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Sevim Bayrak C, Forst CV, Jones DR, Gresham DJ, Pushalkar S, Wu S, Vogel C, Mahal LK, Ghedin E, Ross T, García-Sastre A, Zhang B. Patient subtyping analysis of baseline multi-omic data reveals distinct pre-immune states associated with antibody response to seasonal influenza vaccination. Clin Immunol 2024; 266:110333. [PMID: 39089348 DOI: 10.1016/j.clim.2024.110333] [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: 06/18/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/03/2024]
Abstract
Understanding the molecular mechanisms underpinning diverse vaccination responses is critical for developing efficient vaccines. Molecular subtyping can offer insights into heterogeneous nature of responses and aid in vaccine design. We analyzed multi-omic data from 62 haemagglutinin seasonal influenza vaccine recipients (2019-2020), including transcriptomics, proteomics, glycomics, and metabolomics data collected pre-vaccination. We performed a subtyping analysis on the integrated data revealing five subtypes with distinct molecular signatures. These subtypes differed in the expression of pre-existing adaptive or innate immunity signatures, which were linked to significant variation in baseline immunoglobulin A (IgA) and hemagglutination inhibition (HAI) titer levels. It is worth noting that these differences persisted through day 28 post-vaccination, indicating the effect of initial immune state on vaccination response. These findings highlight the significance of interpersonal variation in baseline immune status as a crucial factor in determining the effectiveness of seasonal vaccines. Ultimately, incorporating molecular profiling could enable personalized vaccine optimization.
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Affiliation(s)
- Cigdem Sevim Bayrak
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt Sinai, New York, NY, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt Sinai, New York, NY, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Microbiology, Icahn School of Medicine at Mt Sinai, New York, NY, USA
| | - Drew R Jones
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, NY, New York, USA
| | - David J Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Smruti Pushalkar
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Shaohuan Wu
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Ted Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA; Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt Sinai, New York, NY, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Tenforde MW, Weber ZA, Yang DH, DeSilva MB, Dascomb K, Irving SA, Naleway AL, Gaglani M, Fireman B, Lewis N, Zerbo O, Goddard K, Timbol J, Hansen JR, Grisel N, Arndorfer J, McEvoy CE, Essien IJ, Rao S, Grannis SJ, Kharbanda AB, Natarajan K, Ong TC, Embi PJ, Ball SW, Dunne MM, Kirshner L, Wiegand RE, Dickerson M, Patel P, Ray C, Flannery B, Garg S, Adams K, Klein NP. Influenza Vaccine Effectiveness Against Influenza A-Associated Emergency Department, Urgent Care, and Hospitalization Encounters Among US Adults, 2022-2023. J Infect Dis 2024; 230:141-151. [PMID: 39052725 PMCID: PMC11306194 DOI: 10.1093/infdis/jiad542] [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: 08/08/2023] [Revised: 11/08/2023] [Accepted: 11/29/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND The 2022-2023 United States influenza season had unusually early influenza activity with high hospitalization rates. Vaccine-matched A(H3N2) viruses predominated, with lower levels of A(H1N1)pdm09 activity also observed. METHODS Using the test-negative design, we evaluated influenza vaccine effectiveness (VE) during the 2022-2023 season against influenza A-associated emergency department/urgent care (ED/UC) visits and hospitalizations from October 2022 to March 2023 among adults (aged ≥18 years) with acute respiratory illness (ARI). VE was estimated by comparing odds of seasonal influenza vaccination among case-patients (influenza A test positive by molecular assay) and controls (influenza test negative), applying inverse-propensity-to-be-vaccinated weights. RESULTS The analysis included 85 389 ED/UC ARI encounters (17.0% influenza A positive; 37.8% vaccinated overall) and 19 751 hospitalizations (9.5% influenza A positive; 52.8% vaccinated overall). VE against influenza A-associated ED/UC encounters was 44% (95% confidence interval [CI], 40%-47%) overall and 45% and 41% among adults aged 18-64 and ≥65 years, respectively. VE against influenza A-associated hospitalizations was 35% (95% CI, 27%-43%) overall and 23% and 41% among adults aged 18-64 and ≥65 years, respectively. CONCLUSIONS VE was moderate during the 2022-2023 influenza season, a season characterized with increased burden of influenza and co-circulation with other respiratory viruses. Vaccination is likely to substantially reduce morbidity, mortality, and strain on healthcare resources.
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Affiliation(s)
- Mark W. Tenforde
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Duck-Hye Yang
- Department of Clinical Resarch, Westat, Rockville, Maryland
| | - Malini B. DeSilva
- Department of Research, HealthPartners Institute, Minneapolis, Minnesota
| | - Kristin Dascomb
- Division of Infectious Diseases and Clinical Epidemiology, Intermountain Healthcare, Salt Lake City, Utah
| | - Stephanie A. Irving
- Department of Science Programs, Kaiser Permanente Center for Health Research, Portland, Oregon
| | - Allison L. Naleway
- Department of Science Programs, Kaiser Permanente Center for Health Research, Portland, Oregon
| | - Manjusha Gaglani
- Section of Pediatric Infectious Diseases, Department of Pediatrics, Baylor Scott & White Health and Baylor College of Medicine, Temple, Texas
- Department of Medical Education, Texas A&M University College of Medicine, Temple, Texas
| | - Bruce Fireman
- Kaiser Permanente Vaccine Study Center, Kaiser Permanente Northern California Division of Research, Oakland, California
| | - Ned Lewis
- Kaiser Permanente Vaccine Study Center, Kaiser Permanente Northern California Division of Research, Oakland, California
| | - Ousseny Zerbo
- Kaiser Permanente Vaccine Study Center, Kaiser Permanente Northern California Division of Research, Oakland, California
| | - Kristin Goddard
- Kaiser Permanente Vaccine Study Center, Kaiser Permanente Northern California Division of Research, Oakland, California
| | - Julius Timbol
- Kaiser Permanente Vaccine Study Center, Kaiser Permanente Northern California Division of Research, Oakland, California
| | - John R. Hansen
- Kaiser Permanente Vaccine Study Center, Kaiser Permanente Northern California Division of Research, Oakland, California
| | - Nancy Grisel
- Division of Infectious Diseases and Clinical Epidemiology, Intermountain Healthcare, Salt Lake City, Utah
| | - Julie Arndorfer
- Division of Infectious Diseases and Clinical Epidemiology, Intermountain Healthcare, Salt Lake City, Utah
| | - Charlene E. McEvoy
- Department of Research, HealthPartners Institute, Minneapolis, Minnesota
| | - Inih J. Essien
- Department of Research, HealthPartners Institute, Minneapolis, Minnesota
| | - Suchitra Rao
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Shaun J. Grannis
- Center for Biomedical Informatics, Regenstrief Institute, Indianapolis, Indiana
- School of Medicine, Indiana University, Indianapolis, Indiana
| | - Anupam B. Kharbanda
- Department of Pediatric Emergency Medicine, Children’s Minnesota, Minneapolis, Minnesota
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
- Medical Informatics Services, NewYork-Presbyterian Hospital, New York, New York
| | - Toan C. Ong
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Peter J. Embi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sarah W. Ball
- Department of Clinical Resarch, Westat, Rockville, Maryland
| | | | | | - Ryan E. Wiegand
- Coronavirus and other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Monica Dickerson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Palak Patel
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Caitlin Ray
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Brendan Flannery
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Shikha Garg
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Katherine Adams
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Nicola P. Klein
- Kaiser Permanente Vaccine Study Center, Kaiser Permanente Northern California Division of Research, Oakland, California
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3
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Lim WW, Feng S, Wong SS, Sullivan SG, Cowling BJ. Hemagglutination Inhibition Antibody Titers as Mediators of Influenza Vaccine Efficacy Against Symptomatic Influenza A(H1N1), A(H3N2), and B/Victoria Virus Infections. J Infect Dis 2024; 230:152-160. [PMID: 39052734 PMCID: PMC11272062 DOI: 10.1093/infdis/jiae122] [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: 07/18/2023] [Revised: 02/24/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND The hemagglutination inhibition antibody (HAI) titer contributes only a part of vaccine-induced protection against influenza virus infections. Using causal mediation analysis, we quantified the proportion of vaccine efficacy mediated by postvaccination HAI titers. METHODS We conducted causal mediation analyses using data from a randomized, active-comparator controlled, phase III, trial of an inactivated, split-virion seasonal quadrivalent influenza vaccine in children conducted from October 2010 to December 2011 in 8 countries. Vaccine efficacy was estimated using a weighted Cox proportional hazards model. Estimates were decomposed into the direct and indirect effects mediated by postvaccination HAI titers. RESULTS The proportions of vaccine efficacy mediated by postvaccination HAI titers were estimated to be 22% (95% confidence interval, 18%--47%) for influenza A(H1N1), 20% (16%-39%) for influenza A(H3N2), and 37% (26%-85%) for influenza B/Victoria. CONCLUSIONS HAI titers partially mediate influenza vaccine efficacy against influenza A(H1N1), A(H3N2), and B/Victoria. Our estimates were lower than in previous studies, possibly reflecting expected heterogeneity in antigenic similarity between vaccine and circulating viruses across seasons.
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Affiliation(s)
- Wey Wen Lim
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Shuo Feng
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Sook-San Wong
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, and Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Epidemiology, University of California, California, Los Angeles, USA
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
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4
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Bloom N, Ramirez SI, Cohn H, Parikh UM, Heaps A, Sieg SF, Greninger A, Ritz J, Moser C, Eron JJ, Bajic G, Currier JS, Klekotka P, Wohl DA, Daar ES, Li J, Hughes MD, Chew KW, Smith DM, Crotty S, Coelho CH. SARS-CoV-2 monoclonal antibody treatment followed by vaccination shifts human memory B cell epitope recognition suggesting antibody feedback. J Infect Dis 2024:jiae371. [PMID: 39036987 DOI: 10.1093/infdis/jiae371] [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: 05/29/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 07/23/2024] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) have been studied in humans, but the impact on immune memory of mAb treatment during an ongoing infection has remained unclear. We evaluated the effect of infusion of the anti-SARS-CoV-2 spike receptor binding domain (RBD) mAb bamlanivimab on memory B cells (MBCs) in SARS-CoV-2-infected individuals. Bamlanivimab treatment skewed the repertoire of memory B cells targeting Spike towards non-RBD epitopes. Furthermore, the relative affinity of RBD memory B cells was weaker in mAb-treated individuals compared to placebo-treated individuals over time. Subsequently, after mRNA COVID-19 vaccination, memory B cell differences persisted and mapped to a specific reduction in recognition of the class II RBD site, the same RBD epitope recognized by bamlanivimab. These findings indicate a substantial role of antibody feedback in regulating memory B cell responses to infection, and single mAb administration can continue to impact memory B cell responses to additional antigen exposures months later.
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Affiliation(s)
- Nathaniel Bloom
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 92037, USA
| | - Hallie Cohn
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Urvi M Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy Heaps
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Scott F Sieg
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio, USA
| | - Alex Greninger
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Justin Ritz
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Carlee Moser
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Judith S Currier
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, USA
| | | | - David A Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Eric S Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jonathan Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael D Hughes
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kara W Chew
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 92037, USA
| | - Shane Crotty
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 92037, USA
| | - Camila H Coelho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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5
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Jiménez-Cabello L, Utrilla-Trigo S, Calvo-Pinilla E, Lorenzo G, Illescas-Amo M, Benavides J, Moreno S, Marín-López A, Nogales A, Ortego J. Co-expression of VP2, NS1 and NS2-Nt proteins by an MVA viral vector induces complete protection against bluetongue virus. Front Immunol 2024; 15:1440407. [PMID: 39072326 PMCID: PMC11272488 DOI: 10.3389/fimmu.2024.1440407] [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: 05/29/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
Introduction Bluetongue (BT), caused by bluetongue virus (BTV), is an important arthropod-borne livestock disease listed by the World Organization for Animal Health. Live-attenuated and inactivated vaccines have permitted to control BT but they do not simultaneously protect against the myriad of BTV serotypes. Recently, we identified the highly conserved BTV nonstructural protein NS1 and the N-terminal region of NS2 as antigens capable of conferring multiserotype protection against BTV. Methods Here, we designed Modified Vaccinia Ankara (MVA) viral vectors that expressed BTV-4 proteins VP2 or VP7 along with NS1 and NS2-Nt as well as MVAs that expressed proteins VP2, VP7 or NS1 and NS2-Nt. Results Immunization of IFNAR(-/-) mice with two doses of MVA-NS1-2A-NS2-Nt protected mice from BTV-4M infection by the induction of an antigen-specific T cell immune response. Despite rMVA expressing VP7 alone were not protective in the IFNAR(-/-) mouse model, inclusion of VP7 in the vaccine formulation amplified the cell-mediated response induced by NS1 and NS2-Nt. Expression of VP2 elicited protective non-cross-reactive neutralizing antibodies (nAbs) in immunized animals and improved the protection observed in the MVA-NS1-2A-NS2-Nt immunized mice when these three BTV antigens were co-expressed. Moreover, vaccines candidates co-expressing VP2 or VP7 along with NS1 and NS2-Nt provided multiserotype protection. We assessed protective efficacy of both vaccine candidates in sheep against virulent challenge with BTV-4M. Discussion Immunization with MVA-VP7-NS1-2A-NS2-Nt partially dumped viral replication and clinical disease whereas administration of MVA-VP2-NS1-2A-NS2-Nt promoted a complete protection, preventing viraemia and the pathology produced by BTV infection.
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Affiliation(s)
- Luis Jiménez-Cabello
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Sergio Utrilla-Trigo
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Eva Calvo-Pinilla
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Gema Lorenzo
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Miguel Illescas-Amo
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Julio Benavides
- Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
| | - Sandra Moreno
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Alejandro Marín-López
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Aitor Nogales
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Javier Ortego
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
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6
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Mitul MT, Kastenschmidt JM, Sureshchandra S, Wagoner ZW, Sorn AM, Mcllwain DR, Hernandez-Davies JE, Jain A, de Assis R, Trask D, Davies DH, Wagar LE. Tissue-specific sex differences in pediatric and adult immune cell composition and function. Front Immunol 2024; 15:1373537. [PMID: 38812520 PMCID: PMC11133680 DOI: 10.3389/fimmu.2024.1373537] [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: 01/19/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Sex-based differences in immune cell composition and function can contribute to distinct adaptive immune responses. Prior work has quantified these differences in peripheral blood, but little is known about sex differences within human lymphoid tissues. Here, we characterized the composition and phenotypes of adaptive immune cells from male and female ex vivo tonsils and evaluated their responses to influenza antigens using an immune organoid approach. In a pediatric cohort, female tonsils had more memory B cells compared to male tonsils direct ex vivo and after stimulation with live-attenuated but not inactivated vaccine, produced higher influenza-specific antibody responses. Sex biases were also observed in adult tonsils but were different from those measured in children. Analysis of peripheral blood immune cells from in vivo vaccinated adults also showed higher frequencies of tissue homing CD4 T cells in female participants. Together, our data demonstrate that distinct memory B and T cell profiles are present in male vs. female lymphoid tissues and peripheral blood respectively and suggest that these differences may in part explain sex biases in response to vaccines and viruses.
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Affiliation(s)
- Mahina Tabassum Mitul
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Center for Virus Research, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
| | - Jenna M. Kastenschmidt
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Center for Virus Research, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
| | - Suhas Sureshchandra
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Center for Virus Research, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
| | - Zachary W. Wagoner
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Center for Virus Research, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
| | - Andrew M. Sorn
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Center for Virus Research, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
| | - David R. Mcllwain
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV, United States
| | - Jenny E. Hernandez-Davies
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Center for Virus Research, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
| | - Aarti Jain
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
| | - Rafael de Assis
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
| | - Douglas Trask
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, CA, United States
| | - D. Huw Davies
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Center for Virus Research, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
| | - Lisa E. Wagar
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
- Institute for Immunology, University of California, Irvine, Irvine, CA, United States
- Center for Virus Research, University of California, Irvine, Irvine, CA, United States
- Vaccine Research and Development Center, University of California, Irvine, Irvine, CA, United States
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7
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Ray R, Nait Mohamed FA, Maurer DP, Huang J, Alpay BA, Ronsard L, Xie Z, Han J, Fernandez-Quintero M, Phan QA, Ursin RL, Vu M, Kirsch KH, Prum T, Rosado VC, Bracamonte-Moreno T, Okonkwo V, Bals J, McCarthy C, Nair U, Kanekiyo M, Ward AB, Schmidt AG, Batista FD, Lingwood D. Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses. Immunity 2024; 57:1141-1159.e11. [PMID: 38670113 PMCID: PMC11096021 DOI: 10.1016/j.immuni.2024.03.022] [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: 12/12/2023] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]
Abstract
Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.
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Affiliation(s)
- Rashmi Ray
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Faez Amokrane Nait Mohamed
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
| | - Daniel P Maurer
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Jiachen Huang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Berk A Alpay
- Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Larance Ronsard
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Zhenfei Xie
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Monica Fernandez-Quintero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020 Innsbruck, Austria
| | - Quynh Anh Phan
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Rebecca L Ursin
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mya Vu
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thavaleak Prum
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Victoria C Rosado
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thalia Bracamonte-Moreno
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Vintus Okonkwo
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Julia Bals
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Caitlin McCarthy
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Usha Nair
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aaron G Schmidt
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Facundo D Batista
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Department of Biology, The Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Daniel Lingwood
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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8
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585703. [PMID: 38746108 PMCID: PMC11092427 DOI: 10.1101/2024.03.19.585703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app .
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9
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. ARXIV 2024:arXiv:2403.12684v2. [PMID: 38745695 PMCID: PMC11092678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app.
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Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Malancha Karmakar
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
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10
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Hay JA, Zhu H, Jiang CQ, Kwok KO, Shen R, Kucharski A, Yang B, Read JM, Lessler J, Cummings DAT, Riley S. Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.18.24304371. [PMID: 38562868 PMCID: PMC10984066 DOI: 10.1101/2024.03.18.24304371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Humans experience many influenza infections over their lives, resulting in complex and varied immunological histories. Although experimental and quantitative analyses have improved our understanding of the immunological processes defining an individual's antibody repertoire, how these within-host processes are linked to population-level influenza epidemiology remains unclear. Here, we used a multi-level mathematical model to jointly infer antibody dynamics and individual-level lifetime influenza A/H3N2 infection histories for 1,130 individuals in Guangzhou, China, using 67,683 haemagglutination inhibition (HI) assay measurements against 20 A/H3N2 strains from repeat serum samples collected between 2009 and 2015. These estimated infection histories allowed us to reconstruct historical seasonal influenza patterns and to investigate how influenza incidence varies over time, space and age in this population. We estimated median annual influenza infection rates to be approximately 18% from 1968 to 2015, but with substantial variation between years. 88% of individuals were estimated to have been infected at least once during the study period (2009-2015), and 20% were estimated to have three or more infections in that time. We inferred decreasing infection rates with increasing age, and found that annual attack rates were highly correlated across all locations, regardless of their distance, suggesting that age has a stronger impact than fine-scale spatial effects in determining an individual's antibody profile. Finally, we reconstructed each individual's expected antibody profile over their lifetime and inferred an age-stratified relationship between probability of infection and HI titre. Our analyses show how multi-strain serological panels provide rich information on long term, epidemiological trends, within-host processes and immunity when analyzed using appropriate inference methods, and adds to our understanding of the life course epidemiology of influenza A/H3N2.
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Affiliation(s)
- James A. Hay
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, Imperial College London
| | - Huachen Zhu
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases/MOE Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou University, Shantou, China
- State Key Laboratory of Emerging Infectious Diseases / World Health Organization Influenza Reference Laboratory, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- 5EKIH (Gewuzhikang) Pathogen Research Institute, Guangdong, China
| | | | - Kin On Kwok
- The Jockey Club School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Hong Kong Institute of Asia-Pacific Studies, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ruiyin Shen
- Guangzhou No.12 Hospital, Guangzhou, Guangdong, China
| | - Adam Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Bingyi Yang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jonathan M. Read
- Centre for Health Informatics Computing and Statistics, Lancaster University, Lancaster, United Kingdom
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
- Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, United States
- UNC Carolina Population Center, Chapel Hill, United States
| | - Derek A. T. Cummings
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Imperial College London
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11
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Maurer DP, Vu M, Schmidt AG. Antigenic drift expands viral escape pathways from imprinted host humoral immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585891. [PMID: 38562862 PMCID: PMC10983950 DOI: 10.1101/2024.03.20.585891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
An initial virus exposure can imprint antibodies such that future responses to antigenically drifted strains are dependent on the identity of the imprinting strain. Subsequent exposure to antigenically distinct strains followed by affinity maturation can guide immune responses toward generation of cross-reactive antibodies. How viruses evolve in turn to escape these imprinted broad antibody responses is unclear. Here, we used clonal antibody lineages from two human donors recognizing conserved influenza virus hemagglutinin (HA) epitopes to assess viral escape potential using deep mutational scanning. We show that even though antibody affinity maturation does restrict the number of potential escape routes in the imprinting strain through repositioning the antibody variable domains, escape is still readily observed in drifted strains and attributed to epistatic networks within HA. These data explain how influenza virus continues to evolve in the human population by escaping even broad antibody responses.
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12
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Loes AN, Tarabi RAL, Huddleston J, Touyon L, Wong SS, Cheng SMS, Leung NHL, Hannon WW, Bedford T, Cobey S, Cowling BJ, Bloom JD. High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584176. [PMID: 38496577 PMCID: PMC10942427 DOI: 10.1101/2024.03.08.584176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately one month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals, and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers six months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. This study demonstrates the utility of high-throughput sequencing-based neutralization assays that enable titers to be simultaneously measured against many different viral strains. We provide a detailed experimental protocol (DOI: https://dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and a computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.
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Affiliation(s)
- Andrea N Loes
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Rosario Araceli L Tarabi
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - John Huddleston
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Lisa Touyon
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Sook San Wong
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Samuel M S Cheng
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Nancy H L Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - William W Hannon
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Benjamin J Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
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13
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Ji W, Guthmiller J. Goldilocks Zone of Preexisting Immunity: Too Little or Too Much Suppresses Diverse Antibody Responses Against Influenza Viruses. J Infect Dis 2024; 229:299-302. [PMID: 37979157 PMCID: PMC10873167 DOI: 10.1093/infdis/jiad494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023] Open
Affiliation(s)
- Wei Ji
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jenna Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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14
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Ellis D, Dosey A, Boyoglu-Barnum S, Park YJ, Gillespie R, Syeda H, Hutchinson GB, Tsybovsky Y, Murphy M, Pettie D, Matheson N, Chan S, Ueda G, Fallas JA, Carter L, Graham BS, Veesler D, Kanekiyo M, King NP. Antigen spacing on protein nanoparticles influences antibody responses to vaccination. Cell Rep 2023; 42:113552. [PMID: 38096058 PMCID: PMC10801709 DOI: 10.1016/j.celrep.2023.113552] [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: 06/20/2023] [Revised: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle vaccine platform based on the receptor-binding domain (RBD) of influenza hemagglutinin (HA) that enables precise control of antigen conformation and spacing. HA RBDs are presented as either monomers or native-like closed trimers that are connected to the underlying nanoparticle by a rigid linker that is modularly extended to precisely control antigen spacing. Nanoparticle immunogens with decreased spacing between trimeric RBDs elicit antibodies with improved hemagglutination inhibition and neutralization potency as well as binding breadth across diverse H1 HAs. Our "trihead" nanoparticle immunogen platform provides insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used in next-generation vaccines against influenza and other viruses.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Rebecca Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Geoffrey B Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nick Matheson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorge A Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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15
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Jost S, Lucar O, Lee E, Yoder T, Kroll K, Sugawara S, Smith S, Jones R, Tweet G, Werner A, Tomezsko PJ, Dugan HL, Ghofrani J, Rascle P, Altfeld M, Müller-Trutwin M, Goepfert P, Reeves RK. Antigen-specific memory NK cell responses against HIV and influenza use the NKG2/HLA-E axis. Sci Immunol 2023; 8:eadi3974. [PMID: 38064568 PMCID: PMC11104516 DOI: 10.1126/sciimmunol.adi3974] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
Multiple studies have broadened the roles of natural killer (NK) cells functioning as purely innate lymphocytes by demonstrating that they are capable of putative antigen-specific immunological memory against multiple infectious agents including HIV-1 and influenza. However, the mechanisms underlying antigen specificity remain unknown. Here, we demonstrate that antigen-specific human NK cell memory develops upon exposure to both HIV and influenza, unified by a conserved and epitope-specific targetable mechanism largely dependent on the activating CD94/NKG2C receptor and its ligand HLA-E. We validated the permanent acquisition of antigen specificity by individual memory NK cells by single-cell cloning. We identified elevated expression of KLRG1, α4β7, and NKG2C as biomarkers of antigen-specific NK cell memory through complex immunophenotyping. Last, we uncovered individual HLA-E-restricted peptides that may constitute the dominant NK cell response in HIV-1- and influenza-infected persons in vivo. Our findings clarify the mechanisms contributing to antigen-specific memory NK cell responses and suggest that they could be potentially targeted therapeutically for vaccines or other therapeutic interventions.
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Affiliation(s)
- Stephanie Jost
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC 27703, USA
| | - Olivier Lucar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Esther Lee
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC 27703, USA
| | - Taylor Yoder
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Kyle Kroll
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC 27703, USA
| | - Sho Sugawara
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC 27703, USA
| | - Scott Smith
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Rhianna Jones
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC 27703, USA
| | - George Tweet
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Werner
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Phillip J. Tomezsko
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Haley L. Dugan
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Joshua Ghofrani
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Philippe Rascle
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC 27703, USA
| | | | - Michaela Müller-Trutwin
- Institut Pasteur, Université Paris-Cité, HIV, Inflammation and Persistence Unit, 75015 Paris, France
| | - Paul Goepfert
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - R. Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC 27703, USA
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA
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16
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Han AX, de Jong SPJ, Russell CA. Co-evolution of immunity and seasonal influenza viruses. Nat Rev Microbiol 2023; 21:805-817. [PMID: 37532870 DOI: 10.1038/s41579-023-00945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
Seasonal influenza viruses cause recurring global epidemics by continually evolving to escape host immunity. The viral constraints and host immune responses that limit and drive the evolution of these viruses are increasingly well understood. However, it remains unclear how most of these advances improve the capacity to reduce the impact of seasonal influenza viruses on human health. In this Review, we synthesize recent progress made in understanding the interplay between the evolution of immunity induced by previous infections or vaccination and the evolution of seasonal influenza viruses driven by the heterogeneous accumulation of antibody-mediated immunity in humans. We discuss the functional constraints that limit the evolution of the viruses, the within-host evolutionary processes that drive the emergence of new virus variants, as well as current and prospective options for influenza virus control, including the viral and immunological barriers that must be overcome to improve the effectiveness of vaccines and antiviral drugs.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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17
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Rijnink WF, Stadlbauer D, Puente-Massaguer E, Okba NMA, Kirkpatrick Roubidoux E, Strohmeier S, Mudd PA, Schmitz A, Ellebedy A, McMahon M, Krammer F. Characterization of non-neutralizing human monoclonal antibodies that target the M1 and NP of influenza A viruses. J Virol 2023; 97:e0164622. [PMID: 37916834 PMCID: PMC10688359 DOI: 10.1128/jvi.01646-22] [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: 10/25/2022] [Accepted: 10/08/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Currently, many groups are focusing on isolating both neutralizing and non-neutralizing antibodies to the mutation-prone hemagglutinin as a tool to treat or prevent influenza virus infection. Less is known about the level of protection induced by non-neutralizing antibodies that target conserved internal influenza virus proteins. Such non-neutralizing antibodies could provide an alternative pathway to induce broad cross-reactive protection against multiple influenza virus serotypes and subtypes by partially overcoming influenza virus escape mediated by antigenic drift and shift. Accordingly, more information about the level of protection and potential mechanism(s) of action of non-neutralizing antibodies targeting internal influenza virus proteins could be useful for the design of broadly protective and universal influenza virus vaccines.
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Affiliation(s)
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eduard Puente-Massaguer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nisreen M. A. Okba
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ericka Kirkpatrick Roubidoux
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Philip A. Mudd
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Aaron Schmitz
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ali Ellebedy
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meagan McMahon
- Department of Microbiology, 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 (C-VaRPP), 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
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18
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Coelho CH, Bloom N, Ramirez SI, Parikh UM, Heaps A, Sieg SF, Greninger A, Ritz J, Moser C, Eron JJ, Currier JS, Klekotka P, Wohl DA, Daar ES, Li J, Hughes MD, Chew KW, Smith DM, Crotty S. SARS-CoV-2 monoclonal antibody treatment followed by vaccination shifts human memory B cell epitope recognition suggesting antibody feedback. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.567575. [PMID: 38045374 PMCID: PMC10690233 DOI: 10.1101/2023.11.21.567575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Therapeutic anti-SARS-CoV-2 monoclonal antibodies (mAbs) have been extensively studied in humans, but the impact on immune memory of mAb treatment during an ongoing immune response has remained unclear. Here, we evaluated the effect of infusion of the anti-SARS-CoV-2 spike receptor binding domain (RBD) mAb bamlanivimab on memory B cells (MBCs) in SARS-CoV-2-infected individuals. Bamlanivimab treatment skewed the repertoire of memory B cells targeting Spike towards non-RBD epitopes. Furthermore, the relative affinity of RBD memory B cells was weaker in mAb-treated individuals compared to placebo-treated individuals over time. Subsequently, after mRNA COVID-19 vaccination, memory B cell differences persisted and mapped to a specific defect in recognition of the class II RBD site, the same RBD epitope recognized by bamlanivimab. These findings indicate a substantial role of antibody feedback in regulating human memory B cell responses, both to infection and vaccination. These data indicate that mAb administration can promote alterations in the epitopes recognized by the B cell repertoire, and the single administration of mAb can continue to determine the fate of B cells in response to additional antigen exposures months later.
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Affiliation(s)
- Camila H Coelho
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
| | - Nathaniel Bloom
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 92037, USA
| | - Urvi M Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy Heaps
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Scott F Sieg
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio, USA
| | - Alex Greninger
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Justin Ritz
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Carlee Moser
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Judith S Currier
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, USA
| | | | - David A Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Eric S Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jonathan Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael D Hughes
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kara W Chew
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 92037, USA
| | - Shane Crotty
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 92037, USA
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19
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Heida R, Frijlink HW, Hinrichs WLJ. Inhalation of vaccines and antiviral drugs to fight respiratory virus infections: reasons to prioritize the pulmonary route of administration. mBio 2023; 14:e0129523. [PMID: 37768057 PMCID: PMC10653782 DOI: 10.1128/mbio.01295-23] [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] [Indexed: 09/29/2023] Open
Abstract
Many of the current pandemic threats are caused by viruses that infect the respiratory tract. Remarkably though, the majority of vaccines and antiviral drugs are administered via alternative routes. In this perspective, we argue that the pulmonary route of administration deserves more attention in the search for novel therapeutic strategies against respiratory virus infections. Firstly, vaccines administered at the viral portal of entry can induce a broader immune response, employing the mucosal arm of the immune system; secondly, direct administration of antiviral drugs at the target site leads to superior bioavailability, enabling lower dosing and reducing the chance of side effects. We further elaborate on why the pulmonary route may induce a superior effect compared to the intranasal route of administration and provide reasons why dry powder formulations for inhalation have significant advantages over standard liquid formulations.
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Affiliation(s)
- Rick Heida
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Henderik W. Frijlink
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Wouter L. J. Hinrichs
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
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20
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Jones RP, Ponomarenko A. COVID-19-Related Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mortality. Infect Dis Rep 2023; 15:600-634. [PMID: 37888139 PMCID: PMC10606787 DOI: 10.3390/idr15050058] [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: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023] Open
Abstract
Since 2020, COVID-19 has caused serious mortality around the world. Given the ambiguity in establishing COVID-19 as the direct cause of death, we first investigate the effects of age and sex on all-cause mortality during 2020 and 2021 in England and Wales. Since infectious agents have their own unique age profile for death, we use a 9-year time series and several different methods to adjust single-year-of-age deaths in England and Wales during 2019 (the pre-COVID-19 base year) to a pathogen-neutral single-year-of-age baseline. This adjusted base year is then used to confirm the widely reported higher deaths in males for most ages above 43 in both 2020 and 2021. During 2020 (+COVID-19 but no vaccination), both male and female population-adjusted deaths significantly increased above age 35. A significant reduction in all-cause mortality among both males and females aged 75+ could be demonstrated in 2021 during the widespread COVID-19 vaccination period; however, deaths below age 75 progressively increased. This finding arises from a mix of vaccination coverage and year-of-age profiles of deaths for the different SARS-CoV-2 variants. In addition, specific effects of age around puberty were demonstrated, where females had higher deaths than males. There is evidence that year-of-birth cohorts may also be involved, indicating that immune priming to specific pathogen outbreaks in the past may have led to lower deaths for some birth cohorts. To specifically identify the age profile for the COVID-19 variants from 2020 to 2023, we employ the proportion of total deaths at each age that are potentially due to or 'with' COVID-19. The original Wuhan strain and the Alpha variant show somewhat limited divergence in the age profile, with the Alpha variant shifting to a moderately higher proportion of deaths below age 84. The Delta variant specifically targeted individuals below age 65. The Omicron variants showed a significantly lower proportion of overall mortality, with a markedly higher relative proportion of deaths above age 65, steeply increasing with age to a maximum around 100 years of age. A similar age profile for the variants can be seen in the age-banded deaths in US states, although they are slightly obscured by using age bands rather than single years of age. However, the US data shows that higher male deaths are greatly dependent on age and the COVID variant. Deaths assessed to be 'due to' COVID-19 (as opposed to 'involving' COVID-19) in England and Wales were especially overestimated in 2021 relative to the change in all-cause mortality. This arose as a by-product of an increase in COVID-19 testing capacity in late 2020. Potential structure-function mechanisms for the age-specificity of SARS-CoV-2 variants are discussed, along with potential roles for small noncoding RNAs (miRNAs). Using data from England, it is possible to show that the unvaccinated do indeed have a unique age profile for death from each variant and that vaccination alters the shape of the age profile in a manner dependent on age, sex, and the variant. The question is posed as to whether vaccines based on different variants carry a specific age profile.
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Affiliation(s)
| | - Andrey Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine
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21
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Früh SP, Adu OF, López-Astacio RA, Weichert WS, Wasik BR, Parrish CR. Isolation, cloning and analysis of parvovirus-specific canine antibodies from peripheral blood B cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104894. [PMID: 37467826 PMCID: PMC10542859 DOI: 10.1016/j.dci.2023.104894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/05/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
B-cell cloning methods enable the analysis of antibody responses against target antigens and can be used to reveal the host antibody repertoire, antigenic sites (epitopes), and details of protective immunity against pathogens. Here, we describe improved methods for isolation of canine peripheral blood B cells producing antibodies against canine parvovirus (CPV) capsids by fluorescence-activated cell sorting, followed by cell cloning. We cultured sorted B cells from an immunized dog in vitro and screened for CPV-specific antibody production. Updated canine-specific primer sets were used to amplify and clone the heavy and light chain immunoglobulin sequences directly from the B cells by reverse transcription and PCR. Monoclonal canine IgGs were produced by cloning heavy and light chain sequences into antibody expression vectors, which were screened for CPV binding. Three different canine monoclonal antibodies were analyzed, including two that shared the same heavy chain, and one that had distinct heavy and light chains. The antibodies showed broad binding to CPV variants, and epitopes were mapped to antigenic sites on the capsid. The methods described here are applicable for the isolation of canine B cells and monoclonal antibodies against many antigens.
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Affiliation(s)
- Simon P Früh
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA; Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Oluwafemi F Adu
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Robert A López-Astacio
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Wendy S Weichert
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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22
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Sokal A, Barba-Spaeth G, Hunault L, Fernández I, Broketa M, Meola A, Fourati S, Azzaoui I, Vandenberghe A, Lagouge-Roussey P, Broutin M, Roeser A, Bouvier-Alias M, Crickx E, Languille L, Fournier M, Michel M, Godeau B, Gallien S, Melica G, Nguyen Y, Canoui-Poitrine F, Pirenne F, Megret J, Pawlotsky JM, Fillatreau S, Reynaud CA, Weill JC, Rey FA, Bruhns P, Mahévas M, Chappert P. SARS-CoV-2 Omicron BA.1 breakthrough infection drives late remodeling of the memory B cell repertoire in vaccinated individuals. Immunity 2023; 56:2137-2151.e7. [PMID: 37543032 DOI: 10.1016/j.immuni.2023.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 08/07/2023]
Abstract
How infection by a viral variant showing antigenic drift impacts a preformed mature human memory B cell (MBC) repertoire remains an open question. Here, we studied the MBC response up to 6 months after SARS-CoV-2 Omicron BA.1 breakthrough infection in individuals previously vaccinated with three doses of the COVID-19 mRNA vaccine. Longitudinal analysis, using single-cell multi-omics and functional analysis of monoclonal antibodies from RBD-specific MBCs, revealed that a BA.1 breakthrough infection mostly recruited pre-existing cross-reactive MBCs with limited de novo response against BA.1-restricted epitopes. Reorganization of clonal hierarchy and new rounds of germinal center reactions, however, combined to maintain diversity and induce progressive maturation of the MBC repertoire against common Hu-1 and BA.1, but not BA.5-restricted, SARS-CoV-2 Spike RBD epitopes. Such remodeling was further associated with a marked improvement in overall neutralizing breadth and potency. These findings have fundamental implications for the design of future vaccination booster strategies.
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Affiliation(s)
- Aurélien Sokal
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris Cité, Clichy, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Giovanna Barba-Spaeth
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Lise Hunault
- Institut Pasteur, Université de Paris Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France; Sorbonne University, ED394, Paris, France; Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
| | - Ignacio Fernández
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Matteo Broketa
- Institut Pasteur, Université de Paris Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France; Sorbonne University, ED394, Paris, France
| | - Annalisa Meola
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Slim Fourati
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Imane Azzaoui
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Alexis Vandenberghe
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Pauline Lagouge-Roussey
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Manon Broutin
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Anais Roeser
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Magali Bouvier-Alias
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Etienne Crickx
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Laetitia Languille
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Morgane Fournier
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Marc Michel
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Bertrand Godeau
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Sébastien Gallien
- Service de Maladies Infectieuses, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Giovanna Melica
- Service de Maladies Infectieuses, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Yann Nguyen
- Service de Médecine Interne, Centre Hospitalier Universitaire Cochin, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Florence Canoui-Poitrine
- Département de Santé Publique, Unité de Recherche Clinique (URC), CEpiA (Clinical Epidemiology and Ageing), EA 7376- Institut Mondor de Recherche Biomédicale (IMRB), Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - France Pirenne
- INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France; Etablissement Français du Sang (EFS) Ile de France, Créteil, France
| | - Jérôme Megret
- Plateforme de Cytométrie en Flux, Structure Fédérative de Recherche Necker, INSERM US24-CNRS UMS3633, Paris, France
| | - Jean-Michel Pawlotsky
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Simon Fillatreau
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMR 8253, Université de Paris, Paris, France
| | - Claude-Agnès Reynaud
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France
| | - Jean-Claude Weill
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France
| | - Félix A Rey
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Pierre Bruhns
- Institut Pasteur, Université de Paris Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France
| | - Matthieu Mahévas
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France.
| | - Pascal Chappert
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France.
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23
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Rojas M, Herrán M, Ramírez-Santana C, Leung PSC, Anaya JM, Ridgway WM, Gershwin ME. Molecular mimicry and autoimmunity in the time of COVID-19. J Autoimmun 2023; 139:103070. [PMID: 37390745 PMCID: PMC10258587 DOI: 10.1016/j.jaut.2023.103070] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/26/2023] [Accepted: 06/03/2023] [Indexed: 07/02/2023]
Abstract
Infectious diseases are commonly implicated as potential initiators of autoimmune diseases (ADs) and represent the most commonly known factor in the development of autoimmunity in susceptible individuals. Epidemiological data and animal studies on multiple ADs suggest that molecular mimicry is one of the likely mechanisms for the loss of peripheral tolerance and the development of clinical disease. Besides molecular mimicry, other mechanisms such as defects in central tolerance, nonspecific bystander activation, epitope-determinant spreading, and/or constant antigenic stimuli, may also contribute for breach of tolerance and to the development of ADs. Linear peptide homology is not the only mechanism by which molecular mimicry is established. Peptide modeling (i.e., 3D structure), molecular docking analyses, and affinity estimation for HLAs are emerging as critical strategies when studying the links of molecular mimicry in the development of autoimmunity. In the current pandemic, several reports have confirmed an influence of SARS-CoV-2 on subsequent autoimmunity. Bioinformatic and experimental evidence support the potential role of molecular mimicry. Peptide dimensional analysis requires more research and will be increasingly important for designing and distributing vaccines and better understanding the role of environmental factors related to autoimmunity.
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Affiliation(s)
- Manuel Rojas
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA; Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia.
| | - María Herrán
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Carolina Ramírez-Santana
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Patrick S C Leung
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - Juan-Manuel Anaya
- Health Research and Innovation Center at Coosalud, Cartagena, 130001, Colombia
| | - William M Ridgway
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
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24
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Einav T, Ma R. Using interpretable machine learning to extend heterogeneous antibody-virus datasets. CELL REPORTS METHODS 2023; 3:100540. [PMID: 37671020 PMCID: PMC10475791 DOI: 10.1016/j.crmeth.2023.100540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/14/2023] [Accepted: 06/30/2023] [Indexed: 09/07/2023]
Abstract
A central challenge in biology is to use existing measurements to predict the outcomes of future experiments. For the rapidly evolving influenza virus, variants examined in one study will often have little to no overlap with other studies, making it difficult to discern patterns or unify datasets. We develop a computational framework that predicts how an antibody or serum would inhibit any variant from any other study. We validate this method using hemagglutination inhibition data from seven studies and predict 2,000,000 new values ± uncertainties. Our analysis quantifies the transferability between vaccination and infection studies in humans and ferrets, shows that serum potency is negatively correlated with breadth, and provides a tool for pandemic preparedness. In essence, this approach enables a shift in perspective when analyzing data from "what you see is what you get" into "what anyone sees is what everyone gets."
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Affiliation(s)
- Tal Einav
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Rong Ma
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
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25
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Kastenschmidt JM, Sureshchandra S, Jain A, Hernandez-Davies JE, de Assis R, Wagoner ZW, Sorn AM, Mitul MT, Benchorin AI, Levendosky E, Ahuja G, Zhong Q, Trask D, Boeckmann J, Nakajima R, Jasinskas A, Saligrama N, Davies DH, Wagar LE. Influenza vaccine format mediates distinct cellular and antibody responses in human immune organoids. Immunity 2023; 56:1910-1926.e7. [PMID: 37478854 PMCID: PMC10433940 DOI: 10.1016/j.immuni.2023.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/11/2023] [Accepted: 06/20/2023] [Indexed: 07/23/2023]
Abstract
Highly effective vaccines elicit specific, robust, and durable adaptive immune responses. To advance informed vaccine design, it is critical that we understand the cellular dynamics underlying responses to different antigen formats. Here, we sought to understand how antigen-specific B and T cells were activated and participated in adaptive immune responses within the mucosal site. Using a human tonsil organoid model, we tracked the differentiation and kinetics of the adaptive immune response to influenza vaccine and virus modalities. Each antigen format elicited distinct B and T cell responses, including differences in their magnitude, diversity, phenotype, function, and breadth. These differences culminated in substantial changes in the corresponding antibody response. A major source of antigen format-related variability was the ability to recruit naive vs. memory B and T cells to the response. These findings have important implications for vaccine design and the generation of protective immune responses in the upper respiratory tract.
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Affiliation(s)
- Jenna M Kastenschmidt
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Suhas Sureshchandra
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Aarti Jain
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Jenny E Hernandez-Davies
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Rafael de Assis
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Zachary W Wagoner
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Andrew M Sorn
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Mahina Tabassum Mitul
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Aviv I Benchorin
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Elizabeth Levendosky
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA
| | - Gurpreet Ahuja
- Department of Pediatric Otolaryngology, Children's Hospital of Orange County, Orange, CA 92868, USA; Department of Otolaryngology-Head and Neck Surgery, University of California Irvine, Orange, CA 92868, USA
| | - Qiu Zhong
- Department of Pediatric Otolaryngology, Children's Hospital of Orange County, Orange, CA 92868, USA; Department of Otolaryngology-Head and Neck Surgery, University of California Irvine, Orange, CA 92868, USA
| | - Douglas Trask
- Department of Otolaryngology-Head and Neck Surgery, University of California Irvine, Orange, CA 92868, USA
| | - Jacob Boeckmann
- Department of Otolaryngology-Head and Neck Surgery, University of California Irvine, Orange, CA 92868, USA
| | - Rie Nakajima
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Algimantas Jasinskas
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Naresha Saligrama
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA; Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA; Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA
| | - D Huw Davies
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Lisa E Wagar
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA.
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26
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Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ. Defining and Studying B Cell Receptor and TCR Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:311-322. [PMID: 37459189 PMCID: PMC10495106 DOI: 10.4049/jimmunol.2300136] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by which the adaptive immune system recognizes foreign and self-antigens, playing an integral part in host defense, as well as the emergence of autoimmunity. Importantly, the interaction between AIRs and their cognate Ags defies a simple key-in-lock paradigm and is instead a complex many-to-many mapping between an individual's massively diverse AIR repertoire, and a similarly diverse antigenic space. Understanding how adaptive immunity balances specificity with epitopic coverage is a key challenge for the field, and terms such as broad specificity, cross-reactivity, and polyreactivity remain ill-defined and are used inconsistently. In this Immunology Notes and Resources article, a group of experimental, structural, and computational immunologists define commonly used terms associated with AIR binding, describe methodologies to study these binding modes, as well as highlight the implications of these different binding modes for therapeutic design.
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Affiliation(s)
| | | | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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27
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Kang M, Lin F, Jiang Z, Tan X, Lin X, Liang Z, Xiao C, Xia Y, Guan W, Yang Z, Yu G, Zanin M, Tang S, Wong S. The impact of pre-existing influenza antibodies and inflammatory status on the influenza vaccine responses in older adults. Influenza Other Respir Viruses 2023; 17:e13172. [PMID: 37457646 PMCID: PMC10339007 DOI: 10.1111/irv.13172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 07/18/2023] Open
Abstract
Age-associated immune changes and pre-existing influenza immunity are hypothesized to reduce influenza vaccine effectiveness in older adults, although the contribution of each factor is unknown. Here, we constructed influenza-specific IgG landscapes and determined baseline concentrations of cytokines typically associated with chronic inflammation in older adults (TNF-α, IL-10, IL-6, and IFN-γ) in 30 high and 29 low influenza vaccine responders (HR and LR, respectively). In a background of high H3 antibody titers, vaccine-specific H3, but not H1, antibody titers were boosted in LRs to titers comparable to HRs. Pre-vaccination concentrations of IL-10 were higher in LRs compared with HRs and inversely correlated with titers of pre-existing influenza antibodies. Baseline TNF-α concentrations were positively correlated with fold-increases in antibody titers in HRs. Our findings indicate that baseline inflammatory status is an important determinant for generating post-vaccination hemagglutinin-inhibition antibodies in older adults, and IgG responses can be boosted in the context of high pre-existing immunity.
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Affiliation(s)
- Min Kang
- School of Public HealthSouthern Medical UniversityGuangzhouP. R. China
- Guangdong Center for Disease Control and PreventionGuangzhouP. R. China
| | - Fangmei Lin
- Guangzhou Medical University, XinzaoGuangzhouP. R. China
- State Key Laboratory for Respiratory Diseases and National Clinical Research Centre for Respiratory DiseaseGuangzhouP.R. China
| | - Zhanpeng Jiang
- Guangzhou Medical University, XinzaoGuangzhouP. R. China
- State Key Laboratory for Respiratory Diseases and National Clinical Research Centre for Respiratory DiseaseGuangzhouP.R. China
| | - Xiaohua Tan
- Guangdong Center for Disease Control and PreventionGuangzhouP. R. China
| | - Xia Lin
- Guangzhou Medical University, XinzaoGuangzhouP. R. China
- State Key Laboratory for Respiratory Diseases and National Clinical Research Centre for Respiratory DiseaseGuangzhouP.R. China
| | - Zaolan Liang
- Guangzhou Medical University, XinzaoGuangzhouP. R. China
- State Key Laboratory for Respiratory Diseases and National Clinical Research Centre for Respiratory DiseaseGuangzhouP.R. China
- HKU‐Pasteur Research Pole, School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Cheng Xiao
- Guangzhou Medical University, XinzaoGuangzhouP. R. China
- State Key Laboratory for Respiratory Diseases and National Clinical Research Centre for Respiratory DiseaseGuangzhouP.R. China
- HKU‐Pasteur Research Pole, School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Yonghe Xia
- Zhongshan Yiyan Bio‐Pharmaceutical Co., LtdZhongshanP. R. China
| | - Wenda Guan
- State Key Laboratory for Respiratory Diseases and National Clinical Research Centre for Respiratory DiseaseGuangzhouP.R. China
- Guangzhou Institute of Respiratory HealthFirst Affiliated Hospital of Guangzhou Medical University, National Center for Respiratory MedicineGuangzhouP.R. China
| | - Zifeng Yang
- State Key Laboratory for Respiratory Diseases and National Clinical Research Centre for Respiratory DiseaseGuangzhouP.R. China
- Guangzhou Institute of Respiratory HealthFirst Affiliated Hospital of Guangzhou Medical University, National Center for Respiratory MedicineGuangzhouP.R. China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical SciencesSouthern Medical UniversityGuangzhouP. R. China
| | - Mark Zanin
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong KongChina
- Centre for Immunology & InfectionShatinHong Kong
| | - Shixing Tang
- School of Public HealthSouthern Medical UniversityGuangzhouP. R. China
| | - Sook‐San Wong
- HKU‐Pasteur Research Pole, School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong KongChina
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong KongChina
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28
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McGrath JJC, Wilson PC. Fate-mapping antibodies to study sinful immune dynamics. Nat Immunol 2023; 24:570-572. [PMID: 36959294 DOI: 10.1038/s41590-023-01467-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- Joshua J C McGrath
- Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
| | - Patrick C Wilson
- Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
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29
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Boudreau CM, Burke JS, Roederer AL, Gorman MJ, Mundle S, Lingwood D, Delagrave S, Sridhar S, Ross TM, Kleanthous H, Alter G. Pre-existing Fc profiles shape the evolution of neutralizing antibody breadth following influenza vaccination. Cell Rep Med 2023; 4:100975. [PMID: 36921600 PMCID: PMC10040413 DOI: 10.1016/j.xcrm.2023.100975] [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: 02/07/2022] [Revised: 12/08/2022] [Accepted: 02/19/2023] [Indexed: 03/16/2023]
Abstract
Under the ever-present threat of a pandemic influenza strain, the evolution of a broadly reactive, neutralizing, functional, humoral immune response may hold the key to protection against both circulating and emerging influenza strains. We apply a systems approach to profile hemagglutinin- and neuraminidase-specific humoral signatures that track with the evolution of broad immunity in a cohort of vaccinated individuals and validate these findings in a second longitudinal cohort. Multivariate analysis reveals the presence of a unique pre-existing Fcγ-receptor-binding antibody profile in individuals that evolved broadly reactive hemagglutination inhibition activity (HAI), marked by the presence of elevated levels of pre-existing FCGR2B-binding antibodies. Moreover, vaccination with FCGR2B-binding antibody-opsonized influenza results in enhanced antibody titers and HAI activity in a murine model. Together, these data suggest that pre-existing FCGR2B binding antibodies are a key correlate of the evolution of broadly protective influenza-specific antibodies, providing insight for the design of next-generation influenza vaccines.
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Affiliation(s)
- Carolyn M Boudreau
- PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - John S Burke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Alexander L Roederer
- PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Matthew J Gorman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Sophia Mundle
- Discovery North America, Sanofi-Pasteur, Inc., Cambridge, MA 02139, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Saranya Sridhar
- Discovery North America, Sanofi-Pasteur, Inc., Cambridge, MA 02139, USA
| | - Ted M Ross
- University of Georgia, Athens, GA 30602, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
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30
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Lindesmith LC, Brewer-Jensen PD, Conrad H, O’Reilly KM, Mallory ML, Kelly D, Williams R, Edmunds WJ, Allen DJ, Breuer J, Baric RS. Emergent variant modeling of the serological repertoire to norovirus in young children. Cell Rep Med 2023; 4:100954. [PMID: 36854303 PMCID: PMC10040388 DOI: 10.1016/j.xcrm.2023.100954] [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: 09/14/2022] [Revised: 12/05/2022] [Accepted: 02/02/2023] [Indexed: 03/02/2023]
Abstract
Human norovirus is the leading cause of acute gastroenteritis. Young children and the elderly bear the greatest burden of disease, representing more than 200,000 deaths annually. Infection prevalence peaks at younger than 2 years and is driven by novel GII.4 variants that emerge and spread globally. Using a surrogate neutralization assay, we characterize the evolution of the serological neutralizing antibody (nAb) landscape in young children as they transition between sequential GII.4 pandemic variants. Following upsurge of the replacement variant, antigenic cartography illustrates remodeling of the nAb landscape to the new variant accompanied by improved nAb titer. However, nAb relative avidity remains focused on the preceding variant. These data support immune imprinting as a mechanism of immune evasion and GII.4 virus persistence across a population. Understanding the complexities of immunity to rapidly evolving and co-circulating viral variants, like those of norovirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), and dengue viruses, will fundamentally inform vaccine design for emerging pathogens.
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Affiliation(s)
- Lisa C. Lindesmith
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paul D. Brewer-Jensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Helen Conrad
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kathleen M. O’Reilly
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1EW 7HT, UK
| | - Michael L. Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel Kelly
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Rachel Williams
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - W. John Edmunds
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1EW 7HT, UK
| | - David J. Allen
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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31
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Phillips AM, Maurer DP, Brooks C, Dupic T, Schmidt AG, Desai MM. Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody. eLife 2023; 12:83628. [PMID: 36625542 PMCID: PMC9995116 DOI: 10.7554/elife.83628] [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: 09/21/2022] [Accepted: 01/09/2023] [Indexed: 01/11/2023] Open
Abstract
Broadly neutralizing antibodies (bnAbs) that neutralize diverse variants of a particular virus are of considerable therapeutic interest. Recent advances have enabled us to isolate and engineer these antibodies as therapeutics, but eliciting them through vaccination remains challenging, in part due to our limited understanding of how antibodies evolve breadth. Here, we analyze the landscape by which an anti-influenza receptor binding site (RBS) bnAb, CH65, evolved broad affinity to diverse H1 influenza strains. We do this by generating an antibody library of all possible evolutionary intermediates between the unmutated common ancestor (UCA) and the affinity-matured CH65 antibody and measure the affinity of each intermediate to three distinct H1 antigens. We find that affinity to each antigen requires a specific set of mutations - distributed across the variable light and heavy chains - that interact non-additively (i.e., epistatically). These sets of mutations form a hierarchical pattern across the antigens, with increasingly divergent antigens requiring additional epistatic mutations beyond those required to bind less divergent antigens. We investigate the underlying biochemical and structural basis for these hierarchical sets of epistatic mutations and find that epistasis between heavy chain mutations and a mutation in the light chain at the VH-VL interface is essential for binding a divergent H1. Collectively, this is the first work to comprehensively characterize epistasis between heavy and light chain mutations and shows that such interactions are both strong and widespread. Together with our previous study analyzing a different class of anti-influenza antibodies, our results implicate epistasis as a general feature of antibody sequence-affinity landscapes that can potentiate and constrain the evolution of breadth.
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Affiliation(s)
- Angela M Phillips
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
| | - Daniel P Maurer
- Ragon Institute of MGH, MIT, and HarvardCambridgeUnited States
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Caelan Brooks
- Department of Physics, Harvard UniversityCambridgeUnited States
| | - Thomas Dupic
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and HarvardCambridgeUnited States
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
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Aguilar-Bretones M, Fouchier RA, Koopmans MP, van Nierop GP. Impact of antigenic evolution and original antigenic sin on SARS-CoV-2 immunity. J Clin Invest 2023; 133:e162192. [PMID: 36594464 PMCID: PMC9797340 DOI: 10.1172/jci162192] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and vaccinations targeting the spike protein (S) offer protective immunity against coronavirus disease 2019 (COVID-19). This immunity may further be shaped by cross-reactivity with common cold coronaviruses. Mutations arising in S that are associated with altered intrinsic virus properties and immune escape result in the continued circulation of SARS-CoV-2 variants. Potentially, vaccine updates will be required to protect against future variants of concern, as for influenza. To offer potent protection against future variants, these second-generation vaccines may need to redirect immunity to epitopes associated with immune escape and not merely boost immunity toward conserved domains in preimmune individuals. For influenza, efficacy of repeated vaccination is hampered by original antigenic sin, an attribute of immune memory that leads to greater induction of antibodies specific to the first-encountered variant of an immunogen compared with subsequent variants. In this Review, recent findings on original antigenic sin are discussed in the context of SARS-CoV-2 evolution. Unanswered questions and future directions are highlighted, with an emphasis on the impact on disease outcome and vaccine design.
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Xie Y, Tian X, Zhang X, Yao H, Wu N. Immune interference in effectiveness of influenza and COVID-19 vaccination. Front Immunol 2023; 14:1167214. [PMID: 37153582 PMCID: PMC10154574 DOI: 10.3389/fimmu.2023.1167214] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
Vaccines are known to function as the most effective interventional therapeutics for controlling infectious diseases, including polio, smallpox, rabies, tuberculosis, influenza and SARS-CoV-2. Smallpox has been eliminated completely and polio is almost extinct because of vaccines. Rabies vaccines and Bacille Calmette-Guérin (BCG) vaccines could effectively protect humans against respective infections. However, both influenza vaccines and COVID-19 vaccines are unable to eliminate these two infectious diseases of their highly variable antigenic sites in viral proteins. Vaccine effectiveness (VE) could be negatively influenced (i.e., interfered with) by immune imprinting of previous infections or vaccinations, and repeated vaccinations could interfere with VE against infections due to mismatch between vaccine strains and endemic viral strains. Moreover, VE could also be interfered with when more than one kind of vaccine is administrated concomitantly (i.e., co-administrated), suggesting that the VE could be modulated by the vaccine-induced immunity. In this review, we revisit the evidence that support the interfered VE result from immune imprinting or repeated vaccinations in influenza and COVID-19 vaccine, and the interference in co-administration of these two types of vaccines is also discussed. Regarding the development of next-generation COVID-19 vaccines, the researchers should focus on the induction of cross-reactive T-cell responses and naive B-cell responses to overcome negative effects from the immune system itself. The strategy of co-administrating influenza and COVID-19 vaccine needs to be considered more carefully and more clinical data is needed to verify this strategy to be safe and immunogenic.
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Affiliation(s)
- Yiwen Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Xuebin Tian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Xiaodi Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
- *Correspondence: Nanping Wu,
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35
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Tashi T, Upadhye A, Kundu P, Wu C, Menant S, Soares RR, Ferreira MU, Longley RJ, Mueller I, Hoang QQ, Tham WH, Rayner JC, Scopel KKG, Lima-Junior JC, Tran TM. Longitudinal IgG antibody responses to Plasmodium vivax blood-stage antigens during and after acute vivax malaria in individuals living in the Brazilian Amazon. PLoS Negl Trop Dis 2022; 16:e0010773. [PMID: 36417454 PMCID: PMC9728838 DOI: 10.1371/journal.pntd.0010773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/07/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND To make progress towards malaria elimination, a highly effective vaccine targeting Plasmodium vivax is urgently needed. Evaluating the kinetics of natural antibody responses to vaccine candidate antigens after acute vivax malaria can inform the design of serological markers of exposure and vaccines. METHODOLOGY/PRINCIPAL FINDINGS The responses of IgG antibodies to 9 P. vivax vaccine candidate antigens were evaluated in longitudinal serum samples from Brazilian individuals collected at the time of acute vivax malaria and 30, 60, and 180 days afterwards. Antigen-specific IgG correlations, seroprevalence, and half-lives were determined for each antigen using the longitudinal data. Antibody reactivities against Pv41 and PVX_081550 strongly correlated with each other at each of the four time points. The analysis identified robust responses in terms of magnitude and seroprevalence against Pv41 and PvGAMA at 30 and 60 days. Among the 8 P. vivax antigens demonstrating >50% seropositivity across all individuals, antibodies specific to PVX_081550 had the longest half-life (100 days; 95% CI, 83-130 days), followed by PvRBP2b (91 days; 95% CI, 76-110 days) and Pv12 (82 days; 95% CI, 64-110 days). CONCLUSION/SIGNIFICANCE This study provides an in-depth assessment of the kinetics of antibody responses to key vaccine candidate antigens in Brazilians with acute vivax malaria. Follow-up studies are needed to determine whether the longer-lived antibody responses induced by natural infection are effective in controlling blood-stage infection and mediating clinical protection.
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Affiliation(s)
- Tenzin Tashi
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Microbiology and Immunology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Aditi Upadhye
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Prasun Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Chunxiang Wu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Sébastien Menant
- Infectious Diseases and Immune Defence Division, Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Roberta Reis Soares
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal
| | - Rhea J. Longley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ivo Mueller
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Quyen Q. Hoang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Wai-Hong Tham
- Infectious Diseases and Immune Defence Division, Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Julian C. Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Kézia KG Scopel
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil
| | - Josué C. Lima-Junior
- Laboratory of Immunoparasitology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Tuan M. Tran
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Microbiology and Immunology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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Aartse A, Mortier D, Mooij P, Hofman S, van Haaren MM, Corcoran M, Karlsson Hedestam GB, Eggink D, Claireaux M, Bogers WMJM, van Gils MJ, Koopman G. Primary antibody response after influenza virus infection is first dominated by low-mutated HA-stem antibodies followed by higher-mutated HA-head antibodies. Front Immunol 2022; 13:1026951. [PMID: 36405682 PMCID: PMC9670313 DOI: 10.3389/fimmu.2022.1026951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 09/12/2023] Open
Abstract
Several studies have shown that the first encounter with influenza virus shapes the immune response to future infections or vaccinations. However, a detailed analysis of the primary antibody response is lacking as this is difficult to study in humans. It is therefore not known what the frequency and dynamics of the strain-specific hemagglutinin (HA) head- and stem-directed antibody responses are directly after primary influenza virus infection. Here, sera of twelve H1N1pdm2009 influenza virus-infected cynomolgus macaques were evaluated for HA-head and HA-stem domain antibody responses. We observed an early induction of HA-stem antibody responses, which was already decreased by day 56. In contrast, responses against the HA-head domain were low early after infection and increased at later timepoint. The HA-specific B cell repertoires in each animal showed diverse VH-gene usage with preferred VH-gene and JH-gene family usage for HA-head or HA-stem B cells but a highly diverse allelic variation within the VH-usage. HA-head B cells had shorter CDRH3s and higher VH-gene somatic hyper mutation levels relative to HA-stem B cells. In conclusion, our data suggest that HA-stem antibodies are the first to react to the infection while HA-head antibodies show a delayed response, but a greater propensity to enter the germinal center and undergo affinity maturation.
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Affiliation(s)
- Aafke Aartse
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
| | - Daniella Mortier
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Petra Mooij
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Sam Hofman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Marlies M. van Haaren
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet (KI), Stockholm, Sweden
| | | | - Dirk Eggink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Mathieu Claireaux
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | | | - Marit J. van Gils
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
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Jaago M, Rähni A, Pupina N, Pihlak A, Sadam H, Tuvikene J, Avarlaid A, Planken A, Planken M, Haring L, Vasar E, Baćević M, Lambert F, Kalso E, Pussinen P, Tienari PJ, Vaheri A, Lindholm D, Timmusk T, Ghaemmaghami AM, Palm K. Differential patterns of cross-reactive antibody response against SARS-CoV-2 spike protein detected for chronically ill and healthy COVID-19 naïve individuals. Sci Rep 2022; 12:16817. [PMID: 36207326 PMCID: PMC9540097 DOI: 10.1038/s41598-022-20849-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Immunity to previously encountered viruses can alter response to unrelated pathogens. We reasoned that similar mechanism may also involve SARS-CoV-2 and thereby affect the specificity and the quality of the immune response against the virus. Here, we employed high-throughput next generation phage display method to explore the link between antibody immune response to previously encountered antigens and spike (S) glycoprotein. By profiling the antibody response in COVID-19 naïve individuals with a diverse clinical history (including cardiovascular, neurological, or oncological diseases), we identified 15 highly antigenic epitopes on spike protein that showed cross-reactivity with antigens of seasonal, persistent, latent or chronic infections from common human viruses. We observed varying degrees of cross-reactivity of different viral antigens with S in an epitope-specific manner. The data show that pre-existing SARS-CoV-2 S1 and S2 cross-reactive serum antibody is readily detectable in pre-pandemic cohort. In the severe COVID-19 cases, we found differential antibody response to the 15 defined antigenic and cross-reactive epitopes on spike. We also noted that despite the high mutation rates of Omicron (B.1.1.529) variants of SARS-CoV-2, some of the epitopes overlapped with the described mutations. Finally, we propose that the resolved epitopes on spike if targeted by re-called antibody response from SARS-CoV-2 infections or vaccinations can function in chronically ill COVID-19 naïve/unvaccinated individuals as immunogenic targets to boost antibodies augmenting the chronic conditions. Understanding the relationships between prior antigen exposure at the antibody epitope level and the immune response to subsequent infections with viruses from a different strain is paramount to guiding strategies to exit the COVID-19 pandemic.
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Affiliation(s)
- Mariliis Jaago
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annika Rähni
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | | | | | - Helle Sadam
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Jürgen Tuvikene
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.,DXLabs LLC, Tallinn, Estonia
| | - Annela Avarlaid
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Anu Planken
- North Estonia Medical Centre Foundation, Tallinn, Estonia
| | - Margus Planken
- North Estonia Medical Centre Foundation, Tallinn, Estonia
| | - Liina Haring
- Institute of Clinical Medicine, Psychiatry Clinic of Tartu University Hospital, University of Tartu, Tartu, Estonia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Center of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Miljana Baćević
- Dental Biomaterial Research Unit (d-BRU), Faculty of Medicine, University of Liege, Liege, Belgium
| | - France Lambert
- Department of Periodontology and Oral Surgery, Faculty of Medicine, University of Liege, Liege, Belgium
| | - Eija Kalso
- Department of Anaesthesiology, Intensive Care and Pain Medicine, Helsinki University Hospital, Helsinki, Finland.,SleepWell Research Programme, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Pirkko Pussinen
- Oral and Maxillofacial Diseases, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Pentti J Tienari
- Translational Immunology Research Program, Department of Neurology, Neurocenter, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Antti Vaheri
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Dan Lindholm
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Tõnis Timmusk
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Amir M Ghaemmaghami
- Immunology and Immuno-Bioengineering Group, School of Life Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
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Jia L, Weng S, Wu J, Tian X, Zhang Y, Wang X, Wang J, Yan D, Wang W, Fang F, Zhu Z, Qiu C, Zhang W, Xu Y, Wan Y. Preexisting antibodies targeting SARS-CoV-2 S2 cross-react with commensal gut bacteria and impact COVID-19 vaccine induced immunity. Gut Microbes 2022; 14:2117503. [PMID: 36100957 PMCID: PMC9481142 DOI: 10.1080/19490976.2022.2117503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The origins of preexisting SARS-CoV-2 cross-reactive antibodies and their potential impacts on vaccine efficacy have not been fully clarified. In this study, we demonstrated that S2 was the prevailing target of the preexisting S protein cross-reactive antibodies in both healthy human and SPF mice. A dominant antibody epitope was identified on the connector domain of S2 (1147-SFKEELDKYFKNHT-1160, P144), which could be recognized by preexisting antibodies in both human and mouse. Through metagenomic sequencing and fecal bacteria transplant, we demonstrated that the generation of S2 cross-reactive antibodies was associated with commensal gut bacteria. Furthermore, six P144 reactive monoclonal antibodies were isolated from naïve SPF mice and were proven to cross-react with commensal gut bacteria collected from both human and mouse. A variety of cross-reactive microbial proteins were identified using LC-MS, of which E. coli derived HSP60 and HSP70 proteins were confirmed to be able to bind to one of the isolated monoclonal antibodies. Mice with high levels of preexisting S2 cross-reactive antibodies mounted higher S protein specific binding antibodies, especially against S2, after being immunized with a SARS-CoV-2 S DNA vaccine. Similarly, we found that levels of preexisting S2 and P144-specific antibodies correlated positively with RBD binding antibody titers after two doses of inactivated SARS-CoV-2 vaccination in human. Collectively, our study revealed an alternative origin of preexisting S2-targeted antibodies and disclosed a previously neglected aspect of the impact of gut microbiota on host anti-SARS-CoV-2 immunity.
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Affiliation(s)
- Liqiu Jia
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shufeng Weng
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China,Ying Xu State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Xiangxiang Tian
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
| | - Yifan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
| | - Xuyang Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Department of Immunology, School of Basic Medical, Jiamusi University, Jiamusi, China
| | - Dongmei Yan
- Department of Immunology, School of Basic Medical, Jiamusi University, Jiamusi, China
| | - Wanhai Wang
- Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
| | - Fang Fang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhaoqin Zhu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Zhaoqin Zhu Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chao Qiu
- Institutes of Biomedical Sciences & Shanghai Key Laboratory of Medical Epigenetics, Fudan University, Shanghai, China,Chao Qiu Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China,State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China,Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China,Wenhong Zhang Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Xu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China,Ying Xu State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Yanmin Wan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China,State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China,Department of Radiology, Shanghai Public Health Clinical Center, Shanghai, China,CONTACT Yanmin Wan Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
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Lu X, Guo Z, Li ZN, Holiday C, Liu F, Jefferson S, Gross FL, Tzeng WP, Kumar A, York IA, Uyeki TM, Tumpey T, Stevens J, Levine MZ. Low quality antibody responses in critically ill patients hospitalized with pandemic influenza A(H1N1)pdm09 virus infection. Sci Rep 2022; 12:14971. [PMID: 36056075 PMCID: PMC9440095 DOI: 10.1038/s41598-022-18977-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Although some adults infected with influenza 2009 A(H1N1)pdm09 viruses mounted high hemagglutination inhibition (HAI) antibody response, they still suffered from severe disease, or even death. Here, we analyzed antibody profiles in patients (n = 31, 17-65 years) admitted to intensive care units (ICUs) with lung failure and invasive mechanical ventilation use due to infection with A(H1N1)pdm09 viruses during 2009-2011. We performed a comprehensive analysis of the quality and quantity of antibody responses using HAI, virus neutralization, biolayer interferometry, enzyme-linked-lectin and enzyme-linked immunosorbent assays. At time of the ICU admission, 45% (14/31) of the patients had HAI antibody titers ≥ 80 in the first serum (S1), most (13/14) exhibited narrowly-focused HAI and/or anti-HA-head binding antibodies targeting single epitopes in or around the receptor binding site. In contrast, 42% (13/31) of the patients with HAI titers ≤ 10 in S1 had non-neutralizing anti-HA-stem antibodies against A(H1N1)pdm09 viruses. Only 19% (6/31) of the patients showed HA-specific IgG1-dominant antibody responses. Three of 5 fatal patients possessed highly focused cross-type HAI antibodies targeting the (K130 + Q223)-epitopes with extremely low avidity. Our findings suggest that narrowly-focused low-quality antibody responses targeting specific HA-epitopes may have contributed to severe infection of the lower respiratory tract.
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Affiliation(s)
- Xiuhua Lu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Zhu Guo
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Zhu-Nan Li
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Crystal Holiday
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Feng Liu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Stacie Jefferson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - F Liaini Gross
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Wen-Ping Tzeng
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Anand Kumar
- Section of Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Ian A York
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Terrence Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - James Stevens
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Min Z Levine
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, MS H17-5, 1600 Clifton Road, Atlanta, GA, 30329, USA.
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Goldblatt D, Alter G, Crotty S, Plotkin SA. Correlates of protection against SARS-CoV-2 infection and COVID-19 disease. Immunol Rev 2022; 310:6-26. [PMID: 35661178 PMCID: PMC9348242 DOI: 10.1111/imr.13091] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Antibodies against epitopes in S1 give the most accurate CoP against infection by the SARS-CoV-2 coronavirus. Measurement of those antibodies by neutralization or binding assays both have predictive value, with binding antibody titers giving the highest statistical correlation. However, the protective functions of antibodies are multiple. Antibodies with multiple functions other than neutralization influence efficacy. The role of cellular responses can be discerned with respect to CD4+ T cells and their augmentation of antibodies, and with respect to CD8+ cells with regard to control of viral replication, particularly in the presence of insufficient antibody. More information is needed on mucosal responses.
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Affiliation(s)
- David Goldblatt
- Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Galit Alter
- Massachusetts General HospitalRagon Institute of MGH, MIT and HarvardCambridgeMassachusettsUSA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine ResearchLa Jolla Institute for Immunology (LJI)La JollaCaliforniaUSA
- Department of Medicine, Division of Infectious Diseases and Global Public HealthUniversity of California San Diego (UCSD)La JollaCaliforniaUSA
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Wang L, Cao Z, Wang Z, Guo J, Wen J. Reactive oxygen species associated immunoregulation post influenza virus infection. Front Immunol 2022; 13:927593. [PMID: 35967412 PMCID: PMC9373727 DOI: 10.3389/fimmu.2022.927593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
An appropriate level of reactive oxygen species (ROS) is necessary for cell proliferation, signaling transduction, and apoptosis due to their highly reactive character. ROS are generated through multiple metabolic pathways under a fine-tuned control between oxidant and antioxidant signaling. A growing number of evidence has proved their highly relevant role in modulating inflammation during influenza virus infection. As a network of biological process for protecting organism from invasion of pathogens, immune system can react and fight back through either innate immune system or adaptive immune system, or both. Herein, we provide a review about the mechanisms of ROS generation when encounter influenza virus infection, and how the imbalanced level of ROS influences the replication of virus. We also summarize the pathways used by both the innate and adaptive immune system to sense and attack the invaded virus and abnormal levels of ROS. We further review the limitation of current strategies and discuss the direction of future work.
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Affiliation(s)
- Lan Wang
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, United States,UCLA Acquired Immune Deficiency Syndrome (AIDS) Institute, University of California Los Angeles (UCLA), Los Angeles, CA, United States
| | - Zheng Cao
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles (UCLA), Los Angeles, CA, United States
| | - Zi Wang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles (UCLA), Los Angeles, CA, United States
| | - Jimin Guo
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, United States,UCLA Acquired Immune Deficiency Syndrome (AIDS) Institute, University of California Los Angeles (UCLA), Los Angeles, CA, United States
| | - Jing Wen
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, United States,UCLA Acquired Immune Deficiency Syndrome (AIDS) Institute, University of California Los Angeles (UCLA), Los Angeles, CA, United States,*Correspondence: Jing Wen,
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Yang F, Zhu L, Liu F, Cheng L, Yao H, Wu N, Wu H, Li L. Generation and characterization of monoclonal antibodies against the hemagglutinin of H3N2 influenza A viruses. Virus Res 2022; 317:198815. [PMID: 35595011 DOI: 10.1016/j.virusres.2022.198815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 01/01/2023]
Abstract
Seasonal influenza viruses are highly contagious, leading to 290,000-650,000 mortalities every year globally. Among the influenza viruses, influenza A virus (H3N2) has attracted much attention due to its high frequency of antigenic variations, resulting in poor protection by vaccination. We generated a panel of murine neutralizing monoclonal antibodies (mAbs) against A/Texas/50/2012 (H3N2) and identified the relevant epitopes that potentially influence the antigenicity by selecting mAb-resistant mutants. The epitopes were mainly in antigenic site A (1/9, 11.1%), B (6/9, 66.7%), and C (1/9, 11.1%), which is consistent with recent reports on the immunodominance of antigenic site B. The amino acid substitutions at positions 156, 157, 159, 160, and 189 at antigenic site B resulted in decreased mAb capability for blocking receptor binding. In addition, the neutralizing spectra of three mAbs (1F8, 1G9 and 1H5) were different, suggesting that their epitopes may be different but partially overlapping, and it required further study. Further, the mAb 3F9 selected a new substitution, D53G/N, at antigenic site C and showed in vitro neutralizing activity against A/Victoria/361/2011 (H3N2), A/Texas/50/2012 (H3N2), and A/Hong Kong/2671/2019 (H3N2), suggesting a potential epitope on H3 hemagglutinin for inducing broad neutralizing antibody responses. Continuous research and regular monitoring of novel epitopes are of great importance for improving vaccine strain selection.
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Affiliation(s)
- Fan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Linwei Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Fumin Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Linfang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Haibo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
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Liu W, Lien YH, Lee PI, Chan TC, Wang LC, Yang CR, Ho MS, Chen JR, Ku CC, King CC. Impact of prior infection and repeated vaccination on post-vaccination antibody titers of the influenza A(H1N1)pdm09 strain in Taiwan schoolchildren: Implications for public health. Vaccine 2022; 40:3402-3411. [PMID: 35525727 DOI: 10.1016/j.vaccine.2022.03.047] [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: 08/27/2021] [Revised: 03/01/2022] [Accepted: 03/18/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND The objective of this study was to evaluate the effects of prior-infection and repeated vaccination on post-vaccination antibody titers. METHODS A(H1N1)pdm09 strain was included in 2009 pandemic monovalent, 2010-2011, and 2011-2012 trivalent influenza vaccines (MIVpdm09, TIV10/11, TIV11/12) in Taiwan. During the 2011-2012 influenza season, we conducted a prospective sero-epidemiological cohort study among schoolchildren from grades 1 - 6 in the two elementary schools in Taipei with documented A(H1N1)pdm09 vaccination records since 2009. Serum samples were collected at pre-vaccination, 1-month, and 4-months post-vaccination (T1, T2, T3). Anti-A(H1N1)pdm09 hemagglutination inhibition titers (HI-Ab-titers) were examined. We also investigated the impact of four vaccination histories [(1) no previous vaccination (None), (2) vaccinated in 2009-2010 season (09v), (3) vaccinated in 2010-2011 season (10v), and (4) vaccinated consecutively in 2009-2010 and 2010-2011 seasons (09v + 10v)] and pre-vaccination HI-Ab levels on post-vaccination HI-Ab responses as well as adjusted vaccine effectiveness (aVE) against serologically-defined infection from T2 to T3. RESULTS TIV11/12 had zero serious adverse events reported. A(H1N1)pdm09 strain in TIV11/12 elicited seroprotective Ab-titers in 98% of children and showed promising protection (aVE: 70.3% [95% confidence interval (CI): 51.0-82.1%]). Previously unvaccinated but infected children had a 3.96 times higher T2 geometric mean titer (T2-GMT) of HI-Ab than those naïve to A(H1N1)pdm09 (GMT [95% CI]: 1039.7[585.3-1845.9] vs. 262.5[65.9-1045], p = 0.046). Previously vaccinated children with seroprotective T1-Ab-titers had a higher T2-GMT and a greater aVE than those with non-seroprotective T1-Ab-titers. Repeatedly vaccinated children had lower T2-GMT than those receiving primary doses of TIV11/12. However, after controlling prior infection and T1-Ab-titers, differences in T2-GMT among the four vaccination histories became insignificant (p = 0.16). CONCLUSION This study supports the implementation of annual mass-vaccination with A(H1N1)pdm09 in schoolchildren for three consecutive influenza seasons when vaccine and circulating strains were well matched, and found that prior infection and pre-vaccination HI-Ab levels positively impacted post-vaccination HI-Ab responses.
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Affiliation(s)
- Wei Liu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei 100, Taiwan, ROC
| | - Yu-Hui Lien
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei 100, Taiwan, ROC
| | - Ping-Ing Lee
- Department of Pediatrics, NTU Hospital and NTU College of Medicine, Taipei 100, Taiwan, ROC
| | - Ta-Chien Chan
- Research Center for Humanities and Social Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | | | - Chin-Rur Yang
- Institute of Immunology, NTU College of Medicine, Taipei 100, Taiwan, ROC
| | - Mei-Shang Ho
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | | | - Chia-Chi Ku
- Institute of Immunology, NTU College of Medicine, Taipei 100, Taiwan, ROC.
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei 100, Taiwan, ROC.
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Bull JJ, Antia R. Which 'imperfect vaccines' encourage the evolution of higher virulence? Evol Med Public Health 2022; 10:202-213. [PMID: 35539897 PMCID: PMC9081871 DOI: 10.1093/emph/eoac015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
Background and objectives Theory suggests that some types of vaccines against infectious pathogens may lead to the evolution of variants that cause increased harm, particularly when they infect unvaccinated individuals. This theory was supported by the observation that the use of an imperfect vaccine to control Marek's disease virus in chickens resulted in the virus evolving to be more lethal to unvaccinated birds. This raises the concern that the use of some other vaccines may lead to similar pernicious outcomes. We examine that theory with a focus on considering the regimes in which such outcomes are expected. Methodology We evaluate the plausibility of assumptions in the original theory. The previous theory rested heavily on a particular form of transmission-mortality-recovery trade-off and invoked other assumptions about the pathways of evolution. We review alternatives to mortality in limiting transmission and consider evolutionary pathways that were omitted in the original theory. Results The regime where the pernicious evolutionary outcome occurs is narrowed by our analysis but remains possible in various scenarios. We propose a more nuanced consideration of alternative models for the within-host dynamics of infections and for factors that limit virulence. Our analysis suggests imperfect vaccines against many pathogens will not lead to the evolution of pathogens with increased virulence in unvaccinated individuals. Conclusions and implications Evolution of greater pathogen mortality driven by vaccination remains difficult to predict, but the scope for such outcomes appears limited. Incorporation of mechanistic details into the framework, especially regarding immunity, may be requisite for prediction accuracy. Lay Summary A virus of chickens appears to have evolved high mortality in response to a vaccine that merely prevented disease symptoms. Theory has predicted this type of evolution in response to a variety of vaccines and other interventions such as drug treatment. Under what circumstances is this pernicious result likely to occur? Analysis of the theory in light of recent changes in our understanding of viral biology raises doubts that medicine-driven, pernicious evolution is likely to be common. But we are far from a mechanistic understanding of the interaction between pathogen and host that can predict when vaccines and other medical interventions will lead to the unwanted evolution of more virulent pathogens. So, while the regime where a pernicious result obtains may be limited, caution remains warranted in designing many types of interventions.
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Affiliation(s)
- James J Bull
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA,Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA. E-mail:
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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Tohma K, Ford-Siltz LA, Kendra JA, Parra GI. Dynamic immunodominance hierarchy of neutralizing antibody responses to evolving GII.4 noroviruses. Cell Rep 2022; 39:110689. [PMID: 35417705 DOI: 10.1016/j.celrep.2022.110689] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/20/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
A paradigm of RNA viruses is their ability to mutate and escape from herd immunity. Because antibody responses are a major effector for viral immunity, antigenic sites are usually under strong diversifying pressure. Here, we use norovirus as a model to study mechanisms of antigenic diversification of non-enveloped, fast-evolving RNA viruses. We comprehensively characterize all variable antigenic sites involved in virus neutralization and find that single neutralizing monoclonal antibodies (mAbs) map to multiple antigenic sites of GII.4 norovirus. Interactions of multiple epitopes on the viral capsid surface provide a broad mAb-binding repertoire with a remarkable difference in the mAb-binding profiles and immunodominance hierarchy for two distantly related GII.4 variants. Time-ordered mutant viruses confirm a progressive change of antibody immunodominance along with point mutations during the process of norovirus evolution. Thus, in addition to point mutations, switches in immunodominance that redirect immune responses could facilitate immune escape in RNA viruses.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1309, Silver Spring, MD 20993, USA
| | - Lauren A Ford-Siltz
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1309, Silver Spring, MD 20993, USA
| | - Joseph A Kendra
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1309, Silver Spring, MD 20993, USA
| | - Gabriel I Parra
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1309, Silver Spring, MD 20993, USA.
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Hendin HE, Lavoie PO, Gravett JM, Pillet S, Saxena P, Landry N, D’Aoust MA, Ward BJ. Elimination of receptor binding by influenza hemagglutinin improves vaccine-induced immunity. NPJ Vaccines 2022; 7:42. [PMID: 35410323 PMCID: PMC9001741 DOI: 10.1038/s41541-022-00463-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/15/2022] [Indexed: 12/05/2022] Open
Abstract
The binding of influenza hemagglutinin (HA) to sialic acid (SA) receptors plays a well-defined role in shaping infection but the impact of such binding on vaccine responses has not yet been explored. We generated a virus-like particle (VLP) vaccine bearing the HA of H1N1 A/California/07/09 that is unable to bind to its α(2,6)-linked SA receptor (H1Y98F-VLP) and compared its immunogenicity and efficacy to a wild-type H1-VLP (H1WT-VLP) in mice. The H1Y98F-VLP elicited significantly stronger and more durable antibody responses (hemagglutination inhibition and microneutralization titers) and greater avidity maturation, likely attributable to improved germinal center formation. H1Y98F-VLP also resulted in a robust population of IL-2+TNFα+IFNγ− CD4+ T cells that correlated with antibody responses. Compared to H1WT-VLP vaccination, mice immunized with H1Y98F-VLP had 2.3-log lower lung viral loads and significantly lower pulmonary inflammatory cytokine levels 5 days post-challenge. These findings suggest that abrogation of HA-SA interactions may be a promising strategy to improve the quality and durability of influenza vaccine-induced humoral responses.
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Fox A, Carolan L, Leung V, Phuong HVM, Khvorov A, Auladell M, Tseng YY, Thai PQ, Barr I, Subbarao K, Mai LTQ, van Doorn HR, Sullivan SG. Opposing Effects of Prior Infection versus Prior Vaccination on Vaccine Immunogenicity against Influenza A(H3N2) Viruses. Viruses 2022; 14:v14030470. [PMID: 35336877 PMCID: PMC8949461 DOI: 10.3390/v14030470] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/10/2021] [Accepted: 11/28/2021] [Indexed: 02/05/2023] Open
Abstract
Prior vaccination can alternately enhance or attenuate influenza vaccine immunogenicity and effectiveness. Analogously, we found that vaccine immunogenicity was enhanced by prior A(H3N2) virus infection among participants of the Ha Nam Cohort, Viet Nam, but was attenuated by prior vaccination among Australian Health Care Workers (HCWs) vaccinated in the same year. Here, we combined these studies to directly compare antibody titers against 35 A(H3N2) viruses spanning 1968–2018. Participants received licensed inactivated vaccines containing A/HongKong/4801/2014 (H3N2). The analysis was limited to participants aged 18–65 Y, and compared those exposed to A(H3N2) viruses circulating since 2009 by infection (Ha Nam) or vaccination (HCWs) to a reference group who had no recent A(H3N2) infection or vaccination (Ha Nam). Antibody responses were compared by fitting titer/titer-rise landscapes across strains, and by estimating titer ratios to the reference group of 2009–2018 viruses. Pre-vaccination, titers were lowest against 2009–2014 viruses among the reference (no recent exposure) group. Post-vaccination, titers were, on average, two-fold higher among participants with prior infection and two-fold lower among participants with 3–5 prior vaccinations compared to the reference group. Titer rise was negligible among participants with 3–5 prior vaccinations, poor among participants with 1–2 prior vaccinations, and equivalent or better among those with prior infection compared to the reference group. The enhancing effect of prior infection versus the incrementally attenuating effect of prior vaccinations suggests that these exposures may alternately promote and constrain the generation of memory that can be recalled by a new vaccine strain.
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Affiliation(s)
- Annette Fox
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
- Correspondence: ; Tel.: +61-393-429-313
| | - Louise Carolan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
| | - Vivian Leung
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
| | - Hoang Vu Mai Phuong
- National Institute of Hygiene and Epidemiology, Ha Noi 100000, Vietnam; (H.V.M.P.); (P.Q.T.); (L.T.Q.M.)
| | - Arseniy Khvorov
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
| | - Maria Auladell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Yeu-Yang Tseng
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
| | - Pham Quang Thai
- National Institute of Hygiene and Epidemiology, Ha Noi 100000, Vietnam; (H.V.M.P.); (P.Q.T.); (L.T.Q.M.)
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Le Thi Quynh Mai
- National Institute of Hygiene and Epidemiology, Ha Noi 100000, Vietnam; (H.V.M.P.); (P.Q.T.); (L.T.Q.M.)
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Africa Asia Programme, National Hospital of Tropical Diseases, Ha Noi 100000, Vietnam;
- Centre of Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Sheena G. Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
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Li L, Changrob S, Fu Y, Stovicek O, Guthmiller JJ, McGrath JJC, Dugan HL, Stamper CT, Zheng NY, Huang M, Wilson PC. Librator: a platform for the optimized analysis, design, and expression of mutable influenza viral antigens. Brief Bioinform 2022; 23:6532539. [PMID: 35183062 PMCID: PMC8921739 DOI: 10.1093/bib/bbac028] [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: 11/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Artificial mutagenesis and protein engineering have laid the foundation for antigenic characterization and universal vaccine design for influenza viruses. However, many methods used in this process require manual sequence editing and protein expression, limiting their efficiency and utility in high-throughput applications. More streamlined in silico tools allowing researchers to properly analyze and visualize influenza viral protein sequences with accurate nomenclature are necessary to improve antigen design and productivity. To address this need, we developed Librator, a system for analyzing and designing custom protein sequences of influenza virus hemagglutinin (HA) and neuraminidase (NA) glycoproteins. Within Librator's graphical interface, users can easily interrogate viral sequences and phylogenies, visualize antigen structures and conservation, mutate target residues and design custom antigens. Librator also provides optimized fragment design for Gibson Assembly of HA and NA expression constructs based on peptide conservation of all historical HA and NA sequences, ensuring fragments are reusable and compatible across related subtypes, thereby promoting reagent savings. Finally, the program facilitates single-cell immune profiling, epitope mapping of monoclonal antibodies and mosaic protein design. Using Librator-based antigen construction, we demonstrate that antigenicity can be readily transferred between HA molecules of H3, but not H1, lineage viruses. Altogether, Librator is a valuable tool for analyzing influenza virus HA and NA proteins and provides an efficient resource for optimizing recombinant influenza antigen synthesis.
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Affiliation(s)
| | | | | | - Olivia Stovicek
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jenna J Guthmiller
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Joshua J C McGrath
- Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | | | - Nai-Ying Zheng
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA,Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Min Huang
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Patrick C Wilson
- Corresponding author: Patrick C. Wilson, Drukier Institute for Children’s Health, Weill Cornell Medicine, New York, NY 10021, USA. E-mail:
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Dugan HL, Wilson PC. Teach 'em young: Influenza vaccines induce broadly neutralizing antibodies in children. Cell Rep Med 2022; 3:100531. [PMID: 35243425 PMCID: PMC8861966 DOI: 10.1016/j.xcrm.2022.100531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Antibodies against the influenza virus hemagglutinin stalk afford broad protection against antigenically drifted viruses. In this issue of Cell Reports Medicine, Yegorov et al.1 identify that current vaccine formulations induce neutralizing stalk antibodies in children—a highly vulnerable population.
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Affiliation(s)
| | - Patrick C Wilson
- Department of Pediatrics, Weill Cornell Medical College, NY 10065, USA
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Ionov S, Lee J. An Immunoproteomic Survey of the Antibody Landscape: Insights and Opportunities Revealed by Serological Repertoire Profiling. Front Immunol 2022; 13:832533. [PMID: 35178051 PMCID: PMC8843944 DOI: 10.3389/fimmu.2022.832533] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
Immunoproteomics has emerged as a versatile tool for analyzing the antibody repertoire in various disease contexts. Until recently, characterization of antibody molecules in biological fluids was limited to bulk serology, which identifies clinically relevant features of polyclonal antibody responses. The past decade, however, has seen the rise of mass-spectrometry-enabled proteomics methods that have allowed profiling of the antibody response at the molecular level, with the disease-specific serological repertoire elucidated in unprecedented detail. In this review, we present an up-to-date survey of insights into the disease-specific immunological repertoire by examining how quantitative proteomics-based approaches have shed light on the humoral immune response to infection and vaccination in pathogenic illnesses, the molecular basis of autoimmune disease, and the tumor-specific repertoire in cancer. We address limitations of this technology with a focus on emerging potential solutions and discuss the promise of high-resolution immunoproteomics in therapeutic discovery and novel vaccine design.
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Affiliation(s)
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
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