1
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Perofsky AC, Huddleston J, Hansen CL, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Lewis N, Whittaker L, Ermetal B, Harvey R, Galiano M, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Sullivan SG, Barr IG, Subbarao K, Krammer F, Bedford T, Viboud C. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. eLife 2024; 13:RP91849. [PMID: 39319780 PMCID: PMC11424097 DOI: 10.7554/elife.91849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024] Open
Abstract
Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here, we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection ynamics, presumably via heterosubtypic cross-immunity.
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MESH Headings
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- United States/epidemiology
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Influenza, Human/immunology
- Humans
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Epidemics
- Antigenic Drift and Shift/genetics
- Child
- Adult
- Neuraminidase/genetics
- Neuraminidase/immunology
- Adolescent
- Child, Preschool
- Antigens, Viral/immunology
- Antigens, Viral/genetics
- Young Adult
- Evolution, Molecular
- Seasons
- Middle Aged
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Affiliation(s)
- Amanda C Perofsky
- Fogarty International Center, National Institutes of Health, Bethesda, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, United States
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, United States
| | - Chelsea L Hansen
- Fogarty International Center, National Institutes of Health, Bethesda, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, United States
| | - John R Barnes
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - Thomas Rowe
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - Xiyan Xu
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - Rebecca Kondor
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - David E Wentworth
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - Nicola Lewis
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Lynne Whittaker
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Burcu Ermetal
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Ruth Harvey
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Monica Galiano
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Rodney Stuart Daniels
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - John W McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Seiichiro Fujisaki
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuya Nakamura
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriko Kishida
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinji Watanabe
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Hasegawa
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Florian Krammer
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, United States
- Department of Genome Sciences, University of Washington, Seattle, United States
- Howard Hughes Medical Institute, Seattle, United States
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, United States
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2
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Loes AN, Tarabi RAL, Huddleston J, Touyon L, Wong SS, Cheng SMS, Leung NHL, Hannon WW, Bedford T, Cobey S, Cowling BJ, Bloom JD. High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains. J Virol 2024:e0068924. [PMID: 39315814 DOI: 10.1128/jvi.00689-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 09/01/2024] [Indexed: 09/25/2024] Open
Abstract
The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes using a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify the infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately 1 month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers 6 months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. We provide an experimental protocol (dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others. IMPORTANCE We describe a new approach that can rapidly measure how the antibodies in human serum inhibit infection by many different influenza strains. This new approach is useful for understanding how viral evolution affects antibody immunity. We apply the approach to study the effect of repeated influenza vaccination.
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Affiliation(s)
- Andrea N Loes
- Howard Hughes Medical Institute, Seattle, Washington, USA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Rosario Araceli L Tarabi
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - John Huddleston
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lisa Touyon
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Sook San Wong
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Samuel M S Cheng
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Nancy H L Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - William W Hannon
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, Washington, USA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Benjamin J Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, Washington, USA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
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3
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Carlock MA, Allen JD, Hanley HB, Ross TM. Longitudinal assessment of human antibody binding to hemagglutinin elicited by split-inactivated influenza vaccination over six consecutive seasons. PLoS One 2024; 19:e0301157. [PMID: 38917104 PMCID: PMC11198804 DOI: 10.1371/journal.pone.0301157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Participants between the ages of 10-86 years old were vaccinated with split-inactivated influenza vaccine (Fluzone®) in six consecutive influenza seasons from 2016-2017 to 2021-2022. Vaccine effectiveness varies from season to season as a result of both host immune responses as well as evolutionary changes in the influenza virus surface glycoproteins that provide challenges to vaccine manufacturers to produce more effective annual vaccines. Next generation influenza vaccines are in development and may provide protective immune responses against a broader number of influenza viruses and reduce the need for annual vaccination. An improved understanding how current influenza vaccines are influenced by human host immune responses in people of different ages and co-morbidities is necessary for designing the next-generation of 'universal' or broadly-protective influenza vaccines. Overall, pre-existing immune responses to previous influenza virus exposures, either by past infections or vaccinations, is a critical factor influencing host responses to seasonal influenza vaccination. Participants vaccinated in consecutive seasons had reduced serum hemagglutination-inhibition (HAI) activity against strains included in the vaccine compared to participants that had not been vaccinated in the preceding 1-2 years prior to entering this study. The magnitude and breadth of these antibody responses were also modulated by the age of the participant. Elderly participants over 65 years of age, in general, had lower pre-existing HAI titers each season prior to vaccination with lower post-vaccination titers compared to children or young adults under the age of 35. The administration of higher doses (HD) of the split-inactivated vaccine enhanced the antibody titers in the elderly. This report showcases 6 consecutive years of antibody HAI activity in human subjects receiving seasonal split-inactivated influenza vaccine.
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Affiliation(s)
- Michael A. Carlock
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
| | - James D. Allen
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
| | - Hannah B. Hanley
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
| | - Ted M. Ross
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
- Department of Infection Biology, Lehner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America
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4
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Perofsky AC, Huddleston J, Hansen C, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Lewis N, Whittaker L, Ermetal B, Harvey R, Galiano M, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Sullivan SG, Barr IG, Subbarao K, Krammer F, Bedford T, Viboud C. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.02.23296453. [PMID: 37873362 PMCID: PMC10593063 DOI: 10.1101/2023.10.02.23296453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection dynamics, presumably via heterosubtypic cross-immunity.
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Affiliation(s)
- Amanda C Perofsky
- Fogarty International Center, National Institutes of Health, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, United States
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, United States
| | - Chelsea Hansen
- Fogarty International Center, National Institutes of Health, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, United States
| | - John R Barnes
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Thomas Rowe
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Xiyan Xu
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Rebecca Kondor
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - David E Wentworth
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Nicola Lewis
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Lynne Whittaker
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Burcu Ermetal
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Ruth Harvey
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Monica Galiano
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Rodney Stuart Daniels
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - John W McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Seiichiro Fujisaki
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Kazuya Nakamura
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Noriko Kishida
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Shinji Watanabe
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Hideki Hasegawa
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Australia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Australia
| | - Florian Krammer
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, United States
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, University of Washington, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, United States
- Department of Genome Sciences, University of Washington, United States
- Howard Hughes Medical Institute, Seattle, United States
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, United States
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5
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Loes AN, Tarabi RAL, Huddleston J, Touyon L, Wong SS, Cheng SMS, Leung NHL, Hannon WW, Bedford T, Cobey S, Cowling BJ, Bloom JD. High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584176. [PMID: 38496577 PMCID: PMC10942427 DOI: 10.1101/2024.03.08.584176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately one month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals, and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers six months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. This study demonstrates the utility of high-throughput sequencing-based neutralization assays that enable titers to be simultaneously measured against many different viral strains. We provide a detailed experimental protocol (DOI: https://dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and a computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.
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Affiliation(s)
- Andrea N Loes
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Rosario Araceli L Tarabi
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - John Huddleston
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Lisa Touyon
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Sook San Wong
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Samuel M S Cheng
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Nancy H L Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - William W Hannon
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Benjamin J Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
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6
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Li L, Guo T, Yuan Y, Xiao J, Yang R, Wang H, Xu W, Yin Y, Zhang X. ΔA146Ply-HA stem protein immunization protects mice against influenza A virus infection and co-infection with Streptococcus pneumoniae. Mol Immunol 2023; 161:91-103. [PMID: 37531919 DOI: 10.1016/j.molimm.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/30/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Influenza virus (IV) is a common pathogen affecting the upper respiratory tract, that causes various diseases. Secondary bacterial pneumonia is a common complication and a major cause of death in influenza patients. Streptococcus pneumoniae (S. pneumoniae) is the predominant co-infected bacteria in the pandemic, which colonizes healthy people but can cause diseases in immunocompromised individuals. Vaccination is a crucial strategy for avoiding infection, however, no universal influenza vaccine (UIV) that is resistant to multiple influenza viruses is available. Despite its limited immunogenicity, the hemagglutinin (HA) stem is a candidate peptide for UIV. ΔA146Ply (pneumolysin with a single deletion of A146) not only retains the Toll-like receptor 4 agonist effect but also is a potential vaccine adjuvant and a candidate protein for the S. pneumoniae vaccine. We constructed the fusion protein ΔA146Ply-HA stem and studied its immunoprotective effect in mice infection models. The results showed that intramuscular immunization of ΔA146Ply-HA stem without adjuvant could induce specific antibodies against HA stem and specific CD4+ T and CD8+ T cellular immunity in BALB/c and C57BL/6 mice, which could improve the survival rate of mice infected with IAV and co-infected with S. pneumoniae, but the protective effect on BALB/c mice was better than that on C57BL/6 mice. ΔA146Ply-HA stem serum antibody could protect BALB/c and C57BL/6 mice from IAV, and recognized HA polypeptides of H3N2, H5N1, H7N9, and H9N2 viruses. Moreover, ΔA146Ply-HA stem intramuscular immunization had a high safety profile with no obvious toxic side effects. The results indicated that coupling ΔA146Ply with influenza protein as a vaccine was a safe and effective strategy against the IV and secondary S. pneumoniae infection.
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Affiliation(s)
- Lian Li
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Ting Guo
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Yuan Yuan
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Jiangming Xiao
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Rui Yang
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Hanyi Wang
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Wenlong Xu
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Yibing Yin
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Xuemei Zhang
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing 400016, China.
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7
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Einav T, Ma R. Using interpretable machine learning to extend heterogeneous antibody-virus datasets. CELL REPORTS METHODS 2023; 3:100540. [PMID: 37671020 PMCID: PMC10475791 DOI: 10.1016/j.crmeth.2023.100540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/14/2023] [Accepted: 06/30/2023] [Indexed: 09/07/2023]
Abstract
A central challenge in biology is to use existing measurements to predict the outcomes of future experiments. For the rapidly evolving influenza virus, variants examined in one study will often have little to no overlap with other studies, making it difficult to discern patterns or unify datasets. We develop a computational framework that predicts how an antibody or serum would inhibit any variant from any other study. We validate this method using hemagglutination inhibition data from seven studies and predict 2,000,000 new values ± uncertainties. Our analysis quantifies the transferability between vaccination and infection studies in humans and ferrets, shows that serum potency is negatively correlated with breadth, and provides a tool for pandemic preparedness. In essence, this approach enables a shift in perspective when analyzing data from "what you see is what you get" into "what anyone sees is what everyone gets."
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Affiliation(s)
- Tal Einav
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Rong Ma
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
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8
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Liu M, Liu J, Song W, Peng Y, Ding X, Deng L, Jiang T. Development of PREDAC-H1pdm to model the antigenic evolution of influenza A/(H1N1) pdm09 viruses. Virol Sin 2023; 38:541-548. [PMID: 37211247 PMCID: PMC10436056 DOI: 10.1016/j.virs.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/17/2023] [Indexed: 05/23/2023] Open
Abstract
The Influenza A (H1N1) pdm09 virus caused a global pandemic in 2009 and has circulated seasonally ever since. As the continual genetic evolution of hemagglutinin in this virus leads to antigenic drift, rapid identification of antigenic variants and characterization of the antigenic evolution are needed. In this study, we developed PREDAC-H1pdm, a model to predict antigenic relationships between H1N1pdm viruses and identify antigenic clusters for post-2009 pandemic H1N1 strains. Our model performed well in predicting antigenic variants, which was helpful in influenza surveillance. By mapping the antigenic clusters for H1N1pdm, we found that substitutions on the Sa epitope were common for H1N1pdm, whereas for the former seasonal H1N1, substitutions on the Sb epitope were more common in antigenic evolution. Additionally, the localized epidemic pattern of H1N1pdm was more obvious than that of the former seasonal H1N1, which could make vaccine recommendation more sophisticated. Overall, the antigenic relationship prediction model we developed provides a rapid determination method for identifying antigenic variants, and the further analysis of evolutionary and epidemic characteristics can facilitate vaccine recommendations and influenza surveillance for H1N1pdm.
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Affiliation(s)
- Mi Liu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Jingze Liu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Wenjun Song
- Guangzhou Laboratory, Guangzhou, 510005, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Xiao Ding
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Lizong Deng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Taijiao Jiang
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Guangzhou Laboratory, Guangzhou, 510005, China; State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, China.
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9
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Kissling E, Pozo F, Martínez‐Baz I, Buda S, Vilcu A, Domegan L, Mazagatos C, Dijkstra F, Latorre‐Margalef N, Kurečić Filipović S, Machado A, Lazar M, Casado I, Dürrwald R, van der Werf S, O'Donnell J, Linares Dopido JA, Meijer A, Riess M, Višekruna Vučina V, Rodrigues AP, Mihai ME, Castilla J, Goerlitz L, Falchi A, Connell J, Castrillejo D, Hooiveld M, Carnahan A, Ilić M, Guiomar R, Ivanciuc A, Maurel M, Omokanye A, Valenciano M. Influenza vaccine effectiveness against influenza A subtypes in Europe: Results from the 2021-2022 I-MOVE primary care multicentre study. Influenza Other Respir Viruses 2023; 17:e13069. [PMID: 36702797 PMCID: PMC9835407 DOI: 10.1111/irv.13069] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 10/26/2022] [Accepted: 10/29/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND In 2021-2022, influenza A viruses dominated in Europe. The I-MOVE primary care network conducted a multicentre test-negative study to measure influenza vaccine effectiveness (VE). METHODS Primary care practitioners collected information on patients presenting with acute respiratory infection. Cases were influenza A(H3N2) or A(H1N1)pdm09 RT-PCR positive, and controls were influenza virus negative. We calculated VE using logistic regression, adjusting for study site, age, sex, onset date, and presence of chronic conditions. RESULTS Between week 40 2021 and week 20 2022, we included over 11 000 patients of whom 253 and 1595 were positive for influenza A(H1N1)pdm09 and A(H3N2), respectively. Overall VE against influenza A(H1N1)pdm09 was 75% (95% CI: 43-89) and 81% (95% CI: 45-93) among those aged 15-64 years. Overall VE against influenza A(H3N2) was 29% (95% CI: 12-42) and 25% (95% CI: -41 to 61), 33% (95% CI: 14-49), and 26% (95% CI: -22 to 55) among those aged 0-14, 15-64, and over 65 years, respectively. The A(H3N2) VE among the influenza vaccination target group was 20% (95% CI: -6 to 39). All 53 sequenced A(H1N1)pdm09 viruses belonged to clade 6B.1A.5a.1. Among 410 sequenced influenza A(H3N2) viruses, all but eight belonged to clade 3C.2a1b.2a.2. DISCUSSION Despite antigenic mismatch between vaccine and circulating strains for influenza A(H3N2) and A(H1N1)pdm09, 2021-2022 VE estimates against circulating influenza A(H1N1)pdm09 were the highest within the I-MOVE network since the 2009 influenza pandemic. VE against A(H3N2) was lower than A(H1N1)pdm09, but at least one in five individuals vaccinated against influenza were protected against presentation to primary care with laboratory-confirmed influenza.
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Affiliation(s)
| | - Francisco Pozo
- National Centre for MicrobiologyInstitute of Health Carlos IIIMadridSpain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP)MadridSpain
| | - Iván Martínez‐Baz
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP)MadridSpain
- Instituto de Salud Pública de Navarra ‐ IdiSNAPamplonaSpain
| | | | - Ana‐Maria Vilcu
- INSERM, Sorbonne UniversitéInstitut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136)ParisFrance
| | - Lisa Domegan
- Health Service Executive‐Health Protection Surveillance CentreDublinIreland
| | - Clara Mazagatos
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP)MadridSpain
- National Centre for EpidemiologyInstitute of Health Carlos IIIMadridSpain
| | - Frederika Dijkstra
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | | | | | | | - Mihaela Lazar
- “Cantacuzino” National Military Medical Institute for Research and DevelopmentBucharestRomania
| | - Itziar Casado
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP)MadridSpain
- Instituto de Salud Pública de Navarra ‐ IdiSNAPamplonaSpain
| | | | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, Institut PasteurUniversité Paris Cité, UMR 3569 CNRSParisFrance
- CNR virus des infections respiratoires, Institut PasteurParisFrance
| | - Joan O'Donnell
- Health Service Executive‐Health Protection Surveillance CentreDublinIreland
| | - Juan Antonio Linares Dopido
- Subdirección de Epidemiología, Dirección General de Salud Pública, Servicio Extremeño de SaludExtremaduraSpain
| | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | | | | | | | - Maria Elena Mihai
- “Cantacuzino” National Military Medical Institute for Research and DevelopmentBucharestRomania
| | - Jesús Castilla
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP)MadridSpain
- Instituto de Salud Pública de Navarra ‐ IdiSNAPamplonaSpain
| | | | | | - Jeff Connell
- National Virus Reference LaboratoryUniversity College DublinDublinIreland
| | - Daniel Castrillejo
- Servicio de Epidemiología, DGSP, Consejería de Políticas Sociales, Salud Pública y Bienestar Animal, Ciudad Autónoma de MelillaMelillaSpain
| | | | | | - Maja Ilić
- Croatian Institute of Public HealthZagrebCroatia
| | - Raquel Guiomar
- Instituto Nacional de Saúde Dr. Ricardo JorgeLisbonPortugal
| | - Alina Ivanciuc
- “Cantacuzino” National Military Medical Institute for Research and DevelopmentBucharestRomania
| | | | - Ajibola Omokanye
- European Centre for Disease Prevention and ControlStockholmSweden
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10
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Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep 2022; 41:111628. [PMID: 36351401 PMCID: PMC9883670 DOI: 10.1016/j.celrep.2022.111628] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/22/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
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Affiliation(s)
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Rachel Hecht
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Anne A Roffler
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Max J Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Daniel P Maurer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elisa Marchiori
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Thomas H Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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11
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Williams BJM, Ogbunugafor CB, Althouse BM, Hébert-Dufresne L. Immunity-induced criticality of the genotype network of influenza A (H3N2) hemagglutinin. PNAS NEXUS 2022; 1:pgac143. [PMID: 36060623 PMCID: PMC9434636 DOI: 10.1093/pnasnexus/pgac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
Abstract
Seasonal influenza kills hundreds of thousands every year, with multiple constantly changing strains in circulation at any given time. A high mutation rate enables the influenza virus to evade recognition by the human immune system, including immunity acquired through past infection and vaccination. Here, we capture the genetic similarity of influenza strains and their evolutionary dynamics with genotype networks. We show that the genotype networks of influenza A (H3N2) hemagglutinin are characterized by heavy-tailed distributions of module sizes and connectivity indicative of critical behavior. We argue that (i) genotype networks are driven by mutation and host immunity to explore a subspace of networks predictable in structure and (ii) genotype networks provide an underlying structure necessary to capture the rich dynamics of multistrain epidemic models. In particular, inclusion of strain-transcending immunity in epidemic models is dependent upon the structure of an underlying genotype network. This interplay is consistent with self-organized criticality where the epidemic dynamics of influenza locates critical regions of its genotype network. We conclude that this interplay between disease dynamics and network structure might be key for future network analysis of pathogen evolution and realistic multistrain epidemic models.
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Affiliation(s)
- Blake J M Williams
- Vermont Complex Systems Center, University of Vermont , Burlington, VT 05405, USA
| | - C Brandon Ogbunugafor
- Vermont Complex Systems Center, University of Vermont , Burlington, VT 05405, USA
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT 06511, USA
- Santa Fe Institute , Santa Fe, NM 87501, USA
- Public Health Modeling Unit, Yale School of Public Health , New Haven, CT 06510, USA
| | - Benjamin M Althouse
- Institute for Disease Modeling, Global Health, Bill & Melinda Gates Foundation , Seattle, WA 98109, USA
- Information School, University of Washington , Seattle, WA 98195, USA
- Department of Biology, New Mexico State University , Las Cruces, NM 88003, USA
| | - Laurent Hébert-Dufresne
- Vermont Complex Systems Center, University of Vermont , Burlington, VT 05405, USA
- Department of Computer Science, University of Vermont , Burlington VT 05405, USA
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12
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Wang Y, Tang CY, Wan XF. Antigenic characterization of influenza and SARS-CoV-2 viruses. Anal Bioanal Chem 2022; 414:2841-2881. [PMID: 34905077 PMCID: PMC8669429 DOI: 10.1007/s00216-021-03806-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.
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Affiliation(s)
- Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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13
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Bivalent H1 and H3 COBRA Recombinant Hemagglutinin Vaccines Elicit Seroprotective Antibodies against H1N1 and H3N2 Influenza Viruses from 2009 to 2019. J Virol 2022; 96:e0165221. [PMID: 35289635 DOI: 10.1128/jvi.01652-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Commercial influenza virus vaccines often elicit strain-specific immune responses and have difficulties preventing illness caused by antigenically drifted viral variants. In the last 20 years, the H3N2 component of the annual vaccine has been updated nearly twice as often as the H1N1 component, and in 2019, a mismatch between the wild-type (WT) H3N2 vaccine strain and circulating H3N2 influenza strains led to a vaccine efficacy of ∼9%. Modern methods of developing computationally optimized broadly reactive antigens (COBRAs) for H3N2 influenza viruses utilize current viral surveillance information to design more broadly reactive vaccine antigens. Here, 7 new recombinant hemagglutinin (rHA) H3 COBRA hemagglutinin (HA) antigens were evaluated in mice. Subsequently, two candidates, J4 and NG2, were selected for further testing in influenza-preimmune animals based on their ability to elicit broadly reactive antibodies against antigenically drifted H3N2 viral isolates. In the preimmune model, monovalent formulations of J4 and NG2 elicited broadly reactive antibodies against recently circulating H3N2 influenza viruses from 2019. Bivalent mixtures of COBRA H1 and H3 rHA, Y2 + J4, and Y2 + NG2 outperformed multiple WT H1+H3 bivalent rHA mixtures by eliciting seroprotective antibodies against H1N1 and H3N2 isolates from 2009 to 2019. Overall, the newly generated COBRA HA antigens, namely, Y2, J4, and NG2, had the ability to induce broadly reactive antibodies in influenza-naive and preimmune animals in both monovalent and bivalent formulations, and these antigens outperformed H1 and H3 WT rHA vaccine antigens by eliciting seroprotective antibodies against panels of antigenically drifted historical H1N1 and H3N2 vaccine strains from 2009 to 2019. IMPORTANCE Standard-of-care influenza virus vaccines are composed of a mixture of antigens from different influenza viral subtypes. For the first time, lead COBRA H1 and H3 HA antigens, formulated as a bivalent vaccine, have been investigated in animals with preexisting immunity to influenza viruses. The cocktail of COBRA HA antigens elicited more broadly reactive anti-HA antibodies than those elicited by a comparator bivalent wild-type HA vaccine against H1 and H3 influenza viruses isolated between 2009 and 2019.
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14
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Tkachuk Z, Melnichuk N, Nikolaiev RO, Szutkowski K, Zhukov I. The Natural Oligoribonucleotides Functionalized by D-Mannitol Affected Interactions of Hemagglutinin with Glycan Receptor Indicating Anti-Influenza Activity. MEMBRANES 2021; 11:membranes11100757. [PMID: 34677523 PMCID: PMC8538433 DOI: 10.3390/membranes11100757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022]
Abstract
Hemagglutinin (HA), the class I influenza A virus protein is responsible for the attachment of virus particles to the cell by binding to glycan receptors, subsequent virion internalization, and cell entry. Consequently, the importance of HA makes it a primary target for the development of anti-influenza drugs. The natural oligoribonucleotides (ORNs) as well as their derivatives functionalized with D-mannitol (ORNs-D-M) possess anti-influenza properties in vitro and in vivo due to interaction with HA receptor sites. This activity suppresses the viral infection in host cells. In the present work, the complexes of ORNs and ORNs-D-M with HA protein were studied by agglutination assay, fluorescence spectroscopy, as well as molecular docking simulations. Acquired experimental data exhibited a decrease in HA titer by 32 times after incubation with the ORNs-D-M for 0.5–24 h. Quenching fluorescence intensity of the HA suggests that titration by ORNs and ORNs-D-M probably leads to changes in the HA structure. Detailed structural data were obtained with the molecular docking simulations performed for ORNs and ORNs-D-M ligands containing three and six oligoribonucleotides. The results reveal that a majority of the ORNs and ORNs-D-M bind in a non-specific way to the receptor-binding domain of the HA protein. The ligand’s affinity to the hemagglutinin was estimated at the micromolar level. Presented experimental data confirmed that both natural ORNs and functionalized ORNs-D-M inhibit the interactions between HA and glycan receptors and demonstrate anti-influenza activity.
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Affiliation(s)
- Zenoviy Tkachuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine; (N.M.); (R.O.N.)
- “Biocell” Subsidiary Company of Biocell Laboratories Inc. (USA), Klovskiy Uzviz 17, 03680 Kyiv, Ukraine
- Correspondence: (Z.T.); (I.Z.); Tel.: +38-067-728-0418 (Z.T.); +48-22-592-2048 (I.Z.)
| | - Nataliia Melnichuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine; (N.M.); (R.O.N.)
| | - Roman O. Nikolaiev
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine; (N.M.); (R.O.N.)
| | - Kosma Szutkowski
- NanoBioMediacal Centre, Adam Mickiewicz University, Ul. Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland;
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Ul. Pawińskiego 5a, 02-106 Warsaw, Poland
- Correspondence: (Z.T.); (I.Z.); Tel.: +38-067-728-0418 (Z.T.); +48-22-592-2048 (I.Z.)
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15
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Allen JD, Ross TM. Evaluation of Next-Generation H3 Influenza Vaccines in Ferrets Pre-Immune to Historical H3N2 Viruses. Front Immunol 2021; 12:707339. [PMID: 34475872 PMCID: PMC8406686 DOI: 10.3389/fimmu.2021.707339] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Each person has a unique immune history to past influenza virus infections. Exposure to influenza viruses early in life establishes memory B cell populations that influence future immune responses to influenza vaccination. Current influenza vaccines elicit antibodies that are typically strain specific and do not offer broad protection against antigenically drifted influenza strains in all age groups of people. This is particularly true for vaccine antigens of the A(H3N2) influenza virus subtype, where continual antigenic drift necessitates frequent vaccine reformulation. Broadly-reactive influenza virus vaccine antigens offer a solution to combat antigenic drift, but they also need to be equally effective in all populations, regardless of prior influenza virus exposure history. This study examined the role that pre-existing immunity plays on influenza virus vaccination. Ferrets were infected with historical A(H3N2) influenza viruses isolated from either the 1970’s, 1980’s, or 1990’s and then vaccinated with computationally optimized broadly reactive antigens (COBRA) or wild-type (WT) influenza virus like particles (VLPs) expressing hemagglutinin (HA) vaccine antigens to examine the expansion of immune breadth. Vaccines with the H3 COBRA HA antigens had more cross-reactive antibodies following a single vaccination in all three pre-immune regimens than vaccines with WT H3 HA antigens against historical, contemporary, and future drifted A(H3N2) influenza viruses. The H3 COBRA HA vaccines also induced antibodies capable of neutralizing live virus infections against modern drifted A(H3N2) strains at higher titers than the WT H3 HA vaccine comparators.
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Affiliation(s)
- James D Allen
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States.,Department of Infectious Diseases, University of Georgia, Athens, GA, United States
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16
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Schnaack OH, Nourmohammad A. Optimal evolutionary decision-making to store immune memory. eLife 2021; 10:61346. [PMID: 33908347 PMCID: PMC8116052 DOI: 10.7554/elife.61346] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 04/23/2021] [Indexed: 12/25/2022] Open
Abstract
The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive immunity, which allows organisms to respond more readily upon re-infections. However, differentiation of memory cells is still one of the least understood cell fate decisions. Here, we introduce a mathematical framework to characterize optimal strategies to store memory to maximize the utility of immune response over an organism's lifetime. We show that memory production should be actively regulated to balance between affinity and cross-reactivity of immune receptors for an effective protection against evolving pathogens. Moreover, we predict that specificity of memory should depend on the organism's lifespan, and shorter lived organisms with fewer pathogenic encounters should store more cross-reactive memory. Our framework provides a baseline to gauge the efficacy of immune memory in light of an organism's coevolutionary history with pathogens.
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Affiliation(s)
- Oskar H Schnaack
- Max Planck Institute for Dynamics and Self-organization, Göttingen, Germany.,Department of Physics, University of Washington, Seattle, United States
| | - Armita Nourmohammad
- Max Planck Institute for Dynamics and Self-organization, Göttingen, Germany.,Department of Physics, University of Washington, Seattle, United States.,Fred Hutchinson Cancer Research Center, Seattle, United States
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17
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Hu Y, Liu Y, Yin Y, Zhang X. Protective efficacy of mucosal and subcutaneous immunization with DnaJ-ΔA146Ply against influenza and Streptococcus pneumoniae co-infection in mice. Microbes Infect 2021; 23:104813. [PMID: 33798714 DOI: 10.1016/j.micinf.2021.104813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/09/2021] [Accepted: 03/16/2021] [Indexed: 02/02/2023]
Abstract
Respiratory tract coinfections, specifically involving influenza A virus (IAV) and Streptococcus pneumoniae (S. pneumoniae), remain a major health problem worldwide. Secondary bacterial pneumonia is a common complication and an important cause of mortality related to seasonal and pandemic influenza infections. Vaccination is a basic control strategy against influenza and S. pneumoniae. The fusion protein DnaJ-ΔA146Ply is a vaccine candidate which can induce immune responses against pneumococcal infections via mucosal and subcutaneous immunization in mice. In the present study, we established a co-infection model using mouse-adapted laboratory strains of IAV (PR8) and S. pneumoniae (19F) in mice intranasally and subcutaneously immunized with DnaJ-ΔA146Ply. Our results showed that vaccinated mice suffered decreased weight loss compared with control mice. The survival rates were higher in intranasally and subcutaneously immunized mice than in control mice. In addition, the bacterial loads in nasal washes and lung homogenates were lower in vaccinated mice than in control mice. Furthermore, lung damage was alleviated in vaccinated mice compared with control mice, with less broken alveoli and less proinflammatory cytokine production. Taken together, these results indicate that vaccination with DnaJ-ΔA146Ply shows protective potential against influenza and S. pneumoniae co-infection in mice.
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Affiliation(s)
- Yi Hu
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China
| | - Yusi Liu
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, 110001, China
| | - Yibing Yin
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China
| | - Xuemei Zhang
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China.
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18
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Mahallawi WH, Ibrahim NA, Alahmadi KS, Al-Harbi AK, Almughthawi MA, Alhazmi OA, Alsehli FH, Khabour OF. Natural immunity to influenza A and B among Saudi blood donors in Al Madinah Al Munawarah, Saudi Arabia. Saudi Med J 2020; 41:1301-1307. [PMID: 33294887 PMCID: PMC7841591 DOI: 10.15537/smj.2020.12.05582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Objectives: To investigate the seroprevalence of influenza viruses (A and B) among blood donors in Kingdom of Saudi Arabia. Methods: The present investigation was conducted between April 2019 and July 2019. Participants were healthy adults recruited from the central blood bank Al Madinah Al Munawarah, Kingdom of Saudi Arabia. Immunoglobulin G (IgG) levels against influenza A and B were measured in serum samples using ELISA. Results: The results showed that 29.2% of the sample had significant concentrations of influenza A IgG antibody, whereas 38.6% had significant concentrations of influenza B IgG antibody. A strong correlation was found between the levels of influenza A and influenza B antibodies (r=0.708, p<0.001). The number of individuals identified as negative for influenza A IgG antibody increased with age (p<0.01). In addition, no correlations were identified between influenza A IgG and influenza B IgG and body mass index (BMI), (p>0.05). Finally, linear regression analysis showed that the level of influenza A antibody can be predicted by age (p<0.05) and body mass index (BMI) (p<0.05). Conclusion: Approximately one-third of Saudi Arabian adults presented significant levels of influenza A and B antibodies in our study. Demographic factors, including age and BMI, might contribute to influenza A antibody levels.
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Affiliation(s)
- Waleed H Mahallawi
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Al Madinah Al Munawarah, Kingdom of Saudi Arabia. E-mail.
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19
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Abstract
Seasonal influenza vaccines prevent influenza-related illnesses, hospitalizations, and deaths. However, these vaccines are not as effective as other viral vaccines, and there is clearly room for improvement. Here, we review the history of seasonal influenza vaccines, describe challenges associated with producing influenza vaccine antigens, and discuss the inherent difficulties of updating influenza vaccine strains each influenza season. We argue that seasonal influenza vaccines can be dramatically improved by modernizing antigen production processes and developing models that are better at predicting viral evolution. Resources should be specifically dedicated to improving seasonal influenza vaccines while developing entirely new vaccine platforms.
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Affiliation(s)
- Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , ,
| | - Elizabeth M Anderson
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , ,
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , ,
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20
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El Zowalaty ME, Järhult JD. From SARS to COVID-19: A previously unknown SARS- related coronavirus (SARS-CoV-2) of pandemic potential infecting humans - Call for a One Health approach. One Health 2020; 9:100124. [PMID: 32195311 PMCID: PMC7075990 DOI: 10.1016/j.onehlt.2020.100124] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 02/07/2023] Open
Abstract
Human coronaviruses continue to pose a threat to human health. The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 which causes coronavirus disease-2019 (COVID-19), an acute respiratory disease marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. This recent emergence of a previously unknown coronavirus in China leads to huge impacts on humans globally. Covid-19 is a challenge to global public health. Here, we discuss the COVID-19 outbreak in a one health context, highlighting the need for the implementation of one health measures and practices to improve human health and reduce the emergence of pandemic viruses.
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Affiliation(s)
- Mohamed E. El Zowalaty
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Infectious Diseases and Anti-Infective Therapy Research Group, College of Pharmacy and Sharjah Medical Research Institute, University of Sharjah, United Arab Emirates
| | - Josef D. Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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21
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Bajic G, Maron MJ, Caradonna TM, Tian M, Mermelstein A, Fera D, Kelsoe G, Kuraoka M, Schmidt AG. Structure-Guided Molecular Grafting of a Complex Broadly Neutralizing Viral Epitope. ACS Infect Dis 2020; 6:1182-1191. [PMID: 32267676 DOI: 10.1021/acsinfecdis.0c00008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Antigenic variation and viral evolution have thwarted traditional influenza vaccination strategies. The broad protection afforded by a "universal" influenza vaccine may come from immunogens that elicit humoral immune responses targeting conserved epitopes on the viral hemagglutinin (HA), such as the receptor-binding site (RBS). Here, we engineered candidate immunogens that use noncirculating, avian influenza HAs as molecular scaffolds to present the broadly neutralizing RBS epitope from historical, circulating H1 influenzas. These "resurfaced" HAs (rsHAs) remove epitopes potentially targeted by strain-specific responses in immune-experienced individuals. Through structure-guided optimization, we improved two antigenically different scaffolds to bind a diverse panel of pan-H1 and H1/H3 cross-reactive bnAbs with high affinity. Subsequent serological and single germinal center B cell analyses from murine prime-boost immunizations show that the rsHAs are both immunogenic and can augment the quality of elicited RBS-directed antibodies. Our structure-guided, RBS grafting approach provides candidate immunogens for selectively presenting a conserved viral epitope.
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Affiliation(s)
- Goran Bajic
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Max J. Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Timothy M. Caradonna
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Ming Tian
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Adam Mermelstein
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina 27710, United States
- Department of Immunology, Duke University, Durham, North Carolina 27710, United States
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, North Carolina 27710, United States
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, United States
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
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22
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Podshivalov DD, Kirilin EM, Konnov SI, Švedas VK. Structural Organization and Dynamic Characteristics of the Binding Site for Conformational Rearrangement Inhibitors in Hemagglutinins from H3N2 and H7N9 Influenza Viruses. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:499-506. [PMID: 32569557 DOI: 10.1134/s0006297920040100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/02/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Computer models of hemagglutinins from the H3N2 and H7N9 influenza viruses were developed to study structural organization and dynamic characteristics of the binding site for the conformational rearrangement inhibitors. The metadynamics was used to map the binding site free energy and to define the volume of its most energetically favorable states. It was demonstrated by simulation of the umifenovir (Arbidol) interaction with hemagglutinin that ligand binding requires an increase in the binding site volume and deformation of its most energetically favorable state. We also identified amino acid residues directly involved in the ligand binding that determine the binding efficiency, as well as the dynamic behavior of the binding site. The revealed features of the binding site structural organization of the influenza virus hemagglutinin should be taken into account when searching for new antiviral drugs capable to modulate its functional properties.
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Affiliation(s)
- D D Podshivalov
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.
| | - E M Kirilin
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - S I Konnov
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - V K Švedas
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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23
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Meade P, Kuan G, Strohmeier S, Maier HE, Amanat F, Balmaseda A, Ito K, Kirkpatrick E, Javier A, Gresh L, Nachbagauer R, Gordon A, Krammer F. Influenza Virus Infection Induces a Narrow Antibody Response in Children but a Broad Recall Response in Adults. mBio 2020; 11:e03243-19. [PMID: 31964741 PMCID: PMC6974575 DOI: 10.1128/mbio.03243-19] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 11/20/2022] Open
Abstract
In contrast to influenza virus vaccination, natural infection induces long-lived and relatively broad immune responses. However, many aspects of the antibody response to natural infection are not well understood. Here, we assessed the immune response after H1N1 influenza virus infection in children and adults in a Nicaraguan household transmission study using an influenza virus protein microarray (IVPM). This technology allows us to simultaneously measure IgG and IgA antibody responses to hemagglutinins of many different virus strains and subtypes quantitatively with a high throughput. We found that children under 6 years of age responded to natural infection with a relatively narrow response that targeted mostly the hemagglutinin of the strain that caused the infection. Adults, however, have a much broader response, including a boost in antibodies to many group 1 subtype hemagglutinins. Also, a strong recall response against historic H1 hemagglutinins that share the K133 epitope with the pandemic H1N1 virus was observed. Of note, some children, while responding narrowly within H1 and group 1 hemagglutinins, induced a boost to H3 and other group 2 hemagglutinins when infected with H1N1 when they had experienced an H3N2 infection earlier in life. This is an interesting phenomenon providing evidence for immune imprinting and a significant new insight which might be leveraged in future universal influenza virus vaccine strategies. Finally, preexisting immunity to pandemic H1 hemagglutinins was significantly associated with protection from infection in both children and adults. In adults, preexisting immunity to non-H1 group 1 hemagglutinins was also significantly associated with protection from infection.IMPORTANCE It is known since Thomas Francis, Jr. published his first paper on original antigenic sin in 1960 that the first infection(s) with influenza virus leaves a special immunological imprint which shapes immune responses to future infections with antigenically related influenza virus strains. Imprinting has been implicated in both protective effects as well as blunting of the immune response to vaccines. Despite the fact that this phenomenon was already described almost 60 years ago, we have very little detailed knowledge of the characteristics and breadth of the immune response to the first exposure(s) to influenza virus in life and how this compares to later exposure as adults. Here, we investigate these immune responses in detail using an influenza virus protein microarray. While our findings are mostly descriptive in nature and based on a small sample size, they provide a strong basis for future large-scale studies to better understand imprinting effects.
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Affiliation(s)
- Philip Meade
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Centers of Excellence for Influenza Research and Surveillance (CEIRS)
- Center for Research on Influenza Pathogenesis (CRIP), New York, New York, USA
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Centers of Excellence for Influenza Research and Surveillance (CEIRS)
- Center for Research on Influenza Pathogenesis (CRIP), New York, New York, USA
| | - Hannah E Maier
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Fatima Amanat
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Centers of Excellence for Influenza Research and Surveillance (CEIRS)
- Center for Research on Influenza Pathogenesis (CRIP), New York, New York, USA
| | - Angel Balmaseda
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Kimihito Ito
- Division of Bioinformatics, Hokkaido University Research Center for Zoonosis Control, Kitaku, Japan
| | - Ericka Kirkpatrick
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Centers of Excellence for Influenza Research and Surveillance (CEIRS)
- Center for Research on Influenza Pathogenesis (CRIP), New York, New York, USA
| | - Andres Javier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lionel Gresh
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Centers of Excellence for Influenza Research and Surveillance (CEIRS)
- Center for Research on Influenza Pathogenesis (CRIP), New York, New York, USA
| | - Aubree Gordon
- Centers of Excellence for Influenza Research and Surveillance (CEIRS)
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- St. Jude Center of Excellence for Influenza Research and Surveillance, Memphis, Tennessee, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Centers of Excellence for Influenza Research and Surveillance (CEIRS)
- Center for Research on Influenza Pathogenesis (CRIP), New York, New York, USA
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24
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Kissling E, Pozo F, Buda S, Vilcu AM, Rizzo C, Gherasim A, Horváth JK, Brytting M, Domegan L, Meijer A, Paradowska-Stankiewicz I, Machado A, Vučina VV, Lazar M, Johansen K, Dürrwald R, van der Werf S, Bella A, Larrauri A, Ferenczi A, Zakikhany K, O'Donnell J, Dijkstra F, Bogusz J, Guiomar R, Filipović SK, Pitigoi D, Penttinen P, Valenciano M. Effectiveness of influenza vaccine against influenza A in Europe in seasons of different A(H1N1)pdm09 and the same A(H3N2) vaccine components (2016-17 and 2017-18). Vaccine X 2019; 3:100042. [PMID: 31660536 PMCID: PMC6807025 DOI: 10.1016/j.jvacx.2019.100042] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/13/2019] [Accepted: 09/15/2019] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION Influenza A(H3N2) viruses predominated in Europe in 2016-17. In 2017-18 A(H3N2) and A(H1N1)pdm09 viruses co-circulated. The A(H3N2) vaccine component was the same in both seasons; while the A(H1N1)pdm09 component changed in 2017-18. In both seasons, vaccine seed A(H3N2) viruses developed adaptations/alterations during propagation in eggs, impacting antigenicity. METHODS We used the test-negative design in a multicentre primary care case-control study in 12 European countries to measure 2016-17 and 2017-18 influenza vaccine effectiveness (VE) against laboratory-confirmed influenza A(H1N1)pdm09 and A(H3N2) overall and by age group. RESULTS During the 2017-18 season, the overall VE against influenza A(H1N1)pdm09 was 59% (95% CI: 47-69). Among those aged 0-14, 15-64 and ≥65 years, VE against A(H1N1)pdm09 was 64% (95% CI: 37-79), 50% (95% CI: 28-66) and 66% (95% CI: 42-80), respectively. Overall VE against influenza A(H3N2) was 28% (95% CI: 17-38) in 2016-17 and 13% (95% CI: -15 to 34) in 2017-18. Among 0-14-year-olds VE against A(H3N2) was 28% (95%CI: -10 to 53) and 29% (95% CI: -87 to 73), among 15-64-year-olds 34% (95% CI: 18-46) and 33% (95% CI: -3 to 56) and among those aged ≥65 years 15% (95% CI: -10 to 34) and -9% (95% CI: -74 to 32) in 2016-17 and 2017-18, respectively. CONCLUSIONS Our study suggests the new A(H1N1)pdm09 vaccine component conferred good protection against circulating strains, while VE against A(H3N2) was <35% in 2016-17 and 2017-18. The egg propagation derived antigenic mismatch of the vaccine seed virus with circulating strains may have contributed to this low effectiveness. A(H3N2) seed viruses for vaccines in subsequent seasons may be subject to the same adaptations; in years with lower than expected VE, recommendations of preventive measures other than vaccination should be given in a timely manner.
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Affiliation(s)
- Esther Kissling
- Epidemiology Department, Epiconcept, 47 rue de Charenton, 75012 Paris, France
| | - Francisco Pozo
- National Centre for Microbiology, National Influenza Reference Laboratory, WHO-National Influenza Centre, Institute of Health Carlos III, Madrid, Spain
| | - Silke Buda
- Robert Koch Institute, Department of Infectious Disease Epidemiology, Respiratory Infections Unit, Seestrasse 10, 13353 Berlin, Germany
| | - Ana-Maria Vilcu
- Sorbonne Université, INSERM, Institut Pierre Louis d’épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France
| | - Caterina Rizzo
- Department of Infectious Diseases, National Institute of Health, Rome, Italy
- Bambino Gesù Children’s Hospital, Rome, Italy
| | - Alin Gherasim
- National Epidemiology Centre, Institute of Health Carlos III, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid Spain
| | | | - Mia Brytting
- Public Health Agency of Sweden, Stockholm, Sweden
| | - Lisa Domegan
- Health Service Executive-Health Protection Surveillance Centre, 25-27 Middle Gardiner Street, Dublin 1 D01 A4A3, Ireland
| | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Ausenda Machado
- Departamento de Epidemiologia, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | | | - Mihaela Lazar
- “Cantacuzino” National Medico-Military Institute for Research and Development, Bucharest, Romania
| | - Kari Johansen
- European Centre for Disease Prevention and Control (ECDC), Gustav III:s boulevard 40, 169 73 Solna, Sweden
| | - Ralf Dürrwald
- Robert Koch Institute, National Reference Center for Influenza, Seestrasse 10, 13353 Berlin, Germany
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université Paris Diderot SPC, France
- CNR des Virus des Infections Respiratoires, WHO National Influenza Center, Institut Pasteur, France
| | - Antonino Bella
- Department of Infectious Diseases, National Institute of Health, Rome, Italy
| | - Amparo Larrauri
- National Epidemiology Centre, Institute of Health Carlos III, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid Spain
| | | | | | - Joan O'Donnell
- Health Service Executive-Health Protection Surveillance Centre, 25-27 Middle Gardiner Street, Dublin 1 D01 A4A3, Ireland
| | - Frederika Dijkstra
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Joanna Bogusz
- National Institute of Public Health-National Institute of Hygiene, Warsaw, Poland
| | - Raquel Guiomar
- Departamento de Doenças Infeciosas, Instituto Nacional de Saúde Dr. Ricardo Jorge, Portugal
| | | | - Daniela Pitigoi
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Pasi Penttinen
- European Centre for Disease Prevention and Control (ECDC), Gustav III:s boulevard 40, 169 73 Solna, Sweden
| | - Marta Valenciano
- Epidemiology Department, Epiconcept, 47 rue de Charenton, 75012 Paris, France
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25
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Auladell M, Nguyen TH, Garcillán B, Mackay F, Kedzierska K, Fox A. Distinguishing naive- from memory-derived human B cells during acute responses. Clin Transl Immunology 2019; 8:e01090. [PMID: 31844520 PMCID: PMC6851823 DOI: 10.1002/cti2.1090] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 12/17/2022] Open
Abstract
Objectives A fundamental question in influenza research is whether antibody titre decline upon successive exposure to variant strains is consequent to recall of cross‐reactive memory B cells that competitively inhibit naive B‐cell responses. In connection, it is not clear whether naive and memory B cells remain phenotypically distinct acutely after activation such that they may be distinguished ex vivo. Methods Here, we first compared the capacity of anti‐Ig and Toll‐like‐receptor (TLR) 7/8 and TLR9 agonists (R848 and CpG) to augment human B‐cell differentiation induced by IL‐21 and sCD40L. The conditions that induced optimal differentiation were then used to compare the post‐activation phenotype of sort‐purified naive and memory B‐cell subsets by FACS and antibody‐secreting cell (ASC) ELISPOT. Results Sort‐purified naive and memory B cells underwent robust plasmablast and ASC formation when stimulated with R848, but not CpG, and co‐cultured with monocytes. This coincided with increased IL‐1β and IL‐6 production when B cells were co‐cultured with monocytes and stimulated with R848, but not CpG. Naive B cells underwent equivalent ASC generation, but exhibited less class‐switch and modulation of CD27, CD38 and CD20 expression than memory B cells after stimulation with R848 and monocytes for 6 days. Conclusion Stimulation with R848, IL‐21 and sCD40L in the presence of monocytes induces robust differentiation and ASC generation from both naive and memory B‐cells. However, naive and memory B cells retain key phenotypic differences after activation that may facilitate ex vivo discrimination and better characterisation of acute responses to variant antigens.
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Affiliation(s)
- Maria Auladell
- Department of Microbiology and Immunology University of Melbourne at the Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Thi Ho Nguyen
- Department of Microbiology and Immunology University of Melbourne at the Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Beatriz Garcillán
- Department of Microbiology and Immunology University of Melbourne at the Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Fabienne Mackay
- Department of Microbiology and Immunology University of Melbourne at the Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology University of Melbourne at the Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Annette Fox
- WHO Collaborating Centre for Reference and Research on Influenza VIDRL at the Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
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26
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Kosikova M, Li L, Radvak P, Ye Z, Wan XF, Xie H. Imprinting of Repeated Influenza A/H3 Exposures on Antibody Quantity and Antibody Quality: Implications for Seasonal Vaccine Strain Selection and Vaccine Performance. Clin Infect Dis 2019; 67:1523-1532. [PMID: 29672713 DOI: 10.1093/cid/ciy327] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/12/2018] [Indexed: 01/04/2023] Open
Abstract
Background Reduced seasonal influenza vaccine effectiveness (VE) was observed in individuals who received repeated annual vaccinations. Preexisting influenza antibody levels were also found inversely correlated with postvaccination titers. These reports suggest that preexisting immunity may affect contemporary seasonal vaccine performance. Methods Influenza A/H3 specific cross-reactivity of postvaccination sera from humans with or without preexisting immunity was assessed by hemagglutination inhibition (HAI) assay. Ferret antisera induced by repeated H3 exposures were also subjected to HAI, antibody affinity, and antibody avidity analyses. Results Human postvaccination sera derived from subjects with or without preexisting immunity showed different cross-reactivity against H3 variant viruses. Similarly, the breadth of cross-reactive ferret antibodies induced by repeated H3 exposures was also broadened. Antigenic differences between H3 viruses characterized by ferret antisera became smaller as the number of exposures increased. Although repeated H3 exposures induced "original antigenic sin" phenomena in HAI titers against later exposed viruses, resultant ferret antibodies showed gradually enhanced avidity for different H3/hemagglutinin. Increased antibody avidity was found to be inversely correlated with decreased antigenic differences among H3 viruses characterized. Conclusions Our results suggest that repeated H3 exposures imprinted not only antibody quantity but also antibody quality. The "naive" ferret model currently used for vaccine strain selection does not recapitulate the complexity of human preexisting immunity. Vaccine strains identified hereby may not provide coverage sufficient for those who were frequently infected and/or vaccinated, leading to the reduced VE observed.
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Affiliation(s)
- Martina Kosikova
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Lei Li
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University
| | - Peter Radvak
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Zhiping Ye
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
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27
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Auladell M, Jia X, Hensen L, Chua B, Fox A, Nguyen THO, Doherty PC, Kedzierska K. Recalling the Future: Immunological Memory Toward Unpredictable Influenza Viruses. Front Immunol 2019; 10:1400. [PMID: 31312199 PMCID: PMC6614380 DOI: 10.3389/fimmu.2019.01400] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/03/2019] [Indexed: 01/09/2023] Open
Abstract
Persistent and durable immunological memory forms the basis of any successful vaccination protocol. Generation of pre-existing memory B cell and T cell pools is thus the key for maintaining protective immunity to seasonal, pandemic and avian influenza viruses. Long-lived antibody secreting cells (ASCs) are responsible for maintaining antibody levels in peripheral blood. Generated with CD4+ T help after naïve B cell precursors encounter their cognate antigen, the linked processes of differentiation (including Ig class switching) and proliferation also give rise to memory B cells, which then can change rapidly to ASC status after subsequent influenza encounters. Given that influenza viruses evolve rapidly as a consequence of antibody-driven mutational change (antigenic drift), the current influenza vaccines need to be reformulated frequently and annual vaccination is recommended. Without that process of regular renewal, they provide little protection against “drifted” (particularly H3N2) variants and are mainly ineffective when a novel pandemic (2009 A/H1N1 “swine” flu) strain suddenly emerges. Such limitation of antibody-mediated protection might be circumvented, at least in part, by adding a novel vaccine component that promotes cross-reactive CD8+ T cells specific for conserved viral peptides, presented by widely distributed HLA types. Such “memory” cytotoxic T lymphocytes (CTLs) can rapidly be recalled to CTL effector status. Here, we review how B cells and follicular T cells are elicited following influenza vaccination and how they survive into a long-term memory. We describe how CD8+ CTL memory is established following influenza virus infection, and how a robust CTL recall response can lead to more rapid virus elimination by destroying virus-infected cells, and recovery. Exploiting long-term, cross-reactive CTL against the continuously evolving and unpredictable influenza viruses provides a possible mechanism for preventing a disastrous pandemic comparable to the 1918-1919 H1N1 “Spanish flu,” which killed more than 50 million people worldwide.
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Affiliation(s)
- Maria Auladell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Luca Hensen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Brendon Chua
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Annette Fox
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Peter C Doherty
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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28
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Bajic G, Maron MJ, Adachi Y, Onodera T, McCarthy KR, McGee CE, Sempowski GD, Takahashi Y, Kelsoe G, Kuraoka M, Schmidt AG. Influenza Antigen Engineering Focuses Immune Responses to a Subdominant but Broadly Protective Viral Epitope. Cell Host Microbe 2019; 25:827-835.e6. [PMID: 31104946 DOI: 10.1016/j.chom.2019.04.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/12/2019] [Accepted: 04/08/2019] [Indexed: 10/26/2022]
Abstract
Viral glycoproteins are under constant immune surveillance by a host's adaptive immune responses. Antigenic variation including glycan introduction or removal is among the mechanisms viruses have evolved to escape host immunity. Understanding how glycosylation affects immunodominance on complex protein antigens may help decipher underlying B cell biology. To determine how B cell responses can be altered by such modifications, we engineered glycans onto the influenza virus hemagglutinin (HA) and characterized the molecular features of the elicited humoral immunity in mice. We found that glycan addition changed the initially diverse antibody repertoire into an epitope-focused, genetically restricted response. Structural analyses showed that one antibody gene family targeted a previously subdominant, occluded epitope at the head interface. Passive transfer of this antibody conferred Fc-dependent protection to influenza virus-challenged mice. These results have potential implications for next-generation viral vaccines aimed at directing B cell responses to preferred epitope(s).
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Affiliation(s)
- Goran Bajic
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Max J Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Yu Adachi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Taishi Onodera
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kevin R McCarthy
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Charles E McGee
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | | | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA.
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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29
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Skowronski DM, Chambers C, Sabaiduc S, De Serres G, Winter AL, Dickinson JA, Gubbay JB, Drews SJ, Martineau C, Charest H, Krajden M, Bastien N, Li Y. Beyond Antigenic Match: Possible Agent-Host and Immuno-epidemiological Influences on Influenza Vaccine Effectiveness During the 2015-2016 Season in Canada. J Infect Dis 2019; 216:1487-1500. [PMID: 29029166 PMCID: PMC5853508 DOI: 10.1093/infdis/jix526] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Vaccine effectiveness (VE) estimates for 2015-2016 seasonal influenza vaccine are reported from Canada's Sentinel Practitioner Surveillance Network (SPSN). This season was characterized by a delayed 2009 pandemic influenza A(H1N1) virus (A[H1N1]pdm09) epidemic and concurrent influenza B(Victoria) virus activity. Potential influences on VE beyond antigenic match are explored, including viral genomic variation, birth cohort effects, prior vaccination, and epidemic period. Methods VE was estimated by a test-negative design comparing the adjusted odds ratio for influenza test positivity among vaccinated compared to unvaccinated participants. Vaccine-virus relatedness was assessed by gene sequencing and hemagglutination inhibition assay. Results Analyses included 596 influenza A(H1N1)pdm09 and 305 B(Victoria) cases and 926 test-negative controls. A(H1N1)pdm09 viruses were considered antigenically related to vaccine (unchanged since 2009), despite phylogenetic clustering within emerging clade 6B.1. The adjusted VE against A(H1N1)pdm09 was 43% (95% confidence interval [CI], 25%-57%). Compared to other age groups, VE against A(H1N1)pdm09 was lower for adults born during 1957-1976 (25%; 95% CI, -16%-51%). The VE against A(H1N1)pdm09 was also lower for participants consecutively vaccinated during both the current and prior seasons (41%; 95% CI, 18%-57%) than for those vaccinated during the current season only (75%; 95% CI, 45%-88%), and the VE among participants presenting in March-April 2016 (19%; 95% CI, -15%-44%) was lower than that among those presenting during January-February 2016 (62%; 95% CI, 44%-74%). The adjusted VE for B(Victoria) viruses was 54% (95% CI, 32%-68%), despite lineage-level mismatch to B(Yamagata) vaccine. The further variation in VE as observed for A(H1N1)pdm09 was not observed for B(Victoria). Conclusions Influenza VE findings may require consideration of other agent-host and immuno-epidemiologic influences on vaccine performance beyond antigenic match, including viral genomic variation, repeat vaccination, birth (immunological) cohort effects, and potential within-season waning of vaccine protection.
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Affiliation(s)
- Danuta M Skowronski
- British Columbia Centre for Disease Control, Vancouver.,University of British Columbia, Vancouver
| | | | | | - Gaston De Serres
- Institut National de Santé Publique du Québec.,Laval University, Québec.,Centre Hospitalier Universitaire de Québec, Québec
| | | | | | | | - Steven J Drews
- Alberta Provincial Laboratory, Edmonton.,University of Alberta, Edmonton
| | | | | | - Mel Krajden
- British Columbia Centre for Disease Control, Vancouver.,University of British Columbia, Vancouver
| | - Nathalie Bastien
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Yan Li
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
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30
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H5N8 and H7N9 packaging signals constrain HA reassortment with a seasonal H3N2 influenza A virus. Proc Natl Acad Sci U S A 2019; 116:4611-4618. [PMID: 30760600 PMCID: PMC6410869 DOI: 10.1073/pnas.1818494116] [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] [Indexed: 12/24/2022] Open
Abstract
Influenza A virus (IAV) has a segmented genome, which (i) allows for exchange of gene segments in coinfected cells, termed reassortment, and (ii) necessitates a selective packaging mechanism to ensure incorporation of a complete set of segments into virus particles. Packaging signals serve as segment identifiers and enable segment-specific packaging. We have previously shown that packaging signals limit reassortment between heterologous IAV strains in a segment-dependent manner. Here, we evaluated the extent to which packaging signals prevent reassortment events that would raise concern for pandemic emergence. Specifically, we tested the compatibility of hemagglutinin (HA) packaging signals from H5N8 and H7N9 avian IAVs with a human seasonal H3N2 IAV. By evaluating reassortment outcomes, we demonstrate that HA segments carrying H5 or H7 packaging signals are significantly disfavored for incorporation into a human H3N2 virus in both cell culture and a guinea pig model. However, incorporation of the heterologous HAs was not excluded fully, and variants with heterologous HA packaging signals were detected at low levels in vivo, including in naïve contact animals. This work indicates that the likelihood of reassortment between human seasonal IAV and avian IAV is reduced by divergence in the RNA packaging signals of the HA segment. These findings offer important insight into the molecular mechanisms governing IAV emergence and inform efforts to estimate the risks posed by H7N9 and H5N8 subtype avian IAVs.
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31
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Mohl G, Liddle N, Nygaard J, Dorius A, Lyons N, Hodek J, Weber J, Michaelis DJ, Busath DD. Novel influenza inhibitors designed to target PB1 interactions with host importin RanBP5. Antiviral Res 2019; 164:81-90. [PMID: 30742842 DOI: 10.1016/j.antiviral.2019.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/30/2019] [Accepted: 02/03/2019] [Indexed: 11/19/2022]
Abstract
In search of novel targets for influenza inhibitors, a site on PB1 was selected for its high conservation and probable interaction with a host protein, RanBP5, that is key to nuclear import of PB1, where it complexes with PB2, PA, and NP to transcribe viral RNA. Docking with libraries of drug-like compounds led to a selection of five candidates that bound tightly and with a pose likely to inhibit protein binding. These were purchased and tested in vitro, found to be active, and then one was synthetically expanded to explore the structure-activity relationship. The top candidates had a carboxylic acid converted to an ester and electron-withdrawing substituents added to a phenyl group in the original structure. Resistance was slow to develop, but cytotoxicity was moderately high. Nuclear localization of PB1 and in vitro polymerase activity were both strongly inhibited.
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Affiliation(s)
- Gregory Mohl
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA.
| | - Nathan Liddle
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Joseph Nygaard
- Department of Chemistry and Biochemistry, Brigham Young University, USA
| | - Alexander Dorius
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Nathan Lyons
- Department of Chemistry and Biochemistry, Brigham Young University, USA
| | - Jan Hodek
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
| | - David J Michaelis
- Department of Chemistry and Biochemistry, Brigham Young University, USA.
| | - David D Busath
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA.
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32
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Zou G, Kosikova M, Kim SR, Kotian S, Wu WW, Shen R, Powers DN, Agarabi C, Xie H, Ju T. Comprehensive analysis of N-glycans in IgG purified from ferrets with or without influenza A virus infection. J Biol Chem 2018; 293:19277-19289. [PMID: 30315103 DOI: 10.1074/jbc.ra118.005294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/24/2018] [Indexed: 11/06/2022] Open
Abstract
Influenza viruses cause contagious respiratory infections, resulting in significant economic burdens to communities. Production of influenza-specific Igs, specifically IgGs, is one of the major protective immune mechanisms against influenza viruses. In humans, N-glycosylation of IgGs plays a critical role in antigen binding and effector functions. The ferret is the most commonly used animal model for studying influenza pathogenesis, virus transmission, and vaccine development, but its IgG structure and functions remain largely undefined. Here we show that ferret IgGs are N-glycosylated and that their N-glycan structures are diverse. Using a comprehensive strategy based on MS and ultra-HPLC analyses in combination with exoglycosidase digestions, we assigned 42 N-glycan structures in ferret IgGs. We observed that N-glycans of ferret IgGs consist mainly of complex-type glycans, including some high-mannose and hybrid glycans, similar to those observed in human IgG. The complex-type glycans of ferret IgGs were primarily core-fucosylated. Furthermore, a fraction of N-glycans carried bisecting GlcNAc. Ferret IgGs also had a minor fraction of glycans carrying α2-6Neu5Ac(s). We noted that, unlike human IgG, ferret IgGs have αGal epitopes on some N-glycans. Interestingly, influenza A infection caused prominent changes in the N-glycans of ferret IgG, mainly because of an increase in bisecting GlcNAc and F1A2G0 and a corresponding decrease in F1A2G1. This suggests that the glycosylation of virus-specific IgG may play a role in its functionality. Our study highlights the need to further elucidate the structure-function relationships of IgGs in universal influenza vaccine development.
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Affiliation(s)
- Guozhang Zou
- From the Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993 and
| | | | - Su-Ryun Kim
- From the Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993 and
| | - Shweta Kotian
- From the Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993 and
| | - Wells W Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | - Rongfong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | - David N Powers
- From the Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993 and
| | - Cyrus Agarabi
- From the Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993 and
| | - Hang Xie
- the Office of Vaccines Research and Review and
| | - Tongzhong Ju
- From the Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993 and
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33
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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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34
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Complexes of Oligoribonucleotides with d-Mannitol Modulate the Innate Immune Response to Influenza A Virus H1N1 (A/FM/1/47) In Vivo. Pharmaceuticals (Basel) 2018; 11:ph11030073. [PMID: 30037133 PMCID: PMC6161188 DOI: 10.3390/ph11030073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 12/16/2022] Open
Abstract
Rapid replication of the influenza A virus and lung tissue damage caused by exaggerated pro-inflammatory host immune responses lead to numerous deaths. Therefore, novel therapeutic agents that have anti-influenza activities and attenuate excessive pro-inflammatory responses that are induced by an influenza virus infection are needed. Oligoribonucleotides-d-mannitol (ORNs-d-M) complexes possess both antiviral and anti-inflammatory activities. The current research was aimed at studying the ORNs-d-M effects on expression of innate immune genes in mice lungs during an influenza virus infection. Expression of genes was determined by RT-qPCR and Western blot assays. In the present studies, we found that the ORNs-d-M reduced the influenza-induced up-expression of Toll-like receptors (TLRs) (tlr3, tlr7, tlr8), nuclear factor NF-kB (nfkbia, nfnb1), cytokines (ifnε, ifnk, ifna2, ifnb1, ifnγ, il6, il1b, il12a, tnf), chemokines (ccl3, ccl4, сcl5, cxcl9, cxcl10, cxcl11), interferon-stimulated genes (ISGs) (oas1a, oas2, oas3, mx1), and pro-oxidation (nos2, xdh) genes. The ORNs-d-M inhibited the mRNA overexpression of tlr3, tlr7, and tlr8 induced by the influenza virus, which suggests that they impair the upregulation of NF-kB, cytokines, chemokines, ISGs, and pro-oxidation genes induced by the influenza virus by inhibiting activation of the TLR-3, TLR-7, and TLR-8 signaling pathways. By impairing activation of the TLR-3, TLR-7, and TLR-8 signaling pathways, the ORNs-d-M can modulate the innate immune response to an influenza virus infection.
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35
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Xie H, Li L, Ye Z, Li X, Plant EP, Zoueva O, Zhao Y, Jing X, Lin Z, Kawano T, Chiang MJ, Finch CL, Kosikova M, Zhang A, Zhu Y, Wan XF. Differential Effects of Prior Influenza Exposures on H3N2 Cross-reactivity of Human Postvaccination Sera. Clin Infect Dis 2018; 65:259-267. [PMID: 28369230 DOI: 10.1093/cid/cix269] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/21/2017] [Indexed: 01/24/2023] Open
Abstract
Background Effectiveness of seasonal influenza vaccines mainly depends upon how well vaccine strains represent circulating viruses; mismatched strains can lead to reduced protection. Humans have complex influenza exposure histories that increase with age, which may lead to different postvaccination responses to emerging influenza variants. Recent observational studies also suggest that prior vaccination may influence the performance of current seasonal vaccines. Methods To elucidate the effects of age and influenza preexposures on cross-reactivity of vaccination-induced human antibodies, we generated antigenic maps based on postvaccination hemagglutination inhibition titers against representative H3 variants circulating during the 2015-2016, 2014-2015, and 2012-2013 influenza seasons. Results Antigenic maps determined using sera from subjects 18-64 and ≥65 years of age correlated well with each other but poorly with those determined using sera from children. Antigenic maps derived from human postvaccination sera with H1 influenza preexposure also correlated poorly with those derived from sera with neither H1 nor type B influenza preexposure, and the correlation lessened considerably over time. In contrast, antigenic maps derived from human postvaccination sera with only type B influenza preexposure consistently showed good correlation with those derived from sera with neither H1 nor type B influenza preexposure. Conclusions Our results suggest an age-specific difference in human postvaccination responses. Our findings also suggest that prior exposure to H1 or type B influenza may differentially affect cross-reactivity of vaccination-induced H3-specific hemagglutination inhibition antibody responses, and consequently might affect vaccine effectiveness. Our study highlights the need to study the impact of prior exposure on influenza vaccine performance.
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Affiliation(s)
- Hang Xie
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Lei Li
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi
| | - Zhiping Ye
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Xing Li
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Ewan P Plant
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Olga Zoueva
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Yangqing Zhao
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Xianghong Jing
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Zhengshi Lin
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Toshiaki Kawano
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Meng-Jung Chiang
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Courtney L Finch
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Martina Kosikova
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Anding Zhang
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Yanhong Zhu
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi
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36
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A small-molecule fragment that emulates binding of receptor and broadly neutralizing antibodies to influenza A hemagglutinin. Proc Natl Acad Sci U S A 2018; 115:4240-4245. [PMID: 29610325 DOI: 10.1073/pnas.1801999115] [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: 11/18/2022] Open
Abstract
The influenza virus hemagglutinin (HA) glycoprotein mediates receptor binding and membrane fusion during viral entry in host cells. Blocking these key steps in viral infection has applications for development of novel antiinfluenza therapeutics as well as vaccines. However, the lack of structural information on how small molecules can gain a foothold in the small, shallow receptor-binding site (RBS) has hindered drug design against this important target on the viral pathogen. Here, we report on the serendipitous crystallization-based discovery of a small-molecule N-cyclohexyltaurine, commonly known as the buffering agent CHES, that is able to bind to both group-1 and group-2 HAs of influenza A viruses. X-ray structural characterization of group-1 H5N1 A/Vietnam/1203/2004 (H5/Viet) and group-2 H3N2 A/Hong Kong/1/1968 (H3/HK68) HAs at 2.0-Å and 2.57-Å resolution, respectively, revealed that N-cyclohexyltaurine binds to the heart of the conserved HA RBS. N-cyclohexyltaurine mimics the binding mode of the natural receptor sialic acid and RBS-targeting bnAbs through formation of similar hydrogen bonds and CH-π interactions with the HA. In H3/HK68, N-cyclohexyltaurine also binds to a conserved pocket in the stem region, thereby exhibiting a dual-binding mode in group-2 HAs. These long-awaited structural insights into RBS recognition by a noncarbohydrate-based small molecule enhance our knowledge of how to target this important functional site and can serve as a template to guide the development of novel broad-spectrum small-molecule therapeutics against influenza virus.
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Clark AM, DeDiego ML, Anderson CS, Wang J, Yang H, Nogales A, Martinez-Sobrido L, Zand MS, Sangster MY, Topham DJ. Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. PLoS One 2017; 12:e0188267. [PMID: 29145498 PMCID: PMC5690631 DOI: 10.1371/journal.pone.0188267] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/05/2017] [Indexed: 11/18/2022] Open
Abstract
Antigenic drift of the hemagglutinin (HA) and neuraminidase (NA) influenza virus proteins contributes to reduced vaccine efficacy. To analyze antigenic drift in human seasonal H1N1 viruses derived from the 2009 pandemic H1N1 virus (pH1N1-like viruses) accounts for the limited effectiveness (around 40%) of vaccination against pH1N1-like viruses during the 2015-2016 season, nasal washes/swabs collected from adult subjects in the Rochester, NY area, were used to sequence and isolate the circulating viruses. The HA and NA proteins from viruses circulating during the 2015-2016 season encoded eighteen and fourteen amino acid differences, respectively, when compared to A/California/04/2009, a strain circulating at the origin of the 2009 pandemic. The circulating strains belonged to subclade 6B.1, defined by HA amino acid substitutions S101N, S179N, and I233T. Hemagglutination-inhibiting (HAI) and HA-specific neutralizing serum antibody (Ab) titers from around 50% of pH1N1-like virus-infected subjects and immune ferrets were 2-4 fold lower for the 2015-2016 circulating strains compared to the vaccine strain. In addition, using a luminex-based mPlex HA assay, the binding of human sera from subjects infected with pH1N1-like viruses to the HA proteins from circulating and vaccine strains was not identical, strongly suggesting antigenic differences in the HA protein. Additionally, NA inhibition (NAI) Ab titers in human sera from pH1N1-like virus-infected subjects increased after the infection and there were measurable antigenic differences between the NA protein of circulating strains and the vaccine strain using both ferret and human antisera. Despite having been vaccinated, infected subjects exhibited low HAI Ab titers against the vaccine and circulating strains. This suggests that poor responses to the H1N1 component of the vaccine as well as antigenic differences in the HA and NA proteins of currently circulating pH1N1-like viruses could be contributing to risk of infection even after vaccination.
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Affiliation(s)
- Amelia M. Clark
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Marta L. DeDiego
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail: (DT); (MD)
| | - Christopher S. Anderson
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Jiong Wang
- Division of Nephrology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Martin S. Zand
- Division of Nephrology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Mark Y. Sangster
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - David J. Topham
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail: (DT); (MD)
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Puig-Barberà J, Guglieri-López B, Tortajada-Girbés M, López-Labrador FX, Carballido-Fernández M, Mollar-Maseres J, Schwarz-Chavarri G, Baselga-Moreno V, Mira-Iglesias A, Díez-Domingo J. Low influenza vaccine effectiveness and the effect of previous vaccination in preventing admission with A(H1N1)pdm09 or B/Victoria-Lineage in patients 60 years old or older during the 2015/2016 influenza season. Vaccine 2017; 35:7331-7338. [PMID: 29128380 DOI: 10.1016/j.vaccine.2017.10.100] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/15/2017] [Accepted: 10/31/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND The 2015/2016 influenza season was characterized in Europe by the circulation of A(H1N1)pdm09 clade 6B.1 and B/Victoria-lineage influenza viruses. The components of the vaccines used in the current and past two seasons in the Valencia region were similar but not well matched to the 2015/2016 dominant influenza-circulating strains. We estimate influenza vaccine effectiveness (IVE) and interference of previous vaccination in preventing admission with A(H1N1)pdm09 or B/Victoria-lineage in this particular season. METHODS The Valencia Hospital Network for the Study of Influenza runs an active surveillance hospital-based study to collect clinical and virological data from consecutive admissions possibly related to influenza. Combined nasopharyngeal and pharyngeal swabs are analyzed by reverse transcription polymerase chain reaction, and the hemagglutinin is sequenced in a sample of positive influenza specimens. Vaccination is ascertained consulting a population vaccine information system. We estimate IVE using a test-negative approach. RESULTS During the 2015-2016 season, we recruited 1049 eligible admissions of patients 60 years or older, and 187 tested positive for influenza. The adjusted IVE in preventing admission with A(H1N1)pdm09 was 20.2%; 95% confidence interval (CI) -21.3-47.5% and -33.2%; 95% CI, -140.1-26.1% in preventing admission with B/Victoria-lineage. The majority of A(H1N1)pdm09 sequenced viruses belonged to the emerging 6B.1 subclade, defined by S162N and I216T mutations in the hemagglutinin protein. When we restricted our analysis to those not vaccinated in the previous year, unadjusted IVE was 84.9% (95% CI 9.9-100.0) overall, 77.9% (-32.7-100.0%) in preventing A(H1N1)pdm09 and 48.8% (-219.5-100.0%) in preventing B/Yamagata-lineage admission. CONCLUSIONS Our findings indicate that IVE was low in preventing A(H1N1)pdm09 and strongly correlated with vaccination in the previous season. No effect in preventing admission with B/Victoria-lineage was observed. For the 2015/2016 season, IVE was low due to a mismatch and lack of concordance between the circulating and vaccine viruses.
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Affiliation(s)
- Joan Puig-Barberà
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain; Centro de Salud Pública de Castellón, Castellón, Spain.
| | - Beatriz Guglieri-López
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain
| | | | - F Xavier López-Labrador
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain; Consorcio de Investigación Biomédica de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | - Víctor Baselga-Moreno
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain
| | - Ainara Mira-Iglesias
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain
| | - Javier Díez-Domingo
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain
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Anderson CS, Ortega S, Chaves FA, Clark AM, Yang H, Topham DJ, DeDiego ML. Natural and directed antigenic drift of the H1 influenza virus hemagglutinin stalk domain. Sci Rep 2017; 7:14614. [PMID: 29097696 PMCID: PMC5668287 DOI: 10.1038/s41598-017-14931-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/18/2017] [Indexed: 12/02/2022] Open
Abstract
The induction of antibodies specific for the influenza HA protein stalk domain is being pursued as a universal strategy against influenza virus infections. However, little work has been done looking at natural or induced antigenic variability in this domain and the effects on viral fitness. We analyzed human H1 HA head and stalk domain sequences and found substantial variability in both, although variability was highest in the head region. Furthermore, using human immune sera from pandemic A/California/04/2009 immune subjects and mAbs specific for the stalk domain, viruses were selected in vitro containing mutations in both domains that partially contributed to immune evasion. Recombinant viruses encoding amino acid changes in the HA stalk domain replicated well in vitro, and viruses incorporating two of the stalk mutations retained pathogenicity in vivo. These findings demonstrate that the HA protein stalk domain can undergo limited drift under immune pressure and the viruses can retain fitness and virulence in vivo, findings which are important to consider in the context of vaccination targeting this domain.
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Affiliation(s)
- Christopher S Anderson
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States
| | - Sandra Ortega
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States
| | - Francisco A Chaves
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States
| | - Amelia M Clark
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States.
| | - Marta L DeDiego
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States.
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Nuñez IA, Carlock MA, Allen JD, Owino SO, Moehling KK, Nowalk P, Susick M, Diagle K, Sweeney K, Mundle S, Vogel TU, Delagrave S, Ramgopal M, Zimmerman RK, Kleanthous H, Ross TM. Impact of age and pre-existing influenza immune responses in humans receiving split inactivated influenza vaccine on the induction of the breadth of antibodies to influenza A strains. PLoS One 2017; 12:e0185666. [PMID: 29091724 PMCID: PMC5665503 DOI: 10.1371/journal.pone.0185666] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 09/14/2017] [Indexed: 12/28/2022] Open
Abstract
Most humans have pre-existing immunity to influenza viruses. In this study, volunteers (ages of 18-85 years) were vaccinated with split, inactivated Fluzone™ influenza vaccine in four consecutive influenza seasons from 2013 to 2016 seasons. The impact of repeated vaccination on breadth and durability of antibodies was assessed as a result of vaccine strain changes. Total IgG anti-hemagglutinin (HA) binding antibodies and hemagglutination-inhibition (HAI) activity increased in all age groups against both influenza A HA components in the vaccine post-vaccination (day 21). However, younger subjects maintained seroprotective titers to the vaccine strains, which resulted in higher seroconversion rates in the elderly, since the HAI titers in elderly subjects were more likely to decline prior to the next season. Young subjects had significant HAI activity against historical, as well as contemporary H1 and H3 vaccine strains from the mid-1980s to present. In contrast, elderly subjects had HAI activity to H1 strains from all years, but were more likely to have HAI activity to older strains from 1918-1950s. They also had a more restricted HAI profile against H3 viruses compared to young subjects recognizing H3N2 influenza viruses from the mid-2000s to present. Vaccine recipients were then categorized by whether subjects seroconverted from a seronegative or seropositive pre-vaccination state. Regardless of age, immunological recall or 'back-boosting' to antigenically related strains were associated with seroconversion to the vaccine strain. Overall, both younger and older people have the ability to mount a breadth of immune responses following influenza vaccination. This report describes how imprinting exposure differs across age groups, influences antibody cross-reactivity to past hemagglutinin antigenic variants, and shapes immune responses elicited by current split inactivated influenza vaccines. Understanding how current influenza vaccines are influenced by pre-existing immunity in people of different ages is critical for designing the next-generation of 'universal' or broadly-protective influenza vaccines.
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Affiliation(s)
- Ivette A. Nuñez
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - Michael A. Carlock
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - James D. Allen
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - Simon O. Owino
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - Krissy K. Moehling
- Department of Family Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Patricia Nowalk
- Department of Family Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael Susick
- Department of Family Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kensington Diagle
- Martin Health System, Clinical Research Division, Stuart, Florida, United States of America
| | - Kristen Sweeney
- Martin Health System, Clinical Research Division, Stuart, Florida, United States of America
| | - Sophia Mundle
- Sanofi Pasteur, Inc., Research North America, Cambridge, Massachusetts, United States of America
| | - Thorsten U. Vogel
- Sanofi Pasteur, Inc., Research North America, Cambridge, Massachusetts, United States of America
| | - Simon Delagrave
- Sanofi Pasteur, Inc., Research North America, Cambridge, Massachusetts, United States of America
| | - Moti Ramgopal
- Martin Health System, Clinical Research Division, Stuart, Florida, United States of America
| | - Richard K. Zimmerman
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Harry Kleanthous
- Martin Health System, Clinical Research Division, Stuart, Florida, United States of America
| | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Kirchenbaum GA, Allen JD, Layman TS, Sautto GA, Ross TM. Infection of Ferrets with Influenza Virus Elicits a Light Chain-Biased Antibody Response against Hemagglutinin. THE JOURNAL OF IMMUNOLOGY 2017; 199:3798-3807. [PMID: 29079697 DOI: 10.4049/jimmunol.1701174] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/27/2017] [Indexed: 01/04/2023]
Abstract
The domestic ferret (Mustela putorius furo) is a commonly used animal model for the study of influenza virus infection and vaccination. Recently, our group has developed murine mAbs with specificity for the κ (Igκ) and λ (Igλ) L chains of ferret Ig. These mAbs were used to quantify the abundance of Igκ and Igλ in serum and to evaluate L chain usage of the Ab response against the hemagglutinin (HA) protein elicited by influenza infection. After influenza A infection of immunologically naive ferrets with various H1N1 or H3N2 strains, the acute Ab response against HA exhibited an inherent bias toward λ L chain usage. In contrast, secondary infection of H1N1 preimmune ferrets with an antigenically distinct H1N1 virus elicited a recall response against the original HA that was no longer biased toward Igλ and possessed differential specificity. Moreover, sequential infection of ferrets with H1N1 influenza viruses elicited an Igκ-biased Ab response directed against the HA globular head and stem regions. Furthermore, sequential infection of ferrets with viral vectors expressing chimeric HA, aimed at boosting Ab reactivity against the HA stem region, also elicited an Igκ-biased response. Collectively, these findings suggest that ferret B cells expressing an Igκ or Igλ BCR possess differential specificities, and highlight the utility of our recently developed mAbs for studying the immune response to influenza virus infection and vaccination in the ferret model.
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Affiliation(s)
- Greg A Kirchenbaum
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602; and
| | - James D Allen
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602; and
| | - Thomas S Layman
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602; and
| | - Giuseppe A Sautto
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602; and
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602; and .,Department of Infectious Diseases, University of Georgia, Athens, GA 30602
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Puig-Barberà J, Mira-Iglesias A, Tortajada-Girbés M, López-Labrador FX, Librero-López J, Díez-Domingo J, Carballido-Fernández M, Carratalá-Munuera C, Correcher-Medina P, Gil-Guillén V, Limón-Ramírez R, Mollar-Maseres J, Otero-Reigada MC, Schwarz H. Waning protection of influenza vaccination during four influenza seasons, 2011/2012 to 2014/2015. Vaccine 2017; 35:5799-5807. [PMID: 28941618 DOI: 10.1016/j.vaccine.2017.09.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 07/06/2017] [Accepted: 09/12/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND Concerns have been raised about intraseasonal waning of the protection conferred by influenza vaccination. METHODS During four influenza seasons, we consecutively recruited individuals aged 18years or older who had received seasonal influenza vaccine and were subsequently admitted to the hospital for influenza infection, asassessed by reverse transcription polymerase chain reaction. We estimated the adjusted odds ratio (aOR) of influenza infection by date of vaccination, defined by tertiles, as early, intermediate or late vaccination. We used a test-negative approach with early vaccination as reference to estimate the aOR of hospital admission with influenza among late vaccinees. We conducted sensitivity analyses by means of conditional logistic regression, Cox proportional hazards regression, and using days between vaccination and hospital admission rather than vaccination date. RESULTS Among 3615 admitted vaccinees, 822 (23%) were positive for influenza. We observed a lower risk of influenza among late vaccinees during the 2011/2012 and 2014/2015A(H3N2)-dominant seasons: aOR=0.68 (95% CI: 0.47-1.00) and 0.69 (95% CI: 0.50-0.95). We found no differences in the risk of admission with influenza among late versus early vaccinees in the 2012/2013A(H1N1)pdm09-dominant or 2013/2014B/Yamagata lineage-dominant seasons: aOR=1.18 (95% CI: 0.58-2.41) and 0.98 (95% CI: 0.56-1.72). When we restricted our analysis to individuals aged 65years or older, we found a statistically significant lower risk of admission with influenza among late vaccinees during the 2011/2012 and 2014/2015A(H3N2)-dominant seasons: aOR=0.61 (95% CI: 0.41-0.91) and 0.69 (95% CI: 0.49-0.96). We observed 39% (95% CI: 9-59%) and 31% (95% CI: 5-50%) waning of vaccine effectiveness among participants aged 65years or older during the two A(H3N2)-dominant seasons. Similar results were obtained in the sensitivity analyses. CONCLUSION Waning of vaccine protection was observed among individuals aged 65years old or over in two A(H3N2)-dominant influenza seasons.
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Affiliation(s)
- J Puig-Barberà
- FISABIO-Salud Pública, 46020 Valencia, Spain; Centro de Salud Pública de Castellón, 12003 Castellón, Spain.
| | | | | | - F X López-Labrador
- FISABIO-Salud Pública, 46020 Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - J Librero-López
- Navarrabiomed - Fundación Miguel Servet, 31008 Pamplona, Spain; REDISSEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - M Carballido-Fernández
- Universidad CEU-UCH, 12006 Castellón, Spain; Hospital General Universitario de Castellón, 12004 Castellón, Spain
| | - C Carratalá-Munuera
- Universidad Miguel Hernández, 03202 Elche, Spain; Hospital San Juan de Alicante, 03550 Alicante, Spain
| | | | | | | | | | | | - H Schwarz
- Hospital General de Alicante, 03010 Alicante, Spain
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Melnichuk N, Semernikova L, Tkachuk Z. Complexes of Oligoribonucleotides with D-Mannitol Inhibit Hemagglutinin-Glycan Interaction and Suppress Influenza A Virus H1N1 (A/FM/1/47) Infectivity In Vitro. Pharmaceuticals (Basel) 2017; 10:ph10030071. [PMID: 28792452 PMCID: PMC5620615 DOI: 10.3390/ph10030071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022] Open
Abstract
The influenza virus hemagglutinin (HA) mediates both receptor (glycan) binding and membrane fusion for cell entry and has been the basis for subtyping influenza viruses. The oligoribonucleotides-d-mannitol (ORNs-d-M) complexes possess an anti-influenza activity in vitro and in vivo. In the present studies, we have found that ORNs-d-M interferes with hemagglutinin (HA)–glycan interaction and suppress viral infection in host cells. HA–glycan interactions were evaluated to indirectly quantify the amount of influenza virus titer by an agglutination assay. Influenza virus infectivity was determined by TCID50 assay. The direct virucidal action of the complexes was evaluated by both cytopathic effects (CPE) reduction assay and cell MTT assay. We found that ORNs-d-M hinders interaction between HA and glycan. These complexes decreased the infectivity of influenza virus and had a direct virucidal action. ORNs-d-M reduces influenza virus infectivity, affecting the HA–glycan interaction in vitro. By suppressing the influenza viral infection, the ORNs-d-M can have direct virucidal action.
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Affiliation(s)
- Nataliia Melnichuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine.
| | - Larisa Semernikova
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine.
| | - Zenoviy Tkachuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine.
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Skowronski DM, Chambers C, De Serres G, Sabaiduc S, Winter AL, Dickinson JA, Gubbay JB, Fonseca K, Drews SJ, Charest H, Martineau C, Krajden M, Petric M, Bastien N, Li Y, Smith DJ. Serial Vaccination and the Antigenic Distance Hypothesis: Effects on Influenza Vaccine Effectiveness During A(H3N2) Epidemics in Canada, 2010-2011 to 2014-2015. J Infect Dis 2017; 215:1059-1099. [PMID: 28180277 PMCID: PMC5853783 DOI: 10.1093/infdis/jix074] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/02/2017] [Indexed: 11/14/2022] Open
Abstract
Background The antigenic distance hypothesis (ADH) predicts that negative interference from prior season's influenza vaccine (v1) on the current season's vaccine (v2) protection may occur when the antigenic distance is small between v1 and v2 (v1 ≈ v2) but large between v1 and the current epidemic (e) strain (v1 ≠ e). Methods Vaccine effectiveness (VE) against medically attended, laboratory-confirmed influenza A(H3N2) illness was estimated by test-negative design during 3 A(H3N2) epidemics (2010-2011, 2012-2013, 2014-2015) in Canada. Vaccine effectiveness was derived with covariate adjustment across v2 and/or v1 categories relative to no vaccine receipt among outpatients aged ≥9 years. Prior vaccination effects were interpreted within the ADH framework. Results Prior vaccination effects varied significantly by season, consistent with the ADH. There was no interference by v1 in 2010-2011 when v1 ≠ v2 and v1 ≠ e, with comparable VE for v2 alone or v2 + v1: 34% (95% confidence interval [CI] = -51% to 71%) versus 34% (95% CI = -5% to 58%). Negative interference by v1 was suggested in 2012-2013 with nonsignificant reduction in VE when v1 ≈ v2 and v1 ≠ e: 49% (95% CI = -47% to 83%) versus 28% (95% CI = -12% to 54%). Negative effects of prior vaccination were pronounced and statistically significant in 2014-2015 when v1 ≡ v2 and v1 ≠ e: 65% (95% CI = 25% to 83%) versus -33% (95% CI = -78% to 1%). Conclusions Effects of repeat influenza vaccination were consistent with the ADH and may have contributed to findings of low VE across recent A(H3N2) epidemics since 2010 in Canada.
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Affiliation(s)
- Danuta M Skowronski
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver
- School of Population and Public Health, University of British Columbia, Vancouver
| | - Catharine Chambers
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver
| | - Gaston De Serres
- Direction of Biological and Occupational Risks, Institut national de santé publique du Québec
- Department of Social and Preventive Medicine, Laval University, Québec
- Infection and Immunity, Centre Hospitalier Universitaire de Québec Research Centre
| | - Suzana Sabaiduc
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver
| | - Anne-Luise Winter
- Communicable Diseases, Emergency Preparedness and Response, Public Health Ontario, Toronto
| | - James A Dickinson
- Departments of Family Medicine and Community Health Sciences, University of Calgary
| | - Jonathan B Gubbay
- Public Health Ontario Laboratory, Public Health Ontario, Toronto
- Departments of Laboratory Medicine and Pathobiology and Paediatrics, University of Toronto
| | - Kevin Fonseca
- Diagnostic Virology, Alberta Provincial Laboratory, Calgary
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary
| | - Steven J Drews
- Diagnostic Virology, Alberta Provincial Laboratory, Edmonton
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton
| | - Hugues Charest
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec
- Département de microbiologie, d'infectiologie et d'immunologie, l'Université de Montréal
| | - Christine Martineau
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver
| | - Martin Petric
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver
| | - Nathalie Bastien
- Infectious Disease Prevention and Control Branch, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; and
| | - Yan Li
- Infectious Disease Prevention and Control Branch, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; and
| | - Derek J Smith
- Department of Zoology, University of Cambridge, England
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46
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Treanor J. Flu Vaccine-Too Much of a Good Thing? J Infect Dis 2017; 215:1017-1019. [PMID: 28180278 PMCID: PMC5853256 DOI: 10.1093/infdis/jix075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- John Treanor
- Infectious Diseases Division, Department of Medicine, University of Rochester Medical Center, Rochester, NY
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47
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Cobey S, Hensley SE. Immune history and influenza virus susceptibility. Curr Opin Virol 2017; 22:105-111. [PMID: 28088686 DOI: 10.1016/j.coviro.2016.12.004] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/14/2016] [Accepted: 12/20/2016] [Indexed: 12/25/2022]
Abstract
Antibody responses to influenza viruses are critical for protection, but the ways in which repeated viral exposures shape antibody evolution and effectiveness over time remain controversial. Early observations demonstrated that viral exposure history has a profound effect on the specificity and magnitude of antibody responses to a new viral strain, a phenomenon called 'original antigenic sin.' Although 'sin' might suppress some aspects of the immune response, so far there is little indication that hosts with pre-existing immunity are more susceptible to viral infections compared to naïve hosts. However, the tendency of the immune response to focus on previously recognized conserved epitopes when encountering new viral strains can create an opportunity cost when mutations arise in these conserved epitopes. Hosts with different exposure histories may continue to experience distinct patterns of infection over time, which may influence influenza viruses' continued antigenic evolution. Understanding the dynamics of B cell competition that underlie the development of antibody responses might help explain the low effectiveness of current influenza vaccines and lead to better vaccination strategies.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 19104, USA.
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
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48
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Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol. Proc Natl Acad Sci U S A 2016; 114:206-214. [PMID: 28003465 DOI: 10.1073/pnas.1617020114] [Citation(s) in RCA: 298] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The broad-spectrum antiviral drug Arbidol shows efficacy against influenza viruses by targeting the hemagglutinin (HA) fusion machinery. However, the structural basis of the mechanism underlying fusion inhibition by Arbidol has remained obscure, thereby hindering its further development as a specific and optimized influenza therapeutic. We determined crystal structures of Arbidol in complex with influenza virus HA from pandemic 1968 H3N2 and recent 2013 H7N9 viruses. Arbidol binds in a hydrophobic cavity in the HA trimer stem at the interface between two protomers. This cavity is distal to the conserved epitope targeted by broadly neutralizing stem antibodies and is ∼16 Å from the fusion peptide. Arbidol primarily makes hydrophobic interactions with the binding site but also induces some conformational rearrangements to form a network of inter- and intraprotomer salt bridges. By functioning as molecular glue, Arbidol stabilizes the prefusion conformation of HA that inhibits the large conformational rearrangements associated with membrane fusion in the low pH of the endosome. This unique binding mode compared with the small-molecule inhibitors of other class I fusion proteins enhances our understanding of how small molecules can function as fusion inhibitors and guides the development of broad-spectrum therapeutics against influenza virus.
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49
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Universal or Specific? A Modeling-Based Comparison of Broad-Spectrum Influenza Vaccines against Conventional, Strain-Matched Vaccines. PLoS Comput Biol 2016; 12:e1005204. [PMID: 27977667 PMCID: PMC5157952 DOI: 10.1371/journal.pcbi.1005204] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 10/15/2016] [Indexed: 01/21/2023] Open
Abstract
Despite the availability of vaccines, influenza remains a major public health challenge. A key reason is the virus capacity for immune escape: ongoing evolution allows the continual circulation of seasonal influenza, while novel influenza viruses invade the human population to cause a pandemic every few decades. Current vaccines have to be updated continually to keep up to date with this antigenic change, but emerging ‘universal’ vaccines—targeting more conserved components of the influenza virus—offer the potential to act across all influenza A strains and subtypes. Influenza vaccination programmes around the world are steadily increasing in their population coverage. In future, how might intensive, routine immunization with novel vaccines compare against similar mass programmes utilizing conventional vaccines? Specifically, how might novel and conventional vaccines compare, in terms of cumulative incidence and rates of antigenic evolution of seasonal influenza? What are their potential implications for the impact of pandemic emergence? Here we present a new mathematical model, capturing both transmission dynamics and antigenic evolution of influenza in a simple framework, to explore these questions. We find that, even when matched by per-dose efficacy, universal vaccines could dampen population-level transmission over several seasons to a greater extent than conventional vaccines. Moreover, by lowering opportunities for cross-protective immunity in the population, conventional vaccines could allow the increased spread of a novel pandemic strain. Conversely, universal vaccines could mitigate both seasonal and pandemic spread. However, where it is not possible to maintain annual, intensive vaccination coverage, the duration and breadth of immunity raised by universal vaccines are critical determinants of their performance relative to conventional vaccines. In future, conventional and novel vaccines are likely to play complementary roles in vaccination strategies against influenza: in this context, our results suggest important characteristics to monitor during the clinical development of emerging vaccine technologies. Influenza vaccines used today offer good protection, but have limitations: they have to be updated regularly, to remain effective in the face of ongoing virus evolution, and they cannot be used in advance of an influenza pandemic. In this study we considered how such ‘conventional’ vaccines might compare on the population level against new ‘universal’ vaccines currently being developed, that may protect against a broad spectrum of influenza viruses. We developed a mathematical model to capture the interactions between vaccination, influenza transmission, and viral evolution. The model suggests that annual vaccination with universal vaccines could control annual influenza epidemics more efficiently than conventional vaccines. In doing so they could slow viral evolution, rather than promoting it, while maintaining the broadly protective immunity that could mitigate against the emergence of a pandemic. These effects depend sensitively on the duration of protection that universal vaccines can afford, an important quantity to monitor in their development. In future, it is likely that conventional and universal vaccines would be deployed in tandem: we suggest that they could fulfill distinct roles, with universal vaccines being prioritised for managing transmission and evolution, and conventional vaccines being focused on protecting specific risk groups.
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50
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López-Labrador FX, Natividad-Sancho A, Pisareva M, Komissarov A, Salvatierra K, Fadeev A, Moya A, Grudinin M, Díez-Domingo J, Afanasieva O, Konovalova N, Sominina A, Puig-Barberà J. Genetic characterization of influenza viruses from influenza-related hospital admissions in the St. Petersburg and Valencia sites of the Global Influenza Hospital Surveillance Network during the 2013/14 influenza season. J Clin Virol 2016; 84:32-38. [PMID: 27690141 DOI: 10.1016/j.jcv.2016.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/06/2016] [Accepted: 09/19/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Continuous surveillance for genetic changes in circulating influenza viruses is needed to guide influenza prevention and control. OBJECTIVES To compare intra-seasonal influenza genetic diversity of hemagglutinin in influenza A strains isolated from influenza hospital admissions collected at two distinct sites during the same season. STUDY DESIGN Comparative phylogenetic analysis of full-length hemagglutinin genes from 77 isolated influenza A viruses from the St. Petersburg, Russian Federation and Valencia, Spain sites of the Global Influenza Hospital Surveillance Network (GIHSN) during the 2013/14 season. RESULTS We found significant variability in A(H3N2) and A(H1N1)pdm09 viruses between the two sites, with nucleotide variation at antigenic positions much lower for A(H1N1)pdm09 than for A(H3N2) viruses. For A(H1N1)pdm09, antigenic sites differed by three to four amino acids from the vaccine strain, two of them common to all tested isolates. For A(H3N2) viruses, antigenic sites differed by six to nine amino acids from the vaccine strain, four of them common to all tested isolates. A fifth amino acid substitution in the antigenic sites of A(H3N2) defined a new clade, 3C.2. For both influenza A subtypes, pairwise amino acid distances between circulating viruses and vaccine strains were significantly higher at antigenic than at non-antigenic sites. Whereas A(H1N1)pdm09 viruses clustered with clade 6B and 94% of A(H3N2) with clade 3C.3, at both study sites A(H3N2) clade 3C.2 viruses emerged towards the end of the season, showing greater pairwise amino acid distances from the vaccine strain compared to the predominant clade 3C.3. CONCLUSIONS Influenza A antigenic variants differed between St. Petersburg and Valencia, and A(H3N2) clade 3C.2 viruses were characterized by more amino acid differences from the vaccine strain, especially at the antigenic sites.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Child
- Child, Preschool
- Epidemiological Monitoring
- Female
- Genetic Variation
- Genome, Viral
- Global Health
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Infant
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Male
- Middle Aged
- Phylogeny
- RNA, Viral/genetics
- Russia/epidemiology
- Seasons
- Sequence Analysis, DNA
- Spain/epidemiology
- Young Adult
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Affiliation(s)
- F Xavier López-Labrador
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain; Joint Units of Infection and of Genomics and Health, FISABIO/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Publica (CIBER-ESP), Instituto de Salud Carlos III, Spain.
| | - Angels Natividad-Sancho
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain.
| | - Maria Pisareva
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Andrey Komissarov
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Karina Salvatierra
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain; Joint Units of Infection and of Genomics and Health, FISABIO/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Spain.
| | - Artem Fadeev
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Andrés Moya
- Joint Units of Infection and of Genomics and Health, FISABIO/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Spain.
| | - Mikhail Grudinin
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Javier Díez-Domingo
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain.
| | - Olga Afanasieva
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Nadezhda Konovalova
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Anna Sominina
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Joan Puig-Barberà
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain.
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