1
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Matz HC, Ellebedy AH. Vaccination against influenza viruses annually: Renewing or narrowing the protective shield? J Exp Med 2025; 222:e20241283. [PMID: 40272481 PMCID: PMC12020744 DOI: 10.1084/jem.20241283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 04/03/2025] [Accepted: 04/09/2025] [Indexed: 04/25/2025] Open
Abstract
Annual vaccines are recommended for the seasonal influenza virus. While yearly updates to the vaccine are necessary due to the constant evolution of influenza viruses, some studies have suggested repeat vaccination may result in a reduction in vaccine effectiveness in subsequent years. This review examines the available evidence that repeated annual influenza virus vaccination may have effects on future vaccine responses, and it synthesizes the available data with studies that may indicate potential immunological mechanisms underlying these effects. The goal is to examine the available literature to determine whether these mechanisms can be subverted to improve seasonal influenza virus vaccine efficacy.
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Affiliation(s)
- Hanover C. Matz
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Ali H. Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
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2
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Stacey H, Carlock MA, Allen JD, Hanley HB, Crotty S, Ross TM, Einav T. Leveraging pre-vaccination antibody titres across multiple influenza H3N2 variants to forecast the post-vaccination response. EBioMedicine 2025; 116:105744. [PMID: 40424667 DOI: 10.1016/j.ebiom.2025.105744] [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: 02/03/2025] [Revised: 04/23/2025] [Accepted: 04/23/2025] [Indexed: 05/29/2025] Open
Abstract
BACKGROUND Despite decades of research on the influenza virus, we still lack a predictive understanding of how vaccination reshapes each person's antibody response, which impedes efforts to design better vaccines. Models using pre-vaccination antibody haemagglutination inhibition (HAI) titres against the vaccine strain alone poorly predict post-vaccination responses. METHODS We combined fifteen prior H3N2 influenza vaccine studies from 1997 to 2021, collectively containing 20,000 data points, and develop of a machine learning model that uses pre-vaccination HAI titres against multiple influenza variants to predict post-vaccination responses. To further test the model, four new vaccine studies were conducted in 2022-2023 spanning two geographic locations and three influenza vaccine types. FINDINGS The most predictive pre-vaccination features were HAI titres against the vaccine strain and against historical influenza variants, with smaller predictive power derived from age, sex, vaccine dose, and geographic location. The resulting model predicted future responses even when the vaccine strain or vaccine formulation changed. A pre-vaccination feature-the time between peak HAI across recent variants-distinguished large versus small post-vaccination responses with 73% accuracy. Model predictions against prior vaccine studies had 2.4-fold error (95% CI: 2.34-2.40x, no large outliers with >4-fold error), yielding more accurate and robust predictions than a null model with 3.2-fold error (95% CI: 3.12-3.21x, 12% large outliers). The four new vaccine studies presented here were predicted with comparable accuracy to the intrinsic 2-fold error of the experimental assay. INTERPRETATION A person's pre-vaccination influenza HAI titres using multiple variants are highly predictive of their post-vaccination response. Many individuals exhibited little-to-no vaccine response, as exhibited by the null model's accuracy, yet the machine learning model identified and accurately predicted both weak and strong responses with statistical superiority. Taken together, this approach paves the way to better utilise current influenza vaccines, especially for individuals that exhibit the weakest responses. FUNDING NIAID, UCSD PREPARE Institute, LJI & Kyowa Kirin, Inc. (KKNA-Kyowa Kirin North America), UGA, Cleveland Clinic, the Georgia Research Alliance, and the Bodman family.
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Affiliation(s)
- Hannah Stacey
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Michael A Carlock
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - James D Allen
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Hannah B Hanley
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Shane Crotty
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Department of Infection Biology, Lehner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Tal Einav
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
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3
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Hao T, Ryan GE, Lydeamore MJ, Cromer D, Wood JG, McVernon J, McCaw JM, Shearer FM, Golding N. Predicting immune protection against outcomes of infectious disease from population-level effectiveness data with application to COVID-19. Vaccine 2025; 55:126987. [PMID: 40117726 DOI: 10.1016/j.vaccine.2025.126987] [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: 11/01/2024] [Revised: 02/20/2025] [Accepted: 02/28/2025] [Indexed: 03/23/2025]
Abstract
Quantifying the extent to which previous infections and vaccinations confer protection against future infection or disease outcomes is critical to managing the transmission and consequences of infectious diseases. We present a general statistical model for predicting the strength of protection conferred by different immunising exposures (numbers, types, and strains of both vaccines and infections), against multiple outcomes of interest, whilst accounting for immune waning. We predict immune protection against key clinical outcomes: developing symptoms, hospitalisation, and death. We also predict transmission-related outcomes: acquisition of infection and onward transmission in breakthrough infections. These enable quantification of the impact of immunity on population-level transmission dynamics. Our model calibrates the level of immune protection, drawing on both population-level data, such as vaccine effectiveness estimates, and neutralising antibody levels as a correlate of protection. This enables the model to learn realised immunity levels beyond those which can be predicted by antibody kinetics or other correlates alone. We demonstrate an application of the model for SARS-CoV-2, and predict the individual-level protective effectiveness conferred by natural infections with the Delta and the Omicron B.1.1.529 variants, and by the BioNTech-Pfizer (BNT162b2), Oxford-AstraZeneca (ChAdOx1), and 3rd-dose mRNA booster vaccines, against outcomes for both Delta and Omicron. We also demonstrate a use case of the model in late 2021 during the emergence of Omicron, showing how the model can be rapidly updated with emerging epidemiological data on multiple variants in the same population, to infer key immunogenicity and intrinsic transmissibility characteristics of the new variant, before the former can be more directly observed via vaccine effectiveness data. This model provided timely inference on rapidly evolving epidemic situations of significant concern during the early stages of the COVID-19 pandemic. The general nature of the model enables it to be used to support management of a range of infectious diseases.
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Affiliation(s)
- Tianxiao Hao
- The Kids Research Institute, Nedlands, Western Australia, Australia; Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia.
| | - Gerard E Ryan
- The Kids Research Institute, Nedlands, Western Australia, Australia; Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Michael J Lydeamore
- Department of Econometrics and Business Statistics, Monash University, Victoria, Australia
| | - Deborah Cromer
- Kirby Institute, University of New South Wales Sydney, New South Wales, Australia
| | - James G Wood
- School of Population Health, University of New South Wales Sydney, New South Wales, Australia
| | - Jodie McVernon
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia; Victorian Infectious Disease Reference Laboratory Epidemiology Unit, The Royal Melbourne Hospital, Victoria, Australia
| | - James M McCaw
- Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia; School of Mathematics and Statistics, The University of Melbourne, Victoria, Australia
| | - Freya M Shearer
- The Kids Research Institute, Nedlands, Western Australia, Australia; Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Nick Golding
- The Kids Research Institute, Nedlands, Western Australia, Australia; Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia; School of Population Health, Curtin University, Western Australia, Australia
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4
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Purushotham JN, Lutz HL, Parker E, Andersen KG. Immunological drivers of zoonotic virus emergence, evolution, and endemicity. Immunity 2025; 58:784-796. [PMID: 40168990 PMCID: PMC11981831 DOI: 10.1016/j.immuni.2025.03.014] [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: 10/10/2024] [Revised: 03/11/2025] [Accepted: 03/12/2025] [Indexed: 04/03/2025]
Abstract
The disruption of natural ecosystems caused by climate change and human activity is amplifying the risk of zoonotic spillover, presenting a growing global health threat. In the past two decades, the emergence of multiple zoonotic viruses has exposed critical gaps in our ability to predict epidemic trajectories and implement effective interventions. RNA viruses, in particular, are challenging to control due to their high mutation rates and ability to adapt and evade immune defenses. To better prepare for future outbreaks, it is vital that we deepen our understanding of the factors driving viral emergence, transmission, and persistence in human populations. Specifically, deciphering the interactions between antibody-mediated immunity and viral evolution will be key. In this perspective, we explore these dynamic relationships and highlight research priorities that may guide the development of more effective strategies to mitigate the impact of emerging infectious diseases.
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Affiliation(s)
- Jyothi N Purushotham
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA; Scripps Research Translational Institute, La Jolla, CA, USA
| | - Holly L Lutz
- Denver Museum of Nature and Science, Denver, CO, USA
| | - Edyth Parker
- The Institute of Genomics and Global Health (IGH), Redeemer's University, Ede, Osun, Nigeria
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA; Scripps Research Translational Institute, La Jolla, CA, USA.
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5
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Kikawa C, Loes AN, Huddleston J, Figgins MD, Steinberg P, Griffiths T, Drapeau EM, Peck H, Barr IG, Englund JA, Hensley SE, Bedford T, Bloom JD. High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.04.641544. [PMID: 40161702 PMCID: PMC11952370 DOI: 10.1101/2025.03.04.641544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Human influenza viruses rapidly acquire mutations in their hemagglutinin (HA) protein that erode neutralization by antibodies from prior exposures. Here, we use a sequencing-based assay to measure neutralization titers for 78 recent H3N2 HA strains against a large set of children and adult sera, measuring ~10,000 total titers. There is substantial person-to-person heterogeneity in the titers against different viral strains, both within and across age cohorts. The growth rates of H3N2 strains in the human population in 2023 are highly correlated with the fraction of sera with low titers against each strain. Notably, strain growth rates are less correlated with neutralization titers against pools of human sera, demonstrating the importance of population heterogeneity in shaping viral evolution. Overall, these results suggest that high-throughput neutralization measurements of human sera against many different viral strains can help explain the evolution of human influenza.
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Affiliation(s)
- Caroline Kikawa
- Division of Basic Sciences and Computational Biology Program, Fred Hutch Cancer Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Medical Scientist Training Program, University of Washington, Seattle, WA
- These authors contributed equally and are listed alphabetically
| | - Andrea N. Loes
- Division of Basic Sciences and Computational Biology Program, Fred Hutch Cancer Center, Seattle, WA
- Howard Hughes Medical Institute, Seattle, WA
- These authors contributed equally and are listed alphabetically
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA
| | - Marlin D. Figgins
- Division of Basic Sciences and Computational Biology Program, Fred Hutch Cancer Center, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA
| | - Philippa Steinberg
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA
| | - Tachianna Griffiths
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth M. Drapeau
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Heidi Peck
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Ian G. Barr
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Janet A. Englund
- Seattle Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA
| | - Jesse D. Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutch Cancer Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Howard Hughes Medical Institute, Seattle, WA
- Lead contact
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6
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Maurer DP, Vu M, Schmidt AG. Antigenic drift expands influenza viral escape pathways from recalled humoral immunity. Immunity 2025; 58:716-727.e6. [PMID: 40023162 PMCID: PMC11906258 DOI: 10.1016/j.immuni.2025.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 11/16/2024] [Accepted: 02/05/2025] [Indexed: 03/04/2025]
Abstract
Initial exposure to a rapidly evolving virus establishes B cell memory that biases later responses to antigenically drifted strains. This "immune imprinting" implies that subsequent exposure to a drifted strain can induce affinity maturation of memory B cells toward cross-reactivity with the drifted strain and hence toward greater overall breadth. Here, we used deep mutational scanning of H1 influenza hemagglutinins (HAs) to investigate how viruses evolve in response to these broad antibody response. We identified escape mutations from clonal antibody lineages that targeted the receptor binding site and lateral patch. By adjusting the antigen-antibody contacts, antibody affinity maturation restricted the potential escape routes for the eliciting strain. However, escape occurred readily in drifted strains. We attribute this escape-prone property of the drifted strains to epistatic networks within HA. Our data explain how the influenza virus continues to evolve in the human population by escaping even broad antibody responses.
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Affiliation(s)
- Daniel P Maurer
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Mya Vu
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Aaron G Schmidt
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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7
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Lane A, Quach HQ, Ovsyannikova IG, Kennedy RB, Ross TM, Einav T. Characterizing the Short- and Long-Term Temporal Dynamics of Antibody Responses to Influenza Vaccination. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.02.26.25322965. [PMID: 40061340 PMCID: PMC11888507 DOI: 10.1101/2025.02.26.25322965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/18/2025]
Abstract
Most influenza vaccine studies evaluate acute antibody responses 1 month post-vaccination, leaving long-term immunity poorly understood. Here, we performed a combined analysis of 14 large-scale vaccine studies and conducted two new studies mapping antibody responses in high resolution from their inception out to 1 year post-vaccination. Vaccine antibody responses were classified as weak (<4x fold-change at 1 month and 1 year), transient (≥4x at 1 month, <4x at 1 year), or durable (≥4x at 1 month and 1 year). Surprisingly, >50% of vaccine recipients were weak across seasons, age groups, sexes, pre-vaccination titers, and high or standard vaccine doses. Peak fold-change at 1 month post-vaccination was strongly associated with the long-term response, with most transient responders achieving a maximum fold-change of 4x, while most durable responders reached ≥16x, with both groups maintaining these titers for 2 months (10-75 days post-vaccination). Using the weak, transient, and durable trajectories, a single time point early in the response (days 7-8 or 21) predicted an individual's response out to 1 year post-vaccination. These results demonstrate that influenza vaccine responses range from little-to-no response to eliciting strong-and-durable immunity, highlighting the stark heterogeneity that is consistently seen across influenza seasons.
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Affiliation(s)
- Aaron Lane
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Huy Q Quach
- Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
- Department of Infection Biology, Lehner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Tal Einav
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
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8
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Murugaiah V, Watson SJ, Cunliffe RF, Temperton NJ, Reece ST, Kellam P, Tregoning JS. A Transgenic Mouse With a Humanized B-Cell Repertoire Mounts an Antibody Response to Influenza Infection and Vaccination. J Infect Dis 2025; 231:e299-e307. [PMID: 39317662 PMCID: PMC11841647 DOI: 10.1093/infdis/jiae472] [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: 06/21/2024] [Revised: 09/16/2024] [Accepted: 09/21/2024] [Indexed: 09/26/2024] Open
Abstract
The development of a universal influenza vaccine likely requires an understanding of previous exposure to influenza virus (through vaccination or infection) and how that shapes the antibody repertoire to vaccination, sometimes called original antigenic sin or antigenic imprinting. While animal models can have a much more defined exposure history, they lack a human B-cell repertoire. Transgenic mice with the complete human immunoglobulin locus enable studies of controlled infection history leading to human-like antibody evolution. Here we evaluated responses to influenza in the Intelliselect transgenic mouse (the Kymouse). We show the Kymouse is susceptible to disease following infection with either H1N1, H3N2, or B/Yamagata influenza viruses and that it induces a robust binding and neutralizing antibody response to all 3 strains of influenza virus. This study demonstrates that human B-cell repertoire mice can be used for influenza virus studies, providing a tool for further interrogation of the antibody response.
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MESH Headings
- Animals
- Mice, Transgenic
- B-Lymphocytes/immunology
- Influenza Vaccines/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Humans
- Mice
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/prevention & control
- Orthomyxoviridae Infections/virology
- Influenza B virus/immunology
- Influenza A Virus, H1N1 Subtype/immunology
- Disease Models, Animal
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza, Human/immunology
- Influenza, Human/prevention & control
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Vaccination
- Antibody Formation
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Affiliation(s)
- Valarmathy Murugaiah
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Simon J Watson
- Kymab, a Sanofi Company, Babraham Research Campus, Cambridge, United Kingdom
| | - Robert F Cunliffe
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Nigel J Temperton
- Viral Pseudotype Unit, University of Kent and Greenwich, Chatham, United Kingdom
| | - Stevo T Reece
- Kymab, a Sanofi Company, Babraham Research Campus, Cambridge, United Kingdom
| | - Paul Kellam
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- Kymab, a Sanofi Company, Babraham Research Campus, Cambridge, United Kingdom
| | - John S Tregoning
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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9
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Chang S, Shin J, Park S, Park H, Kim JH, Kim TW, Jung IK, Song B, Shin KS, Park B, Kim SY, Jeon JH, Yeo J, Lee TY, Kang CY. Continuous Tracking for Effective Tackling: Ad5/35 Platform-Based JN1 Lineage Vaccines Development in Response to Evolving SARS-CoV-2 Variants. J Med Virol 2025; 97:e70206. [PMID: 39891605 DOI: 10.1002/jmv.70206] [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: 10/19/2024] [Revised: 12/20/2024] [Accepted: 01/25/2025] [Indexed: 02/03/2025]
Abstract
The SARS-CoV-2 virus is continuously evolving, such that JN.1 and its subvariants, including KP.2, KP.3, and LB.1, are now predominant variants globally. JN.1 is derived from BA.2.86, which harbors more than 30 mutations in the spike protein compared with those of XBB and BA.2, and it carries an additional L455S mutation. Given the rapid evolution of these variants, assessing the neutralization capacity of current JN.1 lineage vaccines against prevalent variants, such as KP.3, is critical. Phylogenetic trees using spike protein sequences and antigenic cartography based on neutralization results reveal that JN.1 lineage variants are antigenically distant from previously circulating variants. Moreover, JN.1 subvariants showed inadequate neutralization titers compared with other variants against XBB.1.5-containing vaccine in mice. Immunization with vaccines targeting the JN.1, KP.2, KP.3, and LB.1 variants demonstrated significant neutralizing activity against predominant variants in mice. These results highlight the importance of vaccine development to keep pace with the evolution of SARS-CoV-2 variants and the need for updated vaccines targeting the JN.1 variant.
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Affiliation(s)
- Soojeong Chang
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
| | - Jieun Shin
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
| | - Seowoo Park
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
| | - Hyemin Park
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
| | - Jong Heon Kim
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
| | - Tae Wan Kim
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
| | - In Kyung Jung
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
| | - Boyeong Song
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Kwang-Soo Shin
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
| | - Bongju Park
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
| | - Seo-Yeon Kim
- Division of Infectious Disease Vaccine Research, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, South Korea
| | - Ji Hyang Jeon
- Division of Infectious Disease Vaccine Research, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, South Korea
| | - Jinah Yeo
- Division of Infectious Disease Vaccine Research, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, South Korea
| | - Tae-Young Lee
- Division of Infectious Disease Vaccine Research, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, South Korea
| | - Chang-Yuil Kang
- Research & Development Center, Cellid Co. Ltd., Seoul, South Korea
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10
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Lv H, Teo QW, Lee CCD, Liang W, Choi D, Mao KJ, Ardagh MR, Gopal AB, Mehta A, Szlembarski M, Bruzzone R, Wilson IA, Wu NC, Mok CKP. Differential antigenic imprinting effects between influenza H1N1 hemagglutinin and neuraminidase in a mouse model. J Virol 2025; 99:e0169524. [PMID: 39636110 PMCID: PMC11784018 DOI: 10.1128/jvi.01695-24] [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: 10/21/2024] [Accepted: 11/10/2024] [Indexed: 12/07/2024] Open
Abstract
Understanding how immune history influences influenza immunity is essential for developing effective vaccines and therapeutic strategies. This study examines the antigenic imprinting of influenza hemagglutinin (HA) and neuraminidase (NA) using a mouse model with sequential infections by H1N1 virus strains exhibiting substantial antigenic differences in HA. In our pre-2009 influenza infection model, we observed that mice with more extensive infection histories produced higher levels of functional NA-inhibiting antibodies (NAI). However, following further infection with the 2009 pandemic H1N1 strain, these mice demonstrated a reduced NAI to the challenged virus. Interestingly, prior exposure to older strains resulted in a lower HA antibody response (neutralization and HAI) to the challenged virus in both pre- and post-2009 scenarios, potentially due to faster viral clearance facilitated by immune memory recall. Overall, our findings reveal distinct trajectories in HA and NA immune responses, suggesting that immune imprinting can differentially impact these proteins based on the extent of antigenic variation in influenza viruses. IMPORTANCE Influenza viruses continue to pose a significant threat to human health, with vaccine effectiveness remaining a persistent challenge. Individual immune history is a crucial factor that can influence antibody responses to subsequent influenza exposures. While many studies have explored how pre-existing antibodies shape the induction of anti-HA antibodies following influenza virus infections or vaccinations, the impact on anti-NA antibodies has been less extensively studied. Using a mouse model, our study demonstrates that within pre-2009 H1N1 strains, an extensive immune history negatively impacted anti-HA antibody responses but enhanced anti-NA antibody responses. However, in response to the 2009 pandemic H1N1 strain, which experienced an antigenic shift, both anti-HA and anti-NA antibody responses were hindered by antibodies from prior pre-2009 H1N1 virus infections. These findings provide important insights into how antigenic imprinting affects both anti-HA and anti-NA antibody responses and underscore the need to consider immune history in developing more effective influenza vaccination strategies.
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MESH Headings
- Animals
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/genetics
- Neuraminidase/immunology
- Neuraminidase/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Mice
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Disease Models, Animal
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/virology
- Female
- Humans
- Mice, Inbred BALB C
- Influenza Vaccines/immunology
- Antigens, Viral/immunology
- Antibodies, Neutralizing/immunology
- Influenza, Human/immunology
- Influenza, Human/virology
- Antigenic Variation
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Affiliation(s)
- Huibin Lv
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Qi Wen Teo
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA
| | - Weiwen Liang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong, China
| | - Danbi Choi
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin J. Mao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Madison R. Ardagh
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Akshita B. Gopal
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Arjun Mehta
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Matt Szlembarski
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong, China
- Istituto Pasteur Italia, Rome, Italy
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Nicholas C. Wu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Chris K. P. Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- S.H. Ho Research Centre for Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
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11
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Herrera BB, Chaplin B, MBoup S, Abdullahi A, He M, Fisher SM, Akanmu S, Chang CA, Hamel DJ, Gupta RK, Kanki PJ. Pre-pandemic cross-reactive antibody and cellular responses against SARS-CoV-2 among female sex workers in Dakar, Senegal. Front Public Health 2025; 13:1522733. [PMID: 39916712 PMCID: PMC11798920 DOI: 10.3389/fpubh.2025.1522733] [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: 11/26/2024] [Accepted: 01/06/2025] [Indexed: 02/09/2025] Open
Abstract
Background The COVID-19 pandemic had a severe impact globally, yet African populations exhibited unexpectedly lower rates of severe disease and mortality. We investigated the potential role of pre-existing immunity in shaping the epidemiology of COVID-19 in Africa. Methods Plasma collected from Senegalese female sex workers prior to the COVID-19 pandemic was screened for SARS-CoV-2 and human coronavirus (hCoV) antibodies by virion immunoblots. For antibody-reactive plasma, paired peripheral blood mononuclear cells were stimulated by fusion proteins and IFN-γ cellular responses were assessed via ELISPOT. Results We observed substantial levels of pre-existing cross-reactive immunity to SARS-CoV-2, stemming from prior exposure to seasonal hCoVs. Our antibody analysis revealed a 23.5% (47/200) seroprevalence rate against SARS-CoV-2 nucleocapsid (N). These samples were then probed for antibodies against hCoV spike (S) and/or N antigens; 85.1% (40/47), 70.2% (33/47), and 95.7% (45/47) were antibody reactive against hCoV-229E, hCoV-OC43, or hCoV-HKU1, respectively. Our analysis of cellular responses also demonstrated cross-reactivity to SARS-CoV-2 with 80.0% (36/45) and 82.2% (37/45) showing IFN-γ responses against S and N, respectively. A unique pre-pandemic subject had cross-reactive SARS-CoV-2 S antibodies with detectable neutralization and cross-reactive cellular responses. Conclusion These findings suggest that prior hCoV exposure may induce cross-reactive adaptive immunity, potentially contributing to protection against COVID-19. Our study provides unique data on the dynamics of hCoV and SARS-CoV-2 immunity in Senegal and underscores the importance of understanding the role of pre-existing immunity in shaping COVID-19 outcomes globally.
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Affiliation(s)
- Bobby Brooke Herrera
- Rutgers Global Health Institute, Rutgers University, New Brunswick, NJ, United States
- Department of Medicine, Division of Allergy, Immunology, and Infectious Diseases, and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, United States
- Mir Biosciences, Inc., Dunellen, NJ, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Beth Chaplin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Souleymane MBoup
- Institut De Recherche En Santé De Surveillance Épidémiologique Et De Formation (IRESSEF), Dakar, Senegal
| | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Michelle He
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Sydney M. Fisher
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Sulaimon Akanmu
- Lagos University Teaching Hospital, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Charlotte A. Chang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Donald J. Hamel
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Phyllis J. Kanki
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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12
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Sullivan SG, Khvorov A, Carolan L, Dowson L, Hadiprodjo AJ, Sánchez-Ovando S, Liu Y, Leung VKY, Hodgson D, Blyth CC, Macnish M, Cheng AC, Haugenauer M, Clark J, Dougherty S, Macartney K, Koirala A, Khatami A, Jadhav A, Marshall H, Riley KE, Wark PAB, Delahunty C, Subbarao K, Kucharski AJ, Fox A. Antibody responses against influenza A decline with successive years of annual influenza vaccination. NPJ Vaccines 2025; 10:11. [PMID: 39820465 PMCID: PMC11739582 DOI: 10.1038/s41541-024-01057-x] [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: 08/03/2024] [Accepted: 12/19/2024] [Indexed: 01/19/2025] Open
Abstract
Influenza vaccine effectiveness and immunogenicity can be compromised with repeated vaccination. We assessed immunological markers in a cohort of healthcare workers (HCW) from six public hospitals around Australia during 2020-2021. Sera were collected pre-vaccination and ~14 and ~180 days post-vaccination and assessed in haemagglutination inhibition assay against egg-grown vaccine and equivalent cell-grown viruses. Responses to vaccination were compared by the number of prior vaccinations. Baseline sera were available for 595 HCW in 2020 and 1031 in 2021. 5% had not been vaccinated during five years prior to enrolment and 55% had been vaccinated every year. Post-vaccination titres for all vaccine antigens were lowest among HCW vaccinated in all 5-prior years and highest among HCW with 0 or 1 prior vaccinations, even after adjustment. This was observed for both influenza A subtypes and was dependent on pre-vaccination titre. Expanded cohorts are needed to better understand how this translates to vaccine effectiveness.
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Affiliation(s)
- Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
- Department of Epidemiology, University of California, Los Angeles, USA.
- School of Clinical Sciences, Monash University, Clayton, Australia.
| | - Arseniy Khvorov
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Louise Carolan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Leslie Dowson
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - A Jessica Hadiprodjo
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Stephany Sánchez-Ovando
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Yi Liu
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vivian K Y Leung
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Services, Royal Melbourne Hospital, Melbourne, Australia
- Infection Prevention and Surveillance Service, Royal Melbourne Hospital, Melbourne, Australia
| | - David Hodgson
- Department of Infectious Disease Epidemiology and Dynamics, London School of Hygiene and Tropical Medicine, London, UK
| | - Christopher C Blyth
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- School of Medicine, University of Western Australia, Perth, Australia
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Perth, Australia
| | - Marion Macnish
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
| | - Allen C Cheng
- School of Clinical Sciences, Monash University, Clayton, Australia
- Alfred Health, Melbourne, Australia
| | | | - Julia Clark
- Queensland Children's Hospital, Brisbane, Australia
- University of Queensland, Brisbane, Australia
| | | | | | | | - Ameneh Khatami
- The Children's Hospital at Westmead, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - Ajay Jadhav
- The Children's Hospital at Westmead, Sydney, Australia
| | - Helen Marshall
- The Women and Children's Health Network, Adelaide, Australia
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Kathryn E Riley
- The Women and Children's Health Network, Adelaide, Australia
| | - Peter A B Wark
- John Hunter Hospital, Newcastle, Australia
- University of Newcastle, Newcastle, Australia
| | - Catherine Delahunty
- John Hunter Hospital, Newcastle, Australia
- University of Newcastle, Newcastle, Australia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Adam J Kucharski
- Department of Infectious Disease Epidemiology and Dynamics, London School of Hygiene and Tropical Medicine, London, UK
| | - Annette Fox
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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13
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Wickenhagen A, Flagg M, Port JR, Yinda CK, Goldin K, Gallogly S, Schulz JE, Lutterman T, Williamson BN, Kaiser F, Mukesh RK, van Tol S, Smith B, van Doremalen N, Russell CA, de Wit E, Munster VJ. Evolution of Omicron lineage towards increased fitness in the upper respiratory tract in the absence of severe lung pathology. Nat Commun 2025; 16:594. [PMID: 39799119 PMCID: PMC11724920 DOI: 10.1038/s41467-025-55938-3] [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: 07/01/2024] [Accepted: 01/06/2025] [Indexed: 01/15/2025] Open
Abstract
The emergence of the Omicron lineage represented a major genetic drift in SARS-CoV-2 evolution. This was associated with phenotypic changes including evasion of pre-existing immunity and decreased disease severity. Continuous evolution within the Omicron lineage raised concerns of potential increased transmissibility and/or disease severity. To address this, we evaluate the fitness and pathogenesis of contemporary Omicron variants XBB.1.5, XBB.1.16, EG.5.1, and JN.1 in the upper (URT) and lower respiratory tract (LRT). We compare in vivo infection in Syrian hamsters with infection in primary human nasal and lung epithelium cells and assess differences in transmissibility, antigenicity, and innate immune activation. Omicron variants replicate efficiently in the URT but display limited pathology in the lungs compared to previous variants and fail to replicate in human lung organoids. JN.1 is attenuated in both URT and LRT compared to other Omicron variants and fails to transmit in the male hamster model. Our data demonstrate that Omicron lineage evolution has favored increased fitness in the URT.
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Affiliation(s)
- Arthur Wickenhagen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Meaghan Flagg
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Julia R Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
- Laboratory of Transmission Immunology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kerry Goldin
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Shane Gallogly
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jonathan E Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Tessa Lutterman
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Brandi N Williamson
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Franziska Kaiser
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Reshma K Mukesh
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Sarah van Tol
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Brian Smith
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Colin A Russell
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
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14
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Hu YF, Zhang BZ, Chu H, Huang JD. Distinct evolution patterns of influenza viruses and implications for vaccine development. Innovation (N Y) 2025; 6:100739. [PMID: 39872480 PMCID: PMC11763911 DOI: 10.1016/j.xinn.2024.100739] [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: 08/08/2024] [Accepted: 11/19/2024] [Indexed: 01/30/2025] Open
Abstract
In conclusion, the distinct evolution patterns of panzootic influenza A(H5Nx) compared to A(H1N1) and A(H3N2) complicate vaccine development. Effective strategies must consider these unique patterns and the impact of pre-existing immunity. Leveraging AI-based methods for optimized antigen design is essential to mitigate the potential impact of emerging antigenically variable strains and will provide valuable insights for developing more effective vaccines to prepare for future pandemics.
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Affiliation(s)
- Ye-Fan Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong SAR, China
- BayVax Biotech Limited, Hong Kong Science Park, Hong Kong & Shenzhen BayVax Biotech Limited, Guangming, Shenzhen 518107, China
| | - Bao-Zhong Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, HKU, Hong Kong SAR, China
- Materials Innovation Institute for Life Sciences and Energy (MILES), HKU-SIRI, Shenzhen 518048, China
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong SAR, China
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Key Laboratory for Cancer Metastasis and Personalized Therapy, Department of Clinical Oncology, HKU-Shenzhen Hospital, Shenzhen 518053, China
- Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen University, Guangzhou 510120, China
- Materials Innovation Institute for Life Sciences and Energy (MILES), HKU-SIRI, Shenzhen 518048, China
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15
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and Methods for Predicting Viral Evolution. Methods Mol Biol 2025; 2890:253-290. [PMID: 39890732 DOI: 10.1007/978-1-0716-4326-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2025]
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 hemagglutinin 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 1 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 at https://previr.app .
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Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Köln, Germany
| | - Malancha Karmakar
- Institute for Biological Physics, University of Cologne, Köln, Germany
| | - Marta Łuksza
- Departments of Oncological Sciences and Genetics and Genomic Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Köln, Germany.
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16
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Maltseva M, Keeshan A, Cooper C, Langlois MA. Immune imprinting: The persisting influence of the first antigenic encounter with rapidly evolving viruses. Hum Vaccin Immunother 2024; 20:2384192. [PMID: 39149872 PMCID: PMC11328881 DOI: 10.1080/21645515.2024.2384192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/08/2024] [Accepted: 07/21/2024] [Indexed: 08/17/2024] Open
Abstract
Immune imprinting is a phenomenon that stems from the fundamentals of immunological memory. Upon recurrent exposures to an evolving pathogen, the immune system must weigh the benefits of rapidly recalling established antibody repertoires with greater affinity to the initial variant or invest additional time and energy in producing de novo responses specific to the emerging variant. In this review, we delve into the mechanistic complexities of immune imprinting and its role in shaping subsequent immune responses, both de novo and recall, against rapidly evolving respiratory viruses such as influenza and coronaviruses. By exploring the duality of immune imprinting, we examine its potential to both enhance or hinder immune protection against disease, while emphasizing the role of host and viral factors. Finally, we explore how different vaccine platforms may affect immune imprinting and comment on vaccine strategies that can favor de novo variant-specific antibody responses.
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Affiliation(s)
- Mariam Maltseva
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Alexa Keeshan
- School of Epidemiology and Public Health, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Curtis Cooper
- School of Epidemiology and Public Health, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Medicine, University of Ottawa, Ottawa, ON, Canada
- Division of Infectious Diseases, Ottawa Hospital Research Institute Clinical Epidemiology Program, Ottawa, ON, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation (CI3), University of Ottawa, Ottawa, ON, Canada
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17
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Barrat-Charlaix P, Neher RA. Eco-evolutionary dynamics of adapting pathogens and host immunity. eLife 2024; 13:RP97350. [PMID: 39728926 DOI: 10.7554/elife.97350] [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: 12/28/2024] Open
Abstract
As pathogens spread in a population of hosts, immunity is built up, and the pool of susceptible individuals are depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with rapid antigenic evolution and frequent emergence of immune evasive variants. However, the host's immune systems adapt, and older immune responses wane, such that escape variants only enjoy a growth advantage for a limited time. If variant growth dynamics and reshaping of host-immunity operate on comparable time scales, viral adaptation is determined by eco-evolutionary interactions that are not captured by models of rapid evolution in a fixed environment. Here, we use a Susceptible/Infected model to describe the interaction between an evolving viral population in a dynamic but immunologically diverse host population. We show that depending on strain cross-immunity, heterogeneity of the host population, and durability of immune responses, escape variants initially grow exponentially, but lose their growth advantage before reaching high frequencies. Their subsequent dynamics follows an anomalous random walk determined by future escape variants and results in variant trajectories that are unpredictable. This model can explain the apparent contradiction between the clearly adaptive nature of antigenic evolution and the quasi-neutral dynamics of high-frequency variants observed for influenza viruses.
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Affiliation(s)
- Pierre Barrat-Charlaix
- Biozentrum, Universität Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- DISAT, Politecnico di Torino, Torino, Italy
| | - Richard A Neher
- Biozentrum, Universität Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
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18
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Mallajosyula V, Chakraborty S, Sola E, Fong RF, Shankar V, Gao F, Burrell AR, Gupta N, Wagar LE, Mischel PS, Capasso R, Staat MA, Chien YH, Dekker CL, Wang TT, Davis MM. Coupling antigens from multiple subtypes of influenza can broaden antibody and T cell responses. Science 2024; 386:1389-1395. [PMID: 39700292 PMCID: PMC12036609 DOI: 10.1126/science.adi2396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/29/2024] [Accepted: 11/08/2024] [Indexed: 12/21/2024]
Abstract
The seasonal influenza vaccine contains strains of viruses from distinct subtypes that are grown independently and then combined. However, most individuals exhibit a more robust response to one of these strains and thus are vulnerable to infection by others. By studying a monozygotic twin cohort, we found that although prior exposure is a factor, host genetics are a stronger driver of subtype bias to influenza viral strains. We found that covalent coupling of heterologous hemagglutinin (HA) from different viral strains could largely eliminate subtype bias in an animal model and in a human tonsil organoid system. We proposed that coupling of heterologous antigens improves antibody responses across influenza strains by broadening T cell help, and we found that using this approach substantially improved the antibody response to avian influenza HA.
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MESH Headings
- Animals
- Female
- Humans
- Male
- Mice
- Antibodies, Viral/immunology
- Antibody Formation/immunology
- Antigens, Viral/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Influenza A virus/immunology
- Influenza A virus/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza Vaccines/immunology
- Influenza, Human/immunology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Palatine Tonsil/immunology
- Palatine Tonsil/virology
- CD4-Positive T-Lymphocytes/immunology
- Organoids/immunology
- Organoids/virology
- Mice, Inbred C57BL
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Affiliation(s)
- Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Saborni Chakraborty
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - Elsa Sola
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ryan Furuichi Fong
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vishnu Shankar
- Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fei Gao
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Allison R. Burrell
- Department of Pediatrics, Division of Infectious Diseases, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45220, USA
| | - Neha Gupta
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lisa E. Wagar
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Paul S. Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Robson Capasso
- Division of Sleep Surgery, Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mary A. Staat
- Department of Pediatrics, Division of Infectious Diseases, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45220, USA
| | - Yueh-Hsiu Chien
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelia L. Dekker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taia T. Wang
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - Mark M. Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
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19
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Brangel P, Tureli S, Mühlemann B, Liechti N, Zysset D, Engler O, Hunger-Glaser I, Ghiga I, Mattiuzzo G, Eckerle I, Bekliz M, Rössler A, Schmitt MM, Knabl L, Kimpel J, Tort LFL, de Araujo MF, de Oliveira ACA, Caetano BC, Siqueira MM, Budt M, Gensch JM, Wolff T, Hassan T, Selvaraj FA, Hermanus T, Kgagudi P, Crowther C, Richardson SI, Bhiman JN, Moore PL, Cheng SMS, Li JKC, Poon LLM, Peiris M, Corman VM, Drosten C, Lai L, Hunsawong T, Rungrojcharoenkit K, Lohachanakul J, Sigal A, Khan K, Thiel V, Barut GT, Ebert N, Mykytyn AZ, Owusu Donkor I, Aboagye JO, Nartey PA, Van Kerkhove MD, Cunningham J, Haagmans BL, Suthar MS, Smith D, Subissi L. A Global Collaborative Comparison of SARS-CoV-2 Antigenicity Across 15 Laboratories. Viruses 2024; 16:1936. [PMID: 39772242 PMCID: PMC11680265 DOI: 10.3390/v16121936] [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: 11/12/2024] [Revised: 12/08/2024] [Accepted: 12/09/2024] [Indexed: 01/11/2025] Open
Abstract
Setting up a global SARS-CoV-2 surveillance system requires an understanding of how virus isolation and propagation practices, use of animal or human sera, and different neutralisation assay platforms influence assessment of SARS-CoV-2 antigenicity. In this study, with the contribution of 15 independent laboratories across all WHO regions, we carried out a controlled analysis of neutralisation assay platforms using the first WHO International Standard for antibodies to SARS-CoV-2 variants of concern (source: NIBSC). Live virus isolates (source: WHO BioHub or individual labs) or spike plasmids (individual labs) for pseudovirus production were used to perform neutralisation assays using the same serum panels. When comparing fold drops, excellent data consistency was observed across the labs using common reagents, including between pseudovirus and live virus neutralisation assays (RMSD of data from mean fold drop was 0.59). Utilising a Bayesian model, geometric mean titres and assay titre magnitudes (offsets) can describe the data efficiently. Titre magnitudes were seen to vary largely even for labs within the same assay group. We have observed that overall, live Microneutralisation assays tend to have the lowest titres, whereas Pseudovirus Neutralisation have the highest (with a mean difference of 3.2 log2 units between the two). These findings are relevant for laboratory networks, such as the WHO Coronavirus Laboratory Network (CoViNet), that seek to support a global surveillance system for evolution and antigenic characterisation of variants to support monitoring of population immunity and vaccine composition policy.
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Affiliation(s)
| | - Sina Tureli
- Centre for Pathogen Evolution, University of Cambridge, Cambridge CB3 0FD, UK
| | - Barbara Mühlemann
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Virology, Charitéplatz 1, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), Associated Partner Site Charité, Charitéplatz 1, 10117 Berlin, Germany
| | - Nicole Liechti
- WHO BioHub Facility, Spiez Laboratory, 3700 Spiez, Switzerland
| | - Daniel Zysset
- WHO BioHub Facility, Spiez Laboratory, 3700 Spiez, Switzerland
| | - Olivier Engler
- WHO BioHub Facility, Spiez Laboratory, 3700 Spiez, Switzerland
| | | | - Ioana Ghiga
- World Health Organization, 1202 Geneva, Switzerland
| | - Giada Mattiuzzo
- Medicines and Healthcare Products Regulatory Agency, London SW1W 9SZ, UK
| | - Isabella Eckerle
- Department of Medicine, University of Geneva, 1205 Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, 1205 Geneva, Switzerland
| | - Meriem Bekliz
- Department of Medicine, University of Geneva, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, 1205 Geneva, Switzerland
| | - Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Virology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Melanie M. Schmitt
- Institute of Virology, Department of Hygiene, Microbiology and Virology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, 6511 Zams, Austria
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Virology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Luis Fernando Lopez Tort
- Laboratory of Respiratory, Exanthematous and Enteric Viruses and Viral Emergencies (LVRE), Oswaldo Cruz Institute (IOC-Fiocruz), Rio de Janeiro 21.040-900, Brazil
- Laboratory of Molecular Virology, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, Salto 50000, Uruguay
| | - Mia Ferreira de Araujo
- Laboratory of Respiratory, Exanthematous and Enteric Viruses and Viral Emergencies (LVRE), Oswaldo Cruz Institute (IOC-Fiocruz), Rio de Janeiro 21.040-900, Brazil
| | - Any Caroline Alves de Oliveira
- Laboratory of Respiratory, Exanthematous and Enteric Viruses and Viral Emergencies (LVRE), Oswaldo Cruz Institute (IOC-Fiocruz), Rio de Janeiro 21.040-900, Brazil
| | - Braulia Costa Caetano
- Laboratory of Respiratory, Exanthematous and Enteric Viruses and Viral Emergencies (LVRE), Oswaldo Cruz Institute (IOC-Fiocruz), Rio de Janeiro 21.040-900, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory, Exanthematous and Enteric Viruses and Viral Emergencies (LVRE), Oswaldo Cruz Institute (IOC-Fiocruz), Rio de Janeiro 21.040-900, Brazil
| | - Matthias Budt
- Unit 17 “Influenza and Other Respiratory Viruses”, Robert Koch Institut, 13353 Berlin, Germany
| | - Jean-Marc Gensch
- Unit 17 “Influenza and Other Respiratory Viruses”, Robert Koch Institut, 13353 Berlin, Germany
| | - Thorsten Wolff
- Unit 17 “Influenza and Other Respiratory Viruses”, Robert Koch Institut, 13353 Berlin, Germany
| | - Tarteel Hassan
- Reference Laboratory for Infectious Diseases, Purelab, Sheikh Khalifa Medical City, Abu Dhabi 51900, United Arab Emirates
| | - Francis Amirtharaj Selvaraj
- Reference Laboratory for Infectious Diseases, Purelab, Sheikh Khalifa Medical City, Abu Dhabi 51900, United Arab Emirates
| | - Tandile Hermanus
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2001, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg 2131, South Africa
| | - Prudence Kgagudi
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2001, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg 2131, South Africa
| | - Carol Crowther
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2001, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg 2131, South Africa
| | - Simone I. Richardson
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2001, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg 2131, South Africa
| | - Jinal N. Bhiman
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2001, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg 2131, South Africa
| | - Penny L. Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2001, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg 2131, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
| | - Samuel M. S. Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - John K. C. Li
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo L. M. Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Victor M. Corman
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Virology, Charitéplatz 1, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), Associated Partner Site Charité, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian Drosten
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Virology, Charitéplatz 1, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), Associated Partner Site Charité, Charitéplatz 1, 10117 Berlin, Germany
| | - Lilin Lai
- Department of Pediatrics, Center for Childhood Infections and Vaccines, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Taweewun Hunsawong
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok 10500, Thailand
| | - Kamonthip Rungrojcharoenkit
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok 10500, Thailand
| | - Jindarat Lohachanakul
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok 10500, Thailand
| | - Alex Sigal
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Africa Health Research Institute, Durban 4013, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban 4013, South Africa
| | - Volker Thiel
- Multidisciplinary Center for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- Institute of Virology and Immunology, Mittelhäusern and Bern, 3012 Bern, Switzerland
| | - G. Tuba Barut
- Multidisciplinary Center for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- Institute of Virology and Immunology, Mittelhäusern and Bern, 3012 Bern, Switzerland
| | - Nadine Ebert
- Multidisciplinary Center for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- Institute of Virology and Immunology, Mittelhäusern and Bern, 3012 Bern, Switzerland
| | | | - Irene Owusu Donkor
- Medical and Scientific Research Centre, University of Ghana Medical Centre, Accra P.O. Box LG 25, Ghana
| | - James Odame Aboagye
- Medical and Scientific Research Centre, University of Ghana Medical Centre, Accra P.O. Box LG 25, Ghana
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon P.O. Box LG 581, Ghana
| | - Prince Adom Nartey
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon P.O. Box LG 581, Ghana
| | | | | | | | - Mehul S. Suthar
- Department of Pediatrics, Center for Childhood Infections and Vaccines, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Derek Smith
- Centre for Pathogen Evolution, University of Cambridge, Cambridge CB3 0FD, UK
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20
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Lin Y, Wang Y, Li H, Liu T, Zhang J, Guo X, Guo W, Wang Y, Liu X, Huang S, Liao H, Wang X. A platform for the rapid screening of equine immunoglobins F (ab)2 derived from single equine memory B cells able to cross-neutralize to influenza virus. Emerg Microbes Infect 2024; 13:2396864. [PMID: 39331815 PMCID: PMC11441081 DOI: 10.1080/22221751.2024.2396864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/26/2024] [Accepted: 08/22/2024] [Indexed: 09/29/2024]
Abstract
Single B cells-based antibody platforms offer an effective approach for the discovery of useful antibodies for therapeutic or research purposes. Here we present a method for screening equine immunoglobins F(ab)2, which offers the potential advantage of reacting with multiple epitopes on the virus. Using equine influenza virus (EIV) as model, a hemagglutinin (HA) trimer was constructed to bait B cells in vaccinated horses. We screened 370 HA-specific B cells from 1 × 106 PBMCs and identified a diverse set of equine variable region gene sequences of heavy and light chains and then recombined with humanized Ig Fc. Recombinant equine Ig was then self-assembled in co-transfected 293 T cells, and subsequently optimized to obtain HA binding B-cell receptor (s). The recombinant antibodies exhibited a high binding affinity to the HA protein. Antibody H81 exhibited the highest cross neutralizing activities against EIV strains in vitro. Furthermore, it effectively protected EIV-challenged mice, resulting in significantly improved survival, reduced pulmonary inflammation and decreased viral titers. In silico predication identified a functional region of H81 comprising 27 key amino acids cross the main circulating EIV strains. The 12 amino acid residues in this region with the highest binding affinities were screened. Notably, the predicted epitopes of H81 encompassed the documented equine HA receptor binding site, validating its cross-neutralization. In summary, a rapid platform was successfully established to investigate the profiling of equine antigen-recognizing receptors (BCRs) following infection. This platform has the potential to optimize the screening of virus-neutralizing antibodies and aid in vaccine design.
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Affiliation(s)
- Yuezhi Lin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Yayu Wang
- Zhuhai Trinomab Pharmaceutical Co., Ltd, Zhuhai, People’s Republic of China
| | - Hongxin Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Tong Liu
- Zhuhai Trinomab Pharmaceutical Co., Ltd, Zhuhai, People’s Republic of China
| | - Jiaqi Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xing Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Wei Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- Institute of Western Agriculture, the Chinese Academy of Agricultural sciences, Changji, People’s Republic of China
| | - Yaoxin Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xiangning Liu
- Clinical Research Platform for Interdiscipline of Stomatology, The First Affiliated Hospital of Jinan University, Guangzhou, People's Republic of China
- Department of Stomatology, College of Stomatology, Jinan University, Guangzhou, People’s Republic of China
| | - Shaoli Huang
- The Hong Kong University of Science and Technology, School of Engineering, Hong Kong, People’s Republic of China
| | - Huaxin Liao
- Zhuhai Trinomab Pharmaceutical Co., Ltd, Zhuhai, People’s Republic of China
| | - XiaoJun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- Institute of Western Agriculture, the Chinese Academy of Agricultural sciences, Changji, People’s Republic of China
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21
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Hay JA, Routledge I, Takahashi S. Serodynamics: A primer and synthetic review of methods for epidemiological inference using serological data. Epidemics 2024; 49:100806. [PMID: 39647462 DOI: 10.1016/j.epidem.2024.100806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 11/21/2024] [Accepted: 11/25/2024] [Indexed: 12/10/2024] Open
Abstract
We present a review and primer of methods to understand epidemiological dynamics and identify past exposures from serological data, referred to as serodynamics. We discuss processing and interpreting serological data prior to fitting serodynamical models, and review approaches for estimating epidemiological trends and past exposures, ranging from serocatalytic models applied to binary serostatus data, to more complex models incorporating quantitative antibody measurements and immunological understanding. Although these methods are seemingly disparate, we demonstrate how they are derived within a common mathematical framework. Finally, we discuss key areas for methodological development to improve scientific discovery and public health insights in seroepidemiology.
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Affiliation(s)
- James A Hay
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Isobel Routledge
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Saki Takahashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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22
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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] [Key Words] [Grants] [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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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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23
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Luksza M, Lässig M. Concepts and methods for predicting viral evolution. ARXIV 2024:arXiv:2403.12684v3. [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 Luksza
- 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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24
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Wang W, Bhushan G, Paz S, Stauft CB, Selvaraj P, Goguet E, Bishop-Lilly KA, Subramanian R, Vassell R, Lusvarghi S, Cong Y, Agan B, Richard SA, Epsi NJ, Fries A, Fung CK, Conte MA, Holbrook MR, Wang TT, Burgess TH, Pollett SD, Mitre E, Katzelnick LC, Weiss CD. Human and hamster sera correlate well in identifying antigenic drift among SARS-CoV-2 variants, including JN.1. J Virol 2024; 98:e0094824. [PMID: 39365051 DOI: 10.1128/jvi.00948-24] [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: 06/07/2024] [Accepted: 09/14/2024] [Indexed: 10/05/2024] Open
Abstract
Antigenic assessments of SARS-CoV-2 variants inform decisions to update COVID-19 vaccines. Primary infection sera are often used for assessments, but such sera are rare due to population immunity from SARS-CoV-2 infections and COVID-19 vaccinations. Here, we show that neutralization titers and breadth of matched human and hamster pre-Omicron variant primary infection sera correlate well and generate similar antigenic maps. The hamster antigenic map shows modest antigenic drift among XBB sub-lineage variants, with JN.1 and BA.4/BA.5 variants within the XBB cluster, but with fivefold to sixfold antigenic differences between these variants and XBB.1.5. Compared to sera following only ancestral or bivalent COVID-19 vaccinations, or with post-vaccination infections, XBB.1.5 booster sera had the broadest neutralization against XBB sub-lineage variants, although a fivefold titer difference was still observed between JN.1 and XBB.1.5 variants. These findings suggest that antibody coverage of antigenically divergent JN.1 could be improved with a matched vaccine antigen.IMPORTANCEUpdates to COVID-19 vaccine antigens depend on assessing how much vaccine antigens differ antigenically from newer SARS-CoV-2 variants. Human sera from single variant infections are ideal for discriminating antigenic differences among variants, but such primary infection sera are now rare due to high population immunity. It remains unclear whether sera from experimentally infected animals could substitute for human sera for antigenic assessments. This report shows that neutralization titers of variant-matched human and hamster primary infection sera correlate well and recognize variants similarly, indicating that hamster sera can be a proxy for human sera for antigenic assessments. We further show that human sera following an XBB.1.5 booster vaccine broadly neutralized XBB sub-lineage variants but titers were fivefold lower against the more recent JN.1 variant. These findings support updating the current COVID-19 vaccine variant composition and developing a framework for assessing antigenic differences in future variants using hamster primary infection sera.
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Affiliation(s)
- Wei Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Gitanjali Bhushan
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie Paz
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Charles B Stauft
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Prabhuanand Selvaraj
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Emilie Goguet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Kimberly A Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, Maryland, USA
| | - Rahul Subramanian
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Russell Vassell
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Sabrina Lusvarghi
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yu Cong
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Brian Agan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Stephanie A Richard
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Nusrat J Epsi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Anthony Fries
- US Air Force School of Aerospace Medicine, Dayton, Ohio, USA
| | - Christian K Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Michael R Holbrook
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Tony T Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Timothy H Burgess
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Simon D Pollett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carol D Weiss
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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25
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Urdy S, Hanke M, Toledo AI, Ratto N, Jacob E, Peyronnet E, Gourlet JB, Chaves SS, Thommes E, Coudeville L, Boissel JP, Courcelles E, Bruezière L. Multi-strain modeling of influenza vaccine effectiveness in older adults and its dependence on antigenic distance. Sci Rep 2024; 14:27190. [PMID: 39516205 PMCID: PMC11549341 DOI: 10.1038/s41598-024-72716-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 09/10/2024] [Indexed: 11/16/2024] Open
Abstract
Influenza vaccine effectiveness (VE) varies seasonally due to host, virus and vaccine characteristics. To investigate how antigenic matching and dosage impact VE, we developed a mechanistic knowledge-based mathematical model. Immunization with a split vaccine is modeled for exposure to A/H1N1 or A/H3N2 virus strains. The model accounts for cross-reactivity of immune cells elicited during previous immunizations with new antigens. We simulated vaccine effectiveness (sVE) of high dose (HD) versus standard dose (SD) vaccines in the older population, from 2011 to 2022. We find that sVE is highly dependent on antigenic matching and that higher dosage improves immunogenicity, activation and memory formation of immune cells. In alignment with clinical observations, the HD vaccine performs better than the SD vaccine in all simulations, supporting the use of the HD vaccine in the older population. This model could be adapted to predict the impact of alternative virus strain selection on clinical outcomes in future influenza seasons.
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Affiliation(s)
| | | | | | | | | | | | | | - Sandra S Chaves
- Modeling, Edpidemiology and Data Science (MEDS), Sanofi Vaccines, Lyon, France
| | - Edward Thommes
- Modeling, Edpidemiology and Data Science (MEDS), Sanofi Vaccines, Lyon, France
| | - Laurent Coudeville
- Modeling, Edpidemiology and Data Science (MEDS), Sanofi Vaccines, Lyon, France
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26
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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. PLoS Biol 2024; 22:e3002864. [PMID: 39509444 PMCID: PMC11542844 DOI: 10.1371/journal.pbio.3002864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 09/26/2024] [Indexed: 11/15/2024] Open
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 in humans remains unclear. Here, we used a multilevel 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 in humans 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 19% 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 to 2015), and 20% were estimated to have 3 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 analysed 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, London, United Kingdom
| | - 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, The 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, London, 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, Maryland, United States of America
- Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, North Carolina, United States of America
- UNC Carolina Population Center, Chapel Hill, North Carolina, United States of America
| | - Derek A. T. Cummings
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
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27
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Pardi N, Krammer F. mRNA vaccines for infectious diseases - advances, challenges and opportunities. Nat Rev Drug Discov 2024; 23:838-861. [PMID: 39367276 DOI: 10.1038/s41573-024-01042-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 10/06/2024]
Abstract
The concept of mRNA-based vaccines emerged more than three decades ago. Groundbreaking discoveries and technological advancements over the past 20 years have resolved the major roadblocks that initially delayed application of this new vaccine modality. The rapid development of nucleoside-modified COVID-19 mRNA vaccines demonstrated that this immunization platform is easy to develop, has an acceptable safety profile and can be produced at a large scale. The flexibility and ease of antigen design have enabled mRNA vaccines to enter development for a wide range of viruses as well as for various bacteria and parasites. However, gaps in our knowledge limit the development of next-generation mRNA vaccines with increased potency and safety. A deeper understanding of the mechanisms of action of mRNA vaccines, application of novel technologies enabling rational antigen design, and innovative vaccine delivery strategies and vaccination regimens will likely yield potent novel vaccines against a wide range of pathogens.
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Affiliation(s)
- Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), 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.
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria.
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28
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Cobey S. Vaccination against rapidly evolving pathogens and the entanglements of memory. Nat Immunol 2024; 25:2015-2023. [PMID: 39384979 DOI: 10.1038/s41590-024-01970-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/26/2024] [Indexed: 10/11/2024]
Abstract
Immune memory determines infection risk and responses to future infections and vaccinations over potentially decades of life. Despite its centrality, the dynamics of memory to antigenically variable pathogens remains poorly understood. This Review examines how past exposures shape B cell responses to vaccinations with influenza and SARS-CoV-2. An overriding feature of vaccinations with these pathogens is the recall of primary responses, often termed 'imprinting' or 'original antigenic sin'. These recalled responses can inhibit the generation of new responses unless some incompletely defined conditions are met. Depending on the context, immune memory can increase or decrease the total neutralizing antibody response to variant antigens, with apparent consequences for protection. These effects are easier to measure experimentally than epidemiologically, but there is evidence that both early and recent exposures influence vaccine effectiveness. A few immunological interactions between adaptive immune responses and antigens might explain the seemingly discrepant effects of memory. Overall, the complex observations point to a need for more quantitative approaches to integrate high-dimensional immune data from populations with diverse exposure histories. Such approaches could help identify optimal vaccination strategies against antigenically diverse pathogens.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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29
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Kim K, Vieira MC, Gouma S, Weirick ME, Hensley SE, Cobey S. Measures of population immunity can predict the dominant clade of influenza A (H3N2) in the 2017-2018 season and reveal age-associated differences in susceptibility and antibody-binding specificity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.26.23297569. [PMID: 37961288 PMCID: PMC10635207 DOI: 10.1101/2023.10.26.23297569] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background For antigenically variable pathogens such as influenza, strain fitness is partly determined by the relative availability of hosts susceptible to infection with that strain compared to others. Antibodies to the hemagglutinin (HA) and neuraminidase (NA) confer substantial protection against influenza infection. We asked if a cross-sectional antibody-derived estimate of population susceptibility to different clades of influenza A (H3N2) could predict the success of clades in the following season. Methods We collected sera from 483 healthy individuals aged 1 to 90 years in the summer of 2017 and analyzed neutralizing responses to the HA and NA of representative strains using Focus Reduction Neutralization Tests (FNRT) and Enzyme-Linked Lectin Assays (ELLA). We estimated relative population-average and age-specific susceptibilities to circulating viral clades and compared those estimates to changes in clade frequencies in the following 2017-18 season. Results The clade to which neutralizing antibody titers were lowest, indicating greater population susceptibility, dominated the next season. Titer correlations between viral strains varied by age, suggesting age-associated differences in epitope targeting driven by shared past exposures. Yet substantial unexplained variation remains within age groups. Conclusions This study indicates how representative measures of population immunity might improve evolutionary forecasts and inform selective pressures on influenza.
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Affiliation(s)
- Kangchon Kim
- Department of Ecology and Evolution, The University of Chicago, USA
| | - Marcos C. Vieira
- Department of Ecology and Evolution, The University of Chicago, USA
| | - Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, USA
| | - Madison E. Weirick
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, USA
| | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, USA
| | - Sarah Cobey
- Department of Ecology and Evolution, The University of Chicago, USA
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30
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Sylvén KR, Jacobson M, Schwarz L, Zohari S. Reverse zoonotic transmission of human seasonal influenza to a pig herd in Sweden. Tierarztl Prax Ausg G Grosstiere Nutztiere 2024; 52:296-303. [PMID: 39447586 DOI: 10.1055/a-2410-1530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2024]
Abstract
In January 2023, a Swedish piglet-producing farm with 2800 sows in production (SIP) was diagnosed with IAV (Influenza A virus) and the isolates were shown to cluster with the human seasonal influenza (2022/2023). In December 2022, employees with flu like symptoms tended to the pigs and a few weeks later, respiratory signs appeared in different age groups; sows in farrowing units were anorectic and pyrectic. Lung and nasal swabs were tested positive for IAV and other respiratory infectious agents. Blanket vaccination against H1N1pdm09 of sows and gilts was initiated but discontinued for sows after 2 treatments. Biosecurity measures aiming to reduce the spread of virus were implemented. However, the compliance to follow the protocol was moderate.Combining immunity and strict sanitary measures is crucial to control virus circulation. As the farmer discontinued sow vaccination and just partly increased biosecurity, this may have contributed to ongoing virus circulation and clinical signs in pigs, even 5 months post-diagnosis. Although H1N1pdm09 already had been found in the herd in 2017, there were no clinical signs or diagnostic results indicating continuous circulation of this or other IAV strains afterwards. However, this cannot be entirely excluded. Swine IAVs pose a risk of reintroduction into the human population, highlighting the importance of vaccination of farm workers against seasonal influenza.
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Affiliation(s)
| | - Magdalena Jacobson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Lukas Schwarz
- Clinical Centre for Population Medicine in Fish, Pig and Poultry, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine Vienna, Austria
| | - Siamak Zohari
- Department of Microbiology, Swedish Veterinary Agency (SVA), Uppsala, Sweden
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31
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Underwood AP, Gupta M, Wu BR, Eltahla AA, Boo I, Wang JJ, Agapiou D, Abayasingam A, Reynaldi A, Keoshkerian E, Zhao Y, Brasher N, Walker MR, Bukh J, Maher L, Gordon T, Davenport MP, Luciani F, Drummer HE, Lloyd AR, Bull RA. B-cell characteristics define HCV reinfection outcome. J Hepatol 2024; 81:415-428. [PMID: 38604387 DOI: 10.1016/j.jhep.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND & AIMS In individuals highly exposed to HCV, reinfection is common, suggesting that natural development of sterilising immunity is difficult. In those that are reinfected, some will develop a persistent infection, while a small proportion repeatedly clear the virus, suggesting natural protection is possible. The aim of this study was to characterise immune responses associated with rapid natural clearance of HCV reinfection. METHODS Broad neutralising antibodies (nAbs) and Envelope 2 (E2)-specific memory B cell (MBC) responses were examined longitudinally in 15 individuals with varied reinfection outcomes. RESULTS Broad nAb responses were associated with MBC recall, but not with clearance of reinfection. Strong evidence of antigen imprinting was found, and the B-cell receptor repertoire showed a high level of clonality with ongoing somatic hypermutation of many clones over subsequent reinfection events. Single-cell transcriptomic analyses showed that cleared reinfections featured an activated transcriptomic profile in HCV-specific B cells that rapidly expanded upon reinfection. CONCLUSIONS MBC quality, but not necessarily breadth of nAb responses, is important for protection against antigenically diverse variants, which is encouraging for HCV vaccine development. IMPACT AND IMPLICATIONS HCV continues to have a major health burden globally. Limitations in the health infrastructure for diagnosis and treatment, as well as high rates of reinfection, indicate that a vaccine that can protect against chronic HCV infection will greatly complement current efforts to eliminate HCV-related disease. With alternative approaches to testing vaccines, such as controlled human inoculation trials under consideration, we desperately need to identify the correlates of immune protection. In this study, in a small but rare cohort of high-risk injecting drug users who were reinfected multiple times, breadth of neutralisation was not associated with ultimate clearance of the reinfection event. Alternatively, characteristics of the HCV-specific B-cell response associated with B-cell proliferation were. This study indicates that humoral responses are important for protection and suggests that for genetically very diverse viruses, such as HCV, it may be beneficial to look beyond just antibodies as correlates of protection.
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Affiliation(s)
- Alexander P Underwood
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Money Gupta
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Bing-Ru Wu
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Auda A Eltahla
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Irene Boo
- Burnet Institute, Melbourne, VIC, Australia
| | - Jing Jing Wang
- Department of Immunology Flinders Medical Centre and Flinders University, SA Pathology Bedford Park, SA, Australia
| | - David Agapiou
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Arunasingam Abayasingam
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Arnold Reynaldi
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | | | - Yanran Zhao
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Nicholas Brasher
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Melanie R Walker
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lisa Maher
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Tom Gordon
- Department of Immunology Flinders Medical Centre and Flinders University, SA Pathology Bedford Park, SA, Australia
| | - Miles P Davenport
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Fabio Luciani
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Heidi E Drummer
- Burnet Institute, Melbourne, VIC, Australia; Department of Microbiology, Monash University, Clayton, VIC, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew R Lloyd
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Rowena A Bull
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.
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32
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Zhang Y, Cui P, Shi J, Zeng X, Jiang Y, Chen Y, Zhang J, Wang C, Wang Y, Tian G, Chen H, Kong H, Deng G. A broad-spectrum vaccine candidate against H5 viruses bearing different sub-clade 2.3.4.4 HA genes. NPJ Vaccines 2024; 9:152. [PMID: 39160189 PMCID: PMC11333769 DOI: 10.1038/s41541-024-00947-4] [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: 04/01/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
The global spread of H5 clade 2.3.4.4 highly pathogenic avian influenza (HPAI) viruses threatens poultry and public health. The continuous circulation of these viruses has led to their considerable genetic and antigenic evolution, resulting in the formation of eight subclades (2.3.4.4a-h). Here, we examined the antigenic sites that determine the antigenic differences between two H5 vaccine strains, H5-Re8 (clade 2.3.4.4g) and H5-Re11 (clade 2.3.4.4h). Epitope mapping data revealed that all eight identified antigenic sites were located within two classical antigenic regions, with five sites in region A (positions 115, 120, 124, 126, and 140) and three in region B (positions 151, 156, and 185). Through antigenic cartography analysis of mutants with varying numbers of substitutions, we confirmed that a combination of mutations in these eight sites reverses the antigenicity of H5-Re11 to that of H5-Re8, and vice versa. More importantly, our analyses identified H5-Re11_Q115L/R120S/A156T (H5-Re11 + 3) as a promising candidate for a broad-spectrum vaccine, positioned centrally in the antigenic map, and offering potential universal protection against all variants within the clade 2.3.4.4. H5-Re11 + 3 serum has better cross-reactivity than sera generated with other 2.3.4.4 vaccines, and H5-Re11 + 3 vaccine provided 100% protection of chickens against antigenically drifted H5 viruses from various 2.3.4.4 antigenic groups. Our findings suggest that antigenic regions A and B are immunodominant in H5 viruses, and that antigenic cartography-guided vaccine design is a promising strategy for selecting a broad-spectrum vaccine.
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Affiliation(s)
- Yuancheng Zhang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Pengfei Cui
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jianzhong Shi
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xianying Zeng
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yongping Jiang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Chen
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jie Zhang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Congcong Wang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yan Wang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guobin Tian
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hualan Chen
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huihui Kong
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Guohua Deng
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
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33
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Welsh FC, Eguia RT, Lee JM, Haddox HK, Galloway J, Van Vinh Chau N, Loes AN, Huddleston J, Yu TC, Quynh Le M, Nhat NTD, Thi Le Thanh N, Greninger AL, Chu HY, Englund JA, Bedford T, Matsen FA, Boni MF, Bloom JD. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. Cell Host Microbe 2024; 32:1397-1411.e11. [PMID: 39032493 PMCID: PMC11329357 DOI: 10.1016/j.chom.2024.06.015] [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: 04/19/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Human influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population and how this heterogeneity affects virus evolution. Here, we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of two H3N2 strains, A/Hong Kong/45/2019 and A/Perth/16/2009, affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that were fixed in influenza variants after 2020 cause greater escape from sera from younger individuals compared with adults. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups and suggest approaches to understand how this heterogeneous selection shapes viral evolution.
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MESH Headings
- Humans
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Mutation
- Adult
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Influenza, Human/virology
- Influenza, Human/immunology
- Age Factors
- Middle Aged
- Young Adult
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Adolescent
- Evolution, Molecular
- Aged
- Child
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Affiliation(s)
- Frances C Welsh
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA 98109, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Rachel T Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Juhye M Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Hugh K Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jared Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Nguyen Van Vinh Chau
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Timothy C Yu
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA 98109, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mai Quynh Le
- National Institutes for Hygiene and Epidemiology, Hanoi, Vietnam
| | - Nguyen T D Nhat
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nguyen Thi Le Thanh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA 98109, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Maciej F Boni
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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Mühlemann B, Trimpert J, Walper F, Schmidt ML, Jansen J, Schroeder S, Jeworowski LM, Beheim-Schwarzbach J, Bleicker T, Niemeyer D, Richter A, Adler JM, Vidal RM, Langner C, Vladimirova D, Wilks SH, Smith DJ, Voß M, Paltzow L, Martínez Christophersen C, Rose R, Krumbholz A, Jones TC, Corman VM, Drosten C. Antigenic cartography using variant-specific hamster sera reveals substantial antigenic variation among Omicron subvariants. Proc Natl Acad Sci U S A 2024; 121:e2310917121. [PMID: 39078681 PMCID: PMC11317614 DOI: 10.1073/pnas.2310917121] [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: 07/04/2023] [Accepted: 05/31/2024] [Indexed: 07/31/2024] Open
Abstract
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has developed substantial antigenic variability. As the majority of the population now has pre-existing immunity due to infection or vaccination, the use of experimentally generated animal immune sera can be valuable for measuring antigenic differences between virus variants. Here, we immunized Syrian hamsters by two successive infections with one of nine SARS-CoV-2 variants. Their sera were titrated against 16 SARS-CoV-2 variants, and the resulting titers were visualized using antigenic cartography. The antigenic map shows a condensed cluster containing all pre-Omicron variants (D614G, Alpha, Delta, Beta, Mu, and an engineered B.1+E484K variant) and considerably more diversity among a selected panel of Omicron subvariants (BA.1, BA.2, BA.4/BA.5, the BA.5 descendants BF.7 and BQ.1.18, the BA.2.75 descendant BN.1.3.1, the BA.2-derived recombinants XBB.2 and EG.5.1, and the BA.2.86 descendant JN.1). Some Omicron subvariants were as antigenically distinct from each other as the wildtype is from the Omicron BA.1 variant. Compared to titers measured in human sera, titers in hamster sera are of higher magnitude, show less fold change, and result in a more compact antigenic map topology. The results highlight the potential of sera from hamsters for the continued antigenic characterization of SARS-CoV-2.
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Affiliation(s)
- Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Felix Walper
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Marie L. Schmidt
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Jenny Jansen
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Simon Schroeder
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Lara M. Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Anja Richter
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Julia M. Adler
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | | | - Christine Langner
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Daria Vladimirova
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Samuel H. Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Mathias Voß
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
| | - Lea Paltzow
- Labor Dr. Krause und Kollegen Medizinisches Versorgungszentrum GmbH, Kiel24106, Germany
| | | | - Ruben Rose
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
- Labor Dr. Krause und Kollegen Medizinisches Versorgungszentrum GmbH, Kiel24106, Germany
| | - Terry C. Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Victor M. Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
- Labor Berlin–Charité Vivantes GmbH, Berlin13353, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
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Avanthay R, Garcia-Nicolas O, Ruggli N, Grau-Roma L, Párraga-Ros E, Summerfield A, Zimmer G. Evaluation of a novel intramuscular prime/intranasal boost vaccination strategy against influenza in the pig model. PLoS Pathog 2024; 20:e1012393. [PMID: 39116029 PMCID: PMC11309389 DOI: 10.1371/journal.ppat.1012393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/03/2024] [Indexed: 08/10/2024] Open
Abstract
Live-attenuated influenza vaccines (LAIV) offer advantages over the commonly used inactivated split influenza vaccines. However, finding the optimal balance between sufficient attenuation and immunogenicity has remained a challenge. We recently developed an alternative LAIV based on the 2009 pandemic H1N1 virus with a truncated NS1 protein and lacking PA-X protein expression (NS1(1-126)-ΔPAX). This virus showed a blunted replication and elicited a strong innate immune response. In the present study, we evaluated the efficacy of this vaccine candidate in the porcine animal model as a pertinent in vivo system. Immunization of pigs via the nasal route with the novel NS1(1-126)-ΔPAX LAIV did not cause disease and elicited a strong mucosal immune response that completely blocked replication of the homologous challenge virus in the respiratory tract. However, we observed prolonged shedding of our vaccine candidate from the upper respiratory tract. To improve LAIV safety, we developed a novel prime/boost vaccination strategy combining primary intramuscular immunization with a haemagglutinin-encoding propagation-defective vesicular stomatitis virus (VSV) replicon, followed by a secondary immunization with the NS1(1-126)-ΔPAX LAIV via the nasal route. This two-step immunization procedure significantly reduced LAIV shedding, increased the production of specific serum IgG, neutralizing antibodies, and Th1 memory cells, and resulted in sterilizing immunity against homologous virus challenge. In conclusion, our novel intramuscular prime/intranasal boost regimen interferes with virus shedding and transmission, a feature that will help combat influenza epidemics and pandemics.
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MESH Headings
- Animals
- Swine
- Influenza Vaccines/immunology
- Influenza Vaccines/administration & dosage
- Orthomyxoviridae Infections/prevention & control
- Orthomyxoviridae Infections/immunology
- Injections, Intramuscular
- Administration, Intranasal
- Vaccines, Attenuated/immunology
- Vaccines, Attenuated/administration & dosage
- Influenza A Virus, H1N1 Subtype/immunology
- Disease Models, Animal
- Antibodies, Viral/immunology
- Immunization, Secondary/methods
- Vaccination/methods
- Influenza, Human/prevention & control
- Influenza, Human/immunology
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Affiliation(s)
- Robin Avanthay
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Obdulio Garcia-Nicolas
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nicolas Ruggli
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Llorenç Grau-Roma
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, COMPATH, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Ester Párraga-Ros
- Department of Anatomy and Comparative Pathology, Veterinary Faculty, University of Murcia, Murcia, Spain
| | - Artur Summerfield
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gert Zimmer
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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36
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Gong X, Peng L, Wang F, Liu J, Tang Y, Peng Y, Niu S, Yin J, Guo L, Lu H, Liu Y, Yang Y. Repeated Omicron infection dampens immune imprinting from previous vaccination and induces broad neutralizing antibodies against Omicron sub-variants. J Infect 2024; 89:106208. [PMID: 38908522 DOI: 10.1016/j.jinf.2024.106208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/15/2024] [Indexed: 06/24/2024]
Abstract
OBJECTIVE Similar with influenza virus, antigenic drift is highly relevant to SARS-CoV-2 evolution, and immune imprinting has been found to limit the performance of updated vaccines based on the emerging variants of SARS-CoV-2. We aimed to investigate whether repeated exposure to Omicron variant could reduce the immune imprinting from previous vaccination. METHODS A total of 194 participants with different status of vaccination (unvaccinated, regular vaccination and booster vaccination) confirmed for first infection and re-infection with BA.5, BF.7 and XBB variants were enrolled, and the neutralizing profiles against wild type (WT) SARS-CoV-2 and Omicron sub-variants were analyzed. RESULTS Neutralizing potency against the corresponding infected variant is significantly hampered along with the doses of vaccination during first infection. However, for the participants with first infection of BA.5/BF.7 variants and re-infection of XBB variant, immune imprinting was obviously alleviated, indicated as significantly increased ratio of the corresponding infected variant/WT ID50 titers and higher percentage of samples with high neutralizing activities (ID50 > 500) against BA.5, BF.7 and XBB variants. Moreover, repeated Omicron infection could induce strong neutralizing potency with broad neutralizing profiles against a series of other Omicron sub-variants, both in the vaccine naive and vaccine experienced individuals. CONCLUSIONS Our results demonstrate that repeated Omicron infection dampens immune imprinting from vaccination with WT SARS-CoV-2 and induces broad neutralizing profiles against Omicron sub-variants.
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Affiliation(s)
- Xiaohua Gong
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Ling Peng
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Fuxiang Wang
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Jiexiang Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Shenzhen Clinical School of Medicine, Guangzhou University of Chinese Medicine, China
| | - Yimin Tang
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Yun Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Shiyu Niu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China
| | - Juzhen Yin
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China
| | - Liping Guo
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Hongzhou Lu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China.
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China.
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China.
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37
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Edler P, Schwab LSU, Aban M, Wille M, Spirason N, Deng YM, Carlock MA, Ross TM, Juno JA, Rockman S, Wheatley AK, Kent SJ, Barr IG, Price DJ, Koutsakos M. Immune imprinting in early life shapes cross-reactivity to influenza B virus haemagglutinin. Nat Microbiol 2024; 9:2073-2083. [PMID: 38890491 DOI: 10.1038/s41564-024-01732-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024]
Abstract
Influenza exposures early in life are believed to shape future susceptibility to influenza infections by imprinting immunological biases that affect cross-reactivity to future influenza viruses. However, direct serological evidence linked to susceptibility is limited. Here we analysed haemagglutination-inhibition titres in 1,451 cross-sectional samples collected between 1992 and 2020, from individuals born between 1917 and 2008, against influenza B virus (IBV) isolates from 1940 to 2021. We included testing of 'future' isolates that circulated after sample collection. We show that immunological biases are conferred by early life IBV infection and result in lineage-specific cross-reactivity of a birth cohort towards future IBV isolates. This translates into differential estimates of susceptibility between birth cohorts towards the B/Yamagata and B/Victoria lineages, predicting lineage-specific birth-cohort distributions of observed medically attended IBV infections. Our data suggest that immunological measurements of imprinting could be important in modelling and predicting virus epidemiology.
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Affiliation(s)
- Peta Edler
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Lara S U Schwab
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Malet Aban
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Natalie Spirason
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael A Carlock
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
- Florida Research and Innovation Centre, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
- Florida Research and Innovation Centre, Cleveland Clinic, Port Saint Lucie, FL, USA
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Steve Rockman
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Vaccine Product Development, CSL Seqirus Ltd, Parkville, Victoria, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Health, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Ian G Barr
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David J Price
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
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38
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Carlock MA, Allen JD, Hanley HB, Ross TM. Longitudinal assessment of human antibody binding to hemagglutinin elicited by split-inactivated influenza vaccination over six consecutive seasons. PLoS One 2024; 19:e0301157. [PMID: 38917104 PMCID: PMC11198804 DOI: 10.1371/journal.pone.0301157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Participants between the ages of 10-86 years old were vaccinated with split-inactivated influenza vaccine (Fluzone®) in six consecutive influenza seasons from 2016-2017 to 2021-2022. Vaccine effectiveness varies from season to season as a result of both host immune responses as well as evolutionary changes in the influenza virus surface glycoproteins that provide challenges to vaccine manufacturers to produce more effective annual vaccines. Next generation influenza vaccines are in development and may provide protective immune responses against a broader number of influenza viruses and reduce the need for annual vaccination. An improved understanding how current influenza vaccines are influenced by human host immune responses in people of different ages and co-morbidities is necessary for designing the next-generation of 'universal' or broadly-protective influenza vaccines. Overall, pre-existing immune responses to previous influenza virus exposures, either by past infections or vaccinations, is a critical factor influencing host responses to seasonal influenza vaccination. Participants vaccinated in consecutive seasons had reduced serum hemagglutination-inhibition (HAI) activity against strains included in the vaccine compared to participants that had not been vaccinated in the preceding 1-2 years prior to entering this study. The magnitude and breadth of these antibody responses were also modulated by the age of the participant. Elderly participants over 65 years of age, in general, had lower pre-existing HAI titers each season prior to vaccination with lower post-vaccination titers compared to children or young adults under the age of 35. The administration of higher doses (HD) of the split-inactivated vaccine enhanced the antibody titers in the elderly. This report showcases 6 consecutive years of antibody HAI activity in human subjects receiving seasonal split-inactivated influenza vaccine.
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Affiliation(s)
- Michael A. Carlock
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
| | - James D. Allen
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
| | - Hannah B. Hanley
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
| | - Ted M. Ross
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
- Department of Infection Biology, Lehner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America
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39
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McGough L, Cobey S. A speed limit on serial strain replacement from original antigenic sin. Proc Natl Acad Sci U S A 2024; 121:e2400202121. [PMID: 38857397 PMCID: PMC11194583 DOI: 10.1073/pnas.2400202121] [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: 01/04/2024] [Accepted: 05/06/2024] [Indexed: 06/12/2024] Open
Abstract
Many pathogens evolve to escape immunity, yet it remains difficult to predict whether immune pressure will lead to diversification, serial replacement of one variant by another, or more complex patterns. Pathogen strain dynamics are mediated by cross-protective immunity, whereby exposure to one strain partially protects against infection by antigenically diverged strains. There is growing evidence that this protection is influenced by early exposures, a phenomenon referred to as original antigenic sin (OAS) or imprinting. In this paper, we derive constraints on the emergence of the pattern of successive strain replacements demonstrated by influenza, SARS-CoV-2, seasonal coronaviruses, and other pathogens. We find that OAS implies that the limited diversity found with successive strain replacement can only be maintained if [Formula: see text] is less than a threshold set by the characteristic antigenic distances for cross-protection and for the creation of new immune memory. This bound implies a "speed limit" on the evolution of new strains and a minimum variance of the distribution of infecting strains in antigenic space at any time. To carry out this analysis, we develop a theoretical model of pathogen evolution in antigenic space that implements OAS by decoupling the antigenic distances required for protection from infection and strain-specific memory creation. Our results demonstrate that OAS can play an integral role in the emergence of strain structure from host immune dynamics, preventing highly transmissible pathogens from maintaining serial strain replacement without diversification.
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Affiliation(s)
- Lauren McGough
- Department of Ecology and EvolutionThe University of Chicago, Chicago, IL60637
| | - Sarah Cobey
- Department of Ecology and EvolutionThe University of Chicago, Chicago, IL60637
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40
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Wang D, Huot M, Mohanty V, Shakhnovich EI. Biophysical principles predict fitness of SARS-CoV-2 variants. Proc Natl Acad Sci U S A 2024; 121:e2314518121. [PMID: 38820002 PMCID: PMC11161772 DOI: 10.1073/pnas.2314518121] [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: 08/22/2023] [Accepted: 04/19/2024] [Indexed: 06/02/2024] Open
Abstract
SARS-CoV-2 employs its spike protein's receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our understanding of how RBD's biophysical properties contribute to SARS-CoV-2's epidemiological fitness remains largely incomplete. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the identification of a fitness function based on binding thermodynamics, we unravel the relationship between the biophysical properties of RBD variants and their contribution to viral fitness. We developed a biophysical model that uses statistical mechanics to map the molecular phenotype space, characterized by dissociation constants of RBD to ACE2, LY-CoV016, LY-CoV555, REGN10987, and S309, onto an epistatic fitness landscape. We validate our findings through experimentally measured and machine learning (ML) estimated binding affinities, coupled with infectivity data derived from population-level sequencing. Our analysis reveals that this model effectively predicts the fitness of novel RBD variants and can account for the epistatic interactions among mutations, including explaining the later reversal of Q493R. Our study sheds light on the impact of specific mutations on viral fitness and delivers a tool for predicting the future epidemiological trajectory of previously unseen or emerging low-frequency variants. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics.
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Affiliation(s)
- Dianzhuo Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Marian Huot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- École Polytechnique, Institut Polytechnique de Paris, Palaiseau91128, France
| | - Vaibhav Mohanty
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA02115
- Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eugene I. Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
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41
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Mühlemann B, Wilks SH, Baracco L, Bekliz M, Carreño JM, Corman VM, Davis-Gardner ME, Dejnirattisai W, Diamond MS, Douek DC, Drosten C, Eckerle I, Edara VV, Ellis M, Fouchier RAM, Frieman M, Godbole S, Haagmans B, Halfmann PJ, Henry AR, Jones TC, Katzelnick LC, Kawaoka Y, Kimpel J, Krammer F, Lai L, Liu C, Lusvarghi S, Meyer B, Mongkolsapaya J, Montefiori DC, Mykytyn A, Netzl A, Pollett S, Rössler A, Screaton GR, Shen X, Sigal A, Simon V, Subramanian R, Supasa P, Suthar MS, Türeli S, Wang W, Weiss CD, Smith DJ. Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays. Sci Transl Med 2024; 16:eadl1722. [PMID: 38748773 DOI: 10.1126/scitranslmed.adl1722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/11/2024] [Indexed: 08/31/2024]
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires ongoing monitoring to judge the ability of newly arising variants to escape the immune response. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal serum samples. We compared 18 datasets generated using human, hamster, and mouse serum and six different neutralization assays. Datasets using animal model serum samples showed higher titer magnitudes than datasets using human serum samples in this comparison. Fold change in neutralization of variants compared to ancestral SARS-CoV-2, immunodominance patterns, and antigenic maps were similar among serum samples and assays. Most assays yielded consistent results, except for differences in fold change in cytopathic effect assays. Hamster serum samples were a consistent surrogate for human first-infection serum samples. These results inform the transition of surveillance of SARS-CoV-2 antigenic variation from dependence on human first-infection serum samples to the utilization of serum samples from animal models.
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Affiliation(s)
- Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Lauren Baracco
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Meriem Bekliz
- Department of Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, CH-1211, Geneva, Switzerland
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok Noi, Bangkok 10700, Thailand
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Andrew M. and Jane M. Bursky the Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, CH-1211, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, CH-1211 Geneva, Switzerland
| | - Venkata-Viswanadh Edara
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Madison Ellis
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Center, 3015 Rotterdam, Netherlands
| | - Matthew Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bart Haagmans
- Viroscience Department, Erasmus Medical Center, 3015 Rotterdam, Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Terry C Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lilin Lai
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Benjamin Meyer
- Centre of Vaccinology, Department of Pathology and Immunology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anna Mykytyn
- Viroscience Department, Erasmus Medical Center, 3015 Rotterdam, Netherlands
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Simon Pollett
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rahul Subramanian
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Mehul S Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Wei Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Carol D Weiss
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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Astakhova EA, Morozov AA, Vavilova JD, Filatov AV. Antigenic Cartography of SARS-CoV-2. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:862-871. [PMID: 38880647 DOI: 10.1134/s0006297924050079] [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: 11/07/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 06/18/2024]
Abstract
Antigenic cartography is a tool for interpreting and visualizing antigenic differences between virus variants based on virus neutralization data. This approach has been successfully used in the selection of influenza vaccine seed strains. With the emergence of SARS-CoV-2 variants escaping vaccine-induced antibody response, adjusting COVID-19 vaccines has become essential. This review provides information on the antigenic differences between SARS-CoV-2 variants revealed by antigenic cartography and explores a potential of antigenic cartography-based methods (e.g., building antibody landscapes and neutralization breadth gain plots) for the quantitative assessment of the breadth of the antibody response. Understanding the antigenic differences of SARS-CoV-2 and the possibilities of the formed humoral immunity aids in the prompt modification of preventative vaccines against COVID-19.
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Affiliation(s)
- Ekaterina A Astakhova
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia.
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexey A Morozov
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Julia D Vavilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander V Filatov
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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43
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Guiomar R, Pereira da Silva S, Costa I, Conde P, Cristóvão P, Rodrigues A, Fernandes A, Dias A, Couto A, Ramos A, Moita C, Rodrigues C, Vale F, Caldeira F, Bruges Armas J, Pereira‐Vaz J, Alves J, Freitas L, Martins L, Milho L, Mota‐Vieira L, Lopes L, Freitas M, Pessanha M, Correia M, Marques M, Cardoso M, Peres M, Cunha M, Amantegui P, Mota P, Lopes P, Pereira P, Viseu R, Cabral R, Côrte‐Real R, Almeida S, Soares V, Mansinho K, Hungnes O, Nunes B. Seroprevalence of Protective Antibodies Against Influenza and the Reduction of the Influenza Incidence Rate: An Annual Repeated Cross-Sectional Study From 2014 to 2019. Influenza Other Respir Viruses 2024; 18:e13307. [PMID: 38798072 PMCID: PMC11128746 DOI: 10.1111/irv.13307] [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: 12/27/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Seroepidemiological studies provide estimates of population-level immunity, prevalence/incidence of infections, and evaluation of vaccination programs. We assessed the seroprevalence of protective antibodies against influenza and evaluated the correlation of seroprevalence with the cumulative annual influenza incidence rate. METHODS We conducted an annual repeated cross-sectional seroepidemiological survey, during June-August, from 2014 to 2019, in Portugal. A total of 4326 sera from all age groups, sex, and regions was tested by hemagglutination inhibition assay. Seroprevalence and geometric mean titers (GMT) of protective antibodies against influenza were assessed by age group, sex, and vaccine status (65+ years old). The association between summer annual seroprevalence and the difference of influenza incidence rates between one season and the previous one was measured by Pearson correlation coefficient (r). RESULTS Significant differences in seroprevalence of protective antibodies against influenza were observed in the population. Higher seroprevalence and GMT for A(H1N1)pdm09 and A(H3N2) were observed in children (5-14); influenza B seroprevalence in adults 65+ was 1.6-4.4 times than in children (0-4). Vaccinated participants (65+) showed significant higher seroprevalence/GMT for influenza. A strong negative and significant correlation was found between seroprevalence and ILI incidence rate for A(H1N1)pdm09 in children between 5 and 14 (r = -0.84; 95% CI, -0.98 to -0.07); a weak negative correlation was observed for A(H3N2) and B/Yamagata (r ≤ -0.1). CONCLUSIONS The study provides new insight into the anti-influenza antibodies seroprevalence measured in summer on the ILI incidence rate in the next season and the need for adjusted preventive health care measures to prevent influenza infection and transmission.
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Affiliation(s)
- Raquel Guiomar
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Infectious Diseases DepartmentNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | | | - Inês Costa
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Infectious Diseases DepartmentNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | - Patricia Conde
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Infectious Diseases DepartmentNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | - Paula Cristóvão
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Infectious Diseases DepartmentNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | - Ana Paula Rodrigues
- Department of EpidemiologyNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | - Aida Fernandes
- Laboratório de Saúde Pública Dr.ª Laura AyresFaroPortugal
| | - Ana Paula Dias
- Centro Hospitalar de Lisboa Ocidental, E. P. E.LisbonPortugal
| | - Ana Rita Couto
- Hospital de Santo Espírito da Ilha Terceira, E. P. E.R.Angra do HeroísmoPortugal
| | - Angélica Ramos
- Centro Hospitalar Universitário de São João, E. P. E.PortoPortugal
- EPIUnit – Instituto de Saúde PúblicaUniversidade do PortoPortoPortugal
| | - Carina Moita
- Unidade Local de Saúde da Guarda, E. P. E.GuardaPortugal
| | | | - Fátima Vale
- Unidade Local de Saúde da Guarda, E. P. E.GuardaPortugal
| | | | - Jácome Bruges Armas
- Hospital de Santo Espírito da Ilha Terceira, E. P. E.R.Angra do HeroísmoPortugal
| | - João Pereira‐Vaz
- Centro Hospitalar e Universitário de Coimbra, E. P. E.CoimbraPortugal
| | - José Alves
- Hospital Central e Universitário da MadeiraFunchalPortugal
| | | | - Luis Martins
- Instituto Português de Oncologia de Lisboa, Francisco Gentil, E.P. E.LisbonPortugal
| | - Luís Milho
- Laboratório de Saúde Pública Dr.ª Laura AyresFaroPortugal
| | - Luisa Mota‐Vieira
- Hospital do Divino Espirito Santo de Ponta Delgada, E. P. E. R.Ponta DelgadaPortugal
| | - Lurdes Lopes
- Centro Hospitalar e Universitário de Lisboa Central, E. P. E.LisbonPortugal
| | - Margarida Freitas
- Hospital da Senhora da Oliveira Guimarães, E. P. E.GuimarãesPortugal
| | | | - Maria Correia
- Centro Hospitalar e Universitário de Coimbra, E. P. E.CoimbraPortugal
| | | | | | | | - Mário Cunha
- Instituto Português de Oncologia de Lisboa, Francisco Gentil, E.P. E.LisbonPortugal
| | | | - Paula Mota
- Hospital da Senhora da Oliveira Guimarães, E. P. E.GuimarãesPortugal
| | - Paulo Lopes
- Centro Hospitalar de Vila Nova de Gaia/Espinho, E. P. E.Vila Nova de GaiaPortugal
| | - Paulo Pereira
- Centro Hospitalar Universitário do Porto, E. P. E.PortoPortugal
| | - Regina Viseu
- Centro Hospitalar de Setúbal, E. P. E.SetúbalPortugal
| | - Rita Cabral
- Hospital do Divino Espirito Santo de Ponta Delgada, E. P. E. R.Ponta DelgadaPortugal
| | - Rita Côrte‐Real
- Centro Hospitalar e Universitário de Lisboa Central, E. P. E.LisbonPortugal
| | - Sofia Almeida
- Centro Hospitalar Universitário Cova da Beira, E. P. E.CovilhãPortugal
| | - Vânia Soares
- Centro Hospitalar de Vila Nova de Gaia/Espinho, E. P. E.Vila Nova de GaiaPortugal
| | - Kamal Mansinho
- Centro Hospitalar de Lisboa Ocidental, E. P. E.LisbonPortugal
| | - Olav Hungnes
- Norwegian National Influenza CentreNorwegian Institute of Public HealthOsloNorway
| | - Baltazar Nunes
- Department of EpidemiologyNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
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Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead SS, Cauchemez S, Cummings DAT, Salje H. Antigenic distance between primary and secondary dengue infections correlates with disease risk. Sci Transl Med 2024; 16:eadk3259. [PMID: 38657027 DOI: 10.1126/scitranslmed.adk3259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Many pathogens continuously change their protein structure in response to immune-driven selection, resulting in weakened protection even in previously exposed individuals. In addition, for some pathogens, such as dengue virus, poorly targeted immunity is associated with increased risk of severe disease through a mechanism known as antibody-dependent enhancement. However, it remains unclear whether the antigenic distances between an individual's first infection and subsequent exposures dictate disease risk, explaining the observed large-scale differences in dengue hospitalizations across years. Here, we develop a framework that combines detailed antigenic and genetic characterization of viruses with details on hospitalized cases from 21 years of dengue surveillance in Bangkok, Thailand, to identify the role of the antigenic profile of circulating viruses in determining disease risk. We found that the risk of hospitalization depended on both the specific order of infecting serotypes and the antigenic distance between an individual's primary and secondary infections, with risk maximized at intermediate antigenic distances. These findings suggest that immune imprinting helps determine dengue disease risk and provide a pathway to monitor the changing risk profile of populations and to quantifying risk profiles of candidate vaccines.
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Affiliation(s)
- Lin Wang
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Angkana T Huang
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Leah C Katzelnick
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noémie Lefrancq
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Ana Coello Escoto
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Loréna Duret
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Nayeem Chowdhury
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Jarman
- Coalition for Epidemic Preparedness Initiative, Washington, DC 20006, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | | | - Warunee Vandepitte
- Queen Sirikit National Institute of Child Health, Bangkok 10400, Thailand
| | - Stephen S Whitehead
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris 75015, France
| | - Derek A T Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
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45
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McGough L, Cobey S. A speed limit on serial strain replacement from original antigenic sin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574172. [PMID: 38260288 PMCID: PMC10802292 DOI: 10.1101/2024.01.04.574172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Many pathogens evolve to escape immunity, yet it remains difficult to predict whether immune pressure will lead to diversification, serial replacement of one variant by another, or more complex patterns. Pathogen strain dynamics are mediated by cross-protective immunity, whereby exposure to one strain partially protects against infection by antigenically diverged strains. There is growing evidence that this protection is influenced by early exposures, a phenomenon referred to as original antigenic sin (OAS) or imprinting. In this paper, we derive new constraints on the emergence of the pattern of successive strain replacements demonstrated by influenza, SARS-CoV-2, seasonal coronaviruses, and other pathogens. We find that OAS implies that the limited diversity found with successive strain replacement can only be maintained if R 0 is less than a threshold set by the characteristic antigenic distances for cross-protection and for the creation of new immune memory. This bound implies a "speed limit" on the evolution of new strains and a minimum variance of the distribution of infecting strains in antigenic space at any time. To carry out this analysis, we develop a theoretical model of pathogen evolution in antigenic space that implements OAS by decoupling the antigenic distances required for protection from infection and strain-specific memory creation. Our results demonstrate that OAS can play an integral role in the emergence of strain structure from host immune dynamics, preventing highly transmissible pathogens from maintaining serial strain replacement without diversification.
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Affiliation(s)
- Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
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Kasten-Jolly J, Lawrence DA. Cellular and Molecular Immunity to Influenza Viruses and Vaccines. Vaccines (Basel) 2024; 12:389. [PMID: 38675771 PMCID: PMC11154265 DOI: 10.3390/vaccines12040389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Immune responses to influenza (flu) antigens reflect memory of prior infections or vaccinations, which might influence immunity to new flu antigens. Memory of past antigens has been termed "original antigenic sin" or, more recently, "immune imprinting" and "seniority". We have researched a comparison between the immune response to live flu infections and inactivated flu vaccinations. A brief history of antibody generation theories is presented, culminating in new findings about the immune-network theory and suggesting that a network of clones exists between anti-idiotypic antibodies and T cell receptors. Findings regarding the 2009 pandemic flu strain and immune responses to it are presented, including memory B cells and conserved regions within the hemagglutinin protein. The importance of CD4+ memory T cells and cytotoxic CD8+ T cells responding to both infections and vaccinations are discussed and compared. Innate immune cells, like natural killer (NK) cells and macrophages, are discussed regarding their roles in adaptive immune responses. Antigen presentation via macroautophagy processes is described. New vaccines in development are mentioned along with the results of some clinical trials. The manuscript concludes with how repeated vaccinations are impacting the immune system and a sketch of what might be behind the imprinting phenomenon, including future research directions.
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Affiliation(s)
- Jane Kasten-Jolly
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA;
| | - David A. Lawrence
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA;
- Departments of Biomedical Science and Environmental Health Science, University at Albany School of Public Health, Rensselaer, NY 12144, USA
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Wang W, Bhushan GL, Paz S, Stauft CB, Selvaraj P, Goguet E, Bishop-Lilly KA, Subramanian R, Vassell R, Lusvarghi S, Cong Y, Agan B, Richard SA, Epsi NJ, Fries A, Fung CK, Conte MA, Holbrook MR, Wang TT, Burgess TH, Mitre E, Pollett SD, Katzelnick LC, Weiss CD. Antigenic cartography using hamster sera identifies SARS-CoV-2 JN.1 evasion seen in human XBB.1.5 booster sera. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588359. [PMID: 38712124 PMCID: PMC11071293 DOI: 10.1101/2024.04.05.588359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Antigenic assessments of SARS-CoV-2 variants inform decisions to update COVID-19 vaccines. Primary infection sera are often used for assessments, but such sera are rare due to population immunity from SARS-CoV-2 infections and COVID-19 vaccinations. Here, we show that neutralization titers and breadth of matched human and hamster pre-Omicron variant primary infection sera correlate well and generate similar antigenic maps. The hamster antigenic map shows modest antigenic drift among XBB sub-lineage variants, with JN.1 and BA.4/BA.5 variants within the XBB cluster, but with five to six-fold antigenic differences between these variants and XBB.1.5. Compared to sera following only ancestral or bivalent COVID-19 vaccinations, or with post-vaccination infections, XBB.1.5 booster sera had the broadest neutralization against XBB sub-lineage variants, although a five-fold titer difference was still observed between JN.1 and XBB.1.5 variants. These findings suggest that antibody coverage of antigenically divergent JN.1 could be improved with a matched vaccine antigen.
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Affiliation(s)
- Wei Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Gitanjali L. Bhushan
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie Paz
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Charles B. Stauft
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Prabhu Selvaraj
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Emilie Goguet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
| | - Kimberly A. Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, Maryland, USA
| | - Rahul Subramanian
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Russell Vassell
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Sabrina Lusvarghi
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yu Cong
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Ft. Detrick, Frederick, Maryland, USA
| | - Brian Agan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Stephanie A. Richard
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Nusrat J. Epsi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Anthony Fries
- US Air Force School of Aerospace Medicine, Dayton, Ohio, USA
| | - Christian K. Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Matthew A. Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael R. Holbrook
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Ft. Detrick, Frederick, Maryland, USA
| | - Tony T. Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Timothy H. Burgess
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Simon D. Pollett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Leah C. Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carol D. Weiss
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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Roberts MG, Hickson RI, McCaw JM. How immune dynamics shape multi-season epidemics: a continuous-discrete model in one dimensional antigenic space. J Math Biol 2024; 88:48. [PMID: 38538962 PMCID: PMC10973021 DOI: 10.1007/s00285-024-02076-x] [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: 05/18/2023] [Revised: 02/25/2024] [Accepted: 03/05/2024] [Indexed: 04/01/2024]
Abstract
We extend a previously published model for the dynamics of a single strain of an influenza-like infection. The model incorporates a waning acquired immunity to infection and punctuated antigenic drift of the virus, employing a set of coupled integral equations within a season and a discrete map between seasons. The long term behaviour of the model is demonstrated by examples where immunity to infection depends on the time since a host was last infected, and where immunity depends on the number of times that a host has been infected. The first scenario leads to complicated dynamics in some regions of parameter space, and to regions of parameter space with more than one attractor. The second scenario leads to a stable fixed point, corresponding to an identical epidemic each season. We also examine the model with both paradigms in combination, almost always but not exclusively observing a stable fixed point or periodic solution. Adding stochastic perturbations to the between season map fails to destroy the model's qualitative dynamics. Our results suggest that if the level of host immunity depends on the elapsed time since the last infection then the epidemiological dynamics may be unpredictable.
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Affiliation(s)
- M G Roberts
- New Zealand Institute for Advanced Study and the Infectious Disease Research Centre, Massey University, Auckland, New Zealand.
| | - R I Hickson
- Health and Biosecurity, CSIRO, Townsville, QLD, 4814, Australia
- Australian Institute of Tropical Medicine and Hygiene, and College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4814, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - J M McCaw
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
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49
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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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50
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Rössler A, Knabl L, Netzl A, Bante D, Borena W, von Laer D, Smith DJ, Kimpel J. Durability of Cross-Neutralizing Antibodies 5.5 Months After Bivalent Coronavirus Disease 2019 Vaccine Booster. J Infect Dis 2024; 229:644-647. [PMID: 38016020 PMCID: PMC10938204 DOI: 10.1093/infdis/jiad472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
We analyzed neutralizing antibodies in samples from ancestral + BA.1 and ancestral + BA.4/5 boosted individuals, collected around 5.5 months after booster. Titers of neutralizing antibodies generally decreased compared to a time point early after the bivalent booster immunization. This was more pronounced for individuals without infection history and for recently emerged Omicron variants.
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Affiliation(s)
- Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Antonia Netzl
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, United Kingdom
| | - David Bante
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
| | - Wegene Borena
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
| | - Dorothee von Laer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
| | - Derek J Smith
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, United Kingdom
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
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