1
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Mandolesi M, Das H, de Vries L, Yang Y, Kim C, Dhinakaran M, Castro Dopico X, Fischbach J, Kim S, Guryleva MV, Àdori M, Chernyshev M, Stålmarck A, Hanke L, McInerney GM, Sheward DJ, Corcoran M, Hällberg BM, Murrell B, Karlsson Hedestam GB. Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques. Nat Commun 2024; 15:6338. [PMID: 39068149 PMCID: PMC11283548 DOI: 10.1038/s41467-024-50286-0] [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: 02/15/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
The continued evolution of SARS-CoV-2 underscores the need to understand qualitative aspects of the humoral immune response elicited by spike immunization. Here, we combine monoclonal antibody (mAb) isolation with deep B cell receptor (BCR) repertoire sequencing of rhesus macaques immunized with prefusion-stabilized spike glycoprotein. Longitudinal tracing of spike-sorted B cell lineages in multiple immune compartments demonstrates increasing somatic hypermutation and broad dissemination of vaccine-elicited B cells in draining and non-draining lymphoid compartments, including the bone marrow, spleen and, most notably, periaortic lymph nodes. Phylogenetic analysis of spike-specific monoclonal antibody lineages identified through deep repertoire sequencing delineates extensive intra-clonal diversification that shaped neutralizing activity. Structural analysis of the spike in complex with a broadly neutralizing mAb provides a molecular basis for the observed differences in neutralization breadth between clonally related antibodies. Our findings highlight that immunization leads to extensive intra-clonal B cell evolution where members of the same lineage can both retain the original epitope specificity and evolve to recognize additional spike variants not previously encountered.
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MESH Headings
- Animals
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Macaca mulatta
- Antibodies, Neutralizing/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- B-Lymphocytes/immunology
- Antibodies, Viral/immunology
- Phylogeny
- Antibodies, Monoclonal/immunology
- Epitopes/immunology
- COVID-19/immunology
- COVID-19/virology
- Humans
- COVID-19 Vaccines/immunology
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, B-Cell/genetics
- Somatic Hypermutation, Immunoglobulin
- Immunization
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Affiliation(s)
- Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Liset de Vries
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Yiqiu Yang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Manojj Dhinakaran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Julian Fischbach
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mariia V Guryleva
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mark Chernyshev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Aron Stålmarck
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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2
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Metzdorf K, Jacobsen H, Kim Y, Teixeira Alves LG, Kulkarni U, Brdovčak MC, Materljan J, Eschke K, Chaudhry MZ, Hoffmann M, Bertoglio F, Ruschig M, Hust M, Šustić M, Krmpotić A, Jonjić S, Widera M, Ciesek S, Pöhlmann S, Landthaler M, Čičin-Šain L. A single-dose MCMV-based vaccine elicits long-lasting immune protection in mice against distinct SARS-CoV-2 variants. Front Immunol 2024; 15:1383086. [PMID: 39119342 PMCID: PMC11306140 DOI: 10.3389/fimmu.2024.1383086] [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: 02/06/2024] [Accepted: 06/11/2024] [Indexed: 08/10/2024] Open
Abstract
Current vaccines against COVID-19 elicit immune responses that are overall strong but wane rapidly. As a consequence, the necessary booster shots have contributed to vaccine fatigue. Hence, vaccines that would provide lasting protection against COVID-19 are needed, but are still unavailable. Cytomegaloviruses (CMVs) elicit lasting and uniquely strong immune responses. Used as vaccine vectors, they may be attractive tools that obviate the need for boosters. Therefore, we tested the murine CMV (MCMV) as a vaccine vector against COVID-19 in relevant preclinical models of immunization and challenge. We have previously developed a recombinant MCMV vaccine vector expressing the spike protein of the ancestral SARS-CoV-2 (MCMVS). In this study, we show that the MCMVS elicits a robust and lasting protection in young and aged mice. Notably, spike-specific humoral and cellular immunity was not only maintained but also even increased over a period of at least 6 months. During that time, antibody avidity continuously increased and expanded in breadth, resulting in neutralization of genetically distant variants, like Omicron BA.1. A single dose of MCMVS conferred rapid virus clearance upon challenge. Moreover, MCMVS vaccination controlled two variants of concern (VOCs), the Beta (B.1.135) and the Omicron (BA.1) variants. Thus, CMV vectors provide unique advantages over other vaccine technologies, eliciting broadly reactive and long-lasting immune responses against COVID-19.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- Mice
- COVID-19 Vaccines/immunology
- COVID-19/prevention & control
- COVID-19/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Muromegalovirus/immunology
- Muromegalovirus/genetics
- Female
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Mice, Inbred BALB C
- Humans
- Genetic Vectors
- Immunity, Cellular
- Immunity, Humoral
- Disease Models, Animal
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Affiliation(s)
- Kristin Metzdorf
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
| | - Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
| | - Yeonsu Kim
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Upasana Kulkarni
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
| | | | - Jelena Materljan
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Kathrin Eschke
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - M. Zeeshan Chaudhry
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, 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
| | - Federico Bertoglio
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maximilian Ruschig
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marko Šustić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Astrid Krmpotić
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Stipan Jonjić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
- German Centre for Infection Research (DZIF), External Partner Site Frankfurt, Frankfurt, 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
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
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3
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Planchais C, Fernández I, Chalopin B, Bruel T, Rosenbaum P, Beretta M, Dimitrov JD, Conquet L, Donati F, Prot M, Porrot F, Planas D, Staropoli I, Guivel-Benhassine F, Baquero E, van der Werf S, Haouz A, Simon-Lorière E, Montagutelli X, Maillère B, Rey FA, Guardado-Calvo P, Nozach H, Schwartz O, Mouquet H. Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2. iScience 2024; 27:110354. [PMID: 39071888 PMCID: PMC11277385 DOI: 10.1016/j.isci.2024.110354] [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: 04/25/2024] [Revised: 05/27/2024] [Accepted: 06/20/2024] [Indexed: 07/30/2024] Open
Abstract
Antibodies play a pivotal role in protecting from SARS-CoV-2 infection, but their efficacy is challenged by the continuous emergence of viral variants. In this study, we describe two broadly neutralizing antibodies cloned from the memory B cells of a single convalescent individual after infection with ancestral SARS-CoV-2. Cv2.3194, a resilient class 1 anti-RBD antibody, remains active against Omicron sub-variants up to BA.2.86. Cv2.3132, a near pan-Sarbecovirus neutralizer, targets the heptad repeat 2 membrane proximal region. When combined, Cv2.3194 and Cv2.3132 form a complementary SARS-CoV-2 neutralizing antibody cocktail exhibiting a local dose-dependent synergy. Thus, remarkably robust neutralizing memory B cell antibodies elicited in response to ancestral SARS-CoV-2 infection can withstand viral evolution and immune escape. The cooperative effect of such antibody combination may confer a certain level of protection against the latest SARS-CoV-2 variants.
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Affiliation(s)
- Cyril Planchais
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Ignacio Fernández
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Benjamin Chalopin
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Timothée Bruel
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Pierre Rosenbaum
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Maxime Beretta
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Laurine Conquet
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Flora Donati
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Matthieu Prot
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
| | - Françoise Porrot
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Delphine Planas
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Isabelle Staropoli
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Florence Guivel-Benhassine
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Eduard Baquero
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Sylvie van der Werf
- CNRS UMR3569, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Molecular Genetics of RNA Viruses, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Cristallography Platform-C2RT, 75015 Paris, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Xavier Montagutelli
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Bernard Maillère
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Félix A. Rey
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Pablo Guardado-Calvo
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Hervé Nozach
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Olivier Schwartz
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
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4
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Bai H, Zhang X, Gong T, Ma J, Zhang P, Cai Z, Ren D, Zhang C. A systematic mutation analysis of 13 major SARS-CoV-2 variants. Virus Res 2024; 345:199392. [PMID: 38729218 PMCID: PMC11112362 DOI: 10.1016/j.virusres.2024.199392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
SARS-CoV-2 evolves constantly with various novel mutations. Due to their enhanced infectivity, transmissibility and immune evasion, a comprehensive understanding of the association between these mutations and the respective functional changes is crucial. However, previous mutation studies of major SARS-CoV-2 variants remain limited. Here, we performed systematic analyses of full-length amino acids mutation, phylogenetic features, protein physicochemical properties, molecular dynamics and immune escape as well as pseudotype virus infection assays among thirteen major SARS-CoV-2 variants. We found that Omicron exhibited the most abundant and complex mutation sites, higher indices of hydrophobicity and flexibility than other variants. The results of molecular dynamics simulation suggest that Omicron has the highest number of hydrogen bonds and strongest binding free energy between the S protein and ACE2 receptor. Furthermore, we revealed 10 immune escape sites in 13 major variants, some of them were reported previously, but four of which (i.e. 339/373/477/496) are first reported to be specific to Omicron, whereas 462 is specific to Epslion. The infectivity of these variants was confirmed by the pseudotype virus infection assays. Our findings may help us understand the functional consequences of the mutations within various variants and the underlying mechanisms of the immune escapes conferred by the S proteins.
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Affiliation(s)
- Han Bai
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Xuan Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Tian Gong
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Junpeng Ma
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Peng Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Zeqiong Cai
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Doudou Ren
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Chengsheng Zhang
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China; Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China.
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5
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Bruhn M, Obara M, Salam A, Costa B, Ziegler A, Waltl I, Pavlou A, Hoffmann M, Graalmann T, Pöhlmann S, Schambach A, Kalinke U. Diversification of the VH3-53 immunoglobulin gene segment by somatic hypermutation results in neutralization of SARS-CoV-2 virus variants. Eur J Immunol 2024; 54:e2451056. [PMID: 38593351 DOI: 10.1002/eji.202451056] [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: 02/07/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
COVID-19 induces re-circulating long-lived memory B cells (MBC) that, upon re-encounter with the pathogen, are induced to mount immunoglobulin responses. During convalescence, antibodies are subjected to affinity maturation, which enhances the antibody binding strength and generates new specificities that neutralize virus variants. Here, we performed a single-cell RNA sequencing analysis of spike-specific B cells from a SARS-CoV-2 convalescent subject. After COVID-19 vaccination, matured infection-induced MBC underwent recall and differentiated into plasmablasts. Furthermore, the transcriptomic profiles of newly activated B cells transiently shifted toward the ones of atypical and CXCR3+ B cells and several B-cell clonotypes massively expanded. We expressed monoclonal antibodies (mAbs) from all B-cell clones from the largest clonotype that used the VH3-53 gene segment. The in vitro analysis revealed that some somatic hypermutations enhanced the neutralization breadth of mAbs in a putatively stochastic manner. Thus, somatic hypermutation of B-cell clonotypes generates an anticipatory memory that can neutralize new virus variants.
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Affiliation(s)
- Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Maureen Obara
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Abdus Salam
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Bibiana Costa
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Annett Ziegler
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Inken Waltl
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Theresa Graalmann
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- Junior Research Group for Translational Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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6
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Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X. An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep 2024; 43:114265. [PMID: 38805396 DOI: 10.1016/j.celrep.2024.114265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/29/2023] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein continues to evolve antigenically, impacting antibody immunity. D1F6, an affinity-matured non-stereotypic VH1-2 antibody isolated from a patient infected with the SARS-CoV-2 ancestral strain, effectively neutralizes most Omicron variants tested, including XBB.1.5. We identify that D1F6 in the immunoglobulin G (IgG) form is able to overcome the effect of most Omicron mutations through its avidity-enhanced multivalent S-trimer binding. Cryo-electron microscopy (cryo-EM) and biochemical analyses show that three simultaneous epitope mutations are generally needed to substantially disrupt the multivalent S-trimer binding by D1F6 IgG. Antigenic mutations at spike positions 346, 444, and 445, which appeared in the latest variants, have little effect on D1F6 binding individually. However, these mutations are able to act synergistically with earlier Omicron mutations to impair neutralization by affecting the interaction between D1F6 IgG and the S-trimer. These results provide insight into the mechanism by which accumulated antigenic mutations facilitate evasion of affinity-matured antibodies.
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Affiliation(s)
- Banghui Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Yijun Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qian Wang
- Guangzhou Laboratory & Bioland Laboratory, Guangzhou, China
| | - Yuanyi Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Shuangshuang Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingxian Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mengzhen Su
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Science and Technology of China, Hefei, China
| | - Xiancheng Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chuanying Niu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Science and Technology of China, Hefei, China
| | - Yinglin Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenyi Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Ling Chen
- Guangzhou Laboratory & Bioland Laboratory, Guangzhou, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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7
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Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hällberg BM. Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies. Cell Rep Med 2024; 5:101577. [PMID: 38761799 PMCID: PMC11228396 DOI: 10.1016/j.xcrm.2024.101577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 12/15/2023] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Descendants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant now account for almost all SARS-CoV-2 infections. The Omicron variant and its sublineages have spike glycoproteins that are highly diverged from the pandemic founder and first-generation vaccine strain, resulting in significant evasion from monoclonal antibody therapeutics and vaccines. Understanding how commonly elicited antibodies can broaden to cross-neutralize escape variants is crucial. We isolate IGHV3-53, using "public" monoclonal antibodies (mAbs) from an individual 7 months post infection with the ancestral virus and identify antibodies that exhibit potent and broad cross-neutralization, extending to the BA.1, BA.2, and BA.4/BA.5 sublineages of Omicron. Deep mutational scanning reveals these mAbs' high resistance to viral escape. Structural analysis via cryoelectron microscopy of a representative broadly neutralizing antibody, CAB-A17, in complex with the Omicron BA.1 spike highlights the structural underpinnings of this broad neutralization. By reintroducing somatic hypermutations into a germline-reverted CAB-A17, we delineate the role of affinity maturation in the development of cross-neutralization by a public class of antibodies.
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Affiliation(s)
- Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Hyllner
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Robert Dyrdak
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jimin Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pia Dosenovic
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | | | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestraße 85, 22607 Hamburg, Germany.
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8
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Hoeggerl AD, Nunhofer V, Weidner L, Lauth W, Zimmermann G, Badstuber N, Grabmer C, Kartal O, Jungbauer C, Neureiter H, Held N, Ortner T, Flamm M, Osterbrink J, Rohde E, Laner-Plamberger S. Dissecting the dynamics of SARS-CoV-2 reinfections in blood donors with pauci- or asymptomatic COVID-19 disease course at initial infection. Infect Dis (Lond) 2024:1-11. [PMID: 38869944 DOI: 10.1080/23744235.2024.2367112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Understanding the dynamics of SARS-CoV-2 reinfections is crucial for public health policy, vaccine development, and long-term disease management. However, data on reinfections in the general population remains scarce. OBJECTIVES This study aimed to investigate SARS-CoV-2 antibody dynamics among Austrian blood donors, representing healthy adults, over two years following primary infection and to evaluate the reinfection risk. METHODS 117,895 blood donations were analysed for SARS-CoV-2 total anti-N levels from June 2020 to December 2023. We examined anti-N and anti-S antibody dynamics and in vitro functionality in 230 study participants at five defined times during 24 months, assessing associations with demographics, vaccination status, and reinfection awareness. RESULTS The seroprevalence of SARS-CoV-2 infection-derived anti-N antibodies increased over time, reaching 90% by February 2023 and remaining at that level since then. According to serological screenings, we found an 88% reinfection rate, which is in contrast to participants' reports indicating a reinfection rate of 59%. Our data further reveal that about 26% of reinfections went completely unnoticed. Antibody dynamics were independent of age, sex, and ABO blood group. Interestingly, individuals with multiple reinfections reported symptoms more frequently during their primary infection. Our results further show that vaccination modestly affected reinfection risk and disease course. CONCLUSION SARS-CoV-2 reinfections were uncommon until the end of 2021 but became common with the advent of Omicron. This study highlights the underestimation of reinfection rates in healthy adults and underscores the need for continued surveillance, which is an important support for public health policies and intervention strategies.
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Affiliation(s)
- Alexandra Domnica Hoeggerl
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Verena Nunhofer
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Lisa Weidner
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
- Austrian Red Cross, Blood Service for Vienna, Lower Austria and Burgenland, Vienna, Austria
| | - Wanda Lauth
- Team Biostatistics and Big Medical Data, IDA Lab Salzburg, PMU Salzburg, Salzburg, Austria
- Research Programme Biomedical Data Science, PMU Salzburg, Salzburg, Austria
| | - Georg Zimmermann
- Team Biostatistics and Big Medical Data, IDA Lab Salzburg, PMU Salzburg, Salzburg, Austria
- Research Programme Biomedical Data Science, PMU Salzburg, Salzburg, Austria
| | - Natalie Badstuber
- Department of Psychological Assessment, Institute of Psychology, Paris-Lodron-University of Salzburg, Salzburg, Austria
| | - Christoph Grabmer
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Orkan Kartal
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Christof Jungbauer
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
- Austrian Red Cross, Blood Service for Vienna, Lower Austria and Burgenland, Vienna, Austria
| | - Heidrun Neureiter
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Nina Held
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Tuulia Ortner
- Department of Psychological Assessment, Institute of Psychology, Paris-Lodron-University of Salzburg, Salzburg, Austria
| | - Maria Flamm
- Center for Public Health and Healthcare Research, Institute of General Practice, Family Medicine and Preventive Medicine, PMU Salzburg, Salzburg, Austria
| | - Jürgen Osterbrink
- Center for Public Health and Healthcare Research, Institute of Nursing Science and Practice, PMU Salzburg, Salzburg, Austria
| | - Eva Rohde
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
- GMP Laboratory, Paracelsus Medical University, Salzburg, Austria
| | - Sandra Laner-Plamberger
- Department for Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
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9
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Suryawanshi P, Patil‐Takbhate B, Athavale P, Mirza S, Tripathy A, Kanitkar S, Shivnitwar S, Barthwal MS, Dole S, Chavan H, Jali P, Pawale S, Kakad D, Kakrani AL, Bhawalkar J, Gandhi M, Chaturvedi S, Karandikar M, Tripathy S. T-cell responses in COVID-19 survivors 6-8 months after infection: A longitudinal cohort study in Pune. Immun Inflamm Dis 2024; 12:e1238. [PMID: 38860770 PMCID: PMC11165687 DOI: 10.1002/iid3.1238] [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: 10/27/2023] [Revised: 02/26/2024] [Accepted: 03/20/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune response is crucial for disease management, although diminishing immunity raises the possibility of reinfection. METHODS We examined the immunological response to SARS-CoV-2 in a cohort of convalescent COVID-19 patients in matched samples collected at 1 and 6-8 months after infection. The peripheral blood mononuclear cells were isolated from enrolled study participants and flow cytometry analysis was done to assess the lymphocyte subsets of naive, effector, central memory, and effector memory CD4+ or CD8+ T cells in COVID-19 patients at 1 and 6-8 months after infection. Immunophenotypic characterization of immune cell subsets was performed on individuals who were followed longitudinally for 1 month (n = 44) and 6-8 months (n = 25) after recovery from COVID infection. RESULTS We observed that CD4 +T cells in hospitalized SARS-CoV-2 patients tended to decrease, whereas CD8+ T cells steadily recovered after 1 month, while there was a sustained increase in the population of effector T cells and effector memory T cells. Furthermore, COVID-19 patients showed persistently low B cells and a small increase in the NK cell population. CONCLUSION Our findings show that T cell responses were maintained at 6-8 months after infection. This opens new pathways for further research into the long-term effects in COVID-19 immunopathogenesis.
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Affiliation(s)
- Poonam Suryawanshi
- Central Research Facility, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Bhagyashri Patil‐Takbhate
- Central Research Facility, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Prachi Athavale
- Department of Microbiology, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Shahzad Mirza
- Department of Microbiology, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | | | - Shubhangi Kanitkar
- Department of General Medicine, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Sachin Shivnitwar
- Department of General Medicine, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Madhusudan S. Barthwal
- Department of Respiratory Medicine, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, Pimpri, (deemed to be University)PuneIndia
| | - Sachin Dole
- Department of Respiratory Medicine, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, Pimpri, (deemed to be University)PuneIndia
| | - Hanumant Chavan
- Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Priyanka Jali
- Central Research Facility, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Sujata Pawale
- Central Research Facility, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Dhanashree Kakad
- Central Research Facility, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Arjun Lal Kakrani
- Department of General Medicine, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Jitendra Bhawalkar
- Department of Community Medicine, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Madhura Gandhi
- Central Research Facility, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | | | - Mahesh Karandikar
- Central Research Facility, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
| | - Srikanth Tripathy
- Central Research Facility, Dr D. Y. Patil Medical College, Hospital and Research CentreDr D. Y. Patil Vidyapeeth, (deemed to be University)PimpriPuneIndia
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10
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Chang YH, Hsu MF, Chen WN, Wu MH, Kong WL, Lu MYJ, Huang CH, Chang FJ, Chang LY, Tsai HY, Tung CP, Yu JH, Kuo Y, Chou YC, Bai LY, Chang YC, Chen AY, Chen CC, Chen YH, Liao CC, Chang CS, Liang JJ, Lin YL, Angata T, Hsu STD, Lin KI. Functional and structural investigation of a broadly neutralizing SARS-CoV-2 antibody. JCI Insight 2024; 9:e179726. [PMID: 38775156 PMCID: PMC11141937 DOI: 10.1172/jci.insight.179726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/12/2024] [Indexed: 06/02/2024] Open
Abstract
Since its emergence, SARS-CoV-2 has been continuously evolving, hampering the effectiveness of current vaccines against COVID-19. mAbs can be used to treat patients at risk of severe COVID-19. Thus, the development of broadly protective mAbs and an understanding of the underlying protective mechanisms are of great importance. Here, we isolated mAbs from donors with breakthrough infection with Omicron subvariants using a single-B cell screening platform. We identified a mAb, O5C2, which possesses broad-spectrum neutralization and antibody-dependent cell-mediated cytotoxic activities against SARS-CoV-2 variants, including EG.5.1. Single-particle analysis by cryo-electron microscopy revealed that O5C2 targeted an unusually large epitope within the receptor-binding domain of spike protein that overlapped with the angiotensin-converting enzyme 2 binding interface. Furthermore, O5C2 effectively protected against BA.5 Omicron infection in vivo by mediating changes in transcriptomes enriched in genes involved in apoptosis and interferon responses. Our findings provide insights into the development of pan-protective mAbs against SARS-CoV-2.
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Affiliation(s)
- Yi-Hsuan Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | | | - Wei-Nan Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Wye-Lup Kong
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Heng Huang
- Institute of Preventive Medicine
- Graduate Institute of Medical Sciences, and
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Fang-Ju Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Ho-Yang Tsai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jou-Hui Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yali Kuo
- Biomedical Translation Research Center (BioTReC)
| | - Yu-Chi Chou
- Biomedical Translation Research Center (BioTReC)
| | - Li-Yang Bai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yuan-Chih Chang
- Institute of Biological Chemistry and
- Academia Sinica Cryo-EM Center, and
| | - An-Yu Chen
- Institute of Preventive Medicine
- Graduate Institute of Medical Sciences, and
| | - Cheng-Cheung Chen
- Institute of Preventive Medicine
- Graduate Institute of Medical Sciences, and
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lin
- Biomedical Translation Research Center (BioTReC)
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Takashi Angata
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry and
| | - Shang-Te Danny Hsu
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry and
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKC M2, ) Hiroshima University, Hiroshima, Japan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center (BioTReC)
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11
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Jacob-Dolan C, Lifton M, Powers OC, Miller J, Hachmann NP, Vu M, Surve N, Mazurek CR, Fisher JL, Rodrigues S, Patio RC, Anand T, Le Gars M, Sadoff J, Schmidt AG, Barouch DH. B cell somatic hypermutation following COVID-19 vaccination with Ad26.COV2.S. iScience 2024; 27:109716. [PMID: 38655202 PMCID: PMC11035370 DOI: 10.1016/j.isci.2024.109716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/02/2024] [Accepted: 04/07/2024] [Indexed: 04/26/2024] Open
Abstract
The viral vector-based COVID-19 vaccine Ad26.COV2.S has been recommended by the WHO since 2021 and has been administered to over 200 million people. Prior studies have shown that Ad26.COV2.S induces durable neutralizing antibodies (NAbs) that increase in coverage of variants over time, even in the absence of boosting or infection. Here, we studied humoral responses following Ad26.COV2.S vaccination in individuals enrolled in the initial Phase 1/2a trial of Ad26.COV2.S in 2020. Through 8 months post vaccination, serum NAb responses increased to variants, including B.1.351 (Beta) and B.1.617.2 (Delta), without additional boosting or infection. The level of somatic hypermutation, measured by nucleotide changes in the VDJ region of the heavy and light antibody chains, increased in Spike-specific B cells. Highly mutated mAbs from these sequences neutralized more SARS-CoV-2 variants than less mutated comparators. These findings suggest that the increase in NAb breadth over time following Ad26.COV2.S vaccination is mediated by affinity maturation.
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Affiliation(s)
- Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Microbiology, Boston, MA, USA
- Harvard Medical School, Department of Immunology, Boston, MA, USA
| | - Michelle Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Olivia C. Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nicole P. Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mya Vu
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Nehalee Surve
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Camille R. Mazurek
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jana L. Fisher
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Stefanie Rodrigues
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert C. Patio
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Trisha Anand
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mathieu Le Gars
- Janssen Vaccines and Prevention B.V., Leiden, the Netherlands
| | - Jerald Sadoff
- Janssen Vaccines and Prevention B.V., Leiden, the Netherlands
| | - Aaron G. Schmidt
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Microbiology, Boston, MA, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Immunology, Boston, MA, USA
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12
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Girl P, von Buttlar H, Mantel E, Antwerpen MH, Wölfel R, Müller K. Comparative Analysis of Vaccine-Induced Neutralizing Antibodies against the Alpha, Beta, Delta, and Omicron Variants of SARS-CoV-2. Vaccines (Basel) 2024; 12:515. [PMID: 38793766 PMCID: PMC11126034 DOI: 10.3390/vaccines12050515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
The SARS-CoV-2 virus has infected more than 660 million people and caused nearly seven million deaths worldwide. During the pandemic, a number of SARS-CoV-2 vaccines were rapidly developed, and several are currently licensed for use in Europe. However, the optimization of vaccination regimens is still ongoing, particularly with regard to booster vaccinations. At the same time, the emergence of new virus variants poses an ongoing challenge to vaccine efficacy. In this study, we focused on a comparative analysis of the neutralization capacity of vaccine-induced antibodies against four different variants of concern (i.e., Alpha, Beta, Delta, and Omicron) after two and three doses of COVID-19 vaccine. We were able to show that both two (prime/boost) and three (prime/boost/boost) vaccinations elicit highly variable levels of neutralizing antibodies. In addition, we did not observe a significant difference in antibody levels after two and three vaccinations. We also observed a significant decrease in the neutralization susceptibility of all but one SARS-CoV-2 variants to vaccine-induced antibodies. In contrast, a SARS-CoV-2 breakthrough infection between the second and third vaccination results in overall higher levels of neutralizing antibodies with a concomitant improved neutralization of all virus variants. Titer levels remained highly variable across the cohort but a common trend was observed. This may be due to the fact that at the time of this study, all licensed vaccines were still based exclusively on wild-type SARS-CoV-2, whereas infections were caused by virus variants. Overall, our data demonstrate the importance of (booster) vaccinations, but at the same time emphasize the need for the continued adaptation of vaccines to induce a protective immune response against virus variants in order to be prepared for future (seasonal) SARS-CoV-2 outbreaks.
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Affiliation(s)
- Philipp Girl
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany; (P.G.); (H.v.B.); (E.M.); (M.H.A.); (R.W.)
- German Centre for Infection Research (DZIF), Partner Site Munich, 80937 Munich, Germany
- Central Institute of the Bundeswehr Medical Service Munich, 85784 Garching, Germany
- Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Heiner von Buttlar
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany; (P.G.); (H.v.B.); (E.M.); (M.H.A.); (R.W.)
- German Centre for Infection Research (DZIF), Partner Site Munich, 80937 Munich, Germany
| | - Enrico Mantel
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany; (P.G.); (H.v.B.); (E.M.); (M.H.A.); (R.W.)
- German Centre for Infection Research (DZIF), Partner Site Munich, 80937 Munich, Germany
| | - Markus H. Antwerpen
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany; (P.G.); (H.v.B.); (E.M.); (M.H.A.); (R.W.)
- German Centre for Infection Research (DZIF), Partner Site Munich, 80937 Munich, Germany
| | - Roman Wölfel
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany; (P.G.); (H.v.B.); (E.M.); (M.H.A.); (R.W.)
- German Centre for Infection Research (DZIF), Partner Site Munich, 80937 Munich, Germany
| | - Katharina Müller
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany; (P.G.); (H.v.B.); (E.M.); (M.H.A.); (R.W.)
- German Centre for Infection Research (DZIF), Partner Site Munich, 80937 Munich, Germany
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13
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Klingler J, Kowdle S, Bandres JC, Emami-Gorizi R, Alvarez RA, Rao PG, Amanat F, Gleason C, Kleiner G, Simon V, Edelstein A, Perandones C, Upadhyay C, Lee B, Hioe CE. Heterologous Ad26/Ad5 adenovirus-vectored vaccines elicited SARS-CoV-2-specific antibody responses with potent Fc activities. Front Immunol 2024; 15:1382619. [PMID: 38779671 PMCID: PMC11109367 DOI: 10.3389/fimmu.2024.1382619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Antibodies against the SARS-CoV-2 spike protein are a critical immune determinant for protection against the virus. While virus neutralization is a key function of spike-specific antibodies, antibodies also mediate Fc-dependent activities that can play a role in protection or pathogenesis. Methods This study characterized serum antibody responses elicited after two doses of heterologous adenovirus-vectored (Ad26/ Ad5) vaccines. Results Vaccine-induced antibody binding titers and Fc-mediated functions decreased over six months, while neutralization titers remained stable. Comparison of antibody isotypes elicited after Ad26/Ad5 vs. LNP-mRNA vaccination and after infection showed that anti-spike IgG1 were dominant and produced to high levels in all groups. The Ad26/Ad5 vaccines also induced IgG4 but not IgG2 and IgG3, whereas the LNP-mRNA vaccines elicited a full Ig spectrum (IgM, IgG1-4, IgA1-2). Convalescent COVID-19 patients had mainly IgM and IgA1 alongside IgG1. Despite these differences, the neutralization potencies against early variants were similar. However, both vaccine groups had antibodies with greater Fc potencies of binding complement and Fcg receptors than the COVID-19 group. The Ad26/Ad5 group also displayed a greater potency of RBD-specific antibody-mediated cellular phagocytosis. Discussion Antibodies with distinctive quality were induced by different vaccines and infection. The data imply the utility of different vaccine platforms to elicit antibody responses with fine-tuned Fc activities.
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Affiliation(s)
- Jéromine Klingler
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- James J. Peters VA Medical Center, Bronx, NY, United States
| | - Shreyas Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | | | - Raymond A. Alvarez
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Priyanka G. Rao
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Charles Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Giulio Kleiner
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Viviana Simon
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alexis Edelstein
- Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Claudia Perandones
- Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Chitra Upadhyay
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Catarina E. Hioe
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- James J. Peters VA Medical Center, Bronx, NY, United States
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14
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Rubio AA, Baharani VA, Dadonaite B, Parada M, Abernathy ME, Wang Z, Lee YE, Eso MR, Phung J, Ramos I, Chen T, Nesr GE, Bloom JD, Bieniasz PD, Nussenzweig MC, Barnes CO. Bispecific antibodies with broad neutralization potency against SARS-CoV-2 variants of concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592584. [PMID: 38766244 PMCID: PMC11100608 DOI: 10.1101/2024.05.05.592584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The ongoing emergence of SARS-CoV-2 variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that are resilient to viral evolution. Here, we characterized N-terminal domain (NTD) and receptor binding domain (RBD)-specific monoclonal antibodies previously isolated from COVID-19 convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these, the NTD-specific antibody C1596 displayed the greatest breadth of binding to VOCs, with cryo-EM structural analysis revealing recognition of a distinct NTD epitope outside of the site i antigenic supersite. Given C1596's favorable binding profile, we designed a series of bispecific antibodies (bsAbs) termed CoV2-biRNs, that featured both NTD and RBD specificities. Notably, two of the C1596-inclusive bsAbs, CoV2-biRN5 and CoV2-biRN7, retained potent in vitro neutralization activity against all Omicron variants tested, including XBB.1.5, EG.5.1, and BA.2.86, contrasting the diminished potency of parental antibodies delivered as monotherapies or as a cocktail. Furthermore, prophylactic delivery of CoV2-biRN5 significantly reduced the viral load within the lungs of K18-hACE2 mice following challenge with SARS-CoV-2 XBB.1.5. In conclusion, our NTD-RBD bsAbs offer promising potential for the design of resilient, next-generation antibody therapeutics against SARS-CoV-2 VOCs.
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Affiliation(s)
- Adonis A. Rubio
- Stanford Biosciences, Stanford School of Medicine; Stanford, USA
- Department of Biology, Stanford University; Stanford, USA
| | - Viren A. Baharani
- Laboratory of Retrovirology, The Rockefeller University; New York, USA
- Laboratory of Molecular Immunology, The Rockefeller University; New York, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center; Seattle, USA
| | - Megan Parada
- Department of Biology, Stanford University; Stanford, USA
| | | | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University; New York, USA
| | - Yu E. Lee
- Department of Biology, Stanford University; Stanford, USA
| | - Michael R. Eso
- Department of Biology, Stanford University; Stanford, USA
| | - Jennie Phung
- Department of Biology, Stanford University; Stanford, USA
| | - Israel Ramos
- Department of Biology, Stanford University; Stanford, USA
| | - Teresia Chen
- Department of Biology, Stanford University; Stanford, USA
| | - Gina El Nesr
- Stanford Biosciences, Stanford School of Medicine; Stanford, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center; Seattle, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University; New York, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University; New York, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| | - Christopher O. Barnes
- Department of Biology, Stanford University; Stanford, USA
- ChEM-H Institute, Stanford University; Stanford, CA
- Chan Zuckerberg Biohub; San Francisco, USA
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15
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Polmear J, Kealy L, Xu H, Good-Jacobson KL. A Touch of Immunology: improving accessibility to the science of antibodies for people with blindness, low vision and diverse needs. Immunol Cell Biol 2024; 102:326-330. [PMID: 37905389 DOI: 10.1111/imcb.12708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Immunology for all: Most scientific communication has historically been limited to visual imagery and the written or spoken word, often in the form of dense articles obscured by jargon. Clear communication of science is vital to enable the public to engage with important scientific discoveries and to limit medical distrust. However, scientific communication is often executed in a way which neglects people with blindness, low vision and diverse needs. Our aim for the exhibit at the Monash Sensory Science Exhibition on Autoimmunity 2023 at Monash University was to develop novel, tactile and informative models to help better communicate the scientific principles that underpin autoimmune disease and immunology. As B-cell biologists, we decided to focus our exhibit for this workshop on antibody-mediated autoimmunity. Antibodies are key components of the immune system, providing protection against a range of diverse pathogens. However, in the context of autoimmunity, they can also drive pathology.
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Affiliation(s)
- Jack Polmear
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
- Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Liam Kealy
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
- Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Hui Xu
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
- Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kim L Good-Jacobson
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
- Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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16
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Bryan M, Butt JN, Ding Z, Tokranova N, Cady N, Piorek B, Meinhart C, Tice J, Miller BL. A Multiplex "Disposable Photonics" Biosensor Platform and Its Application to Antibody Profiling in Upper Respiratory Disease. ACS Sens 2024; 9:1799-1808. [PMID: 38549498 PMCID: PMC11059096 DOI: 10.1021/acssensors.3c02225] [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: 10/22/2023] [Revised: 02/08/2024] [Accepted: 03/18/2024] [Indexed: 05/02/2024]
Abstract
Photonic technologies promise to deliver quantitative, multiplex, and inexpensive medical diagnostic platforms by leveraging the highly scalable processes developed for the fabrication of semiconductor microchips. However, in practice, the affordability of these platforms is limited by complex and expensive sample handling and optical alignment. We previously reported the development of a disposable photonic assay that incorporates inexpensive plastic micropillar microfluidic cards for sample delivery. That system as developed was limited to singleplex assays due to its optical configuration. To enable multiplexing, we report a new approach addressing multiplex light I/O, in which the outputs of individual grating couplers on a photonic chip are mapped to fibers in a fiber bundle. As demonstrated in the context of detecting antibody responses to influenza and SARS-CoV-2 antigens in human serum and saliva, this enables multiplexing in an inexpensive, disposable, and compact format.
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Affiliation(s)
- Michael
R. Bryan
- Department
of Dermatology, University of Rochester, Rochester, New York 14627, United States
- Department
of Biochemistry and Biophysics, University
of Rochester, Rochester, New York 14627, United States
| | - Jordan N. Butt
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Zhong Ding
- ZDing
Tech, LLC, Pittsford, New York 14534, United States
| | - Natalya Tokranova
- Department
of Nanoscale Science & Engineering, University at Albany, Albany, New York 12203, United States
| | - Nathaniel Cady
- Department
of Nanoscale Science & Engineering, University at Albany, Albany, New York 12203, United States
| | - Brian Piorek
- University
of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Carl Meinhart
- University
of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Joshua Tice
- QuidelOrtho,
Inc., Rochester, New York 14626, United States
| | - Benjamin L. Miller
- Department
of Dermatology, University of Rochester, Rochester, New York 14627, United States
- Department
of Biochemistry and Biophysics, University
of Rochester, Rochester, New York 14627, United States
- The
Institute of Optics, University of Rochester, Rochester, New York 14627, United States
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17
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Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MYS, Sigal A. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation. Nat Commun 2024; 15:2360. [PMID: 38491050 PMCID: PMC10943233 DOI: 10.1038/s41467-024-46673-2] [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: 08/10/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.
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Affiliation(s)
- Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | | | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Strauss van Graan
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | | | | | | | | | - Elizabeth Venter
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zanele Makhado
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Monjurul Hoque
- KwaDabeka Community Health Centre, KwaDabeka, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombulelo Magula
- Department of Internal Medicine, Nelson R. Mandela School of Medicine, University of Kwa-Zulu Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - 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.
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18
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Zedan HT, Smatti MK, Al-Sadeq DW, Al Khatib HA, Nicolai E, Pieri M, Bernardini S, Hssain AA, Taleb S, Qotba H, Issa K, Abu Raddad LJ, Althani AA, Nasrallah GK, Yassine HM. SARS-CoV-2 infection triggers more potent antibody-dependent cellular cytotoxicity (ADCC) responses than mRNA-, vector-, and inactivated virus-based COVID-19 vaccines. J Med Virol 2024; 96:e29527. [PMID: 38511514 DOI: 10.1002/jmv.29527] [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: 05/15/2023] [Revised: 02/08/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Neutralizing antibodies (NAbs) are elicited after infection and vaccination and have been well studied. However, their antibody-dependent cellular cytotoxicity (ADCC) functionality is still poorly characterized. Here, we investigated ADCC activity in convalescent sera from infected patients with wild-type (WT) severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) or omicron variant compared with three coronavirus disease 2019 (COVID-19) vaccine platforms and postvaccination breakthrough infection (BTI). We analyzed ADCC activity targeting SARS-CoV-2 spike (S) and nucleocapsid (N) proteins in convalescent sera following WT SARS-CoV-2-infection (n = 91), including symptomatic and asymptomatic infections, omicron-infection (n = 8), COVID-19 vaccination with messenger RNA- (mRNA)- (BNT162b2 or mRNA-1273, n = 77), adenovirus vector- (n = 41), and inactivated virus- (n = 46) based vaccines, as well as post-mRNA vaccination BTI caused by omicron (n = 28). Correlations between ADCC, binding, and NAb titers were reported. ADCC was elicited within the first month postinfection and -vaccination and remained detectable for ≥3 months. WT-infected symptomatic patients had higher S-specific ADCC levels than asymptomatic and vaccinated individuals. Also, no difference in N-specific ADCC activity was seen between symptomatic and asymptomatic patients, but the levels were higher than the inactivated vaccine. Notably, omicron infection showed reduced overall ADCC activity compared to WT SARS-CoV-2 infection. Although post-mRNA vaccination BTI elicited high levels of binding and NAbs, ADCC activity was significantly reduced. Also, there was no difference in ADCC levels across the four vaccines, although NAbs and binding antibody titers were significantly higher in mRNA-vaccinated individuals. All evaluated vaccine platforms are inferior in inducing ADCC compared to natural infection with WT SARS-CoV-2. The inactivated virus-based vaccine can induce N-specific ADCC activity, but its relevance to clinical outcomes requires further investigation. Our data suggest that ADCC could be used to estimate the extra-neutralization level against COVID-19 and provides evidence that vaccination should focus on other Fc-effector functions besides NAbs. Also, the decreased susceptibility of the omicron variant to ADCC offers valuable guidance for forthcoming efforts to identify the specific targets of antibodies facilitating ADCC.
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Affiliation(s)
- Hadeel T Zedan
- Infectious Diseases Department, Biomedical Research Center, Research Complex, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Maria K Smatti
- Infectious Diseases Department, Biomedical Research Center, Research Complex, Qatar University, Doha, Qatar
| | - Duaa W Al-Sadeq
- College of Medicine, Member of QU Health, Qatar University, Doha, Qatar
| | - Hebah A Al Khatib
- Infectious Diseases Department, Biomedical Research Center, Research Complex, Qatar University, Doha, Qatar
| | - Eleonora Nicolai
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Massimo Pieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Ali Ait Hssain
- Medical Intensive Care Unit, Hamad Medical Corporation, Doha, Qatar
| | - Sara Taleb
- Department of Research, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Hamda Qotba
- Department of Clinical Research, Primary Health Care Centers, Doha, Qatar
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Khodr Issa
- Proteomics, Inflammatory Response, and Mass Spectrometry (PRISM) Laboratory, INSERM U-1192, University of Lille, Lille, France
| | - Laith J Abu Raddad
- Department of Population Health Sciences, Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Asmaa A Althani
- Infectious Diseases Department, Biomedical Research Center, Research Complex, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Gheyath K Nasrallah
- Infectious Diseases Department, Biomedical Research Center, Research Complex, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Hadi M Yassine
- Infectious Diseases Department, Biomedical Research Center, Research Complex, Qatar University, Doha, Qatar
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19
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Zhang F, Schmidt F, Muecksch F, Wang Z, Gazumyan A, Nussenzweig MC, Gaebler C, Caskey M, Hatziioannou T, Bieniasz PD. SARS-CoV-2 spike glycosylation affects function and neutralization sensitivity. mBio 2024; 15:e0167223. [PMID: 38193662 PMCID: PMC10865855 DOI: 10.1128/mbio.01672-23] [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: 06/29/2023] [Accepted: 11/08/2023] [Indexed: 01/10/2024] Open
Abstract
The glycosylation of viral envelope proteins can play important roles in virus biology and immune evasion. The spike (S) glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) includes 22 N-linked glycosylation sequons and 17 O-linked glycosites. We investigated the effect of individual glycosylation sites on SARS-CoV-2 S function in pseudotyped virus infection assays and on sensitivity to monoclonal and polyclonal neutralizing antibodies. In most cases, the removal of individual glycosylation sites decreased the infectiousness of the pseudotyped virus. For glycosylation mutants in the N-terminal domain and the receptor-binding domain (RBD), reduction in pseudotype infectivity was predicted by a commensurate reduction in the level of virion-incorporated S protein and reduced S trafficking to the cell surface. Notably, the presence of a glycan at position N343 within the RBD had diverse effects on neutralization by RBD-specific monoclonal antibodies cloned from convalescent individuals. The N343 glycan reduced the overall sensitivity to polyclonal antibodies in plasma from COVID-19 convalescent individuals, suggesting a role for SARS-CoV-2 S glycosylation in immune evasion. However, vaccination of convalescent individuals produced neutralizing activity that was resilient to the inhibitory effect of the N343 glycan.IMPORTANCEThe attachment of glycans to the spike proteins of viruses during their synthesis and movement through the secretory pathway can affect their properties. This study shows that the glycans attached to the severe acute respiratory syndrome coronavirus-2 spike protein enable its movement to the cell surface and incorporation into virus particles. Certain glycans, including one that is attached to asparagine 343 in the receptor-binding domain of the spike protein, can also affect virus neutralization by antibodies. This glycan can increase or decrease sensitivity to individual antibodies, likely through direct effects on antibody epitopes and modulation of spike conformation. However, the overall effect of the glycan in the context of the polyclonal mixture of antibodies in convalescent serum is to reduce neutralization sensitivity. Overall, this study highlights the complex effects of glycosylation on spike protein function and immune evasion.
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Affiliation(s)
- Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
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20
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Abela IA, Schwarzmüller M, Ulyte A, Radtke T, Haile SR, Ammann P, Raineri A, Rueegg S, Epp S, Berger C, Böni J, Manrique A, Audigé A, Huber M, Schreiber PW, Scheier T, Fehr J, Weber J, Rusert P, Günthard HF, Kouyos RD, Puhan MA, Kriemler S, Trkola A, Pasin C. Cross-protective HCoV immunity reduces symptom development during SARS-CoV-2 infection. mBio 2024; 15:e0272223. [PMID: 38270455 PMCID: PMC10865973 DOI: 10.1128/mbio.02722-23] [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: 10/05/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Numerous clinical parameters link to severe coronavirus disease 2019, but factors that prevent symptomatic disease remain unknown. We investigated the impact of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and endemic human coronavirus (HCoV) antibody responses on symptoms in a longitudinal children cohort (n = 2,917) and a cross-sectional cohort including children and adults (n = 882), all first exposed to SARS-CoV-2 (March 2020 to March 2021) in Switzerland. Saliva (n = 4,993) and plasma (n = 7,486) antibody reactivity to the four HCoVs (subunit S1 [S1]) and SARS-CoV-2 (S1, receptor binding domain, subunit S2 [S2], nucleocapsid protein) was determined along with neutralizing activity against SARS-CoV-2 Wuhan, Alpha, Delta, and Omicron (BA.2) in a subset of individuals. Inferred recent SARS-CoV-2 infection was associated with a strong correlation between mucosal and systemic SARS-CoV-2 anti-spike responses. Individuals with pre-existing HCoV-S1 reactivity exhibited significantly higher antibody responses to SARS-CoV-2 in both plasma (IgG regression coefficients = 0.20, 95% CI = [0.09, 0.32], P < 0.001) and saliva (IgG regression coefficient = 0.60, 95% CI = [0.088, 1.11], P = 0.025). Saliva neutralization activity was modest but surprisingly broad, retaining activity against Wuhan (median NT50 = 32.0, 1Q-3Q = [16.4, 50.2]), Alpha (median NT50 = 34.9, 1Q-3Q = [26.0, 46.6]), and Delta (median NT50 = 28.0, 1Q-3Q = [19.9, 41.7]). In line with a rapid mucosal defense triggered by cross-reactive HCoV immunity, asymptomatic individuals presented with higher pre-existing HCoV-S1 activity in plasma (IgG HKU1, odds ratio [OR] = 0.53, 95% CI = [0.29,0.97], P = 0.038) and saliva (total HCoV, OR = 0.55, 95% CI = [0.33, 0.91], P = 0.019) and higher SARS-CoV-2 reactivity in saliva (IgG S2 fold change = 1.26, 95% CI = [1.03, 1.54], P = 0.030). By investigating the systemic and mucosal immune responses to SARS-CoV-2 and HCoVs in a population without prior exposure to SARS-CoV-2 or vaccination, we identified specific antibody reactivities associated with lack of symptom development.IMPORTANCEKnowledge of the interplay between human coronavirus (HCoV) immunity and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection is critical to understanding the coexistence of current endemic coronaviruses and to building knowledge potential future zoonotic coronavirus transmissions. This study, which retrospectively analyzed a large cohort of individuals first exposed to SARS-CoV-2 in Switzerland in 2020-2021, revealed several key findings. Pre-existing HCoV immunity, particularly mucosal antibody responses, played a significant role in improving SARS-CoV-2 immune response upon infection and reducing symptoms development. Mucosal neutralizing activity against SARS-CoV-2, although low in magnitude, retained activity against SARS-CoV-2 variants underlining the importance of maintaining local mucosal immunity to SARS-CoV-2. While the cross-protective effect of HCoV immunity was not sufficient to block infection by SARS-CoV-2, the present study revealed a remarkable impact on limiting symptomatic disease. These findings support the feasibility of generating pan-protective coronavirus vaccines by inducing potent mucosal immune responses.
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Affiliation(s)
- Irene A. Abela
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Agne Ulyte
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Thomas Radtke
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Sarah R. Haile
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Priska Ammann
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Alessia Raineri
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Sonja Rueegg
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Selina Epp
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Amapola Manrique
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Annette Audigé
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Peter W. Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jan Fehr
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Jacqueline Weber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F. Günthard
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Roger D. Kouyos
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Milo A. Puhan
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Susi Kriemler
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Collegium Helveticum, Zurich, Switzerland
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21
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Hie BL, Shanker VR, Xu D, Bruun TUJ, Weidenbacher PA, Tang S, Wu W, Pak JE, Kim PS. Efficient evolution of human antibodies from general protein language models. Nat Biotechnol 2024; 42:275-283. [PMID: 37095349 PMCID: PMC10869273 DOI: 10.1038/s41587-023-01763-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/28/2023] [Indexed: 04/26/2023]
Abstract
Natural evolution must explore a vast landscape of possible sequences for desirable yet rare mutations, suggesting that learning from natural evolutionary strategies could guide artificial evolution. Here we report that general protein language models can efficiently evolve human antibodies by suggesting mutations that are evolutionarily plausible, despite providing the model with no information about the target antigen, binding specificity or protein structure. We performed language-model-guided affinity maturation of seven antibodies, screening 20 or fewer variants of each antibody across only two rounds of laboratory evolution, and improved the binding affinities of four clinically relevant, highly mature antibodies up to sevenfold and three unmatured antibodies up to 160-fold, with many designs also demonstrating favorable thermostability and viral neutralization activity against Ebola and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudoviruses. The same models that improve antibody binding also guide efficient evolution across diverse protein families and selection pressures, including antibiotic resistance and enzyme activity, suggesting that these results generalize to many settings.
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Affiliation(s)
- Brian L Hie
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Varun R Shanker
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Theodora U J Bruun
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Payton A Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter S Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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22
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Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
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Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
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23
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Röltgen K, Boyd SD. Antibody and B Cell Responses to SARS-CoV-2 Infection and Vaccination: The End of the Beginning. ANNUAL REVIEW OF PATHOLOGY 2024; 19:69-97. [PMID: 37738512 DOI: 10.1146/annurev-pathmechdis-031521-042754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
As the COVID-19 pandemic has evolved during the past years, interactions between human immune systems, rapidly mutating and selected SARS-CoV-2 viral variants, and effective vaccines have complicated the landscape of individual immunological histories. Here, we review some key findings for antibody and B cell-mediated immunity, including responses to the highly mutated omicron variants; immunological imprinting and other impacts of successive viral antigenic variant exposures on antibody and B cell memory; responses in secondary lymphoid and mucosal tissues and non-neutralizing antibody-mediated immunity; responses in populations vulnerable to severe disease such as those with cancer, immunodeficiencies, and other comorbidities, as well as populations showing apparent resistance to severe disease such as many African populations; and evidence of antibody involvement in postacute sequelae of infection or long COVID. Despite the initial phase of the pandemic ending, human populations will continue to face challenges presented by this unpredictable virus.
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Affiliation(s)
- Katharina Röltgen
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA;
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
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24
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Fazli S, Thomas A, Estrada AE, Ross HA, Xthona Lee D, Kazmierczak S, Slifka MK, Montefiori D, Messer WB, Curlin ME. Contralateral second dose improves antibody responses to a 2-dose mRNA vaccination regimen. J Clin Invest 2024; 134:e176411. [PMID: 38227381 PMCID: PMC10940087 DOI: 10.1172/jci176411] [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: 10/06/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUNDVaccination is typically administered without regard to site of prior vaccination, but this factor may substantially affect downstream immune responses.METHODSWe assessed serological responses to initial COVID-19 vaccination in baseline seronegative adults who received second-dose boosters in the ipsilateral or contralateral arm relative to initial vaccination. We measured serum SARS-CoV-2 spike-specific Ig, receptor-binding domain-specific (RBD-specific) IgG, SARS-CoV-2 nucleocapsid-specific IgG, and neutralizing antibody titers against SARS-CoV-2.D614G (early strain) and SARS-CoV-2.B.1.1.529 (Omicron) at approximately 0.6, 8, and 14 months after boosting.RESULTSIn 947 individuals, contralateral boosting was associated with higher spike-specific serum Ig, and this effect increased over time, from a 1.1-fold to a 1.4-fold increase by 14 months (P < 0.001). A similar pattern was seen for RBD-specific IgG. Among 54 pairs matched for age, sex, and relevant time intervals, arm groups had similar antibody levels at study visit 2 (W2), but contralateral boosting resulted in significantly higher binding and neutralizing antibody titers at W3 and W4, with progressive increase over time, ranging from 1.3-fold (total Ig, P = 0.007) to 4.0-fold (pseudovirus neutralization to B.1.1.529, P < 0.001).CONCLUSIONSIn previously unexposed adults receiving an initial vaccine series with the BNT162b2 mRNA COVID-19 vaccine, contralateral boosting substantially increases antibody magnitude and breadth at times beyond 3 weeks after vaccination. This effect should be considered during arm selection in the context of multidose vaccine regimens.FUNDINGM.J. Murdock Charitable Trust, OHSU Foundation, NIH.
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Affiliation(s)
| | - Archana Thomas
- Oregon National Primate Research Center, Division of Neuroscience, and
| | - Abram E. Estrada
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | | | - David Xthona Lee
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Steven Kazmierczak
- Department of Pathology, Oregon Health & Science University, Portland, Oregon, USA
| | - Mark K. Slifka
- Oregon National Primate Research Center, Division of Neuroscience, and
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - William B. Messer
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Division of Infectious Diseases, Oregon Health & Science University, Portland, Oregon, USA
- Program in Epidemiology, Oregon Health & Science University, Portland State University School of Public Health, Portland, Oregon, USA
| | - Marcel E. Curlin
- Department of Occupational Health
- Department of Medicine, Division of Infectious Diseases, Oregon Health & Science University, Portland, Oregon, USA
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, USA
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25
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Zang T, Osei Kuffour E, Baharani VA, Canis M, Schmidt F, Da Silva J, Lercher A, Chaudhary P, Hoffmann HH, Gazumyan A, Miranda IC, MacDonald MR, Rice CM, Nussenzweig MC, Hatziioannou T, Bieniasz PD. Heteromultimeric sarbecovirus receptor binding domain immunogens primarily generate variant-specific neutralizing antibodies. Proc Natl Acad Sci U S A 2023; 120:e2317367120. [PMID: 38096415 PMCID: PMC10740387 DOI: 10.1073/pnas.2317367120] [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: 10/08/2023] [Accepted: 10/23/2023] [Indexed: 12/18/2023] Open
Abstract
Vaccination will likely be a key component of strategies to curtail or prevent future sarbecovirus pandemics and to reduce the prevalence of infection and disease by future SARS-CoV-2 variants. A "pan-sarbecovirus" vaccine, that provides maximum possible mitigation of human disease, should elicit neutralizing antibodies with maximum possible breadth. By positioning multiple different receptor binding domain (RBD) antigens in close proximity on a single immunogen, it is postulated that cross-reactive B cell receptors might be selectively engaged. Heteromultimeric vaccines could therefore elicit individual antibodies that neutralize a broad range of viral species. Here, we use model systems to investigate the ability of multimeric sarbecovirus RBD immunogens to expand cross-reactive B cells and elicit broadly reactive antibodies. Homomultimeric RBD immunogens generated higher serum neutralizing antibody titers than the equivalent monomeric immunogens, while heteromultimeric RBD immunogens generated neutralizing antibodies recognizing each RBD component. Moreover, RBD heterodimers elicited a greater fraction of cross-reactive germinal center B cells and cross-reactive RBD binding antibodies than did homodimers. However, when serum antibodies from RBD heterodimer-immunized mice were depleted using one RBD component, neutralization activity against the homologous viral pseudotype was removed, but neutralization activity against pseudotypes corresponding to the other RBD component was unaffected. Overall, simply combining divergent RBDs in a single immunogen generates largely separate sets of individual RBD-specific neutralizing serum antibodies that are mostly incapable of neutralizing viruses that diverge from the immunogen components.
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Affiliation(s)
- Trinity Zang
- Laboratory of Retrovirology, The Rockefeller University, New York, NY10065
- HHMI, The Rockefeller University, New York, NY10065
| | | | - Viren A. Baharani
- Laboratory of Retrovirology, The Rockefeller University, New York, NY10065
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY10065
| | - Marie Canis
- Laboratory of Retrovirology, The Rockefeller University, New York, NY10065
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY10065
| | - Justin Da Silva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY10065
| | - Alexander Lercher
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY10065
| | - Pooja Chaudhary
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY10065
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY10065
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY10065
| | - Ileana C. Miranda
- Laboratory of Comparative Pathology, The Rockefeller University, New York, NY10065
| | - Margaret R. MacDonald
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY10065
| | - Charles M. Rice
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY10065
| | - Michel C. Nussenzweig
- HHMI, The Rockefeller University, New York, NY10065
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY10065
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY10065
- HHMI, The Rockefeller University, New York, NY10065
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26
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Korenkov M, Zehner M, Cohen-Dvashi H, Borenstein-Katz A, Kottege L, Janicki H, Vanshylla K, Weber T, Gruell H, Koch M, Diskin R, Kreer C, Klein F. Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants. Immunity 2023; 56:2803-2815.e6. [PMID: 38035879 DOI: 10.1016/j.immuni.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/19/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Somatic hypermutation (SHM) drives affinity maturation and continues over months in SARS-CoV-2-neutralizing antibodies (nAbs). However, several potent SARS-CoV-2 antibodies carry no or only a few mutations, leaving the question of how ongoing SHM affects neutralization unclear. Here, we reverted variable region mutations of 92 antibodies and tested their impact on SARS-CoV-2 binding and neutralization. Reverting higher numbers of mutations correlated with decreasing antibody functionality. However, for some antibodies, including antibodies of the public clonotype VH1-58, neutralization of Wu01 remained unaffected. Although mutations were dispensable for Wu01-induced VH1-58 antibodies to neutralize Alpha, Beta, and Delta variants, they were critical for Omicron BA.1/BA.2 neutralization. We exploited this knowledge to convert the clinical antibody tixagevimab into a BA.1/BA.2 neutralizer. These findings broaden our understanding of SHM as a mechanism that not only improves antibody responses during affinity maturation but also contributes to antibody diversification, thus increasing the chances of neutralizing viral escape variants.
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Affiliation(s)
- Michael Korenkov
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Matthias Zehner
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hadas Cohen-Dvashi
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Aliza Borenstein-Katz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Lisa Kottege
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hanna Janicki
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, University of Cologne, 50931 Cologne, Germany
| | - Ron Diskin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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27
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Weber T, Dähling S, Rose S, Affeldt P, Vanshylla K, Ullrich L, Gieselmann L, Teipel F, Gruell H, Di Cristanziano V, Kim DS, Georgiou G, Koch M, Kreer C, Klein F. Enhanced SARS-CoV-2 humoral immunity following breakthrough infection builds upon the preexisting memory B cell pool. Sci Immunol 2023; 8:eadk5845. [PMID: 37976348 DOI: 10.1126/sciimmunol.adk5845] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
The human immune response must continuously adapt to newly emerging SARS-CoV-2 variants. To investigate how B cells respond to repeated SARS-CoV-2 antigen exposure by Wu01 booster vaccination and Omicron breakthrough infection, we performed a molecular longitudinal analysis of the memory B cell pool. We demonstrate that a subsequent breakthrough infection substantially increases the frequency of B cells encoding SARS-CoV-2-neutralizing antibodies. However, this is not primarily attributable to maturation, but to selection of preexisting B cell clones. Moreover, broadly reactive memory B cells arose early and even neutralized highly mutated variants like XBB.1.5 that the individuals had not encountered. Together, our data show that SARS-CoV-2 immunity is largely imprinted on Wu01 over the course of multiple antigen contacts but can respond to new variants through preexisting diversity.
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Affiliation(s)
- Timm Weber
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Sabrina Dähling
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Svea Rose
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Patrick Affeldt
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kanika Vanshylla
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Leon Ullrich
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lutz Gieselmann
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Finn Teipel
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Henning Gruell
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Dae Sung Kim
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - George Georgiou
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA
- Department of Chemical Engineering and Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, Austin, Texas, USA
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty and University of Cologne, Cologne, Germany
| | - Christoph Kreer
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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28
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Seow J, Shalim ZA, Graham C, Kimuda S, Pillai A, Lechmere T, Kurshan A, Khimji AM, Snell LB, Nebbia G, Mant C, Waters A, Fox J, Malim MH, Doores KJ. Broad and potent neutralizing antibodies are elicited in vaccinated individuals following Delta/BA.1 breakthrough infection. mBio 2023; 14:e0120623. [PMID: 37747187 PMCID: PMC10653880 DOI: 10.1128/mbio.01206-23] [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: 05/10/2023] [Accepted: 08/02/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE With the emergence of SARS-CoV-2 viral variants, there has been an increase in infections in vaccinated individuals. Here, we isolated monoclonal antibodies (mAbs) from individuals experiencing a breakthrough infection (Delta or BA.1) to determine how exposure to a heterologous Spike broadens the neutralizing antibody response at the monoclonal level. All mAbs isolated had reactivity to the Spike of the vaccine and infection variant. While many mAbs showed reduced neutralization of current circulating variants, we identified mAbs with broad and potent neutralization of BA.2.75.2, XBB, XBB.1.5, and BQ.1.1 indicating the presence of conserved epitopes on Spike. These results indicate that variant-based vaccine boosters have the potential to broaden the vaccine response.
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Affiliation(s)
- Jeffrey Seow
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Zayed A. Shalim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Simon Kimuda
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Aswin Pillai
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Thomas Lechmere
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ashwini Kurshan
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Atika M. Khimji
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Luke B. Snell
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Christine Mant
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Infectious Diseases Biobank, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Anele Waters
- Harrison Wing, Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Julie Fox
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Harrison Wing, Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Katie J. Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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Ghoula M, Deyawe Kongmeneck A, Eid R, Camproux AC, Moroy G. Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein. J Phys Chem B 2023; 127:8586-8602. [PMID: 37775095 PMCID: PMC10578311 DOI: 10.1021/acs.jpcb.3c01467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/20/2023] [Indexed: 10/01/2023]
Abstract
SARS-CoV-2 strains have made an appearance across the globe, causing over 757 million cases and over 6.85 million deaths at the time of writing. The emergence of these variants shows the amplitude of genetic variation to which the wild-type strains have been subjected. The rise of the different SARS-CoV-2 variants resulting from such genetic modification has significantly affected COVD-19's major impact on proliferation, virulence, and clinics. With the emergence of the variants of concern, the spike protein has been identified as a possible therapeutic target due to its critical role in binding to human cells and pathogenesis. These mutations could be linked to functional heterogeneity and use a different infection strategy. For example, the Omicron variant's multiple mutations should be carefully examined, as they represent one of the most widely spread strains and hint to us that there may be more genetic changes in the virus. As a result, we applied a common protocol where we reconstructed SARS-CoV-2 variants of concern and performed molecular dynamics simulations to study the stability of the ACE2-RBD complex in each variant. We also carried out free energy calculations to compare the binding and biophysical properties of the different SARS-CoV-2 variants when they interact with ACE2. Therefore, we were able to obtain consistent results and uncover new crucial residues that were essential for preserving a balance between maintaining a high affinity for ACE2 and the capacity to evade RBD-targeted antibodies. Our detailed structural analysis showed that SARS-CoV-2 variants of concern show a higher affinity for ACE2 compared to the Wuhan strain. Additionally, residues K417N and E484K/A might play a crucial role in antibody evasion, whereas Q498R and N501Y are specifically mutated to strengthen RBD affinity to ACE2 and, thereby, increase the viral effect of the COVID-19 virus.
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Affiliation(s)
- Mariem Ghoula
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Audrey Deyawe Kongmeneck
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Rita Eid
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Anne-Claude Camproux
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Gautier Moroy
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
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30
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Zhang Z, Wu S, Liu Y, Li K, Fan P, Song X, Wang Y, Zhao Z, Zhang X, Shang J, Zhang J, Xu J, Li Y, Li Y, Zhang J, Fu K, Wang B, Hao M, Zhang G, Long P, Qiu Z, Zhu T, Liu S, Zhang Y, Shao F, Lv P, Yang Y, Zhao X, Sun Y, Hou L, Chen W. Boosting with an aerosolized Ad5-nCoV elicited robust immune responses in inactivated COVID-19 vaccines recipients. Front Immunol 2023; 14:1239179. [PMID: 37868993 PMCID: PMC10585368 DOI: 10.3389/fimmu.2023.1239179] [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: 06/14/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction The SARS-CoV-2 Omicron variant has become the dominant SARS-CoV-2 variant and exhibits immune escape to current COVID-19 vaccines, the further boosting strategies are required. Methods We have conducted a non-randomized, open-label and parallel-controlled phase 4 trial to evaluate the magnitude and longevity of immune responses to booster vaccination with intramuscular adenovirus vectored vaccine (Ad5-nCoV), aerosolized Ad5-nCoV, a recombinant protein subunit vaccine (ZF2001) or homologous inactivated vaccine (CoronaVac) in those who received two doses of inactivated COVID-19 vaccines. Results The aerosolized Ad5-nCoV induced the most robust and long-lasting neutralizing activity against Omicron variant and IFNg T-cell response among all the boosters, with a distinct mucosal immune response. SARS-CoV-2-specific mucosal IgA response was substantially generated in subjects boosted with the aerosolized Ad5-nCoV at day 14 post-vaccination. At month 6, participants boosted with the aerosolized Ad5-nCoV had remarkably higher median titer and seroconversion of the Omicron BA.4/5-specific neutralizing antibody than those who received other boosters. Discussion Our findings suggest that aerosolized Ad5-nCoV may provide an efficient alternative in response to the spread of the Omicron BA.4/5 variant. Clinical trial registration https://www.chictr.org.cn/showproj.html?proj=152729, identifier ChiCTR2200057278.
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Affiliation(s)
- Zhe Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Shipo Wu
- Beijing Institute of Biotechnology, Beijing, China
| | - Yawei Liu
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | - Kailiang Li
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | - Pengfei Fan
- Beijing Institute of Biotechnology, Beijing, China
| | | | - Yudong Wang
- Beijing Institute of Biotechnology, Beijing, China
| | | | - Xianwei Zhang
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | - Jin Shang
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | | | - Jinghan Xu
- Beijing Institute of Biotechnology, Beijing, China
| | - Yao Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Yaohui Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Jipeng Zhang
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | - Kefan Fu
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | - Busen Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Meng Hao
- Beijing Institute of Biotechnology, Beijing, China
| | | | - Pengwei Long
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | - Ziyu Qiu
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | - Tao Zhu
- CanSino Biologics Inc., Tianjin, China
| | - Shuling Liu
- Beijing Institute of Biotechnology, Beijing, China
| | - Yue Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Fangze Shao
- Beijing Institute of Biotechnology, Beijing, China
| | - Peng Lv
- Beijing Institute of Biotechnology, Beijing, China
| | - Yilong Yang
- Beijing Institute of Biotechnology, Beijing, China
| | - Xiaofan Zhao
- Beijing Institute of Biotechnology, Beijing, China
| | - Yufa Sun
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | - Lihua Hou
- Beijing Institute of Biotechnology, Beijing, China
| | - Wei Chen
- Beijing Institute of Biotechnology, Beijing, China
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31
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Hu D, Irving AT. Massively-multiplexed epitope mapping techniques for viral antigen discovery. Front Immunol 2023; 14:1192385. [PMID: 37818363 PMCID: PMC10561112 DOI: 10.3389/fimmu.2023.1192385] [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: 03/23/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Following viral infection, viral antigens bind specifically to receptors on the surface of lymphocytes thereby activating adaptive immunity in the host. An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key sites for the activation of adaptive immunity. The complexity and diverse range of epitopes are essential to study and map for the diagnosis of disease, the design of vaccines and for immunotherapy. Mapping the location of these specific epitopes has become a hot topic in immunology and immune therapy. Recently, epitope mapping techniques have evolved to become multiplexed, with the advent of high-throughput sequencing and techniques such as bacteriophage-display libraries and deep mutational scanning. Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.
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Affiliation(s)
- Diya Hu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Aaron T. Irving
- Department of Clinical Laboratory Studies, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
- Biomedical and Health Translational Research Centre of Zhejiang Province (BIMET), Haining, China
- College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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32
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Quirk GE, Schoenle MV, Peyton KL, Uhrlaub JL, Lau B, Burgess JL, Ellingson K, Beitel S, Romine J, Lutrick K, Fowlkes A, Britton A, Tyner HL, Caban-Martinez AJ, Naleway A, Gaglani M, Yoon S, Edwards L, Olsho L, Dake M, LaFleur BJ, Nikolich JŽ, Sprissler R, Worobey M, Bhattacharya D. Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295384. [PMID: 37745498 PMCID: PMC10516057 DOI: 10.1101/2023.09.12.23295384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Vaccine-induced immunity may impact subsequent de novo responses to drifted epitopes in SARS-CoV-2 variants, but this has been difficult to quantify due to the challenges in recruiting unvaccinated control groups whose first exposure to SARS-CoV-2 is a primary infection. Through local, statewide, and national SARS-CoV-2 testing programs, we were able to recruit cohorts of individuals who had recovered from either primary or post-vaccination infections by either the Delta or Omicron BA.1 variants. Regardless of variant, we observed greater Spike-specific and neutralizing antibody responses in post-vaccination infections than in those who were infected without prior vaccination. Through analysis of variant-specific memory B cells as markers of de novo responses, we observed that Delta and Omicron BA.1 infections led to a marked shift in immunodominance in which some drifted epitopes elicited minimal responses, even in primary infections. Prior immunity through vaccination had a small negative impact on these de novo responses, but this did not correlate with cross-reactive memory B cells, arguing against competitive inhibition of naïve B cells. We conclude that dampened de novo B cell responses against drifted epitopes are mostly a function of altered immunodominance hierarchies that are apparent even in primary infections, with a more modest contribution from pre-existing immunity, perhaps due to accelerated antigen clearance.
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Affiliation(s)
- Grace E Quirk
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marta V Schoenle
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Kameron L Peyton
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Jennifer L Uhrlaub
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Branden Lau
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Jefferey L Burgess
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Katherine Ellingson
- Department of Epidemiology and Biostatistics, Zuckerman College of Public Health, University of Arizona, Tucson
| | - Shawn Beitel
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - James Romine
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Karen Lutrick
- College of Medicine-Tucson, University of Arizona, Tucson, Arizona, USA
| | - Ashley Fowlkes
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Amadea Britton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Harmony L Tyner
- St. Luke's Regional Health Care System, Duluth, Minnesota, USA
| | | | - Allison Naleway
- Kaiser Permanente Northwest Center for Health Research, Portland, Oregon, USA
| | - Manjusha Gaglani
- Baylor Scott & White Health and Texas A&M University College of Medicine, Temple, Texas, USA
| | - Sarang Yoon
- Rocky Mountain Center for Occupational and Environmental Health, Department of Family and Preventive Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | | | | | - Michael Dake
- Office of the Senior Vice-President for Health Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Janko Ž Nikolich
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Ryan Sprissler
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
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33
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Farnsworth CW, O’Neil CA, Dalton C, McDonald D, Vogt L, Hock K, Arter O, Wallace MA, Muenks C, Amor M, Alvarado K, Peacock K, Jolani K, Fraser VJ, Burnham CAD, Babcock HM, Budge PJ, Kwon JH. Association between SARS-CoV-2 Symptoms, Ct Values, and Serological Response in Vaccinated and Unvaccinated Healthcare Personnel. J Appl Lab Med 2023; 8:871-886. [PMID: 37478837 PMCID: PMC10482509 DOI: 10.1093/jalm/jfad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/15/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND SARS-CoV-2 vaccines are effective at reducing symptomatic and asymptomatic COVID-19. Limited studies have compared symptoms, threshold cycle (Ct) values from reverse transcription (RT)-PCR testing, and serological testing results between previously vaccinated vs unvaccinated populations with SARS-CoV-2 infection. METHODS Healthcare personnel (HCP) with a positive SARS-CoV-2 RT-PCR test within the previous 14 to 28 days completed surveys including questions about demographics, medical conditions, social factors, and symptoms of COVID-19. Ct values were observed, and serological testing was performed for anti-nucleocapsid (anti-N) and anti-Spike (anti-S) antibodies at enrollment and 40 to 90 days later. Serological results were compared to HCP with no known SARS-CoV-2 infection and negative anti-N testing. RESULTS There were 104 unvaccinated/not fully vaccinated and 77 vaccinated HCP with 2 doses of an mRNA vaccine at time of infection. No differences in type or duration of symptoms were reported (P = 0.45). The median (interquartile range [IQR]) Ct was 21.4 (17.6-24.6) and 21.5 (18.1-24.6) for the unvaccinated and vaccinated HCP, respectively. Higher anti-N IgG was observed in unvaccinated HCP (5.08 S/CO, 3.08-6.92) than vaccinated (3.61 signal to cutoff ratio [S/CO], 2.16-5.05). Anti-S IgG was highest among vaccinated HCP with infection (34 285 aribitrary units [AU]/mL, 17 672-61 775), followed by vaccinated HCP with no prior infection (1452 AU/mL, 791-2943), then unvaccinated HCP with infection (829 AU/mL, 290-1555). Anti-S IgG decreased 1.56% (0.9%-1.79%) per day in unvaccinated and 0.38% (0.03%-0.94%) in vaccinated HCP. CONCLUSIONS Vaccinated HCP infected with SARS-CoV-2 reported comparable symptoms and had similar Ct values relative to unvaccinated. However, vaccinated HCP had increased and prolonged anti-S and decreased anti-N response relative to unvaccinated.
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Affiliation(s)
- Christopher W Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Caroline A O’Neil
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Claire Dalton
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - David McDonald
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Lucy Vogt
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Karl Hock
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Olivia Arter
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Meghan A Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Carol Muenks
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Mostafa Amor
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Kelly Alvarado
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Kate Peacock
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Kevin Jolani
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Victoria J Fraser
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Hilary M Babcock
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Phillip J Budge
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Jennie H Kwon
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
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Addetia A, Piccoli L, Case JB, Park YJ, Beltramello M, Guarino B, Dang H, de Melo GD, Pinto D, Sprouse K, Scheaffer SM, Bassi J, Silacci-Fregni C, Muoio F, Dini M, Vincenzetti L, Acosta R, Johnson D, Subramanian S, Saliba C, Giurdanella M, Lombardo G, Leoni G, Culap K, McAlister C, Rajesh A, Dellota E, Zhou J, Farhat N, Bohan D, Noack J, Chen A, Lempp FA, Quispe J, Kergoat L, Larrous F, Cameroni E, Whitener B, Giannini O, Cippà P, Ceschi A, Ferrari P, Franzetti-Pellanda A, Biggiogero M, Garzoni C, Zappi S, Bernasconi L, Kim MJ, Rosen LE, Schnell G, Czudnochowski N, Benigni F, Franko N, Logue JK, Yoshiyama C, Stewart C, Chu H, Bourhy H, Schmid MA, Purcell LA, Snell G, Lanzavecchia A, Diamond MS, Corti D, Veesler D. Neutralization, effector function and immune imprinting of Omicron variants. Nature 2023; 621:592-601. [PMID: 37648855 PMCID: PMC10511321 DOI: 10.1038/s41586-023-06487-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023]
Abstract
Currently circulating SARS-CoV-2 variants have acquired convergent mutations at hot spots in the receptor-binding domain1 (RBD) of the spike protein. The effects of these mutations on viral infection and transmission and the efficacy of vaccines and therapies remains poorly understood. Here we demonstrate that recently emerged BQ.1.1 and XBB.1.5 variants bind host ACE2 with high affinity and promote membrane fusion more efficiently than earlier Omicron variants. Structures of the BQ.1.1, XBB.1 and BN.1 RBDs bound to the fragment antigen-binding region of the S309 antibody (the parent antibody for sotrovimab) and human ACE2 explain the preservation of antibody binding through conformational selection, altered ACE2 recognition and immune evasion. We show that sotrovimab binds avidly to all Omicron variants, promotes Fc-dependent effector functions and protects mice challenged with BQ.1.1 and hamsters challenged with XBB.1.5. Vaccine-elicited human plasma antibodies cross-react with and trigger effector functions against current Omicron variants, despite a reduced neutralizing activity, suggesting a mechanism of protection against disease, exemplified by S309. Cross-reactive RBD-directed human memory B cells remained dominant even after two exposures to Omicron spikes, underscoring the role of persistent immune imprinting.
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Affiliation(s)
- Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | - Ha Dang
- Vir Biotechnology, San Francisco, CA, USA
| | - Guilherme Dias de Melo
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | | | - Kaitlin Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Suzanne M Scheaffer
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Dana Bohan
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Alex Chen
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Lauriane Kergoat
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | - Florence Larrous
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | | | - Bradley Whitener
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Pietro Cippà
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Stephanie Zappi
- Division of Nephrology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Luca Bernasconi
- Institute of Laboratory Medicine, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Min Jeong Kim
- Division of Nephrology, Cantonal Hospital Aarau, Aarau, Switzerland
| | | | | | | | | | - Nicholas Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jennifer K Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | | | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Helen Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | | | | | | | | | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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Zhang Y, Li Q, Liu N, Hu J, Lin X, Huang M, Wei Y, Qi X, Chen X. Secure reversal of immune evasion from refractory NSCLC and highly contagious CoV-2 mutants by using 3D-engineered multifunctional biologics. Bioeng Transl Med 2023; 8:e10554. [PMID: 37693048 PMCID: PMC10487317 DOI: 10.1002/btm2.10554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/22/2023] [Accepted: 05/16/2023] [Indexed: 09/12/2023] Open
Abstract
There is an imperative choice to develop a secure feasible strategy to address evasion dynamics of refractory tumors and SARS-CoV-2-variants, while stem cell-based protocol may be more reliable as its unique ability for resetting multifunctional immunity to address progressive tumor and the constantly-evolving virus. In this study, spheroid-embryonoid stem cells from mature somatic cells were engineered as multifunctional biologics (3D-E/BSC) and inoculated in senile rhesus to identify secure potential against immune-evasion from viral-variants. Meanwhile, a cohort of eligible patients with stage IV NSCLC were approved for phase I clinical trials. Subsequently, long-lasting security and efficacy were validated by primate and clinical trials (p < 0.01) in that it could not only stimulate serological immunity, but also reset core immunity for hosts to address variant evasion after 3D-E/BSC withdrawal. Particularly, illustrated by single-cell evolving trajectory, 3D-E/BSC had securely reset senile thymus of aging hosts to remodel core immunity by rearranging naive rhythm to evolve TRGC2+/JCHAIN+NKT clusters to abolish tumoral and viral evasion dynamics with path-feedbacks of NSCLC and COVID-19 simultaneously activated, leading to continuous blockade of breakthrough infection of viral-mutants and long-term survival in one-third of terminal patients without adjuvant required. Our study may pioneer a practical multifunctional strategy to eliminate evasion of SARS-CoV-2 variants and refractory NSCLC so as for victims to restart a new life-equation.
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Affiliation(s)
- Yanna Zhang
- Department of Blood Transfusion, Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
- Department of Biotherapy, Cancer Center and State Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Qian Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Nanxi Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Jianchuan Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xiaojuan Lin
- Department of Gynecology & Obstetrics, West China Second HospitalSichuan UniversityChengduChina
| | - Meijuan Huang
- Division of Thoracic Tumor Multimodality Treatment and Department of Medical Oncology, Cancer Center, West China HospitalSichuan UniversityChengduChina
| | - Yuquan Wei
- Department of Biotherapy, Cancer Center and State Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
- Division of Thoracic Tumor Multimodality Treatment and Department of Medical Oncology, Cancer Center, West China HospitalSichuan UniversityChengduChina
| | - Xiaorong Qi
- Department of Gynecology & Obstetrics, West China Second HospitalSichuan UniversityChengduChina
| | - Xiancheng Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
- Division of Thoracic Tumor Multimodality Treatment and Department of Medical Oncology, Cancer Center, West China HospitalSichuan UniversityChengduChina
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Singh G, Abbad A, Tcheou J, Mendu DR, Firpo-Betancourt A, Gleason C, Srivastava K, Cordon-Cardo C, Simon V, Krammer F, Carreño JM. Binding and Avidity Signatures of Polyclonal Sera From Individuals With Different Exposure Histories to Severe Acute Respiratory Syndrome Coronavirus 2 Infection, Vaccination, and Omicron Breakthrough Infections. J Infect Dis 2023; 228:564-575. [PMID: 37104046 PMCID: PMC10469125 DOI: 10.1093/infdis/jiad116] [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: 11/11/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND The number of exposures to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to vaccine antigens affect the magnitude and avidity of the polyclonal response. METHODS We studied binding and avidity of different antibody isotypes to the spike, the receptor-binding domain (RBD), and the nucleoprotein (NP) of wild-type (WT) and BA.1 SARS-CoV-2 in convalescent, mRNA vaccinated and/or boosted, hybrid immune individuals and in individuals with breakthrough cases during the peak of the BA.1 wave. RESULTS We found an increase in spike-binding antibodies and antibody avidity with increasing number of exposures to infection and/or vaccination. NP antibodies were detectible in convalescent individuals and a proportion of breakthrough cases, but they displayed low avidity. Omicron breakthrough infections elicited high levels of cross-reactive antibodies between WT and BA.1 antigens in vaccinated individuals without prior infection directed against the spike and RBD. The magnitude of the antibody response and avidity correlated with neutralizing activity against WT virus. CONCLUSIONS The magnitude and quality of the antibody response increased with the number of antigenic exposures, including breakthrough infections. However, cross-reactivity of the antibody response after BA.1 breakthroughs, was affected by the number of prior exposures.
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Affiliation(s)
- Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anass Abbad
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Johnstone Tcheou
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Demodara Rao Mendu
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo Firpo-Betancourt
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Charles Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, 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
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, 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
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Plikusiene I, Maciulis V, Vertelis V, Juciute S, Balevicius S, Ramanavicius A, Talbot J, Ramanaviciene A. Revealing the SARS-CoV-2 Spike Protein and Specific Antibody Immune Complex Formation Mechanism for Precise Evaluation of Antibody Affinity. Int J Mol Sci 2023; 24:13220. [PMID: 37686023 PMCID: PMC10487573 DOI: 10.3390/ijms241713220] [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: 06/27/2023] [Revised: 08/04/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
The profound understanding and detailed evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (SCoV2-S) protein and specific antibody interaction mechanism is of high importance in the development of immunosensors for COVID-19. In the present work, we studied a model system of immobilized SCoV2-S protein and specific monoclonal antibodies by molecular dynamics of immune complex formation in real time. We simultaneously applied spectroscopic ellipsometry and quartz crystal microbalance with dissipation to reveal the features and steps of the immune complex formation. We showed direct experimental evidence based on acoustic and optical measurements that the immune complex between covalently immobilized SCoV2-S and specific monoclonal antibodies is formed in two stages. Based on these findings it was demonstrated that applying a two-step binding mathematical model for kinetics analysis leads to a more precise determination of interaction rate constants than that determined by the 1:1 Langmuir binding model. Our investigation showed that the equilibrium dissociation constants (KD) determined by a two-step binding model and the 1:1 Langmuir model could differ significantly. The reported findings can facilitate a deeper understanding of antigen-antibody immune complex formation steps and can open a new way for the evaluation of antibody affinity towards corresponding antigens.
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Affiliation(s)
- Ieva Plikusiene
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Vincentas Maciulis
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Vilius Vertelis
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Silvija Juciute
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
| | - Saulius Balevicius
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Arunas Ramanavicius
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Julian Talbot
- Laboratoire de Physique Théorique de la Matière Condensée, Sorbonne Université, UMR 7600, 4 Place Jussieu, CEDEX 05, 75252 Paris, France
| | - Almira Ramanaviciene
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
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Hayashi H, Sun J, Yanagida Y, Otera T, Tai JA, Nishikawa T, Yamashita K, Sakaguchi N, Yoshida S, Baba S, Chang CY, Shimamura M, Okamoto S, Amaishi Y, Chono H, Mineno J, Rakugi H, Morishita R, Nakagami H. Intradermal administration of DNA vaccine targeting Omicron SARS-CoV-2 via pyro-drive jet injector provides the prolonged neutralizing antibody production via germinal center reaction. Sci Rep 2023; 13:13033. [PMID: 37563266 PMCID: PMC10415318 DOI: 10.1038/s41598-023-40172-y] [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: 03/08/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023] Open
Abstract
Emerging SARS-CoV-2 Omicron variants are highly contagious with enhanced immune escape mechanisms against the initially approved COVID-19 vaccines. Therefore, we require stable alternative-platform vaccines that confer protection against newer variants of SARS-CoV-2. We designed an Omicron B.1.1.529 specific DNA vaccine using our DNA vaccine platform and evaluated the humoral and cellular immune responses. SD rats intradermally administered with Omicron-specific DNA vaccine via pyro-drive jet injector (PJI) thrice at 2-week intervals elicited high antibody titers against the Omicron subvariants as well as the ancestral strain. Indeed, the Omicron B.1.1.529-specific antibody titer and neutralizing antibody were higher than that of other strains. Longitudinal monitoring indicated that anti-spike (ancestral and Omicron) antibody titers decreased toward 30 weeks after the first vaccination dose. However, neutralization activity remained unaltered. Germinal center formation was histologically detected in lymph nodes in rats immunized with Omicron DNA vaccine. Ancestral spike-specific immune cell response was slightly weaker than Omicron spike-specific response in splenocytes with Omicron-adapted DNA vaccine, evaluated by ELISpot assay. Collectively, our findings suggest that Omicron targeting DNA vaccines via PJI can elicit robust durable antibody production mediated by germinal center reaction against this new variant as well as partially against the spike protein of other SARS-CoV-2 variants.
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Affiliation(s)
- Hiroki Hayashi
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
| | - Jiao Sun
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuka Yanagida
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takako Otera
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Anges Inc., Tokyo, Japan
| | - Jiayu A Tai
- Department of Device Application for Molecular Therapeutics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Tomoyuki Nishikawa
- Department of Device Application for Molecular Therapeutics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kunihiko Yamashita
- Department of Device Application for Molecular Therapeutics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Daicel Co, Osaka, Japan
| | | | - Shota Yoshida
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Geriatric Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Satoshi Baba
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Geriatric Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Chin Yang Chang
- Department of Gene and Stem Cell Regenerative Therapy, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Munehisa Shimamura
- Department of Gene and Stem Cell Regenerative Therapy, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | | | | | | | | | - Hiromi Rakugi
- Department of Geriatric Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Ryuichi Morishita
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Hironori Nakagami
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Division of Microbiology and Immunology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
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Li D, Xu M, Hooper AT, Rofail D, Mohammadi KA, Chen Y, Ali S, Norton T, Weinreich DM, Musser BJ, Hamilton JD, Geba GP. Casirivimab + imdevimab accelerates symptom resolution linked to improved COVID-19 outcomes across susceptible antibody and risk profiles. Sci Rep 2023; 13:12784. [PMID: 37550377 PMCID: PMC10406852 DOI: 10.1038/s41598-023-39681-7] [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: 12/21/2022] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
Severe, protracted symptoms are associated with poor outcomes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In a placebo-controlled study of casirivimab and imdevimab (CAS + IMD) in persons at high risk of severe coronavirus disease 2019 (COVID-19; n = 3816), evolution of individual symptoms was assessed for resolution patterns across risk factors, and baseline SARS-CoV-2-specific antibody responses against S1 and N domains. CAS + IMD versus placebo provided statistically significant resolution for 17/23 symptoms, with greater response linked to absence of endogenous anti-SARS-CoV-2 immunoglobulin (Ig)G, IgA, or specific neutralizing antibodies at baseline, or high baseline viral load. Resolution of five key symptoms (onset days 3-5)-dyspnea, cough, feeling feverish, fatigue, and loss of appetite-independently correlated with reduced hospitalization and death (hazard ratio range: 0.31-0.56; P < 0.001-0.043), and was more rapid in CAS + IMD-treated patients lacking robust early antibody responses. Those who seroconverted late still benefited from treatment. Thus, highly neutralizing COVID-19-specific antibodies provided by CAS + IMD treatment accelerated key symptom resolution associated with hospitalization and death in those at high risk for severe disease as well as in those lacking early, endogenous neutralizing antibody responses.
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Affiliation(s)
- Dateng Li
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Meng Xu
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Andrea T Hooper
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Diana Rofail
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Kusha A Mohammadi
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Yiziying Chen
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Shazia Ali
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Thomas Norton
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - David M Weinreich
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Bret J Musser
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Jennifer D Hamilton
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Gregory P Geba
- Global Development, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
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40
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Zhang F, Schmidt F, Muecksch F, Wang Z, Gazumyan A, Nussenzweig MC, Gaebler C, Caskey M, Hatziioannou T, Bieniasz PD. SARS-CoV-2 spike glycosylation affects function and neutralization sensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547241. [PMID: 37425700 PMCID: PMC10327196 DOI: 10.1101/2023.06.30.547241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The glycosylation of viral envelope proteins can play important roles in virus biology and immune evasion. The spike (S) glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) includes 22 N-linked glycosylation sequons and 17 O-linked glycosites. Here, we investigated the effect of individual glycosylation sites on SARS-CoV-2 S function in pseudotyped virus infection assays and on sensitivity to monoclonal and polyclonal neutralizing antibodies. In most cases, removal of individual glycosylation sites decreased the infectiousness of the pseudotyped virus. For glycosylation mutants in the N-terminal domain (NTD) and the receptor binding domain (RBD), reduction in pseudotype infectivity was predicted by a commensurate reduction in the level of virion-incorporated spike protein. Notably, the presence of a glycan at position N343 within the RBD had diverse effects on neutralization by RBD-specific monoclonal antibodies (mAbs) cloned from convalescent individuals. The N343 glycan reduced overall sensitivity to polyclonal antibodies in plasma from COVID-19 convalescent individuals, suggesting a role for SARS-CoV-2 spike glycosylation in immune evasion. However, vaccination of convalescent individuals produced neutralizing activity that was resilient to the inhibitory effect of the N343 glycan.
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Affiliation(s)
- Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
- Current address: King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia. Center for Integrative Infectious Disease Research, Universitätsklinikum Heidelberg, 69120 Heidleberg, Germany
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Current address: Laboratory of Translational Immunology of Viral Infections, Charité - Universitätsmedizin Berlin, Germany
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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41
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Alfonso-Dunn R, Lin J, Lei J, Liu J, Roche M, De Oliveira A, Raisingani A, Kumar A, Kirschner V, Feuer G, Malin M, Sadiq SA. Humoral and cellular responses to repeated COVID-19 exposure in multiple sclerosis patients receiving B-cell depleting therapies: a single-center, one-year, prospective study. Front Immunol 2023; 14:1194671. [PMID: 37449202 PMCID: PMC10338057 DOI: 10.3389/fimmu.2023.1194671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023] Open
Abstract
Multiple sclerosis patients treated with anti-CD20 therapy (aCD20-MS) are considered especially vulnerable to complications from SARS-CoV-2 infection due to severe B-cell depletion with limited viral antigen-specific immunoglobulin production. Therefore, multiple vaccine doses as part of the primary vaccination series and booster updates have been recommended for this group of immunocompromised individuals. Even though much less studied than antibody-mediated humoral responses, T-cell responses play an important role against CoV-2 infection and are induced efficiently in vaccinated aCD20-MS patients. For individuals with such decoupled adaptive immunity, an understanding of the contribution of T-cell mediated immunity is essential to better assess protection against CoV-2 infection. Here, we present results from a prospective, single-center study for the assessment of humoral and cellular immune responses induced in aCD20-MS patients (203 donors/350 samples) compared to a healthy control group (43/146) after initial exposure to CoV-2 spike antigen and subsequent re-challenges. Low rates of seroconversion and RBD-hACE2 blocking activity were observed in aCD20-MS patients, even after multiple exposures (responders after 1st exposure = 17.5%; 2nd exposure = 29.3%). Regarding cellular immunity, an increase in the number of spike-specific monofunctional IFNγ+-, IL-2+-, and polyfunctional IFNγ+/IL-2+-secreting T-cells after 2nd exposure was found most noticeably in healthy controls. Nevertheless, a persistently higher T-cell response was detected in aCD20-MS patients compared to control individuals before and after re-exposure (mean fold increase in spike-specific IFNγ+-, IL-2+-, and IFNγ+/IL-2+-T cells before re-exposure = 3.9X, 3.6X, 3.5X/P< 0.001; after = 3.2X, 1.4X, 2.2X/P = 0.002, P = 0.05, P = 0.004). Moreover, cellular responses against sublineage BA.2 of the currently circulating omicron variant were maintained, to a similar degree, in both groups (15-30% T-cell response drop compared to ancestral). Overall, these results highlight the potential for a severely impaired humoral response in aCD20-MS patients even after multiple exposures, while still generating a strong T-cell response. Evaluating both humoral and cellular responses in vaccinated or infected MS patients on B-cell depletion therapy is essential to better assess individual correlations of immune protection and has implications for the design of future vaccines and healthcare strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Saud A. Sadiq
- Tisch Multiple Sclerosis Research Center of New York, New York, NY, United States
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42
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Onodera T, Sax N, Sato T, Adachi Y, Kotaki R, Inoue T, Shinnakasu R, Nakagawa T, Fukushi S, Terooatea T, Yoshikawa M, Tonouchi K, Nagakura T, Moriyama S, Matsumura T, Isogawa M, Terahara K, Takano T, Sun L, Nishiyama A, Omoto S, Shinkai M, Kurosaki T, Yamashita K, Takahashi Y. CD62L expression marks SARS-CoV-2 memory B cell subset with preference for neutralizing epitopes. SCIENCE ADVANCES 2023; 9:eadf0661. [PMID: 37315144 DOI: 10.1126/sciadv.adf0661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 05/09/2023] [Indexed: 06/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2-neutralizing antibodies primarily target the spike receptor binding domain (RBD). However, B cell antigen receptors (BCRs) on RBD-binding memory B (Bmem) cells have variation in the neutralizing activities. Here, by combining single Bmem cell profiling with antibody functional assessment, we dissected the phenotype of Bmem cell harboring the potently neutralizing antibodies in coronavirus disease 2019 (COVID-19)-convalescent individuals. The neutralizing subset was marked by an elevated CD62L expression and characterized by distinct epitope preference and usage of convergent VH (variable region of immunoglobulin heavy chain) genes, accounting for the neutralizing activities. Concordantly, the correlation was observed between neutralizing antibody titers in blood and CD62L+ subset, despite the equivalent RBD binding of CD62L+ and CD62L- subset. Furthermore, the kinetics of CD62L+ subset differed between the patients who recovered from different COVID-19 severities. Our Bmem cell profiling reveals the unique phenotype of Bmem cell subset that harbors potently neutralizing BCRs, advancing our understanding of humoral protection.
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Affiliation(s)
- Taishi Onodera
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Yu Adachi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryutaro Kotaki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takeshi Inoue
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Ryo Shinnakasu
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | | | - Shuetsu Fukushi
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Keisuke Tonouchi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Takaki Nagakura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
- Laboratory of Viral Infection, Ōmura Satoshi Memorial Institute Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Matsumura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masanori Isogawa
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazutaka Terahara
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomohiro Takano
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Lin Sun
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ayae Nishiyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Osaka, Japan
| | | | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
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43
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Tolbert WD, Chen Y, Sun L, Benlarbi M, Ding S, Manickam R, Pangaro E, Nguyen DN, Gottumukkala S, Côté M, Gonzalez FJ, Finzi A, Tehrani ZR, Sajadi MM, Pazgier M. The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11. Front Immunol 2023; 14:1178355. [PMID: 37334379 PMCID: PMC10272436 DOI: 10.3389/fimmu.2023.1178355] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
SARS-CoV-2, the virus behind the COVID-19 pandemic, has changed over time to the extent that the current virus is substantially different from what originally led to the pandemic in 2019-2020. Viral variants have modified the severity and transmissibility of the disease and continue do so. How much of this change is due to viral fitness versus a response to immune pressure is hard to define. One class of antibodies that continues to afford some level of protection from emerging variants are those that closely overlap the binding site for angiotensin-converting enzyme 2 (ACE2) on the receptor binding domain (RBD). Some members of this class that were identified early in the course of the pandemic arose from the VH 3-53 germline gene (IGHV3-53*01) and had short heavy chain complementarity-determining region 3s (CDR H3s). Here, we describe the molecular basis of the SARS-CoV-2 RBD recognition by the anti-RBD monoclonal antibody CoV11 isolated early in the COVID-19 pandemic and show how its unique mode of binding the RBD determines its neutralization breadth. CoV11 utilizes a heavy chain VH 3-53 and a light chain VK 3-20 germline sequence to bind to the RBD. Two of CoV11's four heavy chain changes from the VH 3-53 germline sequence, T h r F W R H 1 28 to Ile and S e r C D R H 1 31 to Arg, and some unique features in its CDR H3 increase its affinity to the RBD, while the four light chain changes from the VK 3-20 germline sequence sit outside of the RBD binding site. Antibodies of this type can retain significant affinity and neutralization potency against variants of concern (VOCs) that have diverged significantly from original virus lineage such as the prevalent omicron variant. We also discuss the mechanism by which VH 3-53 encoded antibodies recognize spike antigen and show how minimal changes to their sequence, their choice of light chain, and their mode of binding influence their affinity and impact their neutralization breadth.
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Affiliation(s)
- William D. Tolbert
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Mehdi Benlarbi
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Shilei Ding
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Rohini Manickam
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Emily Pangaro
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Dung N. Nguyen
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Suneetha Gottumukkala
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Andrés Finzi
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Zahra R. Tehrani
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mohammad M. Sajadi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, Baltimore Veterans Health Administration (VA) Medical Center, Baltimore, MD, United States
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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44
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Zhang F, Jenkins J, de Carvalho RVH, Nakandakari-Higa S, Chen T, Abernathy ME, Baharani VA, Nyakatura EK, Andrew D, Lebedeva IV, Lorenz IC, Hoffmann HH, Rice CM, Victora GD, Barnes CO, Hatziioannou T, Bieniasz PD. Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies. Nat Microbiol 2023; 8:1051-1063. [PMID: 37188812 PMCID: PMC10234812 DOI: 10.1038/s41564-023-01389-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
Human monoclonal antibodies (mAbs) that target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have been isolated from convalescent individuals and developed into therapeutics for SARS-CoV-2 infection. However, therapeutic mAbs for SARS-CoV-2 have been rendered obsolete by the emergence of mAb-resistant virus variants. Here we report the generation of a set of six human mAbs that bind the human angiotensin-converting enzyme-2 (hACE2) receptor, rather than the SARS-CoV-2 spike protein. We show that these antibodies block infection by all hACE2 binding sarbecoviruses tested, including SARS-CoV-2 ancestral, Delta and Omicron variants at concentrations of ~7-100 ng ml-1. These antibodies target an hACE2 epitope that binds to the SARS-CoV-2 spike, but they do not inhibit hACE2 enzymatic activity nor do they induce cell-surface depletion of hACE2. They have favourable pharmacology, protect hACE2 knock-in mice against SARS-CoV-2 infection and should present a high genetic barrier to the acquisition of resistance. These antibodies should be useful prophylactic and treatment agents against any current or future SARS-CoV-2 variants and might be useful to treat infection with any hACE2-binding sarbecoviruses that emerge in the future.
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Affiliation(s)
- Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Jesse Jenkins
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | | | - Teresia Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Viren A Baharani
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - David Andrew
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, USA
| | - Irina V Lebedeva
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, USA
| | - Ivo C Lorenz
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, USA
| | - H-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Christopher O Barnes
- Department of Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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45
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Feng Y, Yuan M, Powers JM, Hu M, Munt JE, Arunachalam PS, Leist SR, Bellusci L, Kim J, Sprouse KR, Adams LE, Sundaramurthy S, Zhu X, Shirreff LM, Mallory ML, Scobey TD, Moreno A, O’Hagan DT, Kleanthous H, Villinger FJ, Veesler D, King NP, Suthar MS, Khurana S, Baric RS, Wilson IA, Pulendran B. Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine. Sci Transl Med 2023; 15:eadg7404. [PMID: 37163615 PMCID: PMC11032722 DOI: 10.1126/scitranslmed.adg7404] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/11/2023] [Indexed: 05/12/2023]
Abstract
The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that evade immunity elicited by vaccination has placed an imperative on the development of countermeasures that provide broad protection against SARS-CoV-2 and related sarbecoviruses. Here, we identified extremely potent monoclonal antibodies (mAbs) that neutralized multiple sarbecoviruses from macaques vaccinated with AS03-adjuvanted monovalent subunit vaccines. Longitudinal analysis revealed progressive accumulation of somatic mutation in the immunoglobulin genes of antigen-specific memory B cells (MBCs) for at least 1 year after primary vaccination. Antibodies generated from these antigen-specific MBCs at 5 to 12 months after vaccination displayed greater potency and breadth relative to those identified at 1.4 months. Fifteen of the 338 (about 4.4%) antibodies isolated at 1.4 to 6 months after the primary vaccination showed potency against SARS-CoV-2 BA.1, despite the absence of serum BA.1 neutralization. 25F9 and 20A7 neutralized authentic clade 1 sarbecoviruses (SARS-CoV, WIV-1, SHC014, SARS-CoV-2 D614G, BA.1, and Pangolin-GD) and vesicular stomatitis virus-pseudotyped clade 3 sarbecoviruses (BtKY72 and PRD-0038). 20A7 and 27A12 showed potent neutralization against all SARS-CoV-2 variants and multiple Omicron sublineages, including BA.1, BA.2, BA.3, BA.4/5, BQ.1, BQ.1.1, and XBB. Crystallography studies revealed the molecular basis of broad and potent neutralization through targeting conserved sites within the RBD. Prophylactic protection of 25F9, 20A7, and 27A12 was confirmed in mice, and administration of 25F9 particularly provided complete protection against SARS-CoV-2, BA.1, SARS-CoV, and SHC014 challenge. These data underscore the extremely potent and broad activity of these mAbs against sarbecoviruses.
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Affiliation(s)
- Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University; Stanford, CA 94305, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - John M. Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University; Stanford, CA 94305, USA
| | - Jennifer E. Munt
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Prabhu S. Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University; Stanford, CA 94305, USA
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA); Silver Spring, MD 20993, USA
| | - JungHyun Kim
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA); Silver Spring, MD 20993, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Lily E. Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | | | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Lisa M. Shirreff
- New Iberia Research Center, University of Louisiana at Lafayette; New Iberia, LA 70560, USA
| | - Michael L. Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Trevor D. Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Alberto Moreno
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, GA 30322, USA
| | | | | | - Francois J. Villinger
- New Iberia Research Center, University of Louisiana at Lafayette; New Iberia, LA 70560, USA
| | - David Veesler
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, 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
| | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center; Atlanta, GA 30329, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA); Silver Spring, MD 20993, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University; Stanford, CA 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University; Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University; Stanford, CA 94305, USA
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46
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Ruffolo JA, Chu LS, Mahajan SP, Gray JJ. Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies. Nat Commun 2023; 14:2389. [PMID: 37185622 PMCID: PMC10129313 DOI: 10.1038/s41467-023-38063-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Antibodies have the capacity to bind a diverse set of antigens, and they have become critical therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six hypervariable loops that are diversified through genetic recombination and mutation. Even with recent advances, accurate structural prediction of these loops remains a challenge. Here, we present IgFold, a fast deep learning method for antibody structure prediction. IgFold consists of a pre-trained language model trained on 558 million natural antibody sequences followed by graph networks that directly predict backbone atom coordinates. IgFold predicts structures of similar or better quality than alternative methods (including AlphaFold) in significantly less time (under 25 s). Accurate structure prediction on this timescale makes possible avenues of investigation that were previously infeasible. As a demonstration of IgFold's capabilities, we predicted structures for 1.4 million paired antibody sequences, providing structural insights to 500-fold more antibodies than have experimentally determined structures.
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Affiliation(s)
- Jeffrey A Ruffolo
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Lee-Shin Chu
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sai Pooja Mahajan
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeffrey J Gray
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, 21218, USA.
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47
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Shen CF, Fu YC, Ho TS, Chen PL, Lee NY, Tsai BY, Tsai PJ, Ko WC, Liu CC, Cheng CM, Shieh CC. Pre-existing humoral immunity and CD4 + T cell response correlate with cross-reactivity against SARS-CoV-2 Omicron subvariants after heterologous prime-boost vaccination. Clin Immunol 2023; 251:109342. [PMID: 37100338 PMCID: PMC10124102 DOI: 10.1016/j.clim.2023.109342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Information regarding the heterologous prime-boost COVID vaccination has been fully elucidated. The study aimed to evaluate both humoral, cellular immunity and cross-reactivity against variants after heterologous vaccination. METHODS We recruited healthcare workers previously primed with Oxford/AstraZeneca ChAdOx1-S vaccines and boosted with Moderna mRNA-1273 vaccine boost to evaluate the immunological response. Assay used: anti-spike RBD antibody, surrogate virus neutralizing antibody and interferon-γ release assay. RESULTS All participants exhibited higher humoral and cellular immune response after the booster regardless of prior antibody level, but those with higher antibody level demonstrated stronger booster response, especially against omicron BA.1 and BA.2 variants. The pre-booster IFN-γ release by CD4+ T cells correlates with post-booster neutralizing antibody against BA.1 and BA.2 variant after adjustment with age and gender. CONCLUSIONS A heterologous mRNA boost is highly immunogenic. The pre-existing neutralizing antibody level and CD4+ T cells response correlates with post-booster neutralization reactivity against the Omicron variant.
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Affiliation(s)
- Ching-Fen Shen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC; Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Yi-Chen Fu
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Tzong-Shiann Ho
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 70101, Taiwan, ROC; Department of Pediatrics, Tainan Hospital, Ministry of Health and Welfare, Tainan 700007, Taiwan, ROC
| | - Po-Lin Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Nan-Yao Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Bo-Yang Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Pei-Jane Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Ching-Chuan Liu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC.
| | - Chi-Chang Shieh
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC; Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC.
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48
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Chernyshev M, Sakharkar M, Connor RI, Dugan HL, Sheward DJ, Rappazzo CG, Stålmarck A, Forsell MNE, Wright PF, Corcoran M, Murrell B, Walker LM, Karlsson Hedestam GB. Vaccination of SARS-CoV-2-infected individuals expands a broad range of clonally diverse affinity-matured B cell lineages. Nat Commun 2023; 14:2249. [PMID: 37076511 PMCID: PMC10115384 DOI: 10.1038/s41467-023-37972-1] [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: 11/02/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Vaccination of SARS-CoV-2 convalescent individuals generates broad and potent antibody responses. Here, we isolate 459 spike-specific monoclonal antibodies (mAbs) from two individuals who were infected with the index variant of SARS-CoV-2 and later boosted with mRNA-1273. We characterize mAb genetic features by sequence assignments to the donors' personal immunoglobulin genotypes and assess antibody neutralizing activities against index SARS-CoV-2, Beta, Delta, and Omicron variants. The mAbs used a broad range of immunoglobulin heavy chain (IGH) V genes in the response to all sub-determinants of the spike examined, with similar characteristics observed in both donors. IGH repertoire sequencing and B cell lineage tracing at longitudinal time points reveals extensive evolution of SARS-CoV-2 spike-binding antibodies from acute infection until vaccination five months later. These results demonstrate that highly polyclonal repertoires of affinity-matured memory B cells are efficiently recalled by vaccination, providing a basis for the potent antibody responses observed in convalescent persons following vaccination.
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Affiliation(s)
- Mark Chernyshev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Ruth I Connor
- Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | | | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Aron Stålmarck
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Peter F Wright
- Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura M Walker
- Adimab LLC, Lebanon, NH, 03766, USA.
- Invivyd Inc, Waltham, MA, 02451, USA.
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49
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Shitaoka K, Higashiura A, Kawano Y, Yamamoto A, Mizoguchi Y, Hashiguchi T, Nishimichi N, Huang S, Ito A, Ohki S, Kanda M, Taniguchi T, Yoshizato R, Azuma H, Kitajima Y, Yokosaki Y, Okada S, Sakaguchi T, Yasuda T. Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants. Commun Biol 2023; 6:395. [PMID: 37041231 PMCID: PMC10088672 DOI: 10.1038/s42003-023-04782-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/30/2023] [Indexed: 04/13/2023] Open
Abstract
The decrease of antibody efficacy to mutated SARS-CoV-2 spike RBD explains the breakthrough infections and reinfections by Omicron variants. Here, we analyzed broadly neutralizing antibodies isolated from long-term hospitalized convalescent patients of early SARS-CoV-2 strains. One of the antibodies named NCV2SG48 is highly potent to broad SARS-CoV-2 variants including Omicron BA.1, BA.2, and BA.4/5. To reveal the mode of action, we determined the sequence and crystal structure of the Fab fragment of NCV2SG48 in a complex with spike RBD from the original, Delta, and Omicron BA.1. NCV2SG48 is from a minor VH but the multiple somatic hypermutations contribute to a markedly extended binding interface and hydrogen bonds to interact with conserved residues at the core receptor-binding motif of RBD, which efficiently neutralizes a broad spectrum of variants. Thus, eliciting the RBD-specific B cells to the longitudinal germinal center reaction confers potent immunity to broad SARS-CoV-2 variants emerging one after another.
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Affiliation(s)
- Kiyomi Shitaoka
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akifumi Higashiura
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yohei Kawano
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akima Yamamoto
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yoko Mizoguchi
- Department of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Norihisa Nishimichi
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Integrin-Matrix Biomedical Science, Translational Research Center, Hiroshima University, Hiroshima, Japan
| | - Shiyu Huang
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ayano Ito
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shun Ohki
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Miyuki Kanda
- Collaborative laboratory of Liquid Biopsy, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomohiro Taniguchi
- Division of General Internal Medicine and Infectious Diseases, Hiroshima Prefectural Hospital, Hiroshima, Japan
| | - Rin Yoshizato
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hitoshi Azuma
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasuo Kitajima
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasuyuki Yokosaki
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Integrin-Matrix Biomedical Science, Translational Research Center, Hiroshima University, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takemasa Sakaguchi
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoharu Yasuda
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
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50
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Wang J, Huang L, Guo N, Yao YP, Zhang C, Xu R, Jiao YM, Li YQ, Song YR, Wang FS, Fan X. Dynamics of SARS-CoV-2 Antibody Responses up to 9 Months Post-Vaccination in Individuals with Previous SARS-CoV-2 Infection Receiving Inactivated Vaccines. Viruses 2023; 15:v15040917. [PMID: 37112897 PMCID: PMC10145073 DOI: 10.3390/v15040917] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 04/07/2023] Open
Abstract
Humoral immunity confers protection against COVID-19. The longevity of antibody responses after receiving an inactivated vaccine in individuals with previous SARS-CoV-2 infection is unclear. Plasma samples were collected from 58 individuals with previous SARS-CoV-2 infection and 25 healthy donors (HDs) who had been vaccinated with an inactivated vaccine. The neutralizing antibodies (NAbs) and S1 domain-specific antibodies against the SARS-CoV-2 wild-type and Omicron strains and nucleoside protein (NP)-specific antibodies were measured using a chemiluminescent immunoassay. Statistical analysis was performed using clinical variables and antibodies at different timepoints after SARS-CoV-2 vaccination. NAbs targeting the wild-type or Omicron strain were detected in individuals with previous SARS-CoV-2 infection at 12 months after infection (wild-type: 81%, geometric mean (GM): 20.3 AU/mL; Omicron: 44%, GM: 9.4 AU/mL), and vaccination provided further enhancement of these antibody levels (wild-type: 98%, GM: 53.3 AU/mL; Omicron: 75%, GM: 27.8 AU/mL, at 3 months after vaccination), which were significantly higher than those in HDs receiving a third dose of inactivated vaccine (wild-type: 85%, GM: 33.6 AU/mL; Omicron: 45%, GM: 11.5 AU/mL). The level of NAbs in individuals with previous infection plateaued 6 months after vaccination, but the NAb levels in HDs declined continuously. NAb levels in individuals with previous infection at 3 months post-vaccination were strongly correlated with those at 6 months post-vaccination, and weakly correlated with those before vaccination. NAb levels declined substantially in most individuals, and the rate of antibody decay was negatively correlated with the neutrophil-to-lymphocyte ratio in the blood at discharge. These results suggest that the inactivated vaccine induced robust and durable NAb responses in individuals with previous infection up to 9 months after vaccination.
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Affiliation(s)
- Jing Wang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Lei Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Nan Guo
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
- Chinese PLA Medical School, Beijing 100853, China
| | - Ya-Ping Yao
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Chao Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Ruonan Xu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Yan-Mei Jiao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Ya-Qun Li
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Yao-Ru Song
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
- Chinese PLA Medical School, Beijing 100853, China
| | - Fu-Sheng Wang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Xing Fan
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
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