1
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Dadonaite B, Brown J, McMahon TE, Farrell AG, Figgins MD, Asarnow D, Stewart C, Lee J, Logue J, Bedford T, Murrell B, Chu HY, Veesler D, Bloom JD. Spike deep mutational scanning helps predict success of SARS-CoV-2 clades. Nature 2024:10.1038/s41586-024-07636-1. [PMID: 38961298 DOI: 10.1038/s41586-024-07636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
SARS-CoV-2 variants acquire mutations in the spike protein that promote immune evasion1 and affect other properties that contribute to viral fitness, such as ACE2 receptor binding and cell entry2,3. Knowledge of how mutations affect these spike phenotypes can provide insight into the current and potential future evolution of the virus. Here we use pseudovirus deep mutational scanning4 to measure how more than 9,000 mutations across the full XBB.1.5 and BA.2 spikes affect ACE2 binding, cell entry or escape from human sera. We find that mutations outside the receptor-binding domain (RBD) have meaningfully affected ACE2 binding during SARS-CoV-2 evolution. We also measure how mutations to the XBB.1.5 spike affect neutralization by serum from individuals who recently had SARS-CoV-2 infections. The strongest serum escape mutations are in the RBD at sites 357, 420, 440, 456 and 473; however, the antigenic effects of these mutations vary across individuals. We also identify strong escape mutations outside the RBD; however, many of them decrease ACE2 binding, suggesting they act by modulating RBD conformation. Notably, the growth rates of human SARS-CoV-2 clades can be explained in substantial part by the measured effects of mutations on spike phenotypes, suggesting our data could enable better prediction of viral evolution.
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Affiliation(s)
- Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Teagan E McMahon
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ariana G Farrell
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marlin D Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jenni Logue
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Helen Y Chu
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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2
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Connor RI, Sakharkar M, Rappazzo CG, Kaku CI, Curtis NC, Shin S, Wieland-Alter WF, Wentworth J, Mielcarz DW, Weiner JA, Ackerman ME, Walker LM, Lee J, Wright PF. Characteristics and Functions of Infection-enhancing Antibodies to the N-terminal Domain of SARS-CoV-2. Pathog Immun 2024; 9:1-24. [PMID: 38933606 PMCID: PMC11197847 DOI: 10.20411/pai.v9i2.679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024] Open
Abstract
Background Fcγ-receptor (FcγR)-independent enhancement of SARS-CoV-2 infection mediated by N-terminal domain (NTD)-binding monoclonal antibodies (mAbs) has been observed in vitro, but the functional significance of these antibodies in vivo is less clear. Methods We characterized 1,213 SARS-CoV-2 spike (S)-binding mAbs derived from COVID-19 convalescent patients for binding specificity to the SARS-CoV-2 S protein, VH germ-line usage, and affinity maturation. Infection enhancement in a vesicular stomatitis virus (VSV)-SARS-CoV-2 S pseudovirus (PV) assay was characterized in respiratory and intestinal epithelial cell lines, and against SARS-CoV-2 variants of concern (VOC). Proteomic deconvolution of the serum antibody repertoire was used to determine functional attributes of secreted NTD-binding mAbs. Results We identified 72/1213 (5.9%) mAbs that enhanced SARS-CoV-2 infection in a PV assay. The majority (68%) of these mAbs recognized the NTD, were identified in patients with mild and severe disease, and persisted for at least 5 months post-infection. Infection enhancement by NTD-binding mAbs was not observed in intestinal and respiratory epithelial cell lines and was diminished or lost against SARS-CoV-2 VOC. Proteomic deconvolution of the serum antibody repertoire from 2 of the convalescent patients identified, for the first time, NTD-binding, infection-enhancing mAbs among the circulating immunoglobulins directly isolated from serum. Functional analysis of these mAbs demonstrated robust activation of FcγRIIIa associated with antibody binding to recombinant S proteins. Conclusions Functionally active NTD-specific mAbs arise frequently during natural infection and can last as major serum clonotypes during convalescence. These antibodies display functional attributes that include FcγR activation, and may be selected against by mutations in NTD associated with SARS-CoV-2 VOC.
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Affiliation(s)
- Ruth I. Connor
- Department of Pediatrics, Geisel School of Medicine, Dartmouth Health, Lebanon, New Hampshire
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | | | | | | | | | - Seungmin Shin
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | - Wendy F. Wieland-Alter
- Department of Pediatrics, Geisel School of Medicine, Dartmouth Health, Lebanon, New Hampshire
| | - Jordan Wentworth
- DartLab, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire
| | - Daniel W. Mielcarz
- DartLab, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire
| | - Joshua A. Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | | | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | - Peter F. Wright
- Department of Pediatrics, Geisel School of Medicine, Dartmouth Health, Lebanon, New Hampshire
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3
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Bruun TU, Do J, Weidenbacher PAB, Kim PS. Engineering a SARS-CoV-2 vaccine targeting the RBD cryptic-face via immunofocusing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597541. [PMID: 38895327 PMCID: PMC11185595 DOI: 10.1101/2024.06.05.597541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is the main target of neutralizing antibodies. Although they are infrequently elicited during infection or vaccination, antibodies that bind to the conformation-specific cryptic face of the RBD display remarkable breadth of binding and neutralization across Sarbecoviruses. Here, we employed the immunofocusing technique PMD (protect, modify, deprotect) to create RBD immunogens (PMD-RBD) specifically designed to focus the antibody response towards the cryptic-face epitope recognized by the broadly neutralizing antibody S2X259. Immunization with PMD-RBD antigens induced robust binding titers and broad neutralizing activity against homologous and heterologous Sarbecovirus strains. A serum-depletion assay provided direct evidence that PMD successfully skewed the polyclonal antibody response towards the cryptic face of the RBD. Our work demonstrates the ability of PMD to overcome immunodominance and refocus humoral immunity, with implications for the development of broader and more resilient vaccines against current and emerging viruses with pandemic potential.
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Affiliation(s)
- Theodora U.J. Bruun
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305
| | - Jonathan Do
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305
| | - Payton A.-B. Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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4
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Dadonaite B, Brown J, McMahon TE, Farrell AG, Asarnow D, Stewart C, Logue J, Murrell B, Chu HY, Veesler D, Bloom JD. Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566961. [PMID: 38014024 PMCID: PMC10680755 DOI: 10.1101/2023.11.13.566961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
SARS-CoV-2 variants acquire mutations in spike that promote immune evasion and impact other properties that contribute to viral fitness such as ACE2 receptor binding and cell entry. Knowledge of how mutations affect these spike phenotypes can provide insight into the current and potential future evolution of the virus. Here we use pseudovirus deep mutational scanning to measure how >9,000 mutations across the full XBB.1.5 and BA.2 spikes affect ACE2 binding, cell entry, or escape from human sera. We find that mutations outside the receptor-binding domain (RBD) have meaningfully impacted ACE2 binding during SARS-CoV-2 evolution. We also measure how mutations to the XBB.1.5 spike affect neutralization by serum from individuals who recently had SARS-CoV-2 infections. The strongest serum escape mutations are in the RBD at sites 357, 420, 440, 456, and 473-however, the antigenic impacts of these mutations vary across individuals. We also identify strong escape mutations outside the RBD; however many of them decrease ACE2 binding, suggesting they act by modulating RBD conformation. Notably, the growth rates of human SARS-CoV-2 clades can be explained in substantial part by the measured effects of mutations on spike phenotypes, suggesting our data could enable better prediction of viral evolution.
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5
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Lusvarghi S, Stauft CB, Vassell R, Williams B, Baha H, Wang W, Neerukonda SN, Wang T, Weiss CD. Effects of N-glycan modifications on spike expression, virus infectivity, and neutralization sensitivity in ancestral compared to Omicron SARS-CoV-2 variants. PLoS Pathog 2023; 19:e1011788. [PMID: 37943965 PMCID: PMC10662749 DOI: 10.1371/journal.ppat.1011788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/21/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
The SARS-CoV-2 spike glycoprotein has 22 potential N-linked glycosylation sites per monomer that are highly conserved among diverse variants, but how individual glycans affect virus entry and neutralization of Omicron variants has not been extensively characterized. Here we compared the effects of specific glycan deletions or modifications in the Omicron BA.1 and D614G spikes on spike expression, processing, and incorporation into pseudoviruses, as well as on virus infectivity and neutralization by therapeutic antibodies. We found that loss of potential glycans at spike residues N717 and N801 each conferred a loss of pseudovirus infectivity for Omicron but not for D614G or Delta variants. This decrease in infectivity correlated with decreased spike processing and incorporation into Omicron pseudoviruses. Oligomannose-enriched Omicron pseudoviruses generated in GnTI- cells or in the presence of kifunensine were non-infectious, whereas D614G or Delta pseudoviruses generated under similar conditions remained infectious. Similarly, growth of live (authentic) SARS-CoV-2 in the presence of kifunensine resulted in a greater reduction of titers for the BA.1.1 variant than Delta or D614G variants relative to their respective, untreated controls. Finally, we found that loss of some N-glycans, including N343 and N234, increased the maximum percent neutralization by the class 3 S309 monoclonal antibody against D614G but not BA.1 variants, while these glycan deletions altered the neutralization potency of the class 1 COV2-2196 and Etesevimab monoclonal antibodies without affecting maximum percent neutralization. The maximum neutralization by some antibodies also varied with the glycan composition, with oligomannose-enriched pseudoviruses conferring the highest percent neutralization. These results highlight differences in the interactions between glycans and residues among SARS-CoV-2 variants that can affect spike expression, virus infectivity, and susceptibility of variants to antibody neutralization.
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Affiliation(s)
- Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Charles B. Stauft
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Russell Vassell
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Brittany Williams
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Haseebullah Baha
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Wei Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Sabari Nath Neerukonda
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Tony Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Carol D. Weiss
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring Maryland, United States of America
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6
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Liu L, Casner RG, Guo Y, Wang Q, Iketani S, Chan JFW, Yu J, Dadonaite B, Nair MS, Mohri H, Reddem ER, Yuan S, Poon VKM, Chan CCS, Yuen KY, Sheng Z, Huang Y, Bloom JD, Shapiro L, Ho DD. Antibodies targeting a quaternary site on SARS-CoV-2 spike glycoprotein prevent viral receptor engagement by conformational locking. Immunity 2023; 56:2442-2455.e8. [PMID: 37776849 PMCID: PMC10588992 DOI: 10.1016/j.immuni.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/10/2023] [Accepted: 09/06/2023] [Indexed: 10/02/2023]
Abstract
SARS-CoV-2 continues to evolve, with many variants evading clinically authorized antibodies. To isolate monoclonal antibodies (mAbs) with broadly neutralizing capacities against the virus, we screened serum samples from convalescing COVID-19 patients. We isolated two mAbs, 12-16 and 12-19, which neutralized all SARS-CoV-2 variants tested, including the XBB subvariants, and prevented infection in hamsters challenged with Omicron BA.1 intranasally. Structurally, both antibodies targeted a conserved quaternary epitope located at the interface between the N-terminal domain and subdomain 1, uncovering a site of vulnerability on SARS-CoV-2 spike. These antibodies prevented viral receptor engagement by locking the receptor-binding domain (RBD) of spike in the down conformation, revealing a mechanism of virus neutralization for non-RBD antibodies. Deep mutational scanning showed that SARS-CoV-2 could mutate to escape 12-19, but such mutations are rarely found in circulating viruses. Antibodies 12-16 and 12-19 hold promise as prophylactic agents for immunocompromised persons who do not respond robustly to COVID-19 vaccines.
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Affiliation(s)
- Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Ryan G Casner
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Qian Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Eswar R Reddem
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Vincent Kwok-Man Poon
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Chris Chung-Sing Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lawrence Shapiro
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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7
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Wilks SH, Mühlemann B, Shen X, Türeli S, LeGresley EB, Netzl A, Caniza MA, Chacaltana-Huarcaya JN, Corman VM, Daniell X, Datto MB, Dawood FS, Denny TN, Drosten C, Fouchier RAM, Garcia PJ, Halfmann PJ, Jassem A, Jeworowski LM, Jones TC, Kawaoka Y, Krammer F, McDanal C, Pajon R, Simon V, Stockwell MS, Tang H, van Bakel H, Veguilla V, Webby R, Montefiori DC, Smith DJ. Mapping SARS-CoV-2 antigenic relationships and serological responses. Science 2023; 382:eadj0070. [PMID: 37797027 DOI: 10.1126/science.adj0070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/23/2023] [Indexed: 10/07/2023]
Abstract
During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, multiple variants escaping preexisting immunity emerged, causing reinfections of previously exposed individuals. Here, we used antigenic cartography to analyze patterns of cross-reactivity among 21 variants and 15 groups of human sera obtained after primary infection with 10 different variants or after messenger RNA (mRNA)-1273 or mRNA-1273.351 vaccination. We found antigenic differences among pre-Omicron variants caused by substitutions at spike-protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months after a second dose. We found changes in immunodominance of different spike regions, depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine-strain selection.
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Affiliation(s)
- Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Miguela A Caniza
- Department of Global Pediatric Medicine, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Xiaoju Daniell
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Michael B Datto
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | | | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | | | - Patricia J Garcia
- School of Public Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Agatha Jassem
- BC Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Lara M Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Terry C Jones
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Science, 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
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, Japan
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charlene McDanal
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa S Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, and Department of Population and Family Health, Mailman School of Public Health, New York, NY, USA
| | - Haili Tang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vic Veguilla
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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8
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Mühlemann B, Wilks SH, Baracco L, Bekliz M, Carreño JM, Corman VM, Davis-Gardner ME, Dejnirattisai W, Diamond MS, Douek DC, Drosten C, Eckerle I, Edara VV, Ellis M, Fouchier RAM, Frieman M, Godbole S, Haagmans B, Halfmann PJ, Henry AR, Jones TC, Katzelnick LC, Kawaoka Y, Kimpel J, Krammer F, Lai L, Liu C, Lusvarghi S, Meyer B, Mongkolsapaya J, Montefiori DC, Mykytyn A, Netzl A, Pollett S, Rössler A, Screaton GR, Shen X, Sigal A, Simon V, Subramanian R, Supasa P, Suthar M, Türeli S, Wang W, Weiss CD, Smith DJ. Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559689. [PMID: 37808679 PMCID: PMC10557678 DOI: 10.1101/2023.09.27.559689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The antigenic evolution of SARS-CoV-2 requires ongoing monitoring to judge the immune escape of newly arising variants. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal sera. We compared 18 datasets generated using human, hamster, and mouse sera, and six different neutralization assays. Titer magnitude was lowest in human, intermediate in hamster, and highest in mouse sera. Fold change, immunodominance patterns and antigenic maps were similar among sera. Most assays yielded similar results, except for differences in fold change in cytopathic effect assays. Not enough data was available for conclusively judging mouse sera, but hamster sera were a consistent surrogate for human first-infection sera.
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Affiliation(s)
- Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Lauren Baracco
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Meriem Bekliz
- Department of Medicine, Faculty of Medicine, University of Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, Switzerland
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok 10700, Thailand
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky the Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Venkata-Viswanadh Edara
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Madison Ellis
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Matthew Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bart Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Terry C Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, 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 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lilin Lai
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Benjamin Meyer
- Centre of Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Anna Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Simon Pollett
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rahul Subramanian
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Mehul Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Wei Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Carol D Weiss
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
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Connor RI, Sakharkar M, Rappazzo CG, Kaku CI, Curtis NC, Shin S, Wieland-Alter WF, Weiner JA, Ackerman ME, Walker LM, Lee J, Wright PF. Characteristics and functions of infection-enhancing antibodies to the N-terminal domain of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558444. [PMID: 37786672 PMCID: PMC10541592 DOI: 10.1101/2023.09.19.558444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Characterization of functional antibody responses to the N-terminal domain (NTD) of the SARS-CoV-2 spike (S) protein has included identification of both potent neutralizing activity and putative enhancement of infection. Fcγ-receptor (FcγR)-independent enhancement of SARS-CoV-2 infection mediated by NTD-binding monoclonal antibodies (mAbs) has been observed in vitro , but the functional significance of these antibodies in vivo is not clear. Here we studied 1,213 S-binding mAbs derived from longitudinal sampling of B-cells collected from eight COVID-19 convalescent patients and identified 72 (5.9%) mAbs that enhanced infection in a VSV-SARS-CoV-2-S-Wuhan pseudovirus (PV) assay. The majority (68%) of these mAbs recognized the NTD, were identified in patients with mild and severe disease, and persisted for at least five months post-infection. Enhancement of PV infection by NTD-binding mAbs was not observed using intestinal (Caco-2) and respiratory (Calu-3) epithelial cells as infection targets and was diminished or lost against SARS-CoV-2 variants of concern (VOC). Proteomic deconvolution of the serum antibody repertoire from two of the convalescent subjects identified, for the first time, NTD-binding, infection-enhancing mAbs among the circulating immunoglobulins directly isolated from serum ( i.e ., functionally secreted antibody). Functional analysis of these mAbs demonstrated robust activation of FcγRIIIa associated with antibody binding to recombinant S proteins. Taken together, these findings suggest functionally active NTD-specific mAbs arise frequently during natural infection and can last as major serum clonotypes during convalescence. These antibodies display diverse attributes that include FcγR activation, and may be selected against by mutations in NTD associated with SARS-CoV-2 VOC.
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Dickson A, Geerling E, Stone ET, Hassert M, Steffen TL, Makkena T, Smither M, Schwetye KE, Zhang J, Georges B, Roberts MS, Suschak JJ, Pinto AK, Brien JD. The role of vaccination route with an adenovirus-vectored vaccine in protection, viral control, and transmission in the SARS-CoV-2/K18-hACE2 mouse infection model. Front Immunol 2023; 14:1188392. [PMID: 37662899 PMCID: PMC10469340 DOI: 10.3389/fimmu.2023.1188392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/22/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Vaccination is the most effective mechanism to prevent severe COVID-19. However, breakthrough infections and subsequent transmission of SARS-CoV-2 remain a significant problem. Intranasal vaccination has the potential to be more effective in preventing disease and limiting transmission between individuals as it induces potent responses at mucosal sites. Methods Utilizing a replication-deficient adenovirus serotype 5-vectored vaccine expressing the SARS-CoV-2 RBD (AdCOVID) in homozygous and heterozygous transgenic K18-hACE2, we investigated the impact of the route of administration on vaccine immunogenicity, SARS-CoV-2 transmission, and survival. Results Mice vaccinated with AdCOVID via the intramuscular or intranasal route and subsequently challenged with SARS-CoV-2 showed that animals vaccinated intranasally had improved cellular and mucosal antibody responses. Additionally, intranasally vaccinated animals had significantly better viremic control, and protection from lethal infection compared to intramuscularly vaccinated animals. Notably, in a novel transmission model, intranasal vaccination reduced viral transmission to naïve co-housed mice compared to intramuscular vaccination. Discussion Our data provide convincing evidence for the use of intranasal vaccination in protecting against SARS-CoV-2 infection and transmission.
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Affiliation(s)
- Alexandria Dickson
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO, United States
| | - Elizabeth Geerling
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO, United States
| | - E. Taylor Stone
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO, United States
| | - Mariah Hassert
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO, United States
| | - Tara L. Steffen
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO, United States
| | - Taneesh Makkena
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO, United States
| | - Madeleine Smither
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO, United States
| | - Katherine E. Schwetye
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | | | | | | | | | - Amelia K. Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO, United States
| | - James D. Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO, United States
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11
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Chen C, Liang J, Hu H, Li X, Wang L, Wang Z. Research progress in methods for detecting neutralizing antibodies against SARS-CoV-2. Anal Biochem 2023:115199. [PMID: 37257735 DOI: 10.1016/j.ab.2023.115199] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/13/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
The emergence of SARS-CoV-2 has seriously affected the lives of people worldwide. Clarifying the attenuation rule of SARS-CoV-2 neutralizing antibody (NAb) in vivo is the key to prevent reinfection and recurrence of virus. Currently, the commonly used methods for detecting NAb include virus neutralization tests, pseudovirus neutralization assays, lateral flow immunochromatography and enzyme-linked immunosorbent assays. The detection of NAb not only can be used to evaluate the level of immunity after vaccination or infection but also can provide important theoretical support for virus reinfection, recurrence and vaccine iteration. In this research, the related technologies of SARS-CoV-2 NAb detection were reviewed, aiming to provide better research ideas for SARS-CoV-2 epidemic prevention and control.
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Affiliation(s)
- Chunxia Chen
- Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China
| | - Jiahui Liang
- Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China
| | - Hangzhan Hu
- Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China; Heze Municipal Hospital, Heze, 274000, China
| | - Xiaoquan Li
- Heze Municipal Hospital, Heze, 274000, China
| | - Li Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University, Kaifeng, 475004, China.
| | - Zhizeng Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, China; Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China.
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Deliyannis G, Gherardin NA, Wong CY, Grimley SL, Cooney JP, Redmond SJ, Ellenberg P, Davidson KC, Mordant FL, Smith T, Gillard M, Lopez E, McAuley J, Tan CW, Wang JJ, Zeng W, Littlejohn M, Zhou R, Fuk-Woo Chan J, Chen ZW, Hartwig AE, Bowen R, Mackenzie JM, Vincan E, Torresi J, Kedzierska K, Pouton CW, Gordon TP, Wang LF, Kent SJ, Wheatley AK, Lewin SR, Subbarao K, Chung AW, Pellegrini M, Munro T, Nolan T, Rockman S, Jackson DC, Purcell DFJ, Godfrey DI. Broad immunity to SARS-CoV-2 variants of concern mediated by a SARS-CoV-2 receptor-binding domain protein vaccine. EBioMedicine 2023; 92:104574. [PMID: 37148585 PMCID: PMC10159263 DOI: 10.1016/j.ebiom.2023.104574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/02/2023] [Accepted: 04/01/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 global pandemic has fuelled the generation of vaccines at an unprecedented pace and scale. However, many challenges remain, including: the emergence of vaccine-resistant mutant viruses, vaccine stability during storage and transport, waning vaccine-induced immunity, and concerns about infrequent adverse events associated with existing vaccines. METHODS We report on a protein subunit vaccine comprising the receptor-binding domain (RBD) of the ancestral SARS-CoV-2 spike protein, dimerised with an immunoglobulin IgG1 Fc domain. These were tested in conjunction with three different adjuvants: a TLR2 agonist R4-Pam2Cys, an NKT cell agonist glycolipid α-Galactosylceramide, or MF59® squalene oil-in-water adjuvant, using mice, rats and hamsters. We also developed an RBD-human IgG1 Fc vaccine with an RBD sequence of the immuno-evasive beta variant (N501Y, E484K, K417N). These vaccines were also tested as a heterologous third dose booster in mice, following priming with whole spike vaccine. FINDINGS Each formulation of the RBD-Fc vaccines drove strong neutralising antibody (nAb) responses and provided durable and highly protective immunity against lower and upper airway infection in mouse models of COVID-19. The 'beta variant' RBD vaccine, combined with MF59® adjuvant, induced strong protection in mice against the beta strain as well as the ancestral strain. Furthermore, when used as a heterologous third dose booster, the RBD-Fc vaccines combined with MF59® increased titres of nAb against other variants including alpha, delta, delta+, gamma, lambda, mu, and omicron BA.1, BA.2 and BA.5. INTERPRETATION These results demonstrated that an RBD-Fc protein subunit/MF59® adjuvanted vaccine can induce high levels of broadly reactive nAbs, including when used as a booster following prior immunisation of mice with whole ancestral-strain spike vaccines. This vaccine platform offers a potential approach to augment some of the currently approved vaccines in the face of emerging variants of concern, and it has now entered a phase I clinical trial. FUNDING This work was supported by grants from the Medical Research Future Fund (MRFF) (2005846), The Jack Ma Foundation, National Health and Medical Research Council of Australia (NHMRC; 1113293) and Singapore National Medical Research Council (MOH-COVID19RF-003). Individual researchers were supported by an NHMRC Senior Principal Research Fellowship (1117766), NHMRC Investigator Awards (2008913 and 1173871), Australian Research Council Discovery Early Career Research Award (ARC DECRA; DE210100705) and philanthropic awards from IFM investors and the A2 Milk Company.
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Affiliation(s)
- Georgia Deliyannis
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Nicholas A Gherardin
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Chinn Yi Wong
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Samantha L Grimley
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - James P Cooney
- Walter and Eliza Hall Institute, Infectious Diseases & Immune Defence Division, Parkville, Victoria 3052, Australia
| | - Samuel J Redmond
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Paula Ellenberg
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Kathryn C Davidson
- Walter and Eliza Hall Institute, Infectious Diseases & Immune Defence Division, Parkville, Victoria 3052, Australia
| | - Francesca L Mordant
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Tim Smith
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Marianne Gillard
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Ester Lopez
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Julie McAuley
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Chee Wah Tan
- Duke NUS Medical School, Programme for Emerging Infectious Diseases, Singapore
| | - Jing J Wang
- Department of Immunology, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, Adelaide, South Australia 5042, Australia
| | - Weiguang Zeng
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Mason Littlejohn
- Doherty Directorate, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Runhong Zhou
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Zhi-Wei Chen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Airn E Hartwig
- Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Richard Bowen
- Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Jason M Mackenzie
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Elizabeth Vincan
- Victorian Infectious Diseases Reference Laboratory (VIDRL) at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Joseph Torresi
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Katherine Kedzierska
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Colin W Pouton
- Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia
| | - Tom P Gordon
- Department of Immunology, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, Adelaide, South Australia 5042, Australia
| | - Lin-Fa Wang
- Duke NUS Medical School, Programme for Emerging Infectious Diseases, Singapore
| | - Stephen J Kent
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Adam K Wheatley
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, The Alfred Hospital and Monash University, Melbourne, 3010 Australia
| | - Kanta Subbarao
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; WHO Collaborating Centre for Reference and Research on Influenza at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Amy W Chung
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Marc Pellegrini
- Walter and Eliza Hall Institute, Infectious Diseases & Immune Defence Division, Parkville, Victoria 3052, Australia
| | - Trent Munro
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Terry Nolan
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Vaccine and Immunisation Research Group (VIRGo), Department of Infectious Disease, Peter Doherty Institute for Infection and Immunity, University of Melbourne, and Murdoch Children's Research Institute, Victoria 3010, Australia
| | - Steven Rockman
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Seqirus, Vaccine Innovation Unit, Parkville, Victoria, 3052, Australia
| | - David C Jackson
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Damian F J Purcell
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Dale I Godfrey
- Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.
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Liu L, Casner RG, Guo Y, Wang Q, Iketani S, Chan JFW, Yu J, Dadonaite B, Nair MS, Mohri H, Reddem ER, Yuan S, Poon VKM, Chan CCS, Yuen KY, Sheng Z, Huang Y, Bloom JD, Shapiro L, Ho DD. Antibodies that neutralize all current SARS-CoV-2 variants of concern by conformational locking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.08.536123. [PMID: 37090592 PMCID: PMC10120718 DOI: 10.1101/2023.04.08.536123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
SARS-CoV-2 continues to evolve and evade most existing neutralizing antibodies, including all clinically authorized antibodies. We have isolated and characterized two human monoclonal antibodies, 12-16 and 12-19, which exhibited neutralizing activities against all SARS-CoV-2 variants tested, including BQ.1.1 and XBB.1.5. They also blocked infection in hamsters challenged with Omicron BA.1 intranasally. Structural analyses revealed both antibodies targeted a conserved quaternary epitope located at the interface between the N-terminal domain and subdomain 1, revealing a previously unrecognized site of vulnerability on SARS-CoV-2 spike. These antibodies prevent viral receptor engagement by locking the receptor-binding domain of spike in the down conformation, revealing a novel mechanism of virus neutralization for non-RBD antibodies. Deep mutational scanning showed that SARS-CoV-2 could mutate to escape 12-19, but the responsible mutations are rarely found in circulating viruses. Antibodies 12-16 and 12-19 hold promise as prophylactic agents for immunocompromised persons who do not respond robustly to COVID-19 vaccines.
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14
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Dadonaite B, Crawford KHD, Radford CE, Farrell AG, Yu TC, Hannon WW, Zhou P, Andrabi R, Burton DR, Liu L, Ho DD, Chu HY, Neher RA, Bloom JD. A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike. Cell 2023; 186:1263-1278.e20. [PMID: 36868218 PMCID: PMC9922669 DOI: 10.1016/j.cell.2023.02.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/11/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
A major challenge in understanding SARS-CoV-2 evolution is interpreting the antigenic and functional effects of emerging mutations in the viral spike protein. Here, we describe a deep mutational scanning platform based on non-replicative pseudotyped lentiviruses that directly quantifies how large numbers of spike mutations impact antibody neutralization and pseudovirus infection. We apply this platform to produce libraries of the Omicron BA.1 and Delta spikes. These libraries each contain ∼7,000 distinct amino acid mutations in the context of up to ∼135,000 unique mutation combinations. We use these libraries to map escape mutations from neutralizing antibodies targeting the receptor-binding domain, N-terminal domain, and S2 subunit of spike. Overall, this work establishes a high-throughput and safe approach to measure how ∼105 combinations of mutations affect antibody neutralization and spike-mediated infection. Notably, the platform described here can be extended to the entry proteins of many other viruses.
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Affiliation(s)
- Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Caelan E Radford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - Ariana G Farrell
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Timothy C Yu
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - William W Hannon
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, MIT & Harvard, Cambridge, MA 02139, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Helen Y Chu
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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15
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Walker J, Schnell G, Kerr W. Antiviral Agents against Omicron Subvariant BA.4.6 In Vitro. N Engl J Med 2023; 388:e12. [PMID: 36724341 DOI: 10.1056/nejmc2216611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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16
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Dadonaite B, Crawford KHD, Radford CE, Farrell AG, Yu TC, Hannon WW, Zhou P, Andrabi R, Burton DR, Liu L, Ho DD, Neher RA, Bloom JD. A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.13.512056. [PMID: 36263061 PMCID: PMC9580381 DOI: 10.1101/2022.10.13.512056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A major challenge in understanding SARS-CoV-2 evolution is interpreting the antigenic and functional effects of emerging mutations in the viral spike protein. Here we describe a new deep mutational scanning platform based on non-replicative pseudotyped lentiviruses that directly quantifies how large numbers of spike mutations impact antibody neutralization and pseudovirus infection. We demonstrate this new platform by making libraries of the Omicron BA.1 and Delta spikes. These libraries each contain ~7000 distinct amino-acid mutations in the context of up to ~135,000 unique mutation combinations. We use these libraries to map escape mutations from neutralizing antibodies targeting the receptor binding domain, N-terminal domain, and S2 subunit of spike. Overall, this work establishes a high-throughput and safe approach to measure how ~10 5 combinations of mutations affect antibody neutralization and spike-mediated infection. Notably, the platform described here can be extended to the entry proteins of many other viruses.
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Affiliation(s)
- Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, 98109, USA
| | - Caelan E Radford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, Washington, 98109, USA
| | - Ariana G Farrell
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
| | - Timothy C Yu
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, Washington, 98109, USA
| | - William W Hannon
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, Washington, 98109, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of MGH, MIT & Harvard, Cambridge, MA 02139, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Richard A. Neher
- Biozentrum, University of Basel, Basel, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98195, USA
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