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Lu X, Liu F, Tzeng WP, York IA, Tumpey TM, Levine MZ. Antibody-Mediated Suppression Regulates the Humoral Immune Response to Influenza Vaccination in Humans. J Infect Dis 2024; 229:310-321. [PMID: 37981659 DOI: 10.1093/infdis/jiad493] [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: 05/22/2023] [Revised: 09/29/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Preexisting immunity, including memory B cells and preexisting antibodies, can modulate antibody responses to influenza in vivo to antigenically related antigens. We investigated whether preexisting hemagglutination inhibition (HAI) antibodies targeting the K163 epitope on the hemagglutinin (K163 antibodies) could affect antibody responses following vaccination with A/California/07/2009-like A(H1N1)pdm09 influenza viruses in humans. METHODS Pre- and postvaccination sera collected from 300 adults (birth years, 1961-1998) in 6 seasons (2010-2016) were analyzed by HAI assays with 2 reverse genetics viruses and A(H1N1) viruses circulated from 1977 to 2018. Antibody adsorption assays were used to verify the preexisting K163 antibody-mediated suppression effect. RESULTS Preexisting K163 antibody titers ≥80 affected HAI antibody responses following influenza vaccination containing A/California/07/2009-like antigens. At high K163 antibody concentrations (HAI antibody titers ≥160), all HAI antibody responses were suppressed. However, at moderate K163 antibody concentrations (HAI antibody titer, 80), only K163 epitope-specific antibody responses were suppressed, and novel HAI antibody responses targeting the non-K163 epitopes were induced by vaccination. Novel antibodies targeting non-K163 epitopes cross-reacted with newly emerging A(H1N1)pdm09 strains with a K163Q mutation rather than historic 1977-2007 A(H1N1) viruses. CONCLUSIONS K163 antibody-mediated suppression shapes antibody responses to A(H1N1)pdm09 vaccination. Understanding how preexisting antibodies suppress and redirect vaccine-induced antibody responses is of great importance to improve vaccine effectiveness.
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Affiliation(s)
- Xiuhua Lu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Feng Liu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Wen-Ping Tzeng
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ian A York
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Terrence M Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Min Z Levine
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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2
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Yang L, Van Beek M, Wang Z, Muecksch F, Canis M, Hatziioannou T, Bieniasz PD, Nussenzweig MC, Chakraborty AK. Antigen presentation dynamics shape the antibody response to variants like SARS-CoV-2 Omicron after multiple vaccinations with the original strain. Cell Rep 2023; 42:112256. [PMID: 36952347 PMCID: PMC9986127 DOI: 10.1016/j.celrep.2023.112256] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/07/2022] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
The Omicron variant of SARS-CoV-2 is not effectively neutralized by most antibodies elicited by two doses of mRNA vaccines, but a third dose increases anti-Omicron neutralizing antibodies. We reveal mechanisms underlying this observation by combining computational modeling with data from vaccinated humans. After the first dose, limited antigen availability in germinal centers (GCs) results in a response dominated by B cells that target immunodominant epitopes that are mutated in an Omicron-like variant. After the second dose, these memory cells expand and differentiate into plasma cells that secrete antibodies that are thus ineffective for such variants. However, these pre-existing antigen-specific antibodies transport antigen efficiently to secondary GCs. They also partially mask immunodominant epitopes. Enhanced antigen availability and epitope masking in secondary GCs together result in generation of memory B cells that target subdominant epitopes that are less mutated in Omicron. The third dose expands these cells and boosts anti-variant neutralizing antibodies.
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Affiliation(s)
- Leerang Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew Van Beek
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Marie Canis
- Laboratory of Retrovirology, 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
| | - 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.
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
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3
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Gupta A, Konnova A, Smet M, Berkell M, Savoldi A, Morra M, Van Averbeke V, De Winter FH, Peserico D, Danese E, Hotterbeekx A, Righi E, De Nardo P, Tacconelli E, Malhotra-Kumar S, Kumar-Singh S. Host immunological responses facilitate development of SARS-CoV-2 mutations in patients receiving monoclonal antibody treatments. J Clin Invest 2023; 133:166032. [PMID: 36727404 PMCID: PMC10014108 DOI: 10.1172/jci166032] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/05/2023] [Indexed: 02/03/2023] Open
Abstract
BackgroundThe role of host immunity in emergence of evasive SARS-CoV-2 Spike mutations under therapeutic monoclonal antibody (mAb) pressure remains to be explored.MethodsIn a prospective, observational, monocentric ORCHESTRA cohort study, conducted between March 2021 and November 2022, mild-to-moderately ill COVID-19 patients (n = 204) receiving bamlanivimab, bamlanivimab/etesevimab, casirivimab/imdevimab, or sotrovimab were longitudinally studied over 28 days for viral loads, de novo Spike mutations, mAb kinetics, seroneutralization against infecting variants of concern, and T cell immunity. Additionally, a machine learning-based circulating immune-related biomarker (CIB) profile predictive of evasive Spike mutations was constructed and confirmed in an independent data set (n = 19) that included patients receiving sotrovimab or tixagevimab/cilgavimab.ResultsPatients treated with various mAbs developed evasive Spike mutations with remarkable speed and high specificity to the targeted mAb-binding sites. Immunocompromised patients receiving mAb therapy not only continued to display significantly higher viral loads, but also showed higher likelihood of developing de novo Spike mutations. Development of escape mutants also strongly correlated with neutralizing capacity of the therapeutic mAbs and T cell immunity, suggesting immune pressure as an important driver of escape mutations. Lastly, we showed that an antiinflammatory and healing-promoting host milieu facilitates Spike mutations, where 4 CIBs identified patients at high risk of developing escape mutations against therapeutic mAbs with high accuracy.ConclusionsOur data demonstrate that host-driven immune and nonimmune responses are essential for development of mutant SARS-CoV-2. These data also support point-of-care decision making in reducing the risk of mAb treatment failure and improving mitigation strategies for possible dissemination of escape SARS-CoV-2 mutants.FundingThe ORCHESTRA project/European Union's Horizon 2020 research and innovation program.
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Affiliation(s)
- Akshita Gupta
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Angelina Konnova
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Mathias Smet
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Matilda Berkell
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Alessia Savoldi
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Matteo Morra
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Vincent Van Averbeke
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and
| | - Fien Hr De Winter
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and
| | - Denise Peserico
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - Elisa Danese
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - An Hotterbeekx
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and
| | - Elda Righi
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | | | - Pasquale De Nardo
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Samir Kumar-Singh
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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4
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Inoue T, Shinnakasu R, Kawai C, Yamamoto H, Sakakibara S, Ono C, Itoh Y, Terooatea T, Yamashita K, Okamoto T, Hashii N, Ishii-Watabe A, Butler NS, Matsuura Y, Matsumoto H, Otsuka S, Hiraoka K, Teshima T, Murakami M, Kurosaki T. Antibody feedback contributes to facilitating the development of Omicron-reactive memory B cells in SARS-CoV-2 mRNA vaccinees. J Exp Med 2023; 220:213745. [PMID: 36512034 PMCID: PMC9750191 DOI: 10.1084/jem.20221786] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
In contrast to a second dose of the SARS-CoV-2 mRNA vaccine, a third dose elicits potent neutralizing activity against the Omicron variant. To address the underlying mechanism for this differential antibody response, we examined spike receptor-binding domain (RBD)-specific memory B cells in vaccinated individuals. Frequency of Omicron-reactive memory B cells increased ∼9 mo after the second vaccine dose. These memory B cells show an altered distribution of epitopes from pre-second memory B cells, presumably due to an antibody feedback mechanism. This hypothesis was tested using mouse models, showing that an addition or a depletion of RBD-induced serum antibodies results in a concomitant increase or decrease, respectively, of Omicron-reactive germinal center (GC) and memory B cells. Our data suggest that pre-generated antibodies modulate the selection of GC and subsequent memory B cells after the second vaccine dose, accumulating more Omicron-reactive memory B cells over time, which contributes to the generation of Omicron-neutralizing antibodies elicited by the third vaccine dose.
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Affiliation(s)
- 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.,Division of Medical Research Support, Advanced Research Support Center, Ehime University, Ehime, Japan.,Translational Research Center, Ehime University Hospital, Ehime, Japan
| | - Chie Kawai
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Hiromi Yamamoto
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | | | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kanagawa, Japan
| | - Akiko Ishii-Watabe
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kanagawa, Japan
| | - Noah S Butler
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA, USA
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Hisatake Matsumoto
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shinya Otsuka
- Department of Surgery, National Hospital Organization Hakodate National Hospital, Hokkaido, Japan
| | - Kei Hiraoka
- Department of Surgery, National Hospital Organization Hakodate National Hospital, Hokkaido, Japan
| | - Takanori Teshima
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan.,Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Masaaki Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.,Team of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology, Chiba, Japan.,Division of Molecular Neuroimmunology, Department of Homeostatic Regulation, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Aichi, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan.,Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
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5
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Painter MM, Johnston TS, Lundgreen KA, Santos JJS, Qin JS, Goel RR, Apostolidis SA, Mathew D, Fulmer B, Williams JC, McKeague ML, Pattekar A, Goode A, Nasta S, Baxter AE, Giles JR, Skelly AN, Felley LE, McLaughlin M, Weaver J, Kuthuru O, Dougherty J, Adamski S, Long S, Kee M, Clendenin C, da Silva Antunes R, Grifoni A, Weiskopf D, Sette A, Huang AC, Rader DJ, Hensley SE, Bates P, Greenplate AR, Wherry EJ. Prior vaccination enhances immune responses during SARS-CoV-2 breakthrough infection with early activation of memory T cells followed by production of potent neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.05.527215. [PMID: 36798171 PMCID: PMC9934532 DOI: 10.1101/2023.02.05.527215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
SARS-CoV-2 infection of vaccinated individuals is increasingly common but rarely results in severe disease, likely due to the enhanced potency and accelerated kinetics of memory immune responses. However, there have been few opportunities to rigorously study early recall responses during human viral infection. To better understand human immune memory and identify potential mediators of lasting vaccine efficacy, we used high-dimensional flow cytometry and SARS-CoV-2 antigen probes to examine immune responses in longitudinal samples from vaccinated individuals infected during the Omicron wave. These studies revealed heightened Spike-specific responses during infection of vaccinated compared to unvaccinated individuals. Spike-specific CD4 T cells and plasmablasts expanded and CD8 T cells were robustly activated during the first week. In contrast, memory B cell activation, neutralizing antibody production, and primary responses to non-Spike antigens occurred during the second week. Collectively, these data demonstrate the functionality of vaccine-primed immune memory and highlight memory T cells as rapid responders during SARS-CoV-2 infection.
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Affiliation(s)
- Mark M Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Timothy S Johnston
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kendall A Lundgreen
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Jefferson J S Santos
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Juliana S Qin
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Rishi R Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Bria Fulmer
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Justine C Williams
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Michelle L McKeague
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ajinkya Pattekar
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ahmad Goode
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sean Nasta
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Amy E Baxter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Josephine R Giles
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ashwin N Skelly
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Laura E Felley
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Maura McLaughlin
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Joellen Weaver
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oliva Kuthuru
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Jeanette Dougherty
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sharon Adamski
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sherea Long
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Macy Kee
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Cynthia Clendenin
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Alexander C Huang
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott E Hensley
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
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6
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Scharf L, Axelsson H, Emmanouilidi A, Mathew NR, Sheward DJ, Leach S, Isakson P, Smirnov IV, Marklund E, Miron N, Andersson LM, Gisslén M, Murrell B, Lundgren A, Bemark M, Angeletti D. Longitudinal single-cell analysis of SARS-CoV-2-reactive B cells uncovers persistence of early-formed, antigen-specific clones. JCI Insight 2023; 8:165299. [PMID: 36445762 PMCID: PMC9870078 DOI: 10.1172/jci.insight.165299] [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: 09/09/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022] Open
Abstract
Understanding persistence and evolution of B cell clones after COVID-19 infection and vaccination is crucial for predicting responses against emerging viral variants and optimizing vaccines. Here, we collected longitudinal samples from patients with severe COVID-19 every third to seventh day during hospitalization and every third month after recovery. We profiled their antigen-specific immune cell dynamics by combining single-cell RNA-Seq, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), and B cell receptor-Seq (BCR-Seq) with oligo-tagged antigen baits. While the proportion of Spike receptor binding domain-specific memory B cells (MBC) increased from 3 months after infection, the other Spike- and Nucleocapsid-specific B cells remained constant. All patients showed ongoing class switching and sustained affinity maturation of antigen-specific cells, and affinity maturation was not significantly increased early after vaccine. B cell analysis revealed a polyclonal response with limited clonal expansion; nevertheless, some clones detected during hospitalization, as plasmablasts, persisted for up to 1 year, as MBC. Monoclonal antibodies derived from persistent B cell families increased their binding and neutralization breadth and started recognizing viral variants by 3 months after infection. Overall, our findings provide important insights into the clonal evolution and dynamics of antigen-specific B cell responses in longitudinally sampled patients infected with COVID-19.
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Affiliation(s)
- Lydia Scharf
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Hannes Axelsson
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Aikaterini Emmanouilidi
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Nimitha R. Mathew
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Susannah Leach
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pharmacology
| | - Pauline Isakson
- Department of Clinical Immunology and Transfusion Medicine, and
| | - Ilya V. Smirnov
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Emelie Marklund
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Nicolae Miron
- Department of Clinical Immunology and Transfusion Medicine, and
| | - Lars-Magnus Andersson
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lundgren
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, and
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, and
| | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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Bruel T, Stéfic K, Nguyen Y, Toniutti D, Staropoli I, Porrot F, Guivel-Benhassine F, Bolland WH, Planas D, Hadjadj J, Handala L, Planchais C, Prot M, Simon-Lorière E, André E, Baele G, Cuypers L, Mouthon L, Mouquet H, Buchrieser J, Sève A, Prazuck T, Maes P, Terrier B, Hocqueloux L, Schwartz O. Longitudinal analysis of serum neutralization of SARS-CoV-2 Omicron BA.2, BA.4, and BA.5 in patients receiving monoclonal antibodies. Cell Rep Med 2022; 3:100850. [PMID: 36450283 PMCID: PMC9706550 DOI: 10.1016/j.xcrm.2022.100850] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/10/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
The emergence of Omicron sublineages impacts the therapeutic efficacy of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monoclonal antibodies (mAbs). Here, we evaluate neutralization and antibody-dependent cellular cytotoxicity (ADCC) activities of 6 therapeutic mAbs against Delta, BA.2, BA.4, and BA.5. The Omicron subvariants escape most antibodies but remain sensitive to bebtelovimab and cilgavimab. Consistent with their shared spike sequence, BA.4 and BA.5 display identical neutralization profiles. Sotrovimab is the most efficient at eliciting ADCC. We also analyze 121 sera from 40 immunocompromised individuals up to 6 months after infusion of Ronapreve (imdevimab + casirivimab) or Evusheld (cilgavimab + tixagevimab). Sera from Ronapreve-treated individuals do not neutralize Omicron subvariants. Evusheld-treated individuals neutralize BA.2 and BA.5, but titers are reduced. A longitudinal evaluation of sera from Evusheld-treated patients reveals a slow decay of mAb levels and neutralization, which is faster against BA.5. Our data shed light on antiviral activities of therapeutic mAbs and the duration of effectiveness of Evusheld pre-exposure prophylaxis.
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Affiliation(s)
- Timothée Bruel
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France; Vaccine Research Institute, Créteil, France.
| | - Karl Stéfic
- INSERM U1259, Université de Tours, Tours, France; CHRU de Tours, National Reference Center for HIV-Associated Laboratory, Tours, France
| | - Yann Nguyen
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, AP-HP, APHP.CUP, Hopital Cochin, Paris, France
| | - Donatella Toniutti
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Françoise Porrot
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | | | - William-Henry Bolland
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France; Université Paris Cité, École doctorale BioSPC 562, Paris, France
| | - Delphine Planas
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France; Vaccine Research Institute, Créteil, France
| | - Jérôme Hadjadj
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, AP-HP, APHP.CUP, Hopital Cochin, Paris, France
| | - Lynda Handala
- INSERM U1259, Université de Tours, Tours, France; CHRU de Tours, National Reference Center for HIV-Associated Laboratory, Tours, France
| | - Cyril Planchais
- Humoral Immunology Laboratory, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris, France
| | - Matthieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Etienne Simon-Lorière
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Emmanuel André
- University Hospitals Leuven, Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, Leuven, Belgium; KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, Leuven, Belgium
| | - Guy Baele
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Lize Cuypers
- University Hospitals Leuven, Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, Leuven, Belgium
| | - Luc Mouthon
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, AP-HP, APHP.CUP, Hopital Cochin, Paris, France
| | - Hugo Mouquet
- Humoral Immunology Laboratory, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris, France
| | - Julian Buchrieser
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Aymeric Sève
- CHR d'Orléans, Service de Maladies Infectieuses, Orléans, France
| | - Thierry Prazuck
- CHR d'Orléans, Service de Maladies Infectieuses, Orléans, France
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Benjamin Terrier
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, AP-HP, APHP.CUP, Hopital Cochin, Paris, France
| | | | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France; Vaccine Research Institute, Créteil, France.
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