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Zhou J, Sukhova K, Peacock TP, McKay PF, Brown JC, Frise R, Baillon L, Moshe M, Kugathasan R, Shattock RJ, Barclay WS. Omicron breakthrough infections in vaccinated or previously infected hamsters. Proc Natl Acad Sci U S A 2023; 120:e2308655120. [PMID: 37903249 PMCID: PMC10636328 DOI: 10.1073/pnas.2308655120] [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: 05/26/2023] [Accepted: 09/17/2023] [Indexed: 11/01/2023] Open
Abstract
The ongoing SARS-CoV-2 epidemic was marked by the repeated emergence and replacement of "variants" with genetic and phenotypic distance from the ancestral strains, the most recent examples being viruses of the Omicron lineage. Here, we describe a hamster direct contact exposure challenge model to assess protection against reinfection conferred by either vaccination or prior infection. We found that two doses of self-amplifying RNA vaccine based on the ancestral Spike ameliorated weight loss following Delta infection and decreased viral loads but had minimal effect on Omicron BA.1 infection. Prior vaccination followed by Delta or BA.1 breakthrough infections led to a high degree of cross-reactivity to all tested variants, suggesting that repeated exposure to antigenically distinct Spikes, via infection and/or vaccination drives a cross-reactive immune response. Prior infection with ancestral or Alpha variant was partially protective against BA.1 infection, whereas all animals previously infected with Delta and exposed to BA.1 became reinfected, although they shed less virus than BA.1-infected naive hamsters. Hamsters reinfected with BA.1 after prior Delta infection emitted infectious virus into the air, indicating that they could be responsible for onwards airborne transmission. We further tested whether prior infection with BA.1 protected from reinfection with Delta or later Omicron sublineages BA.2, BA.4, or BA.5. BA.1 was protective against BA.2 but not against Delta, BA.4, or BA.5 reinfection. These findings suggest that cohorts whose only immune experience of COVID-19 is Omicron BA.1 infection may be vulnerable to future circulation of reemerged Delta-like derivatives, as well as emerging Omicron sublineages.
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Affiliation(s)
- Jie Zhou
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Thomas P. Peacock
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Paul F. McKay
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Jonathan C. Brown
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Maya Moshe
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Ruthiran Kugathasan
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Robin J. Shattock
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
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2
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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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3
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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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4
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Branche AR, Rouphael NG, Diemert DJ, Falsey AR, Losada C, Baden LR, Frey SE, Whitaker JA, Little SJ, Anderson EJ, Walter EB, Novak RM, Rupp R, Jackson LA, Babu TM, Kottkamp AC, Luetkemeyer AF, Immergluck LC, Presti RM, Bäcker M, Winokur PL, Mahgoub SM, Goepfert PA, Fusco DN, Malkin E, Bethony JM, Walsh EE, Graciaa DS, Samaha H, Sherman AC, Walsh SR, Abate G, Oikonomopoulou Z, El Sahly HM, Martin TCS, Kamidani S, Smith MJ, Ladner BG, Porterfield L, Dunstan M, Wald A, Davis T, Atmar RL, Mulligan MJ, Lyke KE, Posavad CM, Meagher MA, Stephens DS, Neuzil KM, Abebe K, Hill H, Albert J, Telu K, Mu J, Lewis TC, Giebeig LA, Eaton A, Netzl A, Wilks SH, Türeli S, Makhene M, Crandon S, Montefiori DC, Makowski M, Smith DJ, Nayak SU, Roberts PC, Beigel JH. Comparison of bivalent and monovalent SARS-CoV-2 variant vaccines: the phase 2 randomized open-label COVAIL trial. Nat Med 2023; 29:2334-2346. [PMID: 37640860 PMCID: PMC10504073 DOI: 10.1038/s41591-023-02503-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Vaccine protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection wanes over time, requiring updated boosters. In a phase 2, open-label, randomized clinical trial with sequentially enrolled stages at 22 US sites, we assessed safety and immunogenicity of a second boost with monovalent or bivalent variant vaccines from mRNA and protein-based platforms targeting wild-type, Beta, Delta and Omicron BA.1 spike antigens. The primary outcome was pseudovirus neutralization titers at 50% inhibitory dilution (ID50 titers) with 95% confidence intervals against different SARS-CoV-2 strains. The secondary outcome assessed safety by solicited local and systemic adverse events (AEs), unsolicited AEs, serious AEs and AEs of special interest. Boosting with prototype/wild-type vaccines produced numerically lower ID50 titers than any variant-containing vaccine against all variants. Conversely, boosting with a variant vaccine excluding prototype was not associated with decreased neutralization against D614G. Omicron BA.1 or Beta monovalent vaccines were nearly equivalent to Omicron BA.1 + prototype or Beta + prototype bivalent vaccines for neutralization of Beta, Omicron BA.1 and Omicron BA.4/5, although they were lower for contemporaneous Omicron subvariants. Safety was similar across arms and stages and comparable to previous reports. Our study shows that updated vaccines targeting Beta or Omicron BA.1 provide broadly crossprotective neutralizing antibody responses against diverse SARS-CoV-2 variants without sacrificing immunity to the ancestral strain. ClinicalTrials.gov registration: NCT05289037 .
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Affiliation(s)
- Angela R Branche
- Department of Medicine, Division of Infectious Diseases, University of Rochester, Rochester, NY, USA.
| | | | - David J Diemert
- George Washington Vaccine Research Unit, George Washington University, Washington D.C., WA, USA
| | - Ann R Falsey
- Department of Medicine, Division of Infectious Diseases, University of Rochester, Rochester, NY, USA
| | | | - Lindsey R Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sharon E Frey
- Center for Vaccine Development, Saint Louis University, St. Louis, MO, USA
| | - Jennifer A Whitaker
- Departments of Molecular Virology and Microbiology and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Susan J Little
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Evan J Anderson
- Center for Childhood Infections and Vaccines (CCIV) of Children's Healthcare of Atlanta and Emory University Department of Pediatrics, Atlanta, GA, USA
| | - Emmanuel B Walter
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Richard M Novak
- Project WISH, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard Rupp
- University of Texas Medical Branch, Galveston, TX, USA
| | - Lisa A Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Tara M Babu
- Departments of Medicine, Epidemiology and Laboratory Medicine and Pathology, University of Washington, Vaccines and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Angelica C Kottkamp
- NYU VTEU Manhattan Research Clinic, NYU Grossman School of Medicine, New York, NY, USA
| | - Anne F Luetkemeyer
- Zuckerberg San Francisco General, University of California San Francisco, San Francisco, CA, USA
| | - Lilly C Immergluck
- Department of Microbiology, Biochemistry and Immunology, and Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, USA
| | - Rachel M Presti
- Washington University School of Medicine, St. Louis, MO, USA
| | - Martín Bäcker
- NYU VTEU Long Island Research Clinic, NYU Long Island School of Medicine, Mineola, NY, USA
| | | | - Siham M Mahgoub
- Howard University College of Medicine, Howard University Hospital, Washington D.C., WA, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Elissa Malkin
- George Washington Vaccine Research Unit, George Washington University, Washington D.C., WA, USA
| | - Jeffrey M Bethony
- George Washington Vaccine Research Unit, George Washington University, Washington D.C., WA, USA
| | - Edward E Walsh
- Department of Medicine, Division of Infectious Diseases, University of Rochester, Rochester, NY, USA
| | | | - Hady Samaha
- Hope Clinic, Emory University, Decatur, GA, USA
| | - Amy C Sherman
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen R Walsh
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Getahun Abate
- Center for Vaccine Development, Saint Louis University, St. Louis, MO, USA
| | | | - Hana M El Sahly
- Departments of Molecular Virology and Microbiology and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Thomas C S Martin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Satoshi Kamidani
- Center for Childhood Infections and Vaccines (CCIV) of Children's Healthcare of Atlanta and Emory University Department of Pediatrics, Atlanta, GA, USA
| | - Michael J Smith
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | | | - Maya Dunstan
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Anna Wald
- Departments of Medicine, Epidemiology and Laboratory Medicine and Pathology, University of Washington, Vaccines and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tamia Davis
- NYU VTEU Manhattan Research Clinic, NYU Grossman School of Medicine, New York, NY, USA
| | - Robert L Atmar
- Departments of Molecular Virology and Microbiology and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Mark J Mulligan
- NYU VTEU Manhattan Research Clinic, NYU Grossman School of Medicine, New York, NY, USA
| | - Kirsten E Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine Baltimore, Baltimore, MD, USA
| | - Christine M Posavad
- IDCRC Laboratory Operations Unit, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Megan A Meagher
- IDCRC Laboratory Operations Unit, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David S Stephens
- Department of Medicine and Woodruff Health Sciences Center, Emory University, Atlanta, GA, USA
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine Baltimore, Baltimore, MD, USA
| | | | - Heather Hill
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Jim Albert
- The Emmes Company, LLC, Rockville, MD, USA
| | | | - Jinjian Mu
- The Emmes Company, LLC, Rockville, MD, USA
| | - Teri C Lewis
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa A Giebeig
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mamodikoe Makhene
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sonja Crandon
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | | | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Seema U Nayak
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paul C Roberts
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John H Beigel
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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5
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Rössler A, Netzl A, Knabl L, Bante D, Wilks SH, Borena W, von Laer D, Smith DJ, Kimpel J. Characterizing SARS-CoV-2 neutralization profiles after bivalent boosting using antigenic cartography. Nat Commun 2023; 14:5224. [PMID: 37633965 PMCID: PMC10460376 DOI: 10.1038/s41467-023-41049-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023] Open
Abstract
Since emergence of the initial SARS-CoV-2 BA.1, BA.2 and BA.5 variants, Omicron has diversified substantially. Antigenic characterization of these new variants is important to analyze their potential immune escape from population immunity and implications for future vaccine composition. Here, we describe an antigenic map based on human single-exposure sera and live-virus isolates that includes a broad selection of recently emerged Omicron variants such as BA.2.75, BF.7, BQ, XBB and XBF variants. Recent Omicron variants clustered around BA.1 and BA.5 with some variants further extending the antigenic space. Based on this antigenic map we constructed antibody landscapes to describe neutralization profiles after booster immunization with bivalent mRNA vaccines based on ancestral virus and either BA.1 or BA.4/5. Immune escape of BA.2.75, BQ, XBB and XBF variants was also evident in bivalently boosted individuals, however, cross-neutralization was improved for those with hybrid immunity. Our results indicate that future vaccine updates are needed to induce cross-neutralizing antibodies against currently circulating variants.
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Affiliation(s)
- Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Antonia Netzl
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, Hauptplatz 4, 6511, Zams, Austria
| | - David Bante
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Samuel H Wilks
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Wegene Borena
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Dorothee von Laer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Derek J Smith
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK.
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria.
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6
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Wagh K, Shen X, Theiler J, Girard B, Marshall JC, Montefiori DC, Korber B. Mutational basis of serum cross-neutralization profiles elicited by infection or vaccination with SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.13.553144. [PMID: 37645950 PMCID: PMC10461964 DOI: 10.1101/2023.08.13.553144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
A series of SARS-CoV-2 variants emerged during the pandemic under selection for neutralization resistance. Convalescent and vaccinated sera show consistently different cross-neutralization profiles depending on infecting or vaccine variants. To understand the basis of this heterogeneity, we modeled serum cross-neutralization titers for 165 sera after infection or vaccination with historically prominent lineages tested against 18 variant pseudoviruses. Cross-neutralization profiles were well captured by models incorporating autologous neutralizing titers and combinations of specific shared and differing mutations between the infecting/vaccine variants and pseudoviruses. Infecting/vaccine variant-specific models identified mutations that significantly impacted cross-neutralization and quantified their relative contributions. Unified models that explained cross-neutralization profiles across all infecting and vaccine variants provided accurate predictions of holdout neutralization data comprising untested variants as infecting or vaccine variants, and as test pseudoviruses. Finally, comparative modeling of 2-dose versus 3-dose mRNA-1273 vaccine data revealed that the third dose overcame key resistance mutations to improve neutralization breadth. HIGHLIGHTS Modeled SARS-CoV-2 cross-neutralization using mutations at key sitesIdentified resistance mutations and quantified relative impactAccurately predicted holdout variant and convalescent/vaccine sera neutralizationShowed that the third dose of mRNA-1273 vaccination overcomes resistance mutations.
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7
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Springer DN, Bauer M, Medits I, Camp JV, Aberle SW, Burtscher C, Höltl E, Weseslindtner L, Stiasny K, Aberle JH. Bivalent COVID-19 mRNA booster vaccination (BA.1 or BA.4/BA.5) increases neutralization of matched Omicron variants. NPJ Vaccines 2023; 8:110. [PMID: 37542025 PMCID: PMC10403593 DOI: 10.1038/s41541-023-00708-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/12/2023] [Indexed: 08/06/2023] Open
Abstract
We report SARS-CoV-2 neutralizing antibody titers in sera of triple-vaccinated individuals who received a booster dose of an original monovalent or a bivalent BA.1- or BA.4/BA.5-adapted vaccine or had a breakthrough infection with Omicron variants BA.1, BA.2 or BA.4/BA.5. A bivalent BA.4/BA.5 booster or Omicron-breakthrough infection induced increased Omicron-neutralization titers compared with the monovalent booster. The XBB.1.5 variant effectively evaded neutralizing-antibody responses elicited by current vaccines and/or infection with previous variants.
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Affiliation(s)
- David N Springer
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Michael Bauer
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Iris Medits
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Jeremy V Camp
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | | | - Eva Höltl
- Health Center Erste Bank, Erste Bank, Vienna, Austria
- Center for Public Health, Medical University of Vienna, Vienna, Austria
| | | | - Karin Stiasny
- Center for Virology, Medical University of Vienna, Vienna, Austria.
| | - Judith H Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria.
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8
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Harthaller T, Falkensammer B, Bante D, Huber M, Schmitt M, Benainouna H, Rössler A, Fleischer V, von Laer D, Kimpel J, Würzner R, Borena W. Retained avidity despite reduced cross-binding and cross-neutralizing antibody levels to Omicron after SARS-COV-2 wild-type infection or mRNA double vaccination. Front Immunol 2023; 14:1196988. [PMID: 37545492 PMCID: PMC10401431 DOI: 10.3389/fimmu.2023.1196988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction The rapid evolution of SARS-CoV-2 has posed a challenge to long-lasting immunity against the novel virus. Apart from neutralizing function, binding antibodies induced by vaccination or infection play an important role in containing the infection. Methods To determine the proportion of wild-type (WT)-generated antibodies recognizant of more recent variants, plasma samples from either SARS-CoV-2 WT-infected (n = 336) or double-mRNA (Comirnaty)-vaccinated individuals (n = 354, age and sex matched to the convalescent group) were analyzed for binding antibody capacity against the S1 protein of the BA.1 omicron variant. Results Overall, 38.59% (95% CI, 37.01- 40.20) of WT-generated antibodies recognized Omicron BA.1 S1 protein [28.83% (95% CI, 26.73-30.91) after infection and 43.46% (95% CI, 41.61-45.31) after vaccination; p < 0.001]. Although the proportion of WT-generated binding and neutralizing antibodies also binding to BA.1 is substantially reduced, the avidity of the remaining antibodies against the Omicron variant was non-inferior to that of the ancestral virus: Omicron: 39.7% (95% CI: 38.1-41.3) as compared to the avidity to WT: 27.0% (95% CI, 25.5-28.4), respectively (p < 0.001). Furthermore, we noticed a modestly yet statistically significant higher avidity toward the Omicron epitopes among the vaccinated group (42.2%; 95% CI, 40.51-43.94) as compared to the convalescent counterparts (36.4%; 95% CI, 33.42-38.76) (p = 0.003), even after adjusting for antibody concentration. Discussion Our results suggest that an aspect of functional immunity against the novel strain was considerably retained after WT contact, speculatively counteracting the impact of immune evasion toward neutralization of the strain. Higher antibody levels and cross-binding capacity among vaccinated individuals suggest an advantage of repeated exposure in generating robust immunity.
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Affiliation(s)
- Teresa Harthaller
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Barbara Falkensammer
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - David Bante
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Maria Huber
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Melanie Schmitt
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Habib Benainouna
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Annika Rössler
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Verena Fleischer
- Department of Hygiene, Microbiology and Public Health, Institute of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - Dorothee von Laer
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Janine Kimpel
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Reinhard Würzner
- Department of Hygiene, Microbiology and Public Health, Institute of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - Wegene Borena
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
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9
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Mykytyn AZ, Rosu ME, Kok A, Rissmann M, van Amerongen G, Geurtsvankessel C, de Vries RD, Munnink BBO, Smith DJ, Koopmans MPG, Lamers MM, Fouchier RAM, Haagmans BL. Antigenic mapping of emerging SARS-CoV-2 omicron variants BM.1.1.1, BQ.1.1, and XBB.1. THE LANCET. MICROBE 2023; 4:e294-e295. [PMID: 36657480 PMCID: PMC9842387 DOI: 10.1016/s2666-5247(22)00384-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Miruna E Rosu
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Adinda Kok
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Melanie Rissmann
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | | | | | - Rory D de Vries
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Bas B Oude Munnink
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Marion P G Koopmans
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Mart M Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands.
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10
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Nair MS, Ribeiro RM, Wang M, Bowen AD, Liu L, Guo Y, Chang JY, Wang P, Sheng Z, Sobieszczyk ME, Perelson AS, Huang Y, Ho DD. Changes in serum-neutralizing antibody potency and breadth post-SARS-CoV-2 mRNA vaccine boost. iScience 2023; 26:106345. [PMID: 36925721 PMCID: PMC9987605 DOI: 10.1016/j.isci.2023.106345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
A better understanding of the durability and breadth of serum-neutralizing antibody responses against multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants elicited by COVID-19 vaccines is crucial in addressing the current pandemic. In this study, we quantified the decay of serum neutralization antibodies (nAbs) after second and third doses of the original COVID-19 mRNA vaccine. Using an authentic virus-neutralization assay, we found that decay half-lives of WA1- and Delta-nAbs were both ∼60 days after second and third vaccine dose. Unexpectedly, the durability of serum antibodies that neutralize three different Omicron subvariants (BA.1.1, BA.5, BA.2.12.1) was substantially better, with half-lives of ≥6 months. A booster dose of the original COVID-19 vaccine was also found to broaden antibody responses against SARS-CoV and four other sarbecoviruses, in addition to multiple SARS-CoV-2 strains. These findings suggest that repeated vaccinations with the COVID-19 vaccine may confer a degree of protection against future spillover of sarbecoviruses from animal reservoirs.
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Affiliation(s)
- Manoj S. Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Anthony D. Bowen
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, 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
| | - Jennifer Y. Chang
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Magdalena E. Sobieszczyk
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, 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 Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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11
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Grant R, Sacks JA, Abraham P, Chunsuttiwat S, Cohen C, Figueroa JP, Fleming T, Fine P, Goldblatt D, Hasegawa H, MacIntrye CR, Memish ZA, Miller E, Nishioka S, Sall AA, Sow S, Tomori O, Wang Y, Van Kerkhove MD, Wambo MA, Cohen HA, Mesfin S, Otieno JR, Subissi L, Briand S, Wentworth DE, Subbarao K. When to update COVID-19 vaccine composition. Nat Med 2023; 29:776-780. [PMID: 36807683 DOI: 10.1038/s41591-023-02220-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Rebecca Grant
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Jilian A Sacks
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Priya Abraham
- Indian Council of Medical Research - National Institute of Virology, Pune, India
| | | | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Thomas Fleming
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Paul Fine
- London School of Hygiene and Tropical Medicine, London, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Hideki Hasegawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - C Raina MacIntrye
- Biosecurity Program, The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Ziad A Memish
- Research and Innovation Centre, King Saud Medical City, Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth Miller
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Samba Sow
- Centre for Vaccine Development, Ministry of Health, Bamako, Mali
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
| | - Youchun Wang
- Institute for Biological Product Control, National Institutes for Food and Drug Control, Beijing, China
| | - Maria D Van Kerkhove
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Marie-Ange Wambo
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Homa Attar Cohen
- Department of Acute Response Coordination, World Health Organization, Geneva, Switzerland
| | - Samuel Mesfin
- Department of Acute Response Coordination, World Health Organization, Geneva, Switzerland
| | - James R Otieno
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Lorenzo Subissi
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Sylvie Briand
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland.
| | - David E Wentworth
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
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12
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Wang Q, Iketani S, Li Z, Liu L, Guo Y, Huang Y, Bowen AD, Liu M, Wang M, Yu J, Valdez R, Lauring AS, Sheng Z, Wang HH, Gordon A, Liu L, Ho DD. Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell 2023; 186:279-286.e8. [PMID: 36580913 PMCID: PMC9747694 DOI: 10.1016/j.cell.2022.12.018] [Citation(s) in RCA: 405] [Impact Index Per Article: 405.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022]
Abstract
The BQ and XBB subvariants of SARS-CoV-2 Omicron are now rapidly expanding, possibly due to altered antibody evasion properties deriving from their additional spike mutations. Here, we report that neutralization of BQ.1, BQ.1.1, XBB, and XBB.1 by sera from vaccinees and infected persons was markedly impaired, including sera from individuals boosted with a WA1/BA.5 bivalent mRNA vaccine. Titers against BQ and XBB subvariants were lower by 13- to 81-fold and 66- to 155-fold, respectively, far beyond what had been observed to date. Monoclonal antibodies capable of neutralizing the original Omicron variant were largely inactive against these new subvariants, and the responsible individual spike mutations were identified. These subvariants were found to have similar ACE2-binding affinities as their predecessors. Together, our findings indicate that BQ and XBB subvariants present serious threats to current COVID-19 vaccines, render inactive all authorized antibodies, and may have gained dominance in the population because of their advantage in evading antibodies.
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Affiliation(s)
- Qian Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zhiteng Li
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Liyuan Liu
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yiming Huang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Anthony D Bowen
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Michael Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Riccardo Valdez
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 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; Division of Infectious Diseases, Department of Medicine, 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, USA.
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13
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Aguilar-Bretones M, Fouchier RA, Koopmans MP, van Nierop GP. Impact of antigenic evolution and original antigenic sin on SARS-CoV-2 immunity. J Clin Invest 2023; 133:e162192. [PMID: 36594464 PMCID: PMC9797340 DOI: 10.1172/jci162192] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and vaccinations targeting the spike protein (S) offer protective immunity against coronavirus disease 2019 (COVID-19). This immunity may further be shaped by cross-reactivity with common cold coronaviruses. Mutations arising in S that are associated with altered intrinsic virus properties and immune escape result in the continued circulation of SARS-CoV-2 variants. Potentially, vaccine updates will be required to protect against future variants of concern, as for influenza. To offer potent protection against future variants, these second-generation vaccines may need to redirect immunity to epitopes associated with immune escape and not merely boost immunity toward conserved domains in preimmune individuals. For influenza, efficacy of repeated vaccination is hampered by original antigenic sin, an attribute of immune memory that leads to greater induction of antibodies specific to the first-encountered variant of an immunogen compared with subsequent variants. In this Review, recent findings on original antigenic sin are discussed in the context of SARS-CoV-2 evolution. Unanswered questions and future directions are highlighted, with an emphasis on the impact on disease outcome and vaccine design.
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14
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Brinkkemper M, Veth TS, Brouwer PJ, Turner H, Poniman M, Burger JA, Bouhuijs JH, Olijhoek W, Bontjer I, Snitselaar JL, Caniels TG, van der Linden CA, Ravichandran R, Villaudy J, van der Velden YU, Sliepen K, van Gils MJ, Ward AB, King NP, Heck AJ, Sanders RW. Co-display of diverse spike proteins on nanoparticles broadens sarbecovirus neutralizing antibody responses. iScience 2022; 25:105649. [PMID: 36439375 PMCID: PMC9678814 DOI: 10.1016/j.isci.2022.105649] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/07/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses continuous challenges in combating the virus. Here, we describe vaccination strategies to broaden SARS-CoV-2 and sarbecovirus immunity by combining spike proteins based on different viruses or viral strains displayed on two-component protein nanoparticles. First, we combined spike proteins based on ancestral and Beta SARS-CoV-2 strains to broaden SARS-CoV-2 immune responses. Inclusion of Beta spike improved neutralizing antibody responses against SARS-CoV-2 Beta, Gamma, and Omicron BA.1 and BA.4/5. A third vaccination with ancestral SARS-CoV-2 spike also improved cross-neutralizing antibody responses against SARS-CoV-2 variants, in particular against the Omicron sublineages. Second, we combined SARS-CoV and SARS-CoV-2 spike proteins to broaden sarbecovirus immune responses. Adding SARS-CoV spike to a SARS-CoV-2 spike vaccine improved neutralizing responses against SARS-CoV and SARS-like bat sarbecoviruses SHC014 and WIV1. These results should inform the development of broadly active SARS-CoV-2 and pan-sarbecovirus vaccines and highlight the versatility of two-component nanoparticles for displaying diverse antigens.
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Affiliation(s)
- Mitch Brinkkemper
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tim S. Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Philip J.M. Brouwer
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hannah Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meliawati Poniman
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Judith A. Burger
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joey H. Bouhuijs
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Wouter Olijhoek
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Jonne L. Snitselaar
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tom G. Caniels
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Cynthia A. van der Linden
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Julien Villaudy
- J&S Preclinical Solutions, 5345 RR, OSS, the Netherlands
- AIMM Therapeutics BV, 1105 BA Amsterdam, the Netherlands
| | - Yme U. van der Velden
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Kwinten Sliepen
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Marit J. van Gils
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Rogier W. Sanders
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
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15
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Hauser BM, Feldman J, Sangesland M, Ronsard L, St Denis KJ, Sheehan ML, Cao Y, Boucau J, Windsor IW, Cheng AH, Vu ML, Cardoso MR, Kannegieter T, Balazs AB, Lingwood D, Garcia-Beltran WF, Schmidt AG. Cross-reactive SARS-CoV-2 epitope targeted across donors informs immunogen design. Cell Rep Med 2022; 3:100834. [PMID: 36423634 PMCID: PMC9663748 DOI: 10.1016/j.xcrm.2022.100834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/07/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
The emergence of the antigenically distinct and highly transmissible Omicron variant highlights the possibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune escape due to viral evolution. This continued evolution, along with the possible introduction of new sarbecoviruses from zoonotic reservoirs, may evade host immunity elicited by current SARS-CoV-2 vaccines. Identifying cross-reactive antibodies and defining their epitope(s) can provide templates for rational immunogen design strategies for next-generation vaccines. Here, we characterize the receptor-binding-domain-directed, cross-reactive humoral repertoire across 10 human vaccinated donors. We identify cross-reactive antibodies from diverse gene rearrangements targeting two conserved receptor-binding domain epitopes. An engineered immunogen enriches antibody responses to one of these conserved epitopes in mice with pre-existing SARS-CoV-2 immunity; elicited responses neutralize SARS-CoV-2, variants, and related sarbecoviruses. These data show how immune focusing to a conserved epitope targeted by human cross-reactive antibodies may guide pan-sarbecovirus vaccine development, providing a template for identifying such epitopes and translating to immunogen design.
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Affiliation(s)
- Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kerri J St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Maegan L Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Yi Cao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ian W Windsor
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Agnes H Cheng
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mya L Vu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Ty Kannegieter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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16
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Wang W, Lusvarghi S, Subramanian R, Epsi NJ, Wang R, Goguet E, Fries AC, Echegaray F, Vassell R, Coggins SA, Richard SA, Lindholm DA, Mende K, Ewers EC, Larson DT, Colombo RE, Colombo CJ, Joseph JO, Rozman JS, Smith A, Lalani T, Berjohn CM, Maves RC, Jones MU, Mody R, Huprikar N, Livezey J, Saunders D, Hollis-Perry M, Wang G, Ganesan A, Simons MP, Broder CC, Tribble DR, Laing ED, Agan BK, Burgess TH, Mitre E, Pollett SD, Katzelnick LC, Weiss CD. Antigenic cartography of well-characterized human sera shows SARS-CoV-2 neutralization differences based on infection and vaccination history. Cell Host Microbe 2022; 30:1745-1758.e7. [PMID: 36356586 PMCID: PMC9584854 DOI: 10.1016/j.chom.2022.10.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/31/2022] [Accepted: 10/18/2022] [Indexed: 01/26/2023]
Abstract
The rapid emergence of SARS-CoV-2 variants challenges vaccination strategies. Here, we collected 201 serum samples from persons with a single infection or multiple vaccine exposures, or both. We measured their neutralization titers against 15 natural variants and 7 variants with engineered spike mutations and analyzed antigenic diversity. Antigenic maps of primary infection sera showed that Omicron sublineages BA.2, BA.4/BA.5, and BA.2.12.1 are distinct from BA.1 and more similar to Beta/Gamma/Mu variants. Three mRNA COVID-19 vaccinations increased neutralization of BA.1 more than BA.4/BA.5 or BA.2.12.1. BA.1 post-vaccination infection elicited higher neutralization titers to all variants than three vaccinations alone, although with less neutralization to BA.2.12.1 and BA.4/BA.5. Those with BA.1 infection after two or three vaccinations had similar neutralization titer magnitude and antigenic recognition. Accounting for antigenic differences among variants when interpreting neutralization titers can aid the understanding of complex patterns in humoral immunity that informs the selection of future COVID-19 vaccine strains.
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Affiliation(s)
- Wei Wang
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Sabrina Lusvarghi
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 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
| | - Nusrat J Epsi
- Infectious Diseases 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
| | - Richard Wang
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Emilie Goguet
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Anthony C Fries
- U.S. Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, Fairborn, OH, USA
| | - Fernando Echegaray
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Russell Vassell
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Si'Ana A Coggins
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Stephanie A Richard
- Infectious Diseases 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
| | - David A Lindholm
- Brooke Army Medical Center, Joint Base San Antonio-Fort Sam Houston, San Antonio, TX, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Katrin Mende
- Infectious Diseases 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
| | - Evan C Ewers
- Fort Belvoir Community Hospital, Fort Belvoir, VA, USA
| | | | - Rhonda E Colombo
- Infectious Diseases 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; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Madigan Army Medical Center, Tacoma, WA, USA
| | - Christopher J Colombo
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Madigan Army Medical Center, Tacoma, WA, USA
| | - Janet O Joseph
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julia S Rozman
- Infectious Diseases 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
| | - Alfred Smith
- Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Tahaniyat Lalani
- Infectious Diseases 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; Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Catherine M Berjohn
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Naval Medical Center San Diego, San Diego, CA, USA
| | - Ryan C Maves
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Section of Infectious Diseases, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | | | - Rupal Mody
- William Beaumont Army Medical Center, El Paso, TX, USA
| | - Nikhil Huprikar
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Jeffrey Livezey
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - David Saunders
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Monique Hollis-Perry
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, USA
| | - Gregory Wang
- General Dynamics Information Technology, Falls Church, VA, USA
| | - Anuradha Ganesan
- Infectious Diseases 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; Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Mark P Simons
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - David R Tribble
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Brian K Agan
- Infectious Diseases 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
| | - Timothy H Burgess
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Simon D Pollett
- Infectious Diseases 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.
| | - 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, USA.
| | - Carol D Weiss
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
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17
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Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones. Nat Commun 2022; 13:7733. [PMID: 36517467 PMCID: PMC9748393 DOI: 10.1038/s41467-022-35456-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. However, the basis for such cross-protection at the molecular level is incompletely understood. Here, we characterized the repertoire and epitope specificity of antibodies elicited by infection with the Beta, Gamma and WA1 ancestral variants and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a method to obtain immunoglobulin sequences with concurrent rapid production and functional assessment of monoclonal antibodies from hundreds of single B cells sorted by flow cytometry. Infection with any variant elicited similar cross-binding antibody responses exhibiting a conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may account for the continued efficacy of vaccines based on a single ancestral variant.
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18
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Rössler A, Netzl A, Knabl L, Schäfer H, Wilks SH, Bante D, Falkensammer B, Borena W, von Laer D, Smith DJ, Kimpel J. BA.2 and BA.5 omicron differ immunologically from both BA.1 omicron and pre-omicron variants. Nat Commun 2022; 13:7701. [PMID: 36513653 PMCID: PMC9745279 DOI: 10.1038/s41467-022-35312-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Several studies have shown that SARS-CoV-2 BA.1 omicron is an immune escape variant. Meanwhile, however, omicron BA.2 and BA.5 became dominant in many countries and replaced BA.1. As both have several mutations compared to BA.1, we analyzed whether BA.2 and BA.5 show further immune escape relative to BA.1. Here, we characterized neutralization profiles against the BA.2 and BA.5 omicron sub-variants in plasma samples from individuals with different history of exposures to infection/vaccination and found that unvaccinated individuals after a single exposure to BA.2 had limited cross-neutralizing antibodies to pre-omicron variants and to BA.1. Consequently, our antigenic map including all Variants of Concern and BA.1, BA.2 and BA.5 omicron sub-variants, showed that all omicron sub-variants are distinct to pre-omicron variants, but that the three omicron variants are also antigenically distinct from each other. The antibody landscapes illustrate that cross-neutralizing antibodies against the current antigenic space, as described in our maps, are generated only after three or more exposures to antigenically close variants but also after two exposures to antigenically distant variants. Here, we describe the antigenic space inhabited by the relevant SARS-CoV-2 variants, the understanding of which will have important implications for further vaccine strain adaptations.
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Affiliation(s)
- Annika Rössler
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Antonia Netzl
- grid.5335.00000000121885934University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, Hauptplatz 4, 6511 Zams, Austria
| | - Helena Schäfer
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Samuel H. Wilks
- grid.5335.00000000121885934University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - David Bante
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Barbara Falkensammer
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Wegene Borena
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Dorothee von Laer
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Derek J. Smith
- grid.5335.00000000121885934University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Janine Kimpel
- grid.5361.10000 0000 8853 2677Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
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19
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Fischer C, Maponga TG, Yadouleton A, Abílio N, Aboce E, Adewumi P, Afonso P, Akorli J, Andriamandimby SF, Anga L, Ashong Y, Beloufa MA, Bensalem A, Birtles R, Boumba ALM, Bwanga F, Chaponda M, Chibukira P, Chico RM, Chileshe J, Chongwe G, Cissé A, D'Alessandro U, de Lamballerie XN, de Morais JFM, Derrar F, Dia N, Diarra Y, Doumbia L, Drosten C, Dussart P, Echodu R, Eggers Y, Eloualid A, Faye O, Feldt T, Frühauf A, Halatoko A, Ilouga PV, Ismael N, Jambou R, Jarju S, Kamprad A, Katowa B, Kayiwa J, King'wara L, Koita O, Lacoste V, Lagare A, Landt O, Lekana-Douki SE, Lekana-Douki JB, Iipumbu E, Loemba H, Lutwama J, Mamadou S, Maman I, Manyisa B, Martinez PA, Matoba J, Mhuulu L, Moreira-Soto A, Mwangi J, N Dilimabaka N, Nassuna CA, Ndiath MO, Nepolo E, Njouom R, Nourlil J, Nyanjom SG, Odari EO, Okeng A, Ouoba JB, Owusu M, Owusu Donkor I, Phadu KK, Phillips RO, Preiser W, Ruhanya V, Salah F, Salifou S, Sall AA, Sylverken AA, Tagnouokam-Ngoupo PA, Tarnagda Z, Tchikaya FO, Tufa TB, Drexler JF. RETRACTED: Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa. Science 2022; 378:eadd8737. [PMID: 36454863 DOI: 10.1126/science.add8737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.
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Affiliation(s)
- Carlo Fischer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Tongai Gibson Maponga
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Anges Yadouleton
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Nuro Abílio
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Praise Adewumi
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Pedro Afonso
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Jewelna Akorli
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Latifa Anga
- Institut Pasteur du Maroc, Casablanca, Morocco
| | - Yvonne Ashong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Aicha Bensalem
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Richard Birtles
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Anicet Luc Magloire Boumba
- Faculty of Health Sciences, Marien Ngouabi University, Pointe-Noire, Congo.,Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo
| | - Freddie Bwanga
- MBN Clinical Laboratories, Kampala, Uganda.,Makerere University College of Health Sciences, Kampala, Uganda
| | - Mike Chaponda
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Paradzai Chibukira
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | - Justin Chileshe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Gershom Chongwe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Assana Cissé
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | - Umberto D'Alessandro
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | | | | | - Fawzi Derrar
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Ndongo Dia
- Institut Pasteur de Dakar (IPD), Dakar, Senegal
| | - Youssouf Diarra
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Lassina Doumbia
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Richard Echodu
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Yannik Eggers
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Torsten Feldt
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Frühauf
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | | | | | | | - Ronan Jambou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Sheikh Jarju
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Antje Kamprad
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Ben Katowa
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Leonard King'wara
- National Public Health Reference Laboratory, Ministry of Health, Nairobi, Kenya
| | - Ousmane Koita
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | | | - Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | | | | | - Etuhole Iipumbu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Hugues Loemba
- Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo.,Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Santou Mamadou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | - Brendon Manyisa
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | - Pedro A Martinez
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Japhet Matoba
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Lusia Mhuulu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Andres Moreira-Soto
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Judy Mwangi
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Nadine N Dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Mamadou Ousmane Ndiath
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Emmanuel Nepolo
- School of Medicine, University of Namibia, Windhoek, Namibia
| | | | | | - Steven Ger Nyanjom
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eddy Okoth Odari
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | | | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Irene Owusu Donkor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karabo Kristen Phadu
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.,National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa
| | - Vurayai Ruhanya
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | | | | | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.,Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana
| | | | - Zekiba Tarnagda
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | | | - Tafese Beyene Tufa
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Felix Drexler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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20
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Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters. Nat Commun 2022; 13:6644. [PMID: 36333374 PMCID: PMC9636174 DOI: 10.1038/s41467-022-34439-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Current COVID-19 vaccines are based on prototypic spike sequences from ancestral 2019 SARS-CoV-2 strains. However, the ongoing pandemic is fueled by variants of concern (VOC) escaping vaccine-mediated protection. Here we demonstrate how immunization in hamsters using prototypic spike expressed from yellow fever 17D (YF17D) as vector blocks ancestral virus (B lineage) and VOC Alpha (B.1.1.7) yet fails to fully protect from Beta (B.1.351). However, the same YF17D vectored vaccine candidate with an evolved antigen induced considerably improved neutralizing antibody responses against VOCs Beta, Gamma (P.1) and the recently predominant Omicron (B.1.1.529), while maintaining immunogenicity against ancestral virus and VOC Delta (B.1.617.2). Thus vaccinated animals resisted challenge by all VOCs, including vigorous high titre exposure to the most difficult to cover Beta, Delta and Omicron variants, eliminating detectable virus and markedly improving lung pathology. Finally, vaccinated hamsters did not transmit Delta variant to non-vaccinated cage mates. Overall, our data illustrate how current first-generation COVID-19 vaccines may need to be updated to maintain efficacy against emerging VOCs and their spread at community level.
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21
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Babady NE, Burckhardt RM, Krammer F, Moore PL, Enquist LW. Building a Resilient Scientific Network for COVID-19 and Beyond. mBio 2022; 13:e0222322. [PMID: 36125317 PMCID: PMC9600431 DOI: 10.1128/mbio.02223-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitates that the global scientific community monitor, assess, and respond to the evolving coronavirus disease (COVID-19) pandemic. But the current reactive approach to emerging variants is ill-suited to address the quickly evolving and ever-changing pandemic. To tackle this challenge, investments in pathogen surveillance, systematic variant characterization, and data infrastructure and sharing across public and private sectors will be critical for planning proactive responses to emerging variants. Additionally, an emphasis on incorporating real-time variant identification in point-of-care diagnostics can help inform patient treatment. Active approaches to understand and identify "immunity gaps" can inform design of future vaccines, therapeutics, and diagnostics that will be more resistant to novel variants. Approaches where the scientific community actively plans for and anticipates changes to infectious diseases will result in a more resilient system, capable of adapting to evolving pathogens quickly and effectively.
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Affiliation(s)
- N. Esther Babady
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Penny L. Moore
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa, University of Kwazulu-Natal, Durban, South Africa
| | - Lynn W. Enquist
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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22
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Mykytyn AZ, Rissmann M, Kok A, Rosu ME, Schipper D, Breugem TI, van den Doel PB, Chandler F, Bestebroer T, de Wit M, van Royen ME, Molenkamp R, Oude Munnink BB, de Vries RD, GeurtsvanKessel C, Smith DJ, Koopmans MPG, Rockx B, Lamers MM, Fouchier R, Haagmans BL. Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct. Sci Immunol 2022; 7:eabq4450. [PMID: 35737747 PMCID: PMC9273038 DOI: 10.1126/sciimmunol.abq4450] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/14/2022] [Indexed: 12/16/2022]
Abstract
The emergence and rapid spread of SARS-CoV-2 variants may affect vaccine efficacy substantially. The Omicron variant termed BA.2, which differs substantially from BA.1 based on genetic sequence, is currently replacing BA.1 in several countries, but its antigenic characteristics have not yet been assessed. Here, we used antigenic cartography to quantify and visualize antigenic differences between early SARS-CoV-2 variants (614G, Alpha, Beta, Gamma, Zeta, Delta, and Mu) using hamster antisera obtained after primary infection. We first verified that the choice of the cell line for the neutralization assay did not affect the topology of the map substantially. Antigenic maps generated using pseudo-typed SARS-CoV-2 on the widely used VeroE6 cell line and the human airway cell line Calu-3 generated similar maps. Maps made using authentic SARS-CoV-2 on Calu-3 cells also closely resembled those generated with pseudo-typed viruses. The antigenic maps revealed a central cluster of SARS-CoV-2 variants, which grouped on the basis of mutual spike mutations. Whereas these early variants are antigenically similar, clustering relatively close to each other in antigenic space, Omicron BA.1 and BA.2 have evolved as two distinct antigenic outliers. Our data show that BA.1 and BA.2 both escape vaccine-induced antibody responses as a result of different antigenic characteristics. Thus, antigenic cartography could be used to assess antigenic properties of future SARS-CoV-2 variants of concern that emerge and to decide on the composition of novel spike-based (booster) vaccines.
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Affiliation(s)
- Anna Z. Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Melanie Rissmann
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Adinda Kok
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Miruna E. Rosu
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Tim I. Breugem
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Felicity Chandler
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Theo Bestebroer
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Maurice de Wit
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Martin E. van Royen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Richard Molenkamp
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Rory D. de Vries
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | | | - Barry Rockx
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Mart M. Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ron Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Bart L. Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
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23
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Moyo-Gwete T, Madzivhandila M, Mkhize NN, Kgagudi P, Ayres F, Lambson BE, Manamela NP, Richardson SI, Makhado Z, van der Mescht MA, de Beer Z, de Villiers TR, Burgers WA, Ntusi NAB, Rossouw T, Ueckermann V, Boswell MT, Moore PL. Shared N417-Dependent Epitope on the SARS-CoV-2 Omicron, Beta, and Delta Plus Variants. J Virol 2022; 96:e0055822. [PMID: 35867572 PMCID: PMC9364786 DOI: 10.1128/jvi.00558-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, several variants of concern (VOCs) have arisen which are defined by multiple mutations in their spike proteins. These VOCs have shown variable escape from antibody responses and have been shown to trigger qualitatively different antibody responses during infection. By studying plasma from individuals infected with either the original D614G, Beta, or Delta variants, we showed that the Beta and Delta variants elicit antibody responses that are overall more cross-reactive than those triggered by D614G. Patterns of cross-reactivity varied, and the Beta and Delta variants did not elicit cross-reactive responses to each other. However, Beta-elicited plasma was highly cross-reactive against Delta Plus (Delta+), which differs from Delta by a single K417N mutation in the receptor binding domain, suggesting that the plasma response targets the N417 residue. To probe this further, we isolated monoclonal antibodies from a Beta-infected individual with plasma responses against Beta, Delta+, and Omicron, which all possess the N417 residue. We isolated an N417-dependent antibody, 084-7D, which showed similar neutralization breadth to the plasma. The 084-7D MAb utilized the IGHV3-23*01 germ line gene and had somatic hypermutations similar to those of previously described public antibodies which target the 417 residue. Thus, we have identified a novel antibody which targets a shared epitope found on three distinct VOCs, enabling their cross-neutralization. Understanding antibodies targeting escape mutations, such as K417N, which repeatedly emerge through convergent evolution in SARS-CoV-2 variants, may aid in the development of next-generation antibody therapeutics and vaccines. IMPORTANCE The evolution of SARS-CoV-2 has resulted in variants of concern (VOCs) with distinct spike mutations conferring various immune escape profiles. These variable mutations also influence the cross-reactivity of the antibody response mounted by individuals infected with each of these variants. This study sought to understand the antibody responses elicited by different SARS-CoV-2 variants and to define shared epitopes. We show that Beta and Delta infections resulted in antibody responses that were more cross-reactive than the original D614G variant, but they had differing patterns of cross-reactivity. We further isolated an antibody from Beta infection which targeted the N417 site, enabling cross-neutralization of Beta, Delta+, and Omicron, all of which possess this residue. The discovery of antibodies which target escape mutations common to multiple variants highlights conserved epitopes to target in future vaccines and therapeutics.
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Affiliation(s)
- Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mashudu Madzivhandila
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nonhlanhla N. Mkhize
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Prudence Kgagudi
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Frances Ayres
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bronwen E. Lambson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nelia P. Manamela
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Simone I. Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Makhado
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mieke A. van der Mescht
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | | | | | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Ntobeko A. B. Ntusi
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Theresa Rossouw
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Veronica Ueckermann
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Michael T. Boswell
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Penny L. Moore
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
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24
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Wilhelm A, Widera M, Grikscheit K, Toptan T, Schenk B, Pallas C, Metzler M, Kohmer N, Hoehl S, Marschalek R, Herrmann E, Helfritz FA, Wolf T, Goetsch U, Ciesek S. Limited neutralisation of the SARS-CoV-2 Omicron subvariants BA.1 and BA.2 by convalescent and vaccine serum and monoclonal antibodies. EBioMedicine 2022; 82:104158. [PMID: 35834885 DOI: 10.1101/2021.12.07.21267432] [Citation(s) in RCA: 157] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND In recent months, Omicron variants of SARS-CoV-2 have become dominant in many regions of the world, and case numbers with Omicron subvariants BA.1 and BA.2 continue to increase. Due to numerous mutations in the spike protein, the efficacy of currently available vaccines, which are based on Wuhan-Hu 1 isolate of SARS-CoV-2, is reduced, leading to breakthrough infections. Efficacy of monoclonal antibody therapy is also likely impaired. METHODS In our in vitro study using A549-AT cells constitutively expressing ACE2 and TMPRSS2, we determined and compared the neutralizing capacity of vaccine-elicited sera, convalescent sera and monoclonal antibodies against authentic SARS-CoV-2 Omicron BA.1 and BA.2 compared with Delta. FINDINGS Almost no neutralisation of Omicron BA.1 and BA.2 was observed using sera from individuals vaccinated with two doses 6 months earlier, regardless of the type of vaccine taken. Shortly after the booster dose, most sera from triple BNT162b2-vaccinated individuals were able to neutralise both Omicron variants. In line with waning antibody levels three months after the booster, only weak residual neutralisation was observed for BA.1 (26%, n = 34, 0 median NT50) and BA.2 (44%, n = 34, 0 median NT50). In addition, BA.1 but not BA.2 was resistant to the neutralising monoclonal antibodies casirivimab/imdevimab, while BA.2 exhibited almost a complete evasion from the neutralisation induced by sotrovimab. INTERPRETATION Both SARS-CoV-2 Omicron subvariants BA.1 and BA.2 escape antibody-mediated neutralisation elicited by vaccination, previous infection with SARS-CoV-2, and monoclonal antibodies. Waning immunity renders the majority of tested sera obtained three months after booster vaccination negative in BA.1 and BA.2 neutralisation. Omicron subvariant specific resistance to the monoclonal antibodies casirivimab/imdevimab and sotrovimab emphasizes the importance of genotype-surveillance and guided application. FUNDING This study was supported in part by the Goethe-Corona-Fund of the Goethe University Frankfurt (M.W.) and the Federal Ministry of Education and Research (COVIDready; grant 02WRS1621C (M.W.).
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany.
| | - Katharina Grikscheit
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Barbara Schenk
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Melinda Metzler
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Niko Kohmer
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Sebastian Hoehl
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe University, Frankfurt am Main, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modelling, Goethe University Frankfurt, 60596 Frankfurt, Germany
| | - Fabian A Helfritz
- Bürgerhospital Frankfurt, Nibelungenallee 37-41, 60318 Frankfurt am Main, Germany
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Udo Goetsch
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; German Centre for Infection Research (DZIF), partner site Frankfurt, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch Translational Medicine and Pharmacology, 60596 Frankfurt am Main, Germany.
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25
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Seidel A, Zanoni M, Groß R, Krnavek D, Erdemci-Evin S, von Maltitz P, Albers DPJ, Conzelmann C, Liu S, Weil T, Mayer B, Hoffmann M, Pöhlmann S, Beil A, Kroschel J, Kirchhoff F, Münch J, Müller JA. BNT162b2 booster after heterologous prime-boost vaccination induces potent neutralizing antibodies and T cell reactivity against SARS-CoV-2 Omicron BA.1 in young adults. Front Immunol 2022; 13:882918. [PMID: 35958601 PMCID: PMC9357986 DOI: 10.3389/fimmu.2022.882918] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/28/2022] [Indexed: 01/14/2023] Open
Abstract
In light of the decreasing immune protection against symptomatic SARS-CoV-2 infection after initial vaccinations and the now dominant immune-evasive Omicron variants, 'booster' vaccinations are regularly performed to restore immune responses. Many individuals have received a primary heterologous prime-boost vaccination with long intervals between vaccinations, but the resulting long-term immunity and the effects of a subsequent 'booster', particularly against Omicron BA.1, have not been defined. We followed a cohort of 23 young adults, who received a primary heterologous ChAdOx1 nCoV-19 BNT162b2 prime-boost vaccination, over a 7-month period and analysed how they responded to a BNT162b2 'booster'. We show that already after the primary heterologous vaccination, neutralization titers against Omicron BA.1 are recognizable but that humoral and cellular immunity wanes over the course of half a year. Residual responsive memory T cells recognized spike epitopes of the early SARS-CoV-2 B.1 strain as well as the Delta and BA.1 variants of concern (VOCs). However, the remaining antibody titers hardly neutralized these VOCs. The 'booster' vaccination was well tolerated and elicited both high antibody titers and increased memory T cell responses against SARS-CoV-2 including BA.1. Strikingly, in this young heterologously vaccinated cohort the neutralizing activity after the 'booster' was almost as potent against BA.1 as against the early B.1 strain. Our results suggest that a 'booster' after heterologous vaccination results in effective immune maturation and potent protection against the Omicron BA.1 variant in young adults.
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Affiliation(s)
- Alina Seidel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Michelle Zanoni
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniela Krnavek
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Dan P. J. Albers
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Sichen Liu
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Tatjana Weil
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Benjamin Mayer
- Institute for Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Alexandra Beil
- Central Department for Clinical Chemistry, University Hospital Ulm, Ulm, Germany
| | - Joris Kroschel
- Central Department for Clinical Chemistry, University Hospital Ulm, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Janis A. Müller
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute of Virology, Philipps University of Marburg, Marburg, Germany
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26
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Branche AR, Rouphael NG, Diemert DJ, Falsey AR, Losada C, Baden LR, Frey SE, Whitaker JA, Little SJ, Anderson EJ, Walter EB, Novak RM, Rupp R, Jackson LA, Babu TM, Kottkamp AC, Luetkemeyer AF, Immergluck LC, Presti RM, Bäcker M, Winokur PL, Mahgoub SM, Goepfert PA, Fusco DN, Malkin E, Bethony JM, Walsh EE, Graciaa DS, Samaha H, Sherman AC, Walsh SR, Abate G, Oikonomopoulou Z, El Sahly HM, Martin TCS, Rostad CA, Smith MJ, Ladner BG, Porterfield L, Dunstan M, Wald A, Davis T, Atmar RL, Mulligan MJ, Lyke KE, Posavad CM, Meagher MA, Stephens DS, Neuzil KM, Abebe K, Hill H, Albert J, Lewis TC, Giebeig LA, Eaton A, Netzl A, Wilks SH, Türeli S, Makhene M, Crandon S, Lee M, Nayak SU, Montefiori DC, Makowski M, Smith DJ, Roberts PC, Beigel JH. SARS-CoV-2 Variant Vaccine Boosters Trial: Preliminary Analyses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.07.12.22277336. [PMID: 35898343 PMCID: PMC9327623 DOI: 10.1101/2022.07.12.22277336] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background Protection from SARS-CoV-2 vaccines wanes over time and is compounded by emerging variants including Omicron subvariants. This study evaluated safety and immunogenicity of SARS-CoV-2 variant vaccines. Methods This phase 2 open-label, randomized trial enrolled healthy adults previously vaccinated with a SARS-CoV-2 primary series and a single boost. Eligible participants were randomized to one of six Moderna COVID19 mRNA vaccine arms (50µg dose): Prototype (mRNA-1273), Omicron BA.1+Beta (1 or 2 doses), Omicron BA.1+Delta, Omicron BA.1 monovalent, and Omicron BA.1+Prototype. Neutralization antibody titers (ID 50 ) were assessed for D614G, Delta, Beta and Omicron BA.1 variants and Omicron BA.2.12.1 and BA.4/BA.5 subvariants 15 days after vaccination. Results From March 30 to May 6, 2022, 597 participants were randomized and vaccinated. Median age was 53 years, and 20% had a prior SARS-CoV-2 infection. All vaccines were safe and well-tolerated. Day 15 geometric mean titers (GMT) against D614G were similar across arms and ages, and higher with prior infection. For uninfected participants, Day 15 Omicron BA.1 GMTs were similar across Omicron-containing vaccine arms (3724-4561) and higher than Prototype (1,997 [95%CI:1,482-2,692]). The Omicron BA.1 monovalent and Omicron BA.1+Prototype vaccines induced a geometric mean ratio (GMR) to Prototype for Omicron BA.1 of 2.03 (97.5%CI:1.37-3.00) and 1.56 (97.5%CI:1.06-2.31), respectively. A subset of samples from uninfected participants in four arms were also tested in a different laboratory at Day 15 for neutralizing antibody titers to D614G and Omicron subvariants BA.1, BA.2.12.2 and BA.4/BA.5. Omicron BA.4/BA.5 GMTs were approximately one third BA.1 GMTs (Prototype 517 [95%CI:324-826] vs. 1503 [95%CI:949-2381]; Omicron BA.1+Beta 628 [95%CI:367-1,074] vs. 2125 [95%CI:1139-3965]; Omicron BA.1+Delta 765 [95%CI:443-1,322] vs. 2242 [95%CI:1218-4128] and Omicron BA.1+Prototype 635 [95%CI:447-903] vs. 1972 [95%CI:1337-2907). Conclusions Higher Omicron BA.1 titers were observed with Omicron-containing vaccines compared to Prototype vaccine and titers against Omicron BA.4/BA.5 were lower than against BA.1 for all candidate vaccines. Clinicaltrialsgov NCT05289037.
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27
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Tennøe S, Gheorghe M, Stratford R, Clancy T. The T Cell Epitope Landscape of SARS-CoV-2 Variants of Concern. Vaccines (Basel) 2022; 10:1123. [PMID: 35891287 PMCID: PMC9315645 DOI: 10.3390/vaccines10071123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 02/01/2023] Open
Abstract
During the COVID-19 pandemic, several SARS-CoV-2 variants of concern (VOC) emerged, bringing with them varying degrees of health and socioeconomic burdens. In particular, the Omicron VOC displayed distinct features of increased transmissibility accompanied by antigenic drift in the spike protein that partially circumvented the ability of pre-existing antibody responses in the global population to neutralize the virus. However, T cell immunity has remained robust throughout all the different VOC transmission waves and has emerged as a critically important correlate of protection against SARS-CoV-2 and its VOCs, in both vaccinated and infected individuals. Therefore, as SARS-CoV-2 VOCs continue to evolve, it is crucial that we characterize the correlates of protection and the potential for immune escape for both B cell and T cell human immunity in the population. Generating the insights necessary to understand T cell immunity, experimentally, for the global human population is at present a critical but a time consuming, expensive, and laborious process. Further, it is not feasible to generate global or universal insights into T cell immunity in an actionable time frame for potential future emerging VOCs. However, using computational means we can expedite and provide early insights into the correlates of T cell protection. In this study, we generated and revealed insights on the T cell epitope landscape for the five main SARS-CoV-2 VOCs observed to date. We demonstrated using a unique AI prediction platform, a significant conservation of presentable T cell epitopes across all mutated peptides for each VOC. This was modeled using the most frequent HLA alleles in the human population and covers the most common HLA haplotypes in the human population. The AI resource generated through this computational study and associated insights may guide the development of T cell vaccines and diagnostics that are even more robust against current and future VOCs, and their emerging subvariants.
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Affiliation(s)
| | | | | | - Trevor Clancy
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo, Norway; (S.T.); (M.G.); (R.S.)
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28
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Lima NS, Musayev M, Johnston TS, Wagner DA, Henry AR, Wang L, Yang ES, Zhang Y, Birungi K, Black WP, O’Dell S, Schmidt SD, Moon D, Lorang CG, Zhao B, Chen M, Boswell KL, Roberts-Torres J, Davis RL, Peyton L, Narpala SR, O’Connell S, Wang J, Schrager A, Talana CA, Leung K, Shi W, Khashab R, Biber A, Zilberman T, Rhein J, Vetter S, Ahmed A, Novik L, Widge A, Gordon I, Guech M, Teng IT, Phung E, Ruckwardt TJ, Pegu A, Misasi J, Doria-Rose NA, Gaudinski M, Koup RA, Kwong PD, McDermott AB, Amit S, Schacker TW, Levy I, Mascola JR, Sullivan NJ, Schramm CA, Douek DC. Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.28.486152. [PMID: 35378757 PMCID: PMC8978934 DOI: 10.1101/2022.03.28.486152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. The basis for such cross-protection at the molecular level is incompletely understood. Here we characterized the repertoire and epitope specificity of antibodies elicited by Beta, Gamma and ancestral variant infection and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a high-throughput approach to obtain immunoglobulin sequences and produce monoclonal antibodies for functional assessment from single B cells. Infection with any variant elicited similar cross-binding antibody responses exhibiting a remarkably conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may represent a general immunological principle that accounts for the continued efficacy of vaccines based on a single ancestral variant.
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Affiliation(s)
- Noemia S. Lima
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Maryam Musayev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Timothy S. Johnston
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Danielle A. Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Amy R. Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Kevina Birungi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Walker P. Black
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Stephen D. Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Damee Moon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Cynthia G. Lorang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Bingchun Zhao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Kristin L. Boswell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Jesmine Roberts-Torres
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Rachel L. Davis
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Lowrey Peyton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Sandeep R. Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Sarah O’Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Jennifer Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Alexander Schrager
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Chloe Adrienna Talana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Rawan Khashab
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan 5262112, Israel
| | - Asaf Biber
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan 5262112, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tal Zilberman
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan 5262112, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Joshua Rhein
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Sara Vetter
- Minnesota Department of Health, St Paul, MN 55164, USA
| | - Afeefa Ahmed
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Laura Novik
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Alicia Widge
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Ingelise Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Mercy Guech
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Tracy J. Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Martin Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Sharon Amit
- Clinical Microbiology, Sheba Medical Center, Ramat-Gan 5262112, Israel
| | - Timothy W. Schacker
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Itzchak Levy
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan 5262112, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv 6997801, Israel
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Chaim A. Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
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Chivu-Economescu M, Vremera T, Ruta SM, Grancea C, Leustean M, Chiriac D, David A, Matei L, Diaconu CC, Gatea A, Ilie C, Radu I, Cornienco AM, Iancu LS, Cirstoiu C, Pop CS, Petru R, Strambu V, Malciolu S, Popescu CP, Florescu SA, Rafila A, Furtunescu FL, Pistol A. Assessment of the Humoral Immune Response Following COVID-19 Vaccination in Healthcare Workers: A One Year Longitudinal Study. Biomedicines 2022; 10:1526. [PMID: 35884831 PMCID: PMC9312940 DOI: 10.3390/biomedicines10071526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 11/17/2022] Open
Abstract
The continuous variability of SARS-CoV-2 and the rapid waning of specific antibodies threatens the efficacy of COVID-19 vaccines. We aimed to evaluate antibody kinetics one year after SARS-CoV-2 vaccination with an mRNA vaccine in healthcare workers (HCW), with or without a booster. A marked decline in anti-Spike(S)/Receptor Binding Domain (RBD) antibody levels was registered during the first eight months post-vaccination, followed by a transitory increase after the booster. At three months post-booster an increased antibody level was maintained only in HCW vaccinated after a prior infection, who also developed a higher and long-lasting level of anti-S IgA antibodies. Still, IgG anti-nucleocapsid (NCP) fades five months post-SARS-CoV-2 infection. Despite the decline in antibodies one-year post-vaccination, 68.2% of HCW preserved the neutralization capacity against the ancestral variant, with a decrease of only 17.08% in the neutralizing capacity against the Omicron variant. Nevertheless, breakthrough infections were present in 6.65% of all participants, without any correlation with the previous level of anti-S/RBD IgG. Protection against the ancestral and Omicron variants is maintained at least three months after a booster in HCW, possibly reflecting a continuous antigenic stimulation in the professional setting.
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Affiliation(s)
- Mihaela Chivu-Economescu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (M.C.-E.); (C.G.); (D.C.); (L.M.); (C.C.D.)
| | - Teodora Vremera
- National Institute of Public Health Bucharest, 050463 Bucharest, Romania; (T.V.); (M.L.); (A.D.); (A.G.); (C.I.); (I.R.); (A.M.C.)
- ECDC Fellowship Programme, Public Health Microbiology Path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), 16973 Solna, Sweden
| | - Simona Maria Ruta
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
| | - Camelia Grancea
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (M.C.-E.); (C.G.); (D.C.); (L.M.); (C.C.D.)
| | - Mihaela Leustean
- National Institute of Public Health Bucharest, 050463 Bucharest, Romania; (T.V.); (M.L.); (A.D.); (A.G.); (C.I.); (I.R.); (A.M.C.)
| | - Daniela Chiriac
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (M.C.-E.); (C.G.); (D.C.); (L.M.); (C.C.D.)
| | - Adina David
- National Institute of Public Health Bucharest, 050463 Bucharest, Romania; (T.V.); (M.L.); (A.D.); (A.G.); (C.I.); (I.R.); (A.M.C.)
| | - Lilia Matei
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (M.C.-E.); (C.G.); (D.C.); (L.M.); (C.C.D.)
| | - Carmen C. Diaconu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (M.C.-E.); (C.G.); (D.C.); (L.M.); (C.C.D.)
| | - Adina Gatea
- National Institute of Public Health Bucharest, 050463 Bucharest, Romania; (T.V.); (M.L.); (A.D.); (A.G.); (C.I.); (I.R.); (A.M.C.)
| | - Ciprian Ilie
- National Institute of Public Health Bucharest, 050463 Bucharest, Romania; (T.V.); (M.L.); (A.D.); (A.G.); (C.I.); (I.R.); (A.M.C.)
| | - Iuliana Radu
- National Institute of Public Health Bucharest, 050463 Bucharest, Romania; (T.V.); (M.L.); (A.D.); (A.G.); (C.I.); (I.R.); (A.M.C.)
| | - Ana Maria Cornienco
- National Institute of Public Health Bucharest, 050463 Bucharest, Romania; (T.V.); (M.L.); (A.D.); (A.G.); (C.I.); (I.R.); (A.M.C.)
| | - Luminita Smaranda Iancu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
- Regional Center of Public Health Iași, 700465 Iași, Romania
| | - Catalin Cirstoiu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
- University Emergency Hospital, 050098 Bucharest, Romania
| | - Corina Silvia Pop
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
- University Emergency Hospital, 050098 Bucharest, Romania
| | - Radu Petru
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
- Dr. Carol Davila Nephrology Clinical Hospital, 010731 Bucharest, Romania
| | - Victor Strambu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
- Dr. Carol Davila Nephrology Clinical Hospital, 010731 Bucharest, Romania
| | - Stefan Malciolu
- Victor Babes Hospital for Infectious and Tropical Diseases, 030303 Bucharest, Romania;
| | - Corneliu Petru Popescu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
- Victor Babes Hospital for Infectious and Tropical Diseases, 030303 Bucharest, Romania;
| | - Simin Aysel Florescu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
- Victor Babes Hospital for Infectious and Tropical Diseases, 030303 Bucharest, Romania;
| | - Alexandru Rafila
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
- National Institute of Infectious Diseases “Matei Bals”, 021105 Bucharest, Romania
| | - Florentina Ligia Furtunescu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
| | - Adriana Pistol
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.C.); (C.S.P.); (R.P.); (V.S.); (C.P.P.); (S.A.F.); (A.R.); (F.L.F.); (A.P.)
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30
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Affiliation(s)
- Etienne Simon-Loriere
- Institut Pasteur, Université de Paris, G5 Evolutionary Genomics of RNA viruses, Paris, France.
| | - Olivier Schwartz
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, Paris, France.
- Vaccine Research Institute, Créteil, France.
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31
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Chalkias S, Eder F, Essink B, Khetan S, Nestorova B, Feng J, Chen X, Chang Y, Zhou H, Montefiori D, Edwards DK, Girard B, Pajon R, Dutko FJ, Leav B, Walsh SR, Baden LR, Miller JM, Das R. Safety, immunogenicity and antibody persistence of a bivalent Beta-containing booster vaccine against COVID-19: a phase 2/3 trial. Nat Med 2022; 28:2388-2397. [PMID: 36202997 PMCID: PMC9671805 DOI: 10.1038/s41591-022-02031-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/01/2022] [Indexed: 01/14/2023]
Abstract
Updated immunization strategies are needed to address multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Here we report interim results from an ongoing, open-label phase 2/3 trial evaluating the safety and immunogenicity of the bivalent Coronavirus Disease 2019 (COVID-19) vaccine candidate mRNA-1273.211, which contains equal mRNA amounts encoding the ancestral SARS-CoV-2 and Beta variant spike proteins, as 50-µg (n = 300) and 100-µg (n = 595) first booster doses administered approximately 8.7-9.7 months after the mRNA-1273 primary vaccine series ( NCT04927065 ). The primary objectives were to evaluate the safety and reactogenicity of mRNA-1273.211 and to demonstrate non-inferior antibody responses compared to the mRNA-1273 100-µg primary series. Additionally, a pre-specified immunogenicity objective was to demonstrate superior antibody responses compared to the previously authorized mRNA-1273 50-µg booster. The mRNA-1273.211 booster doses (50-µg or 100-µg) 28 days after immunization elicited higher neutralizing antibody responses against the ancestral SARS-CoV-2 and Beta variant than those elicited 28 days after the second mRNA‑1273 dose of the primary series ( NCT04470427 ). Antibody responses 28 days and 180 days after the 50-µg mRNA-1273.211 booster dose were also higher than those after a 50-µg mRNA-1273 booster dose ( NCT04405076 ) against the ancestral SARS-CoV-2 and Beta, Omicron BA.1 and Delta variants, and all pre-specified immunogenicity objectives were met. The safety and reactogenicity profile of the bivalent mRNA-1273.211 booster (50-µg) was similar to the booster dose of mRNA-1273 (50-µg). Immunization with the primary series does not set a ceiling to the neutralizing antibody response, and a booster dose of the bivalent vaccine elicits a robust response with titers that are likely to be protective against COVID-19. These results indicate that bivalent booster vaccines can induce potent, durable and broad antibody responses against multiple variants, providing a new tool in response to emerging variants.
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Affiliation(s)
- Spyros Chalkias
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - Frank Eder
- grid.477652.5Meridian Clinical Research, Binghamton, NY USA
| | | | - Shishir Khetan
- grid.477652.5Meridian Clinical Research, Rockville, MD USA
| | | | - Jing Feng
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - Xing Chen
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - Ying Chang
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - Honghong Zhou
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - David Montefiori
- grid.26009.3d0000 0004 1936 7961Department of Surgery and Duke Human Vaccine Institute, Durham, NC USA
| | - Darin K. Edwards
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - Bethany Girard
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - Rolando Pajon
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - Frank J. Dutko
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - Brett Leav
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
| | - Stephen R. Walsh
- grid.62560.370000 0004 0378 8294Brigham and Women’s Hospital, Boston, MA USA
| | - Lindsey R. Baden
- grid.62560.370000 0004 0378 8294Brigham and Women’s Hospital, Boston, MA USA
| | | | - Rituparna Das
- grid.479574.c0000 0004 1791 3172Moderna, Inc., Cambridge, MA USA
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32
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Markov PV, Katzourakis A, Stilianakis NI. Antigenic evolution will lead to new SARS-CoV-2 variants with unpredictable severity. Nat Rev Microbiol 2022; 20:251-252. [PMID: 35288685 PMCID: PMC8919145 DOI: 10.1038/s41579-022-00722-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Peter V. Markov
- grid.434554.70000 0004 1758 4137European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Aris Katzourakis
- grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK
| | - Nikolaos I. Stilianakis
- grid.434554.70000 0004 1758 4137European Commission, Joint Research Centre (JRC), Ispra, Italy ,grid.5330.50000 0001 2107 3311Department of Biometry and Epidemiology, University of Erlangen-Nuremberg, Erlangen, Germany
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