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Panwar P, Jhala D, Tamrakar A, Joshi C, Patel A. Bacterially expressed full length Hemagglutinin of Avian Influenza Virus H5N1 forms oligomers and exhibits hemagglutination. Protein Expr Purif 2024; 223:106541. [PMID: 38971212 DOI: 10.1016/j.pep.2024.106541] [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: 03/21/2024] [Revised: 06/11/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Avian influenza poses a significant global health threat, with the potential for widespread pandemics and devastating consequences. Hemagglutinin (HA), a critical surface glycoprotein of influenza viruses, plays a pivotal role in viral entry and serves as a primary target for subunit vaccine development. In this study, we successfully cloned, expressed, and purified hemagglutinin from the circulating strain of H5N1 influenza virus using a robust molecular biology approach. The cloning process involved insertion of the synthetic HA gene into the pET21b vector, confirmed through double digestion and sequencing. SDS-PAGE analysis confirmed the presence of the expected 60 kDa protein band post-induction. Following expression, the protein was subjected to purification via Ni-NTA affinity chromatography, yielding pure protein fractions. Native PAGE analysis confirmed the protein's oligomeric forms, essential for optimal antigenicity. Western blot analysis further validated protein identity using anti-His and anti-HA antibodies. MALDI-TOF analysis confirmed the protein's sequence integrity, while hemagglutination assay demonstrated its biological activity in binding to N-acetyl neuraminic acid. These findings underscore the potential of recombinant hemagglutinin as a valuable antigen for diagnosis and biochemical assays as well as for vaccine development against avian influenza. In conclusion, this study represents a critical guide for bacterial production of H5N1 HA, which can be a cost-effective and simpler strategy compared to mammalian protein expression. Further research into optimizing vaccine candidates and production methods will be essential in combating the ongoing threat of avian influenza pandemics.
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Affiliation(s)
- Priyanka Panwar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382010, India
| | - Dhwani Jhala
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382010, India
| | - Anubhav Tamrakar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382010, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382010, India.
| | - Amrutlal Patel
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382010, India.
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2
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Yang YR, Han J, Perrett HR, Richey ST, Rodriguez AJ, Jackson AM, Gillespie RA, O'Connell S, Raab JE, Cominsky LY, Chopde A, Kanekiyo M, Houser KV, Chen GL, McDermott AB, Andrews SF, Ward AB. Immune memory shapes human polyclonal antibody responses to H2N2 vaccination. Cell Rep 2024; 43:114171. [PMID: 38717904 PMCID: PMC11156625 DOI: 10.1016/j.celrep.2024.114171] [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: 08/24/2023] [Revised: 03/25/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase 1 clinical trial investigating a ferritin nanoparticle vaccine displaying H2 hemagglutinin (HA) in H2-naive and H2-exposed adults enabled us to perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited. We temporally map the epitopes targeted by serum antibodies after vaccine prime and boost, revealing that previous H2 exposure results in higher responses to the variable HA head domain. In contrast, initial responses in H2-naive participants are dominated by antibodies targeting conserved epitopes. We use cryoelectron microscopy and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the HA head, including the receptor-binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses post-vaccination.
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Affiliation(s)
- Yuhe R Yang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Chinese Academy of Sciences Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alesandra J Rodriguez
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah O'Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Julie E Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Lauren Y Cominsky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Ankita Chopde
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Katherine V Houser
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Grace L Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA.
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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3
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Li Y, Huo S, Yin Z, Tian Z, Huang F, Liu P, Liu Y, Yu F. Retracted and republished from: "The current state of research on influenza antiviral drug development: drugs in clinical trial and licensed drugs". mBio 2024; 15:e0017524. [PMID: 38551343 PMCID: PMC11077966 DOI: 10.1128/mbio.00175-24] [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] [Indexed: 05/09/2024] Open
Abstract
Influenza viruses (IVs) threaten global human health due to the high morbidity, infection, and mortality rates. Currently, the influenza drugs recommended by the Food and Drug Administration are oseltamivir, zanamivir, peramivir, and baloxavir marboxil. These recommended antivirals are currently effective for major subtypes of IVs as the compounds target conserved domains in neuraminidase or polymerase acidic (PA) protein. However, this trend may gradually change due to the selection of antiviral drugs and the natural evolution of IVs. Therefore, there is an urgent need to develop drugs related to the treatment of influenza to deal with the next pandemic. Here, we summarized the cutting-edge research in mechanism of action, inhibitory activity, and clinical efficacy of drugs that have been approved and drugs that are still in clinical trials for influenza treatment. We hope this review will provide up-to-date and comprehensive information on influenza antivirals and generate hypotheses for screens and development of new broad-spectrum influenza drugs in the near future.
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Affiliation(s)
- Yanbai Li
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shanshan Huo
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhe Yin
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zuguang Tian
- Department of High-Tech Development, Baoding City Science and Technology Bureau, Baoding, China
| | - Fang Huang
- Epidemic Prevention Laboratory, Tongzhou District Center For Animal Disease Control and Prevention, Beijing, China
| | - Peng Liu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yue Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Fei Yu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
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4
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Han AX, de Jong SPJ, Russell CA. Co-evolution of immunity and seasonal influenza viruses. Nat Rev Microbiol 2023; 21:805-817. [PMID: 37532870 DOI: 10.1038/s41579-023-00945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
Seasonal influenza viruses cause recurring global epidemics by continually evolving to escape host immunity. The viral constraints and host immune responses that limit and drive the evolution of these viruses are increasingly well understood. However, it remains unclear how most of these advances improve the capacity to reduce the impact of seasonal influenza viruses on human health. In this Review, we synthesize recent progress made in understanding the interplay between the evolution of immunity induced by previous infections or vaccination and the evolution of seasonal influenza viruses driven by the heterogeneous accumulation of antibody-mediated immunity in humans. We discuss the functional constraints that limit the evolution of the viruses, the within-host evolutionary processes that drive the emergence of new virus variants, as well as current and prospective options for influenza virus control, including the viral and immunological barriers that must be overcome to improve the effectiveness of vaccines and antiviral drugs.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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5
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Li Y, Huo S, Yin Z, Tian Z, Huang F, Liu P, Liu Y, Yu F. The current state of research on influenza antiviral drug development: drugs in clinical trial and licensed drugs. mBio 2023; 14:e0127323. [PMID: 37610204 PMCID: PMC10653855 DOI: 10.1128/mbio.01273-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Abstract
Influenza viruses (IVs) threaten global human health due to the high morbidity, infection, and mortality rates. Currently, the influenza drugs recommended by the FDA are oseltamivir, zanamivir, peramivir, and baloxavir marboxil. Notably, owing to the high variability of IVs, no drug exists that can effectively treat all types and subtypes of IVs. Moreover, the current trend of drug resistance is likely to continue as the viral genome is constantly mutating. Therefore, there is an urgent need to develop drugs related to the treatment of influenza to deal with the next pandemic. Here, we summarized the cutting-edge research in mechanism of action, inhibitory activity, and clinical efficacy of drugs that have been approved and drugs that are still in clinical trials for influenza treatment. We hope this review will provide up-to-date and comprehensive information on influenza antivirals and generate hypotheses for screens and development of new broad-spectrum influenza drugs in the near future.
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Affiliation(s)
- Yanbai Li
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shanshan Huo
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhe Yin
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zuguang Tian
- Baoding City Science and Technology Bureau, Baoding, China
| | - Fang Huang
- Tongzhou District Center For Animal Disease Control and Prevention, Beijing, China
| | - Peng Liu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yue Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Fei Yu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
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6
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Wilkins D, Langedijk AC, Lebbink RJ, Morehouse C, Abram ME, Ahani B, Aksyuk AA, Baraldi E, Brady T, Chen AT, Chi H, Choi EH, Cohen R, Danilenko DM, Gopalakrishnan V, Greenough A, Heikkinen T, Hosoya M, Keller C, Kelly EJ, Kragten-Tabatabaie L, Martinón-Torres F, de Los Santos AHM, Nunes MC, Palomino MA, Papenburg J, Pernica JM, Richmond P, Stein RT, Tuffy KM, Verwey C, Esser MT, Tabor DE, Bont LJ. Nirsevimab binding-site conservation in respiratory syncytial virus fusion glycoprotein worldwide between 1956 and 2021: an analysis of observational study sequencing data. THE LANCET. INFECTIOUS DISEASES 2023; 23:856-866. [PMID: 36940703 DOI: 10.1016/s1473-3099(23)00062-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 03/19/2023]
Abstract
BACKGROUND Nirsevimab is an extended half-life monoclonal antibody to the respiratory syncytial virus (RSV) fusion protein that has been developed to protect infants for an entire RSV season. Previous studies have shown that the nirsevimab binding site is highly conserved. However, investigations of the geotemporal evolution of potential escape variants in recent (ie, 2015-2021) RSV seasons have been minimal. Here, we examine prospective RSV surveillance data to assess the geotemporal prevalence of RSV A and B, and functionally characterise the effect of the nirsevimab binding-site substitutions identified between 2015 and 2021. METHODS We assessed the geotemporal prevalence of RSV A and B and nirsevimab binding-site conservation between 2015 and 2021 from three prospective RSV molecular surveillance studies (the US-based OUTSMART-RSV, the global INFORM-RSV, and a pilot study in South Africa). Nirsevimab binding-site substitutions were assessed in an RSV microneutralisation susceptibility assay. We contextualised our findings by assessing fusion-protein sequence diversity from 1956 to 2021 relative to other respiratory-virus envelope glycoproteins using RSV fusion protein sequences published in NCBI GenBank. FINDINGS We identified 5675 RSV A and RSV B fusion protein sequences (2875 RSV A and 2800 RSV B) from the three surveillance studies (2015-2021). Nearly all (25 [100%] of 25 positions of RSV A fusion proteins and 22 [88%] of 25 positions of RSV B fusion proteins) amino acids within the nirsevimab binding site remained highly conserved between 2015 and 2021. A highly prevalent (ie, >40·0% of all sequences) nirsevimab binding-site Ile206Met:Gln209Arg RSV B polymorphism arose between 2016 and 2021. Nirsevimab neutralised a diverse set of recombinant RSV viruses, including new variants containing binding-site substitutions. RSV B variants with reduced susceptibility to nirsevimab neutralisation were detected at low frequencies (ie, prevalence <1·0%) between 2015 and 2021. We used 3626 RSV fusion-protein sequences published in NCBI GenBank between 1956 and 2021 (2024 RSV and 1602 RSV B) to show that the RSV fusion protein had lower genetic diversity than influenza haemagglutinin and SARS-CoV-2 spike proteins. INTERPRETATION The nirsevimab binding site was highly conserved between 1956 and 2021. Nirsevimab escape variants were rare and have not increased over time. FUNDING AstraZeneca and Sanofi.
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Affiliation(s)
- Deidre Wilkins
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Annefleur C Langedijk
- Division of Paediatric Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, Netherlands
| | | | - Michael E Abram
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Bahar Ahani
- Bioinformatics, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Anastasia A Aksyuk
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Eugenio Baraldi
- Woman's and Child's Health, Neonatal Intensive Care Unit, University of Padova, Padova, Italy; Institute of Pediatric Research, Città della Speranza, Padova, Italy
| | - Tyler Brady
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Albert Tian Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - Hsin Chi
- Department of Paediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, South Korea
| | - Robert Cohen
- Université Paris XII, Créteil, FranceAssociation Clinique et Thérapeutique Infantile du Val-de-Marne (ACTIV), Créteil, France; Clinical Research Center, Centre Hospitalier Intercommunal de Créteil (CHIC), Créteil, France
| | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | | | - Anne Greenough
- Department of Women and Children's Health, King's College London, London, UK; ReSViNET foundation, Zeist, Netherlands
| | - Terho Heikkinen
- ReSViNET foundation, Zeist, Netherlands; Department of Pediatrics, University of Turku, Turku, Finland; Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Mitsuaki Hosoya
- School of Medicine, Fukushima Medical University, Fukushima, Japan
| | | | - Elizabeth J Kelly
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Federico Martinón-Torres
- ReSViNET foundation, Zeist, Netherlands; Translational Paediatrics and Infectious Diseases, Paediatrics Department, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, University of Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Translational Pediatrics and Infectious Diseases Section, Pediatrics Department, Hospital Clínico Universitario de Santiago, Galicia, Spain
| | | | - Marta C Nunes
- ReSViNET foundation, Zeist, Netherlands; South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Jesse Papenburg
- Department of Pediatrics, McGill University Health Centre, Montreal, QC, Canada
| | - Jeffrey M Pernica
- Division of Infectious Diseases, McMaster University, Hamilton, ON, Canada
| | - Peter Richmond
- Division of Pediatrics, School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Renato T Stein
- ReSViNET foundation, Zeist, Netherlands; Pontificia Universidade Catolica de Rio Grande do Sul, Porto Alegre, Brazil
| | - Kevin M Tuffy
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Charl Verwey
- Department of Paediatrics and Child Health, School of Clinical Medicine and South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mark T Esser
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA.
| | - David E Tabor
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Louis J Bont
- Department of Paediatrics, University Medical Centre Utrecht, Utrecht, Netherlands; ReSViNET foundation, Zeist, Netherlands
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7
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Ghafoori SM, Petersen GF, Conrady DG, Calhoun BM, Stigliano MZZ, Baydo RO, Grice R, Abendroth J, Lorimer DD, Edwards TE, Forwood JK. Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site. Sci Rep 2023; 13:6940. [PMID: 37117205 PMCID: PMC10140725 DOI: 10.1038/s41598-023-33529-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/14/2023] [Indexed: 04/30/2023] Open
Abstract
Influenza virus (IV) causes several outbreaks of the flu each year resulting in an economic burden to the healthcare system in the billions of dollars. Several influenza pandemics have occurred during the last century and estimated to have caused 100 million deaths. There are four genera of IV, A (IVA), B (IVB), C (IVC), and D (IVD), with IVA being the most virulent to the human population. Hemagglutinin (HA) is an IVA surface protein that allows the virus to attach to host cell receptors and enter the cell. Here we have characterised the high-resolution structures of seven IVA HAs, with one in complex with the anti-influenza head-binding antibody C05. Our analysis revealed conserved receptor binding residues in all structures, as seen in previously characterised IV HAs. Amino acid conservation is more prevalent on the stalk than the receptor binding domain (RBD; also called the head domain), allowing the virus to escape from antibodies targeting the RBD. The equivalent site of C05 antibody binding to A/Denver/57 HA appears hypervariable in the other H1N1 IV HAs. Modifications within this region appear to disrupt binding of the C05 antibody, as these HAs no longer bind the C05 antibody by analytical SEC. Our study brings new insights into the structural and functional recognition of IV HA proteins and can contribute to further development of anti-influenza vaccines.
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Affiliation(s)
- Seyed Mohammad Ghafoori
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Gayle F Petersen
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Deborah G Conrady
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Brandy M Calhoun
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Matthew Z Z Stigliano
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Ruth O Baydo
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Rena Grice
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Donald D Lorimer
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Thomas E Edwards
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia.
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8
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Lee CY, Raghunathan V, Caceres C, Geiger G, Seibert B, Cargnin Faccin F, Gay L, Ferreri L, Kaul D, Wrammert J, Tan G, Perez D, Lowen A. Epistasis reduces fitness costs of influenza A virus escape from stem-binding antibodies. Proc Natl Acad Sci U S A 2023; 120:e2208718120. [PMID: 37068231 PMCID: PMC10151473 DOI: 10.1073/pnas.2208718120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 02/15/2023] [Indexed: 04/19/2023] Open
Abstract
The hemagglutinin (HA) stem region is a major target of universal influenza vaccine efforts owing to the presence of highly conserved epitopes across multiple influenza A virus (IAV) strains and subtypes. To explore the potential impact of vaccine-induced immunity targeting the HA stem, we examined the fitness effects of viral escape from stem-binding broadly neutralizing antibodies (stem-bnAbs). Recombinant viruses containing each individual antibody escape substitution showed diminished replication compared to wild-type virus, indicating that stem-bnAb escape incurred fitness costs. A second-site mutation in the HA head domain (N129D; H1 numbering) reduced the fitness effects observed in primary cell cultures and likely enabled the selection of escape mutations. Functionally, this putative permissive mutation increased HA avidity for its receptor. These results suggest a mechanism of epistasis in IAV, wherein modulating the efficiency of attachment eases evolutionary constraints imposed by the requirement for membrane fusion. Taken together, the data indicate that viral escape from stem-bnAbs is costly but highlights the potential for epistatic interactions to enable evolution within the functionally constrained HA stem domain.
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Affiliation(s)
- Chung-Young Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, The Republic of Korea
| | - Vedhika Raghunathan
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - C. Joaquin Caceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Flavio Cargnin Faccin
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - L. Claire Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Lucas M. Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Jens Wrammert
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
| | - Gene S. Tan
- J. Craig Venter Institute, La Jolla, CA 92037
- Division of Infectious Disease, Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
- Emory-University of Georgia Center of Excellence for Influenza Research and Surveillance, Atlanta, GA 30322
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9
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Chu JT, Gu H, Sun W, Fan RL, Nicholls JM, Valkenburg SA, Poon LL. Heterosubtypic immune pressure accelerates emergence of influenza A virus escape phenotypes in mice. Virus Res 2023; 323:198991. [PMID: 36302472 PMCID: PMC10194115 DOI: 10.1016/j.virusres.2022.198991] [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: 09/29/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2022]
Abstract
Rapid antigenic evolution of the influenza A virus surface antigen hemagglutinin undermines protection conferred by seasonal vaccines. Protective correlates targeted by universal vaccines such as cytotoxic T cells or HA stem directed broadly neutralizing antibodies have been shown to select for immune escape mutants during infection. We developed an in vivo serial passage mouse model for viral adaptation and used next generation sequencing to evaluate full genome viral evolution in the context of broadly protective immunity. Heterosubtypic immune pressure increased the incidence of genome-wide single nucleotide variants, though mutations found in early adapted populations were predominantly stochastic in nature. Prolonged adaptation under heterosubtypic immune selection resulted in the manifestation of highly virulent phenotypes that ablated vaccine mediated protection from mortality. High frequency mutations unique to escape phenotypes were identified within the polymerase encoding segments. These findings suggest that a suboptimial usage of population-wide universal influenza vaccine may drive formation of escape variants attributed to polygenic changes.
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Affiliation(s)
- Julie Ts Chu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wanying Sun
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Rebecca Ly Fan
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - John M Nicholls
- Department of Pathology, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sophie A Valkenburg
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Leo Lm Poon
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong Special Administrative Region, China.
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10
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Christensen SR, Martin ET, Petrie JG, Monto AS, Hensley SE. The 2009 Pandemic H1N1 Hemagglutinin Stalk Remained Antigenically Stable after Circulating in Humans for a Decade. J Virol 2022; 96:e0220021. [PMID: 35588275 PMCID: PMC9175623 DOI: 10.1128/jvi.02200-21] [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: 12/24/2021] [Accepted: 04/21/2022] [Indexed: 11/20/2022] Open
Abstract
An H1N1 influenza virus caused a pandemic in 2009, and descendants of this virus continue to circulate seasonally in humans. Upon infection with the 2009 H1N1 pandemic strain (pH1N1), many humans produced antibodies against epitopes in the hemagglutinin (HA) stalk. HA stalk-focused antibody responses were common among pH1N1-infected individuals because HA stalk epitopes were conserved between the pH1N1 strain and previously circulating H1N1 strains. Here, we completed a series of experiments to determine if the pH1N1 HA stalk has acquired substitutions since 2009 that prevent the binding of human antibodies. We identified several amino acid substitutions that accrued in the pH1N1 HA stalk from 2009 to 2019. We completed enzyme-linked immunosorbent assays, absorption-based binding assays, and surface plasmon resonance experiments to determine if these substitutions affect antibody binding. Using sera collected from 230 humans (aged 21 to 80 years), we found that pH1N1 HA stalk substitutions that have emerged since 2009 do not affect antibody binding. Our data suggest that the HA stalk domain of pH1N1 viruses remained antigenically stable after circulating in humans for a decade. IMPORTANCE In 2009, a new pandemic H1N1 (pH1N1) virus began circulating in humans. Many individuals mounted hemagglutinin (HA) stalk-focused antibody responses upon infection with the 2009 pH1N1 strain, since the HA stalk of this virus was relatively conserved with other seasonal H1N1 strains. Here, we completed a series of studies to determine if the 2009 pH1N1 strain has undergone antigenic drift in the HA stalk domain over the past decade. We found that serum antibodies from 230 humans could not antigenically distinguish the 2009 and 2019 HA stalk. These data suggest that the HA stalk of pH1N1 has remained antigenically stable, despite the presence of high levels of HA stalk antibodies within the human population.
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Affiliation(s)
- Shannon R. Christensen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emily T. Martin
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Joshua G. Petrie
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Arnold S. Monto
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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11
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Decker CH, Rapier-Sharman N, Pickett BE. Mutation in Hemagglutinin Antigenic Sites in Influenza A pH1N1 Viruses from 2015-2019 in the United States Mountain West, Europe, and the Northern Hemisphere. Genes (Basel) 2022; 13:909. [PMID: 35627294 PMCID: PMC9141826 DOI: 10.3390/genes13050909] [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: 04/02/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
H1N1 influenza A virus is a respiratory pathogen that undergoes antigenic shift and antigenic drift to improve viral fitness. Tracking the evolutionary trends of H1N1 aids with the current detection and the future response to new viral strains as they emerge. Here, we characterize antigenic drift events observed in the hemagglutinin (HA) sequence of the pandemic H1N1 lineage from 2015-2019. We observed the substitutions S200P, K147N, and P154S, together with other mutations in structural, functional, and/or epitope regions in 2015-2019 HA protein sequences from the Mountain West region of the United States, the larger United States, Europe, and other Northern Hemisphere countries. We reconstructed multiple phylogenetic trees to track the relationships and spread of these mutations and tested for evidence of selection pressure on HA. We found that the prevalence of amino acid substitutions at positions 147, 154, 159, 200, and 233 significantly changed throughout the studied geographical regions between 2015 and 2019. We also found evidence of coevolution among a subset of these amino acid substitutions. The results from this study could be relevant for future epidemiological tracking and vaccine prediction efforts. Similar analyses in the future could identify additional sequence changes that could affect the pathogenicity and/or infectivity of this virus in its human host.
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Affiliation(s)
| | | | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA; (C.H.D.); (N.R.-S.)
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12
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Kirkpatrick Roubidoux E, Sano K, McMahon M, Carreño JM, Capuano C, Jiang K, Simon V, van Bakel H, Wilson P, Krammer F. Novel Epitopes of the Influenza Virus N1 Neuraminidase Targeted by Human Monoclonal Antibodies. J Virol 2022; 96:e0033222. [PMID: 35446141 PMCID: PMC9093090 DOI: 10.1128/jvi.00332-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/16/2022] [Indexed: 12/30/2022] Open
Abstract
Influenza virus neuraminidase (NA)-targeting antibodies are an independent correlate of protection against influenza. Antibodies against the NA act by blocking enzymatic activity, preventing virus release and transmission. As we advance the development of improved influenza virus vaccines that incorporate standard amounts of NA antigen, it is important to identify the antigenic targets of human monoclonal antibodies (mAbs). Here, we describe escape mutants generated by serial passage of A/Netherlands/602/2009 (H1N1)pdm09 in the presence of human anti-N1 mAbs. We observed escape mutations on the head domain of the N1 protein around the enzymatic site (S364N, N369T, and R430Q) and also detected escape mutations located on the sides and bottom of the NA (N88D, N270D, and Q313K/R). This work increases our understanding of how human antibody responses target the N1 protein. IMPORTANCE As improved influenza virus vaccines are being developed, the influenza virus neuraminidase (NA) is becoming an important new target for immune responses. By identifying novel epitopes of anti-NA antibodies, we can improve vaccine design. Additionally, characterizing escape mutations in these epitopes aids in identifying NA antigenic drift in circulating viruses.
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Affiliation(s)
- Ericka Kirkpatrick Roubidoux
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kaori Sano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christina Capuano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kaijun Jiang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patrick Wilson
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, Illinois, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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13
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Hernandez-Mejia G, Hernandez-Vargas EA. Uncovering antibody cross-reaction dynamics in influenza A infections. Bioinformatics 2021; 37:229-235. [PMID: 32730562 DOI: 10.1093/bioinformatics/btaa691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/03/2020] [Accepted: 07/23/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Influenza viruses are a cause of large outbreaks and pandemics with high death tolls. A key obstacle is that flu vaccines have inconsistent performance, in the best cases up to 60% effectiveness, but it can be as low as 10%. Uncovering the hidden pathways of how antibodies (Abs) induced by one influenza strain are effective against another, cross-reaction, is a central vexation for the design of universal flu vaccines. RESULTS We conceive a stochastic model that successfully represents the antibody cross-reactive data from mice infected with H3N2 influenza strains and further validation with cross-reaction data of H1N1 strains. Using a High-Performance Computing cluster, several aspects and parameters in the model were tested. Computational simulations highlight that changes in time of infection and the B-cells population are relevant, however, the affinity threshold of B-cells between consecutive infections is a necessary condition for the successful Abs cross-reaction. Our results suggest a 3-D reformulation of the current influenza antibody landscape for the representation and modeling of cross-reactive data. AVAILABILITY AND IMPLEMENTATION The full code as a testing/simulation platform is freely available here: https://github.com/systemsmedicine/Antibody_cross-reaction_dynamics. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gustavo Hernandez-Mejia
- Frankfurt Institute for Advanced Studies, 60438 Frankfurt am Main, Germany.,Faculty of Biological Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Esteban A Hernandez-Vargas
- Frankfurt Institute for Advanced Studies, 60438 Frankfurt am Main, Germany.,Instituto de Matemáticas, Universidad Nacional Autonoma de Mexico, Blv. Juriquilla 3001, 76230 Juriquilla, Querétaro, México
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14
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Dhar N, Kwatra G, Nunes MC, Cutland C, Izu A, Nachbagauer R, Krammer F, Madhi SA. Hemagglutinin Stalk Antibody Responses Following Trivalent Inactivated Influenza Vaccine Immunization of Pregnant Women and Association With Protection From Influenza Virus Illness. Clin Infect Dis 2021; 71:1072-1079. [PMID: 31565750 PMCID: PMC7428398 DOI: 10.1093/cid/ciz927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 09/17/2019] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The conserved, immuno-subdominant influenza virus hemagglutinin (HA) stalk region is a potential universal group-specific influenza virus vaccine epitope. We analyzed antibody responses to H1 hemagglutinin stalk domain (H1/stalk) following trivalent influenza inactivated vaccine (IIV3) immunization in pregnant women, and association with protection against influenza virus illness. METHODS One hundred forty-five human immunodeficiency virus (HIV)-uninfected pregnant women (68 IIV3 and 77 placebo recipients) and 140 pregnant women with HIV infection (72 IIV3 and 68 placebo recipients) were independently randomized in placebo-controlled efficacy trials of IIV3. Plasma samples were tested for H1/stalk immunoglobulin G (IgG) and hemagglutination inhibition (HAI) antibodies prevaccination and 1 month postvaccination. Women had weekly surveillance for influenza illness, confirmed by polymerase chain reaction. RESULTS Increases in H1/stalk IgG (and HAI) antibody levels were elicited post-IIV3, with responses being higher in HIV-uninfected women than in women living with HIV. Among HIV-uninfected vaccinees, there was no correlation (postvaccination) between H1/stalk and HAI antibody responses, whereas a strong correlation was observed in vaccinees with HIV. The H1/stalk IgG concentration was lower among women developing A/H1N1 illness (85.3 arbitrary units [AU]/mL) than those without A/H1N1 illness (219.6 AU/mL; P = .001). H1/stalk IgG concentration ≥215 AU/mL was associated with 90% lower odds (odds ratio, 0.09; P = .005) of A/H1N1 illness. Also, H1/stalk IgG was significantly lower among women with influenza B illness (93.9 AU/mL) than among their counterparts (215.5 AU/mL) (P = .04); however, no association was observed after adjusting for HAI titers. CONCLUSIONS H1/stalk IgG concentration was associated with lower odds for A/H1N1 influenza virus illness, indicating its potential as an epitope for a universal vaccine against group 1 influenza virus.
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Affiliation(s)
- Nisha Dhar
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clare Cutland
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alane Izu
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Shabir A Madhi
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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15
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Hernandez-Mejia G, Hernandez-Vargas EA. Uncovering antibody cross-reaction dynamics in influenza A infections. BIOINFORMATICS (OXFORD, ENGLAND) 2021; 37:229-235. [PMID: 32730562 DOI: 10.1101/2020.01.06.896274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/03/2020] [Accepted: 07/23/2020] [Indexed: 05/27/2023]
Abstract
MOTIVATION Influenza viruses are a cause of large outbreaks and pandemics with high death tolls. A key obstacle is that flu vaccines have inconsistent performance, in the best cases up to 60% effectiveness, but it can be as low as 10%. Uncovering the hidden pathways of how antibodies (Abs) induced by one influenza strain are effective against another, cross-reaction, is a central vexation for the design of universal flu vaccines. RESULTS We conceive a stochastic model that successfully represents the antibody cross-reactive data from mice infected with H3N2 influenza strains and further validation with cross-reaction data of H1N1 strains. Using a High-Performance Computing cluster, several aspects and parameters in the model were tested. Computational simulations highlight that changes in time of infection and the B-cells population are relevant, however, the affinity threshold of B-cells between consecutive infections is a necessary condition for the successful Abs cross-reaction. Our results suggest a 3-D reformulation of the current influenza antibody landscape for the representation and modeling of cross-reactive data. AVAILABILITY AND IMPLEMENTATION The full code as a testing/simulation platform is freely available here: https://github.com/systemsmedicine/Antibody_cross-reaction_dynamics. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gustavo Hernandez-Mejia
- Frankfurt Institute for Advanced Studies, 60438 Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Esteban A Hernandez-Vargas
- Frankfurt Institute for Advanced Studies, 60438 Frankfurt am Main, Germany
- Instituto de Matemáticas, Universidad Nacional Autonoma de Mexico, Blv. Juriquilla 3001, 76230 Juriquilla, Querétaro, México
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16
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Zhou L, Feng Z, Liu J, Chen Y, Yang L, Liu S, Li X, Gao R, Zhu W, Wang D, Shu Y. A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. Emerg Microbes Infect 2021; 9:1853-1863. [PMID: 32746754 PMCID: PMC7473139 DOI: 10.1080/22221751.2020.1806005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Influenza B virus (IBV) is one of the most important human respiratory viruses: it causes approximately one-third of the global influenza-related disease burden each year. However, compared with the several pathogenicity-related molecular markers that have been identified for influenza A virus (IAV), little is known about potential IBV pathogenicity-related markers. Here, although the IBV strain B/Anhui-Tunxi/1528/2014 (AH1528/14) exhibited a more efficient replication ability in vitro and higher pathogenicity in vivo compared with IBV strain B/Anhui-Baohe/127/2015 (AH127/15), only three amino acids differences (HAA390E, NAN342D and PB1V212I) were observed among their full genomes. The contributions of each amino acid difference to the virus pathogenicity were further investigated. Compared with the wild type IBV virus rAH127, the recombinant virus harbouring a single substitution of HAA390E had a similar phenotype, whereas the recombinant virus harbouring PB1V212I replicated to a moderately higher titre in both MDCK cells and in mice. Notably, the virus harbouring NAN342D showed significantly better growth properties in MDCK cells and higher fatality rates in mice. In addition, the presence of NAN342D dramatically enhanced the viral neuraminidase activity. In conclusion, our study identified a novel IBV molecular marker, NAN342D, that could significantly increase the virulence of IBV in mice.
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Affiliation(s)
- Lijuan Zhou
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People's Republic of China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zhaomin Feng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jia Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yongkun Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People's Republic of China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Suli Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People's Republic of China
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Rongbao Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People's Republic of China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
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17
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Mutations in the Hemagglutinin Stalk Domain Do Not Permit Escape from a Protective, Stalk-Based Vaccine-Induced Immune Response in the Mouse Model. mBio 2021; 12:mBio.03617-20. [PMID: 33593972 PMCID: PMC8545130 DOI: 10.1128/mbio.03617-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Current seasonal influenza virus vaccines target regions of the hemagglutinin (HA) head domain that undergo constant antigenic change, forcing the painstaking annual reformulation of vaccines. The development of broadly protective or universal influenza virus vaccines that induce cross-reactive, protective immune responses could circumvent the need to reformulate current seasonal vaccines. Many of these vaccine candidates target the HA stalk domain, which displays epitopes conserved within and across influenza virus subtypes, including those with pandemic potential. While HA head-mediated antigenic drift is well understood, the potential for antigenic drift in the stalk domain is understudied. Using a panel of HA stalk-specific monoclonal antibodies (MAbs), we applied selection pressure to the stalk domain of A/Netherlands/602/2009 (pdmH1N1) to determine fitness and phenotypes of escape mutant viruses (EMVs). We found that HA stalk MAbs with lower cross-reactivity caused single HA stalk escape mutations, whereas MAbs with broader cross-reactivity forced multiple mutations in the HA. Each escape mutant virus greatly decreased mAb neutralizing activity, but escape mutations did not always ablate MAb binding or Fc-Fc receptor-based effector functions. Escape mutant viruses were not attenuated in vitro but showed attenuation in an in vivo mouse model. Importantly, mice vaccinated with a chimeric HA universal vaccine candidate were protected from lethal challenge with EMVs despite these challenge viruses containing escape mutations in the stalk domain. Our study indicates that while the HA stalk domain can mutate under strong MAb selection pressure, mutant viruses may have attenuated phenotypes and do not evade a polyclonal, stalk-based vaccine-induced response.
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18
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Han J, Schmitz AJ, Richey ST, Dai YN, Turner HL, Mohammed BM, Fremont DH, Ellebedy AH, Ward AB. Polyclonal epitope mapping reveals temporal dynamics and diversity of human antibody responses to H5N1 vaccination. Cell Rep 2021; 34:108682. [PMID: 33503432 PMCID: PMC7888560 DOI: 10.1016/j.celrep.2020.108682] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/03/2020] [Accepted: 12/30/2020] [Indexed: 11/03/2022] Open
Abstract
Novel influenza A virus (IAV) strains elicit recall immune responses to conserved epitopes, making them favorable antigenic choices for universal influenza virus vaccines. Evaluating these immunogens requires a thorough understanding of the antigenic sites targeted by the polyclonal antibody (pAb) response, which single-particle electron microscopy (EM) can sensitively detect. In this study, we employ EM polyclonal epitope mapping (EMPEM) to extensively characterize the pAb response to hemagglutinin (HA) after H5N1 immunization in humans. Cross-reactive pAbs originating from memory B cells immediately bound the stem of HA and persisted for more than a year after vaccination. In contrast, de novo pAb responses to multiple sites on the head of HA, targeting previously determined key neutralizing sites on H5 HA, expanded after the second immunization and waned quickly. Thus, EMPEM provides a robust tool for comprehensively tracking the specificity and durability of immune responses elicited by novel universal influenza vaccine candidates.
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Affiliation(s)
- Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aaron J Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ya-Nan Dai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bassem M Mohammed
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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19
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Han A, Czajkowski L, Rosas LA, Cervantes-Medina A, Xiao Y, Gouzoulis M, Lumbard K, Hunsberger S, Reed S, Athota R, Baus HA, Lwin A, Sadoff J, Taubenberger JK, Memoli MJ. Safety and Efficacy of CR6261 in an Influenza A H1N1 Healthy Human Challenge Model. Clin Infect Dis 2020; 73:e4260-e4268. [PMID: 33211860 DOI: 10.1093/cid/ciaa1725] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/11/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND It is imperative to identify new targets for improved vaccines and therapeutics against influenza and one such target is the relatively conserved stalk region of the influenza A hemagglutinin (HA) surface protein. METHODS We conducted a randomized, double-blind, Phase II placebo-controlled trial of a monoclonal antibody that targets the HA stalk (CR6261) in a H1N1pdm09 healthy volunteer human challenge model. A single 50mg/kg dose of CR6261 was infused 24 hours after challenge and the primary efficacy outcome was area under the curve of viral RNA detection over time. RESULTS Ninety-one healthy volunteers were randomized and underwent influenza challenge; 49 received CR6261 and 42 placebo. CR6261 had no statistically significant effect on AUC (AUC 48.56 log (copies/mL) x days, IQR 202 vs. AUC 25.53 log (copies/mL) x days, IQR 155), P=0.315), and no clinically significant effect on influenza disease measures including number of symptoms, duration of symptoms, or FLU-PRO scores. Preexisting anti-NA antibody titers were most predictive of reduced influenza disease. CR6261 reached a mean peak serum concentration of 1x10 6 ng/ml 15 minutes after infusion, and a mean peak of 5.97x10 2 ng/ml in the nasal mucosa 2-3 days after infusion. CONCLUSIONS The results of this study suggest that a monoclonal anti-stalk approach to prevent or treat influenza infection may be limited in efficacy. Future approaches should consider including and evaluating anti-stalk antibodies as part of a multi-faceted strategy rather than as a standalone therapeutic.
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Affiliation(s)
- Alison Han
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lindsay Czajkowski
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luz Angela Rosas
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adriana Cervantes-Medina
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yongli Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Monica Gouzoulis
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Keith Lumbard
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sally Hunsberger
- Biostatistics Research Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Susan Reed
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rani Athota
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Holly Ann Baus
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy Lwin
- Janssen Infectious Diseases and Vaccines, Leiden, Netherlands
| | - Jerald Sadoff
- Janssen Infectious Diseases and Vaccines, Leiden, Netherlands
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matthew J Memoli
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Characterization of Novel Cross-Reactive Influenza B Virus Hemagglutinin Head Specific Antibodies That Lack Hemagglutination Inhibition Activity. J Virol 2020; 94:JVI.01185-20. [PMID: 32907980 DOI: 10.1128/jvi.01185-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022] Open
Abstract
Humoral immune responses to influenza virus vaccines in elderly individuals are poorly adapted toward new antigenically drifted influenza virus strains. Instead, older individuals respond in an original antigenic sin fashion and produce much more cross-reactive but less potent antibodies. Here, we investigated four influenza B virus hemagglutinin (HA) head specific, hemagglutination inhibition-inactive monoclonal antibodies (MAbs) from elderly individuals. We found that they were broadly reactive within the B/Victoria/2/1987-like lineage, and two were highly cross-reactive with B/Yamagata/16/1988-like lineage viruses. The MAbs were found to be neutralizing, to utilize Fc effector functions, and to be protective against lethal viral challenge in a mouse model. In order to identify residues on the influenza B virus hemagglutinin interacting with the MAbs, we generated escape mutant viruses. Interestingly, escape from these MAbs led to numerous HA mutations within the head domain, including in the defined antigenic sites. We observed that each individual escape mutant virus was able to avoid neutralization by its respective MAb along with other MAbs in the panel, although in many cases binding activity was maintained. Point mutant viruses indicated that K90 is critical for the neutralization of two MAbs, while escape from the other two MAbs required a combination of mutations in the hemagglutinin. Three of four escape mutant viruses had increased lethality in the DBA2/J mouse model. Our work indicates that these cross-reactive antibodies have the potential to cause antigenic drift in the viral population by driving mutations that increase virus fitness. However, binding activity and cross-neutralization were maintained by a majority of antibodies in the panel, suggesting that this drift may not lead to escape from antibody-mediated protection.IMPORTANCE Understanding the immune response that older individuals mount to influenza virus vaccination and infection is critical in order to design better vaccines for this age group. Here, we show that older individuals make broadly neutralizing antibodies that have no hemagglutination-inhibiting activity and are less potent than strain-specific antibodies. These antibodies could drive viral escape from neutralization but did not result in escape from binding. Given their different mechanisms of action, they might retain protective activity even against escape variants.
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21
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Viboud C, Gostic K, Nelson MI, Price GE, Perofsky A, Sun K, Sequeira Trovão N, Cowling BJ, Epstein SL, Spiro DJ. Beyond clinical trials: Evolutionary and epidemiological considerations for development of a universal influenza vaccine. PLoS Pathog 2020; 16:e1008583. [PMID: 32970783 PMCID: PMC7514029 DOI: 10.1371/journal.ppat.1008583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The prospect of universal influenza vaccines is generating much interest and research at the intersection of immunology, epidemiology, and viral evolution. While the current focus is on developing a vaccine that elicits a broadly cross-reactive immune response in clinical trials, there are important downstream questions about global deployment of a universal influenza vaccine that should be explored to minimize unintended consequences and maximize benefits. Here, we review and synthesize the questions most relevant to predicting the population benefits of universal influenza vaccines and discuss how existing information could be mined to begin to address these questions. We review three research topics where computational modeling could bring valuable evidence: immune imprinting, viral evolution, and transmission. We address the positive and negative consequences of imprinting, in which early childhood exposure to influenza shapes and limits immune responses to future infections via memory of conserved influenza antigens. However, the mechanisms at play, their effectiveness, breadth of protection, and the ability to "reprogram" already imprinted individuals, remains heavily debated. We describe instances of rapid influenza evolution that illustrate the plasticity of the influenza virus in the face of drug pressure and discuss how novel vaccines could introduce new selective pressures on the evolution of the virus. We examine the possible unintended consequences of broadly protective (but infection-permissive) vaccines on the dynamics of epidemic and pandemic influenza, compared to conventional vaccines that have been shown to provide herd immunity benefits. In conclusion, computational modeling offers a valuable tool to anticipate the benefits of ambitious universal influenza vaccine programs, while balancing the risks from endemic influenza strains and unpredictable pandemic viruses. Moving forward, it will be important to mine the vast amount of data generated in clinical studies of universal influenza vaccines to ensure that the benefits and consequences of these vaccine programs have been carefully modeled and explored.
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Affiliation(s)
- Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States
- * E-mail:
| | - Katelyn Gostic
- Dept. of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States
- Dept. of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States
| | - Graeme E. Price
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Amanda Perofsky
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States
| | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States
| | - Nídia Sequeira Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States
| | - Benjamin J. Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Suzanne L. Epstein
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States
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22
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Jang YH, Seong BL. Call for a paradigm shift in the design of universal influenza vaccines by harnessing multiple correlates of protection. Expert Opin Drug Discov 2020; 15:1441-1455. [PMID: 32783765 DOI: 10.1080/17460441.2020.1801629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The genetic variability and diversity of influenza viruses, and the expansion of their hosts, present a significant threat to human health. The development of a universal influenza vaccine is urgently needed to tackle seasonal epidemics, pandemics, vaccine mismatch, and zoonotic transmissions to humans. AREAS COVERED Despite the identification of broadly neutralizing antibodies against influenza viruses, designing a universal influenza vaccine that induces such broadly neutralizing antibodies at protective levels in humans has remained challenging. Besides neutralizing antibodies, multiple correlates of protection have recently emerged as crucially important for eliciting broad protection against diverse influenza viruses. This review discusses the immune responses required for broad protection against influenza viruses, and suggests a paradigm shift from an HA stalk-based approach to other approaches that can induce multiple immunological correlates of protection for the development of a universal influenza vaccine. EXPERT OPINION To develop a truly universal influenza vaccine, multiple correlates of protection should be considered, including antibody responses and T cell immunity. Balanced induction of neutralizing antibodies, antibody effector functions, and T cell immunity will contribute to the most effective vaccination strategy. Live-attenuated influenza vaccines provide an attractive platform to improve the breadth and potency of vaccines for broader protection.
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Affiliation(s)
- Yo Han Jang
- Department of Biological Sciences and Biotechnology Major in Bio-Vaccine Engineering, Andong National University , Andong, South Korea
| | - Baik L Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University , Seoul, South Korea.,Vaccine Innovation Technology Alliance (VITAL)-Korea, Yonsei University , Seoul, South Korea
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Li Y, Wang L, Si H, Yu Z, Tian S, Xiang R, Deng X, Liang R, Jiang S, Yu F. Influenza virus glycoprotein-reactive human monoclonal antibodies. Microbes Infect 2020; 22:263-271. [PMID: 32569735 PMCID: PMC7303604 DOI: 10.1016/j.micinf.2020.06.003] [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: 05/01/2020] [Accepted: 06/08/2020] [Indexed: 11/05/2022]
Abstract
Influenza continues to be a significant public health challenge. Two glycoproteins on the surface of influenza virus, hemagglutinin and neuraminidase, play a prominent role in the process of influenza virus infection and release. Monoclonal antibodies targeting glycoproteins can effectively prevent the spread of the virus. In this review, we summarized currently reported human monoclonal antibodies targeting glycoproteins of influenza A and B viruses.
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Affiliation(s)
- Yanbai Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Helong Si
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhengsen Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shijun Tian
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Rong Xiang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Fei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China.
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24
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Park JK, Xiao Y, Ramuta MD, Rosas LA, Fong S, Matthews AM, Freeman AD, Gouzoulis MA, Batchenkova NA, Yang X, Scherler K, Qi L, Reed S, Athota R, Czajkowski L, Han A, Morens DM, Walters KA, Memoli MJ, Kash JC, Taubenberger JK. Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Nat Med 2020; 26:1240-1246. [PMID: 32601336 DOI: 10.1038/s41591-020-0937-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 05/08/2020] [Indexed: 01/07/2023]
Abstract
The conserved region of influenza hemagglutinin (HA) stalk (or stem) has gained attention as a potent target for universal influenza vaccines1-5. Although the HA stalk region is relatively well conserved, the evolutionarily dynamic nature of influenza viruses6 raises concerns about the possible emergence of viruses carrying stalk escape mutation(s) under sufficient immune pressure. Here we show that immune pressure on the HA stalk can lead to expansion of escape mutant viruses in study participants challenged with a 2009 H1N1 pandemic influenza virus inoculum containing an A388V polymorphism in the HA stalk (45% wild type and 55% mutant). High level of stalk antibody titers was associated with the selection of the mutant virus both in humans and in vitro. Although the mutant virus showed slightly decreased replication in mice, it was not observed in cell culture, ferrets or human challenge participants. The A388V mutation conferred resistance to some of the potent HA stalk broadly neutralizing monoclonal antibodies (bNAbs). Co-culture of wild-type and mutant viruses in the presence of either a bNAb or human serum resulted in rapid expansion of the mutant. These data shed light on a potential obstacle for the success of HA-stalk-targeting universal influenza vaccines-viral escape from vaccine-induced stalk immunity.
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Affiliation(s)
- Jae-Keun Park
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yongli Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell D Ramuta
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Luz Angela Rosas
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sharon Fong
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alexis M Matthews
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ashley D Freeman
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Monica A Gouzoulis
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Natalia A Batchenkova
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xingdong Yang
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Li Qi
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Susan Reed
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rani Athota
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lindsay Czajkowski
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alison Han
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David M Morens
- Office of the Director, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Matthew J Memoli
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John C Kash
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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25
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Wu NC, Thompson AJ, Lee JM, Su W, Arlian BM, Xie J, Lerner RA, Yen HL, Bloom JD, Wilson IA. Different genetic barriers for resistance to HA stem antibodies in influenza H3 and H1 viruses. Science 2020; 368:1335-1340. [PMID: 32554590 PMCID: PMC7412937 DOI: 10.1126/science.aaz5143] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
The discovery and characterization of broadly neutralizing human antibodies (bnAbs) to the highly conserved stem region of influenza hemagglutinin (HA) have contributed to considerations of a universal influenza vaccine. However, the potential for resistance to stem bnAbs also needs to be more thoroughly evaluated. Using deep mutational scanning, with a focus on epitope residues, we found that the genetic barrier to resistance to stem bnAbs is low for the H3 subtype but substantially higher for the H1 subtype owing to structural differences in the HA stem. Several strong resistance mutations in H3 can be observed in naturally circulating strains and do not reduce in vitro viral fitness and in vivo pathogenicity. This study highlights a potential challenge for development of a truly universal influenza vaccine.
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Affiliation(s)
- Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew J Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Juhye M Lee
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Wen Su
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Britni M Arlian
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jia Xie
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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26
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Anderson CS, Sangster MY, Yang H, Mariani TJ, Chaudhury S, Topham DJ. Implementing sequence-based antigenic distance calculation into immunological shape space model. BMC Bioinformatics 2020; 21:256. [PMID: 32560624 PMCID: PMC7303933 DOI: 10.1186/s12859-020-03594-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In 2009, a novel influenza vaccine was distributed worldwide to combat the H1N1 influenza "swine flu" pandemic. However, antibodies induced by the vaccine display differences in their specificity and cross-reactivity dependent on pre-existing immunity. Here, we present a computational model that can capture the effect of pre-existing immunity on influenza vaccine responses. The model predicts the region of the virus hemagglutinin (HA) protein targeted by antibodies after vaccination as well as the level of cross-reactivity induced by the vaccine. We tested our model by simulating a scenario similar to the 2009 pandemic vaccine and compared the results to antibody binding data obtained from human subjects vaccinated with the monovalent 2009 H1N1 influenza vaccine. RESULTS We found that both specificity and cross-reactivity of the antibodies induced by the 2009 H1N1 influenza HA protein were affected by the viral strain the individual was originally exposed. Specifically, the level of antigenic relatedness between the original exposure HA antigen and the 2009 HA protein affected antigenic-site immunodominance. Moreover, antibody cross-reactivity was increased when the individual's pre-existing immunity was specific to an HA protein antigenically distinct from the 2009 pandemic strain. Comparison of simulation data with antibody binding data from human serum samples demonstrated qualitative and quantitative similarities between the model and real-life immune responses to the 2009 vaccine. CONCLUSION We provide a novel method to evaluate expected outcomes in antibody specificity and cross-reactivity after influenza vaccination in individuals with different influenza HA antigen exposure histories. The model produced similar outcomes as what has been previously reported in humans after receiving the 2009 influenza pandemic vaccine. Our results suggest that differences in cross-reactivity after influenza vaccination should be expected in individuals with different exposure histories.
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Affiliation(s)
- Christopher S Anderson
- Department of Pediatrics, University of Rochester Medical Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Mark Y Sangster
- New York Influenza Center of Excellence at David Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Thomas J Mariani
- Department of Pediatrics, University of Rochester Medical Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sidhartha Chaudhury
- Center for Enabling Capabilities, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - David J Topham
- New York Influenza Center of Excellence at David Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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27
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Sharma J, Shepardson K, Johns LL, Wellham J, Avera J, Schwarz B, Rynda-Apple A, Douglas T. A Self-Adjuvanted, Modular, Antigenic VLP for Rapid Response to Influenza Virus Variability. ACS APPLIED MATERIALS & INTERFACES 2020; 12:18211-18224. [PMID: 32233444 DOI: 10.1021/acsami.9b21776] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The continuous evolution of influenza A virus (IAV) requires the influenza vaccine formulations to be updated annually to provide adequate protection. Recombinant protein-based vaccines provide safer, faster, and a more scalable alternative to the conventional embryonated egg approach for developing vaccines. However, these vaccines are typically poorer in immunogenicity than the vaccines containing inactivated or attenuated influenza viruses and require administration of a large antigen dosage together with potent adjuvants. The presentation of protein antigens on the surface of virus-like particles (VLP) provides an attractive strategy to rapidly induce stronger antigen-specific immune responses. Here we have examined the immunogenic potential and protective efficacy of P22 VLPs conjugated with multiple copies of the globular head domain of the hemagglutinin (HA) protein from the PR8 strain of IAV in a murine model of influenza pathogenesis. Using a covalent attachment strategy (SpyTag/SpyCatcher), we conjugated the HA globular head, which was recombinantly expressed in a genetically modified E. coli strain and found to refold as a monomer, to preassembled P22 VLPs. Immunization of mice with this P22-HAhead conjugate provided full protection from morbidity and mortality following infection with a homologous IAV strain. Moreover, the P22-HAhead conjugate also elicited an accelerated and enhanced HA head specific IgG response, which was significantly higher than the soluble HA head, or the admixture of P22 and HA head without the need for adjuvants. Thus, our results show that the HA head can be easily prepared by in vitro refolding in a modified E. coli strain, maintaining its intact structure and enabling the induction of a strong immune response when conjugated to P22 VLPs, even when presented as a monomer. These results also demonstrate that the P22 VLPs can be rapidly modified in a modular fashion, resulting in an effective vaccine construct that can generate protective immunity without the need for additional adjuvants.
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Affiliation(s)
- Jhanvi Sharma
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Kelly Shepardson
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, United States
| | - Laura L Johns
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, United States
| | - Julia Wellham
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, United States
| | - John Avera
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
- Matrivax Research and Development Corporation, Boston, Massachusetts 02118, United Sates
| | - Benjamin Schwarz
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
- Immunity to Pulmonary Pathogens section, Laboratory of Bacteriology, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana 59840, United States
| | - Agnieszka Rynda-Apple
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Biswas A, Chakrabarti AK, Dutta S. Current challenges: from the path of “original antigenic sin” towards the development of universal flu vaccines. Int Rev Immunol 2019; 39:21-36. [DOI: 10.1080/08830185.2019.1685990] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Asim Biswas
- Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Alok K. Chakrabarti
- Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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Paules CI, McDermott AB, Fauci AS. Immunity to Influenza: Catching a Moving Target To Improve Vaccine Design. THE JOURNAL OF IMMUNOLOGY 2019; 202:327-331. [PMID: 30617113 DOI: 10.4049/jimmunol.1890025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Catharine I Paules
- Milton S. Hershey Medical Center, Penn State College of Medicine, Hershey, PA 17033
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Anthony S Fauci
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
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30
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Jang YH, Seong BL. The Quest for a Truly Universal Influenza Vaccine. Front Cell Infect Microbiol 2019; 9:344. [PMID: 31649895 PMCID: PMC6795694 DOI: 10.3389/fcimb.2019.00344] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/24/2019] [Indexed: 12/17/2022] Open
Abstract
There is an unmet public health need for a universal influenza vaccine (UIV) to provide broad and durable protection from influenza virus infections. The identification of broadly protective antibodies and cross-reactive T cells directed to influenza viral targets present a promising prospect for the development of a UIV. Multiple targets for cross-protection have been identified in the stalk and head of hemagglutinin (HA) to develop a UIV. Recently, neuraminidase (NA) has received significant attention as a critical component for increasing the breadth of protection. The HA stalk-based approaches have shown promising results of broader protection in animal studies, and their feasibility in humans are being evaluated in clinical trials. Mucosal immune responses and cross-reactive T cell immunity across influenza A and B viruses intrinsic to live attenuated influenza vaccine (LAIV) have emerged as essential features to be incorporated into a UIV. Complementing the weakness of the stand-alone approaches, prime-boost vaccination combining HA stalk, and LAIV is under clinical evaluation, with the aim to increase the efficacy and broaden the spectrum of protection. Preexisting immunity in humans established by prior exposure to influenza viruses may affect the hierarchy and magnitude of immune responses elicited by an influenza vaccine, limiting the interpretation of preclinical data based on naive animals, necessitating human challenge studies. A consensus is yet to be achieved on the spectrum of protection, efficacy, target population, and duration of protection to define a “universal” vaccine. This review discusses the recent advancements in the development of UIVs, rationales behind cross-protection and vaccine designs, and challenges faced in obtaining balanced protection potency, a wide spectrum of protection, and safety relevant to UIVs.
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Affiliation(s)
- Yo Han Jang
- Molecular Medicine Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Baik Lin Seong
- Molecular Medicine Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Vaccine Translational Research Center, Yonsei University, Seoul, South Korea
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31
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Influenza Virus with Increased pH of Hemagglutinin Activation Has Improved Replication in Cell Culture but at the Cost of Infectivity in Human Airway Epithelium. J Virol 2019; 93:JVI.00058-19. [PMID: 31189708 PMCID: PMC6694820 DOI: 10.1128/jvi.00058-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/02/2019] [Indexed: 01/09/2023] Open
Abstract
The pH stability of the hemagglutinin surface protein varies between different influenza strains and subtypes and can affect the virus’ ability to replicate and transmit. Here, we demonstrate a delicate balance that the virus strikes within and without the target cell. We show that a pH-stable hemagglutinin enables a human influenza virus to replicate more effectively in human airway cells and mouse lungs by facilitating virus survival in the extracellular environment of the upper respiratory tract. Conversely, after entering target cells, being more pH stable confers a relative disadvantage, resulting in less efficient delivery of the viral genome to the host cell nucleus. Since the balance we describe will be affected differently in different host environments, it may restrict a virus’ ability to cross species. In addition, our findings imply that different influenza viruses may show variation in how well they are controlled by antiviral strategies targeting pH-dependent steps in the virus replication cycle. Pandemic H1N1 (pH1N1) influenza virus emerged from swine in 2009 with an adequate capability to infect and transmit between people. In subsequent years, it has circulated as a seasonal virus and evolved further human-adapting mutations. Mutations in the hemagglutinin (HA) stalk that increase pH stability have been associated with human adaptation and airborne transmission of pH1N1 virus. Yet, our understanding of how pH stability impacts virus-host interactions is incomplete. Here, using recombinant viruses with point mutations that alter the pH stability of pH1N1 HA, we found distinct effects on virus phenotypes in different experimental models. Increased pH sensitivity enabled viruses to uncoat in endosomes more efficiently, manifesting as increased replication rate in typical continuous cell cultures under single-cycle conditions. A more acid-labile HA also conferred a small reduction in sensitivity to antiviral therapeutics that act at the pH-sensitive HA fusion step. Conversely, in primary human airway epithelium cultured at the air-liquid interface, increased pH sensitivity attenuated multicycle viral replication by compromising virus survival in the extracellular microenvironment. In a mouse model of influenza pathogenicity, there was an optimum HA activation pH, and viruses with either more- or less-pH-stable HA were less virulent. Opposing pressures inside and outside the host cell that determine pH stability may influence zoonotic potential. The distinct effects that changes in pH stability exert on viral phenotypes underscore the importance of using the most appropriate systems for assessing virus titer and fitness, which has implications for vaccine manufacture, antiviral drug development, and pandemic risk assessment. IMPORTANCE The pH stability of the hemagglutinin surface protein varies between different influenza strains and subtypes and can affect the virus’ ability to replicate and transmit. Here, we demonstrate a delicate balance that the virus strikes within and without the target cell. We show that a pH-stable hemagglutinin enables a human influenza virus to replicate more effectively in human airway cells and mouse lungs by facilitating virus survival in the extracellular environment of the upper respiratory tract. Conversely, after entering target cells, being more pH stable confers a relative disadvantage, resulting in less efficient delivery of the viral genome to the host cell nucleus. Since the balance we describe will be affected differently in different host environments, it may restrict a virus’ ability to cross species. In addition, our findings imply that different influenza viruses may show variation in how well they are controlled by antiviral strategies targeting pH-dependent steps in the virus replication cycle.
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Xiao Y, Park JK, Williams S, Ramuta M, Cervantes-Medina A, Bristol T, Smith S, Czajkowski L, Han A, Kash JC, Memoli MJ, Taubenberger JK. Deep sequencing of 2009 influenza A/H1N1 virus isolated from volunteer human challenge study participants and natural infections. Virology 2019; 534:96-107. [PMID: 31226666 PMCID: PMC6652224 DOI: 10.1016/j.virol.2019.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 10/26/2022]
Abstract
Nasal wash samples from 15 human volunteers challenged with GMP manufactured influenza A/California/04/2009(H1N1) and from 5 naturally infected influenza patients of the 2009 pandemic were deep sequenced using viral targeted hybridization enrichment. Ten single nucleotide polymorphism (SNP) positions were found in the challenge virus. Some of the nonsynonymous changes in the inoculant virus were maintained in some challenge participants, but not in others, indicating that virus is evolving away from the Vero cell adapted inoculant, for example SNPs in the neuraminidase. Many SNP sites in challenge patients and naturally infected patients were found, many not identified previously. The SNPs identified, and phylogenetic analyses, showed that intrahost evolution of the virus are different in challenge participants and naturally infected patients. This study, using hybridization enrichment without PCR, provided an accurate and unbiased assessment of differential intrahost viral evolution from a uniform influenza inoculant in humans and comparison to naturally infected patients.
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Affiliation(s)
- Yongli Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Jae-Keun Park
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Williams
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell Ramuta
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adriana Cervantes-Medina
- Clinical Studies Unit, Laboratory if Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Bristol
- Clinical Studies Unit, Laboratory if Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah Smith
- Clinical Studies Unit, Laboratory if Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lindsay Czajkowski
- Clinical Studies Unit, Laboratory if Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alison Han
- Clinical Studies Unit, Laboratory if Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John C Kash
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matthew J Memoli
- Clinical Studies Unit, Laboratory if Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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33
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Khurana S, Hahn M, Coyle EM, King LR, Lin TL, Treanor J, Sant A, Golding H. Repeat vaccination reduces antibody affinity maturation across different influenza vaccine platforms in humans. Nat Commun 2019; 10:3338. [PMID: 31350391 PMCID: PMC6659679 DOI: 10.1038/s41467-019-11296-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 06/26/2019] [Indexed: 01/09/2023] Open
Abstract
Several vaccines are approved in the United States for seasonal influenza vaccination every year. Here we compare the impact of repeat influenza vaccination on hemagglutination inhibition (HI) titers, antibody binding and affinity maturation to individual hemagglutinin (HA) domains, HA1 and HA2, across vaccine platforms. Fold change in HI and antibody binding to HA1 trends higher for H1N1pdm09 and H3N2 but not against B strains in groups vaccinated with FluBlok compared with FluCelvax and Fluzone. Antibody-affinity maturation occurs against HA1 domain of H1N1pdm09, H3N2 and B following vaccination with all vaccine platforms, but not against H1N1pdm09-HA2. Importantly, prior year vaccination of subjects receiving repeat vaccinations demonstrated reduced antibody-affinity maturation to HA1 of all three influenza virus strains irrespective of the vaccine platform. This study identifies an important impact of repeat vaccination on antibody-affinity maturation following vaccination, which may contribute to lower vaccine effectiveness of seasonal influenza vaccines in humans Here, Khurana et al. report the results of a phase 4 clinical trial with three FDA approved influenza vaccines and show that repeat influenza vaccination results in reduced antibody affinity maturation to hemagglutinin domain 1 irrespective of vaccine platform.
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Affiliation(s)
- Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA.
| | - Megan Hahn
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - Elizabeth M Coyle
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - Lisa R King
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - Tsai-Lien Lin
- Division of Biostatistics, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - John Treanor
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Andrea Sant
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
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Wu NC, Yamayoshi S, Ito M, Uraki R, Kawaoka Y, Wilson IA. Recurring and Adaptable Binding Motifs in Broadly Neutralizing Antibodies to Influenza Virus Are Encoded on the D3-9 Segment of the Ig Gene. Cell Host Microbe 2019; 24:569-578.e4. [PMID: 30308159 PMCID: PMC6327842 DOI: 10.1016/j.chom.2018.09.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/16/2018] [Accepted: 08/13/2018] [Indexed: 11/27/2022]
Abstract
Discovery and characterization of broadly neutralizing antibodies (bnAbs) to the influenza hemagglutinin (HA) stem have provided insights for the development of a universal flu vaccine. Identification of signature features common to bnAbs from different individuals will be key to guiding immunogen design. S9-3-37 is a bnAb isolated from a healthy H5N1 vaccinee. Here, structural characterization reveals that the D3-9 gene segment of S9-3-37 contributes most of the interaction surface with the highly conserved stem epitope on HA. Comparison with other influenza bnAb crystal structures indicates that the D3-9 segment provides a general mechanism for targeting HA stem. Interestingly, such bnAbs can approach the HA stem with vastly different angles and orientations. Moreover, D3-9 can be translated in different reading frames in different bnAbs yet still target the same HA stem pocket. Thus, the D3-9 gene segment in the human immune repertoire can provide a robust defense against influenza virus.
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Affiliation(s)
- Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Mutsumi Ito
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Ryuta Uraki
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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35
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Qiu X, Duvvuri VR, Bahl J. Computational Approaches and Challenges to Developing Universal Influenza Vaccines. Vaccines (Basel) 2019; 7:E45. [PMID: 31141933 PMCID: PMC6631137 DOI: 10.3390/vaccines7020045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/15/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022] Open
Abstract
The traditional design of effective vaccines for rapidly-evolving pathogens, such as influenza A virus, has failed to provide broad spectrum and long-lasting protection. With low cost whole genome sequencing technology and powerful computing capabilities, novel computational approaches have demonstrated the potential to facilitate the design of a universal influenza vaccine. However, few studies have integrated computational optimization in the design and discovery of new vaccines. Understanding the potential of computational vaccine design is necessary before these approaches can be implemented on a broad scale. This review summarizes some promising computational approaches under current development, including computationally optimized broadly reactive antigens with consensus sequences, phylogenetic model-based ancestral sequence reconstruction, and immunomics to compute conserved cross-reactive T-cell epitopes. Interactions between virus-host-environment determine the evolvability of the influenza population. We propose that with the development of novel technologies that allow the integration of data sources such as protein structural modeling, host antibody repertoire analysis and advanced phylodynamic modeling, computational approaches will be crucial for the development of a long-lasting universal influenza vaccine. Taken together, computational approaches are powerful and promising tools for the development of a universal influenza vaccine with durable and broad protection.
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Affiliation(s)
- Xueting Qiu
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Venkata R Duvvuri
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA 30606, USA.
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
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36
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V H1-69 antiviral broadly neutralizing antibodies: genetics, structures, and relevance to rational vaccine design. Curr Opin Virol 2019; 34:149-159. [PMID: 30884330 DOI: 10.1016/j.coviro.2019.02.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022]
Abstract
Broadly neutralizing antibodies (bnAbs) are potential therapeutic molecules and valuable tools for studying conserved viral targets for vaccine and drug design. Interestingly, antibody responses to conserved epitopes can be highly convergent at the molecular level. Human antibodies targeting a number of viral antigens have often been found to utilize a restricted set of immunoglobulin germline genes in different individuals. Here we review recent knowledge on VH1-69-encoded antibodies in antiviral responses to influenza virus, HCV, and HIV-1. These antibodies share common genetic and structural features, and often develop neutralizing activity against a broad spectrum of viral strains. Understanding the genetic and structural characteristics of such antibodies and the target epitopes should help advance novel strategies to elicit bnAbs through vaccination.
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Coughlan L, Palese P. Overcoming Barriers in the Path to a Universal Influenza Virus Vaccine. Cell Host Microbe 2019; 24:18-24. [PMID: 30001520 DOI: 10.1016/j.chom.2018.06.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Influenza viruses are important pathogens which pose an ongoing threat to public health due to their ability to mutate and evade immunity elicited by prior infection or vaccination. Their evolutionary diversity is facilitated by the plasticity of the antigenically variable head domain of the major surface glycoprotein, hemagglutinin (HA), which tolerates the accumulation of extensive mutations. To date, vaccines have focused on eliciting largely strain-specific immune responses toward the HA head. However, novel universal influenza vaccines aim to refocus immunity toward the immunosubdominant but conserved influenza virus HA stalk domain. Such vaccines could provide heterologous protection against diverse influenza viruses.
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Affiliation(s)
- Lynda Coughlan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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38
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Nogales A, Martinez-Sobrido L, Topham DJ, DeDiego ML. Modulation of Innate Immune Responses by the Influenza A NS1 and PA-X Proteins. Viruses 2018; 10:v10120708. [PMID: 30545063 PMCID: PMC6315843 DOI: 10.3390/v10120708] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Influenza A viruses (IAV) can infect a broad range of animal hosts, including humans. In humans, IAV causes seasonal annual epidemics and occasional pandemics, representing a serious public health and economic problem, which is most effectively prevented through vaccination. The defense mechanisms that the host innate immune system provides restrict IAV replication and infection. Consequently, to successfully replicate in interferon (IFN)-competent systems, IAV has to counteract host antiviral activities, mainly the production of IFN and the activities of IFN-induced host proteins that inhibit virus replication. The IAV multifunctional proteins PA-X and NS1 are virulence factors that modulate the innate immune response and virus pathogenicity. Notably, these two viral proteins have synergistic effects in the inhibition of host protein synthesis in infected cells, although using different mechanisms of action. Moreover, the control of innate immune responses by the IAV NS1 and PA-X proteins is subject to a balance that can determine virus pathogenesis and fitness, and recent evidence shows co-evolution of these proteins in seasonal viruses, indicating that they should be monitored for enhanced virulence. Importantly, inhibition of host gene expression by the influenza NS1 and/or PA-X proteins could be explored to develop improved live-attenuated influenza vaccines (LAIV) by modulating the ability of the virus to counteract antiviral host responses. Likewise, both viral proteins represent a reasonable target for the development of new antivirals for the control of IAV infections. In this review, we summarize the role of IAV NS1 and PA-X in controlling the antiviral response during viral infection.
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Affiliation(s)
- Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- Centro de Investigación en Sanidad Animal (CISA)-INIA, Valdeolmos, 28130 Madrid, Spain.
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
| | - Marta L DeDiego
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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39
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Epstein SL. Universal Influenza Vaccines: Progress in Achieving Broad Cross-Protection In Vivo. Am J Epidemiol 2018; 187:2603-2614. [PMID: 30084906 DOI: 10.1093/aje/kwy145] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/09/2018] [Indexed: 01/08/2023] Open
Abstract
Despite all we have learned since 1918 about influenza virus and immunity, available influenza vaccines remain inadequate to control outbreaks of unexpected strains. Universal vaccines not requiring strain matching would be a major improvement. Their composition would be independent of predicting circulating viruses and thus potentially effective against unexpected drift or pandemic strains. This commentary explores progress with candidate universal vaccines based on various target antigens. Candidates include vaccines based on conserved viral proteins such as nucleoprotein and matrix, on the conserved hemagglutinin (HA) stem, and various combinations. Discussion covers the differing evidence for each candidate vaccine demonstrating protection in animals against influenza viruses of widely divergent HA subtypes and groups; durability of protection; routes of administration, including mucosal, providing local immunity; and reduction of transmission. Human trials of some candidate universal vaccines have been completed or are underway. Interestingly, the HA stem, like nucleoprotein and matrix, induces immunity that permits some virus replication and emergence of escape mutants fit enough to cause disease. Vaccination with multiple target antigens will thus have advantages over use of single antigens. Ultimately, a universal vaccine providing long-term protection against all influenza virus strains might contribute to pandemic control and routine vaccination.
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Affiliation(s)
- Suzanne L Epstein
- Division of Cellular and Gene Therapies, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
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40
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Fedson DS. Influenza, evolution, and the next pandemic. EVOLUTION MEDICINE AND PUBLIC HEALTH 2018; 2018:260-269. [PMID: 30455951 PMCID: PMC6234328 DOI: 10.1093/emph/eoy027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Mortality rates in influenza appear to have been shaped by evolution. During the 1918 pandemic, mortality rates were lower in children compared with adults. This mortality difference occurs in a wide variety of infectious diseases. It has been replicated in mice and might be due to greater tolerance of infection, not greater resistance. Importantly, combination treatment with inexpensive and widely available generic drugs (e.g. statins and angiotensin receptor blockers) might change the damaging host response in adults to a more tolerant response in children. These drugs might work by modifying endothelial dysfunction, mitochondrial biogenesis and immunometabolism. Treating the host response might be the only practical way to reduce global mortality during the next influenza pandemic. It might also help reduce mortality due to seasonal influenza and other forms of acute critical illness. To realize these benefits, we need laboratory and clinical studies of host response treatment before and after puberty.
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41
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Directed selection of amino acid changes in the influenza hemagglutinin and neuraminidase affecting protein antigenicity. Vaccine 2018; 36:6383-6392. [PMID: 30224200 DOI: 10.1016/j.vaccine.2018.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/22/2018] [Accepted: 09/02/2018] [Indexed: 11/23/2022]
Abstract
Influenza virus hemagglutinin (HA) and neuraminidase (NA) proteins elicit protective antibody responses and therefore, are used as targets for vaccination, especially the HA protein. However, these proteins are subject to antigenic drift, decreasing vaccine efficacy, and few to no studies have analyzed antigenic variability of these proteins by growing the viruses under immune pressure provided by human sera. In this work, we show that after growing different influenza virus strains under immune pressure, the selection of amino acid changes in the NA protein is much more limited than the selection in the HA protein, suggesting that the NA protein could remain more conserved under immune pressure. Interestingly, all the mutations in the HA and NA proteins affected protein antigenicity, and many of the selected amino acid changes were located at the same positions found in viruses circulating. These studies could help to inform HA and NA protein residues targeted by antibody responses after virus infection in humans and are very relevant to update the strains used for influenza virus vaccination each year and to improve the currently available vaccines.
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42
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Sicca F, Neppelenbroek S, Huckriede A. Effector mechanisms of influenza-specific antibodies: neutralization and beyond. Expert Rev Vaccines 2018; 17:785-795. [PMID: 30145912 DOI: 10.1080/14760584.2018.1516553] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Antibodies directed against influenza virus execute their protective function by exploiting a variety of effector mechanisms. Neutralizing antibodies have been thoroughly studied because of their pivotal role in preventing influenza virus infection and their presence in host serum is correlated with protection. Influenza antibodies can also exploit non-neutralizing effector mechanisms, which until recently have been largely overlooked. AREAS COVERED Here, we discuss the antibody response to influenza virus in its entire breadth. Neutralizing antibodies mostly target variable epitopes on influenza surface proteins and interfere with virus binding, fusion, or egress. Non-neutralizing antibodies instead usually target conserved epitopes which can be located on surface as well as internal proteins. They drive viral clearance via interaction of their Fc region with components of the innate immune system such as immune effector cells (e.g. NK cells, macrophages) or the complement system. EXPERT COMMENTARY Recent research has unraveled that influenza-specific antibodies target multiple proteins and make use of diverse effector mechanisms. Often these antibodies are cross-reactive among virus strains of the same subtype or even between subtypes. As such they are induced early in life and are boosted by regular encounters with virus or vaccine. Designing strategies to optimally exploit these pre-existing antibodies may represent the key for the development of new broadly protective influenza vaccines.
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Affiliation(s)
- Federica Sicca
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , The Netherlands
| | - Sam Neppelenbroek
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , The Netherlands
| | - Anke Huckriede
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , The Netherlands
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Zhang H, Henry C, Anderson CS, Nogales A, DeDiego ML, Bucukovski J, Martinez-Sobrido L, Wilson PC, Topham DJ, Miller BL. Crowd on a Chip: Label-Free Human Monoclonal Antibody Arrays for Serotyping Influenza. Anal Chem 2018; 90:9583-9590. [PMID: 29985597 PMCID: PMC6082710 DOI: 10.1021/acs.analchem.8b02479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rapid changes in influenza A virus (IAV) antigenicity create challenges in surveillance, disease diagnosis, and vaccine development. Further, serological methods for studying antigenic properties of influenza viruses often rely on animal models and therefore may not fully reflect the dynamics of human immunity. We hypothesized that arrays of human monoclonal antibodies (hmAbs) to influenza could be employed in a pattern-recognition approach to expedite IAV serology and to study the antigenic evolution of newly emerging viruses. Using the multiplex, label-free Arrayed Imaging Reflectometry (AIR) platform, we have demonstrated that such arrays readily discriminated among various subtypes of IAVs, including H1, H3 seasonal strains, and avian-sourced human H7 viruses. Array responses also allowed the first determination of antigenic relationships among IAV strains directly from hmAb responses. Finally, correlation analysis of antibody binding to all tested IAV subtypes allowed efficient identification of broadly reactive clones. In addition to specific applications in the context of understanding influenza biology with potential utility in "universal" flu vaccine development, these studies validate AIR as a platform technology for studying antigenic properties of viruses and also antibody properties in a high-throughput manner. We further anticipate that this approach will facilitate advances in the study of other viral pathogens.
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Affiliation(s)
- Hanyuan Zhang
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York 14642
- Materials Science Program, University of Rochester, Rochester, New York 14627
| | - Carole Henry
- Department of Medicine, University of Chicago, Chicago, Illinois 60637
| | - Christopher S. Anderson
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Marta L. DeDiego
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Joseph Bucukovski
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York 14642
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Patrick C. Wilson
- Department of Medicine, University of Chicago, Chicago, Illinois 60637
| | - David J. Topham
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York 14642
- Materials Science Program, University of Rochester, Rochester, New York 14627
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Kirkpatrick E, Qiu X, Wilson PC, Bahl J, Krammer F. The influenza virus hemagglutinin head evolves faster than the stalk domain. Sci Rep 2018; 8:10432. [PMID: 29992986 PMCID: PMC6041311 DOI: 10.1038/s41598-018-28706-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/28/2018] [Indexed: 01/12/2023] Open
Abstract
The limited ability of current influenza virus vaccines to protect from antigenically drifted or shifted viruses creates a public health problem that has led to the need to develop effective, broadly protective vaccines. While current influenza virus vaccines mostly induce an immune response against the immunodominant and variable head domain of the hemagglutinin, the major surface glycoprotein of the virus, the hemagglutinin stalk domain has been identified to harbor neutralizing B-cell epitopes that are conserved among and even between influenza A virus subtypes. A complete understanding of the differences in evolution between the main target of current vaccines and this more conserved stalk region are missing. Here, we performed an evolutionary analysis of the stalk domains of the hemagglutinin of pre-pandemic seasonal H1N1, pandemic H1N1, seasonal H3N2, and influenza B viruses and show quantitatively for the first time that the stalk domain is evolving at a rate that is significantly slower than that of the head domain. Additionally, we found that the cross-reactive epitopes in the stalk domain targeted by broadly neutralizing monoclonal antibodies are evolving at an even slower rate compared to the full head and stalk regions of the protein. Finally, a fixed-effects likelihood selection analysis was performed for these virus groups in both the head and stalk domains. While several positive selection sites were found in the head domain, only a single site in the stalk domain of pre-pandemic seasonal H1 hemagglutinin was identified at amino acid position 468 (H1 numbering from methionine). This site is not located in or close to the epitopes of cross-reactive anti-stalk monoclonal antibodies. Furthermore, we found that changes in this site do not significantly impact virus binding or neutralization by human anti-stalk antibodies, suggesting that some positive selection in the stalk domain is independent of immune pressures. We conclude that, while the stalk domain does evolve over time, this evolution is slow and, historically, is not directed to aid in evading neutralizing antibody responses.
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MESH Headings
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Epitopes/immunology
- Evolution, Molecular
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinins/chemistry
- Hemagglutinins/genetics
- Hemagglutinins/immunology
- Humans
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/immunology
- Influenza, Human/immunology
- Influenza, Human/virology
- Kinetics
- Protein Domains/genetics
- Protein Domains/immunology
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Affiliation(s)
- Ericka Kirkpatrick
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xueting Qiu
- University of Texas School of Public Health, Houston, TX, USA
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Justin Bahl
- University of Texas School of Public Health, Houston, TX, USA.
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Topham DJ, Nguyen P, Sangster MY. Pandemic influenza vaccines: what they have taught us about B cell immunology. Curr Opin Immunol 2018; 53:203-208. [PMID: 29957457 DOI: 10.1016/j.coi.2018.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
Abstract
The emergence of avian influenza viruses stimulated pandemic concerns and efforts to develop protective vaccines. Studies of the immune responses to experimental vaccines for pandemic influenza have taught us lessons about human immunity to influenza in general that can be applied to seasonal, pandemic, and even universal vaccine responses. For example, the concepts of targeting the hemagglutinin stalk and elicitation of stalk reactive antibodies grew out of studies of the 2009 pandemic H1N1 vaccines. More recently, the phenomenon of imprinting, the influence of early life exposure to influenza modifying responses to the viruses or vaccines later in life, has been reinforced through the study of potential pandemic influenza virus vaccines such as H7N9. These studies have also revealed potential strategies to improve responses to novel influenza strains and produce more broadly cross-reactive B cell and antibody responses. These concepts are discussed in detail in this review.
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Affiliation(s)
- David J Topham
- New York Influenza Center of Excellence, David H. Smith Center for Vaccine Biology & Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 609, Rochester, NY 14642, USA.
| | - Phuong Nguyen
- New York Influenza Center of Excellence, David H. Smith Center for Vaccine Biology & Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 609, Rochester, NY 14642, USA
| | - Mark Y Sangster
- New York Influenza Center of Excellence, David H. Smith Center for Vaccine Biology & Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 609, Rochester, NY 14642, USA
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The Potential Role of Fc-Receptor Functions in the Development of a Universal Influenza Vaccine. Vaccines (Basel) 2018; 6:vaccines6020027. [PMID: 29772781 PMCID: PMC6027188 DOI: 10.3390/vaccines6020027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/08/2018] [Accepted: 05/10/2018] [Indexed: 01/02/2023] Open
Abstract
Despite global vaccination efforts, influenza virus continues to cause yearly epidemics and periodic pandemics throughout most of the world. Many of us consider the generation of broader, potent and long-lasting immunity against influenza viruses as critical in curtailing the global health and economic impact that influenza currently plays. To date, classical vaccinology has relied on the generation of neutralizing antibodies as the benchmark to measure vaccine effectiveness. However, recent developments in numerous related fields of biomedical research including, HIV, HSV and DENV have emphasized the importance of Fc-mediate effector functions in pathogenesis and immunity. The concept of Fc effector functions in contributing to protection from illness is not a new concept and has been investigated in the field for over four decades. However, in recent years the application and study of Fc effector functions has become revitalized with new knowledge and technologies to characterize their potential importance in immunity. In this perspective, we describe the current state of the field of Influenza Fc effector functions and discuss its potential utility in universal vaccine design in the future.
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Saletti G, Gerlach T, Rimmelzwaan GF. Influenza vaccines: 'tailor-made' or 'one fits all'. Curr Opin Immunol 2018; 53:102-110. [PMID: 29734023 DOI: 10.1016/j.coi.2018.04.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 02/02/2023]
Abstract
Currently used inactivated influenza vaccines aim at the induction of virus-neutralizing antibodies directed to the variable head domain of the viral hemagglutinin. Although these vaccines are effective against antigenically matching virus strains, they offer little protection against antigenically distinct drift variants or potentially pandemic viruses of alternative subtypes. In the last decades, the threat of novel influenza pandemics has sparked research efforts to develop vaccines that induce more broadly protective immunity. Here, we discuss the immune responses induced by conventional 'tailor-made' inactivated and live influenza vaccines and novel 'one fits all' candidate vaccines able to induce cross-reactive virus-specific antibody and T cell responses and to afford protection to a wider range of influenza viruses.
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Affiliation(s)
- Giulietta Saletti
- University of Veterinary Medicine (TiHo), Research Center for Emerging Infections and Zoonoses (RIZ), Bünteweg 17, 30559 Hannover, Germany
| | - Thomas Gerlach
- University of Veterinary Medicine (TiHo), Research Center for Emerging Infections and Zoonoses (RIZ), Bünteweg 17, 30559 Hannover, Germany
| | - Guus F Rimmelzwaan
- University of Veterinary Medicine (TiHo), Research Center for Emerging Infections and Zoonoses (RIZ), Bünteweg 17, 30559 Hannover, Germany.
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How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin. Nat Commun 2018; 9:1386. [PMID: 29643370 PMCID: PMC5895760 DOI: 10.1038/s41467-018-03665-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 02/28/2018] [Indexed: 01/19/2023] Open
Abstract
Influenza virus can escape most antibodies with single mutations. However, rare antibodies broadly neutralize many viral strains. It is unclear how easily influenza virus might escape such antibodies if there was strong pressure to do so. Here, we map all single amino-acid mutations that increase resistance to broad antibodies to H1 hemagglutinin. Our approach not only identifies antigenic mutations but also quantifies their effect sizes. All antibodies select mutations, but the effect sizes vary widely. The virus can escape a broad antibody to hemagglutinin's receptor-binding site the same way it escapes narrow strain-specific antibodies: via single mutations with huge effects. In contrast, broad antibodies to hemagglutinin's stalk only select mutations with small effects. Therefore, among the antibodies we examine, breadth is an imperfect indicator of the potential for viral escape via single mutations. Antibodies targeting the H1 hemagglutinin stalk are quantifiably harder to escape than the other antibodies tested here.
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49
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Chen YQ, Wohlbold TJ, Zheng NY, Huang M, Huang Y, Neu KE, Lee J, Wan H, Rojas KT, Kirkpatrick E, Henry C, Palm AKE, Stamper CT, Lan LYL, Topham DJ, Treanor J, Wrammert J, Ahmed R, Eichelberger MC, Georgiou G, Krammer F, Wilson PC. Influenza Infection in Humans Induces Broadly Cross-Reactive and Protective Neuraminidase-Reactive Antibodies. Cell 2018; 173:417-429.e10. [PMID: 29625056 PMCID: PMC5890936 DOI: 10.1016/j.cell.2018.03.030] [Citation(s) in RCA: 267] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/08/2018] [Accepted: 03/09/2018] [Indexed: 12/12/2022]
Abstract
Antibodies to the hemagglutinin (HA) and neuraminidase (NA) glycoproteins are the major mediators of protection against influenza virus infection. Here, we report that current influenza vaccines poorly display key NA epitopes and rarely induce NA-reactive B cells. Conversely, influenza virus infection induces NA-reactive B cells at a frequency that approaches (H1N1) or exceeds (H3N2) that of HA-reactive B cells. NA-reactive antibodies display broad binding activity spanning the entire history of influenza A virus circulation in humans, including the original pandemic strains of both H1N1 and H3N2 subtypes. The antibodies robustly inhibit the enzymatic activity of NA, including oseltamivir-resistant variants, and provide robust prophylactic protection, including against avian H5N1 viruses, in vivo. When used therapeutically, NA-reactive antibodies protected mice from lethal influenza virus challenge even 48 hr post infection. These findings strongly suggest that influenza vaccines should be optimized to improve targeting of NA for durable and broad protection against divergent influenza strains.
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Affiliation(s)
- Yao-Qing Chen
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Teddy John Wohlbold
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Yunping Huang
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Karlynn E Neu
- The Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Jiwon Lee
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78731, USA
| | - Hongquan Wan
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Karla Thatcher Rojas
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Ericka Kirkpatrick
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carole Henry
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Anna-Karin E Palm
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | | | - Linda Yu-Ling Lan
- The Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - David J Topham
- Center for Vaccine Biology & Immunology, Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - John Treanor
- Division of Infectious Disease, Department of Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jens Wrammert
- Emory Vaccine Center, Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maryna C Eichelberger
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78731, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA.
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Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody. Proc Natl Acad Sci U S A 2017; 115:168-173. [PMID: 29255041 PMCID: PMC5776812 DOI: 10.1073/pnas.1715471115] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Circulating influenza viruses evade neutralization in their human hosts by acquiring escape mutations at epitopes of prevalent antibodies. A goal for next-generation influenza vaccines is to reduce escape likelihood by selectively eliciting antibodies recognizing conserved surfaces on the viral hemagglutinin (HA). The receptor-binding site (RBS) on the HA "head" and a region near the fusion peptide on the HA "stem" are two such sites. We describe here a human antibody clonal lineage, designated CL6649, members of which bind a third conserved site ("lateral patch") on the side of the H1-subtype, HA head. A crystal structure of HA with bound Fab6649 shows the conserved antibody footprint. The site was invariant in isolates from 1977 (seasonal) to 2012 (pdm2009); antibodies in CL6649 recognize HAs from the entire period. In 2013, human H1 viruses acquired mutations in this epitope that were retained in subsequent seasons, prompting modification of the H1 vaccine component in 2017. The mutations inhibit Fab6649 binding. We infer from the rapid spread of these mutations in circulating H1 influenza viruses that the previously subdominant, conserved lateral patch had become immunodominant for individuals with B-cell memory imprinted by earlier H1 exposure. We suggest that introduction of the pdm2009 H1 virus, to which most of the broadly prevalent, neutralizing antibodies did not bind, conferred a selective advantage in the immune systems of infected hosts to recall of memory B cells that recognized the lateral patch, the principal exposed epitope that did not change when pdm2009 displaced previous seasonal H1 viruses.
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