020; 183:1024-1042.e21. [PMID: 32991844 PMCID: PMC7494283 DOI: 10.1016/j.cell.2020.09.037] [Citation(s) in RCA: 924] [Impact Index Per Article: 231.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 09/11/2020] [Indexed: 12/28/2022]
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. 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
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Affiliation(s)
- Luca Piccoli
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, 75015 Paris, France
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Dora Pinto
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Oliver J Acton
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Stefano Jaconi
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Andrea Minola
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Jessica Bassi
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alessia Peter
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Anna De Marco
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Federico Mele
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Sandra Jovic
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | | | - Feng Jin
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Giovanni Piumatti
- Division of Primary Care, Geneva University Hospitals, 1205 Geneva, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Giorgia Lo Presti
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | | | - Maira Biggiogero
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Maciej Tarkowski
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Matteo S Pizzuto
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | | | - David Hong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Emiliano Albanese
- Institute of Public Health, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 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
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, Ospedale Civico and Ospedale Italiano, 6900 Lugano, Switzerland
| | - Luigia Elzi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, Ospedale Regionale Bellinzona e Valli and Ospedale Regionale, 6600 Locarno, Switzerland
| | - Paolo Ferrari
- Department of Nephrology, Ospedale Civico Lugano, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland; Prince of Wales Hospital Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - 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
| | | | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Katja Fink
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Davide Corti
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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Case JB, Rothlauf PW, Chen RE, Liu Z, Zhao H, Kim AS, Bloyet LM, Zeng Q, Tahan S, Droit L, Ilagan MXG, Tartell MA, Amarasinghe G, Henderson JP, Miersch S, Ustav M, Sidhu S, Virgin HW, Wang D, Ding S, Corti D, Theel ES, Fremont DH, Diamond MS, Whelan SPJ. Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2. Cell Host Microbe 2020; 28:475-485.e5. [PMID: 32735849 PMCID: PMC7332453 DOI: 10.1016/j.chom.2020.06.021] [Citation(s) in RCA: 313] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/18/2020] [Accepted: 06/24/2020] [Indexed: 01/08/2023]
Abstract
Antibody-based interventions against SARS-CoV-2 could limit morbidity, mortality, and possibly transmission. An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, which engages with host ACE2 receptor for entry. Using an infectious molecular clone of vesicular stomatitis virus (VSV) expressing eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput-imaging-based neutralization assay at biosafety level 2. We also developed a focus-reduction neutralization test with a clinical isolate of SARS-CoV-2 at biosafety level 3. Comparing the neutralizing activities of various antibodies and ACE2-Fc soluble decoy protein in both assays revealed a high degree of concordance. These assays will help define correlates of protection for antibody-based countermeasures and vaccines against SARS-CoV-2. Additionally, replication-competent VSV-eGFP-SARS-CoV-2 provides a tool for testing inhibitors of SARS-CoV-2 mediated entry under reduced biosafety containment.
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Affiliation(s)
- James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & 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
| | - Haiyan Zhao
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Arthur S Kim
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Qiru Zeng
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen Tahan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lindsay Droit
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ma Xenia G Ilagan
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael A Tartell
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Gaya Amarasinghe
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jeffrey P Henderson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Shane Miersch
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Mart Ustav
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Sachdev Sidhu
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | | | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Inc., CH-6500, Bellinzona, Switzerland
| | - Elitza S Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Daved H Fremont
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biochemistry & Molecular Biophysics, 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
| | - Michael S Diamond
- 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; Department of Pathology & Immunology, 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.
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
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Spreafico R, Soriaga LB, Grosse J, Virgin HW, Telenti A. Advances in Genomics for Drug Development. Genes (Basel) 2020; 11:E942. [PMID: 32824125 PMCID: PMC7465049 DOI: 10.3390/genes11080942] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022] Open
Abstract
Drug development (target identification, advancing drug leads to candidates for preclinical and clinical studies) can be facilitated by genetic and genomic knowledge. Here, we review the contribution of population genomics to target identification, the value of bulk and single cell gene expression analysis for understanding the biological relevance of a drug target, and genome-wide CRISPR editing for the prioritization of drug targets. In genomics, we discuss the different scope of genome-wide association studies using genotyping arrays, versus exome and whole genome sequencing. In transcriptomics, we discuss the information from drug perturbation and the selection of biomarkers. For CRISPR screens, we discuss target discovery, mechanism of action and the concept of gene to drug mapping. Harnessing genetic support increases the probability of drug developability and approval.
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Affiliation(s)
| | | | | | | | - Amalio Telenti
- Vir Biotechnology, Inc., San Francisco, CA 94158, USA; (R.S.); (L.B.S.); (J.G.); (H.W.V.)
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Xavier RJ, Virgin HW. Beth Levine (1960–2020). Cell 2020. [DOI: 10.1016/j.cell.2020.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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48
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Xavier RJ, Virgin HW. Beth Levine (1960–2020). Dev Cell 2020. [DOI: 10.1016/j.devcel.2020.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Xavier RJ, Virgin HW. Beth Levine (1960–2020). Mol Cell 2020. [DOI: 10.1016/j.molcel.2020.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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Affiliation(s)
- Herbert W. Virgin
- Vir Biotechnology, San Francisco,
CA, USA
- Washington University School of
Medicine, St. Louis, MO, USA
| | - Ana Maria Cuervo
- Department of Developmental and
Molecular Biology and Institute for Aging
Research, Albert Einstein College of Medicine, New
York, NY, USA
| | - Ramnik J. Xavier
- Broad Institute, Cambridge, MA,
USA
- Massachusetts General Hospital,
Harvard Medical School, Boston, MA,
USA
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