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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Bahojb Mahdavi SZ, Jebelli A, Aghbash PS, Baradaran B, Amini M, Oroojalian F, Pouladi N, Baghi HB, de la Guardia M, Mokhtarzadeh AA. A comprehensive overview on the crosstalk between microRNAs and viral pathogenesis and infection. Med Res Rev 2024. [PMID: 39185567 DOI: 10.1002/med.22073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 04/11/2023] [Accepted: 08/04/2024] [Indexed: 08/27/2024]
Abstract
Infections caused by viruses as the smallest infectious agents, pose a major threat to global public health. Viral infections utilize different host mechanisms to facilitate their own propagation and pathogenesis. MicroRNAs (miRNAs), as small noncoding RNA molecules, play important regulatory roles in different diseases, including viral infections. They can promote or inhibit viral infection and have a pro-viral or antiviral role. Also, viral infections can modulate the expression of host miRNAs. Furthermore, viruses from different families evade the host immune response by producing their own miRNAs called viral miRNAs (v-miRNAs). Understanding the replication cycle of viruses and their relation with host miRNAs and v-miRNAs can help to find new treatments against viral infections. In this review, we aim to outline the structure, genome, and replication cycle of various viruses including hepatitis B, hepatitis C, influenza A virus, coronavirus, human immunodeficiency virus, human papillomavirus, herpes simplex virus, Epstein-Barr virus, Dengue virus, Zika virus, and Ebola virus. We also discuss the role of different host miRNAs and v-miRNAs and their role in the pathogenesis of these viral infections.
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Affiliation(s)
- Seyedeh Zahra Bahojb Mahdavi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Asiyeh Jebelli
- Department of Biological Science, Faculty of Basic Science, Higher Education Institute of Rab-Rashid, Tabriz, Iran
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Nasser Pouladi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Burjassot, Valencia, Spain
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3
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Misra S, Gilbride E, Ramasamy S, Pond SLK, Kuchipudi SV. Enhanced Diversifying Selection on Polymerase Genes in H5N1 Clade 2.3.4.4b: A Key Driver of Altered Species Tropism and Host Range Expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.606826. [PMID: 39229076 PMCID: PMC11370473 DOI: 10.1101/2024.08.19.606826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses have shown unprecedented host range and pathogenicity, including infections in cattle, previously not susceptible to H5N1. We investigated whether selection pressures on clade 2.3.4.4b viral genes could shed light on their unique epidemiological features. Our analysis revealed that while the gene products of clade 2.3.4.4b H5N1 primarily undergo purifying selection, there are notable instances of episodic diversifying selection. Specifically, the polymerase genes PB2, PB1, and PA exhibit significantly greater selection pressures in clade 2.3.4.4b than all earlier H5N1 virus clades. Polymerases play critical roles in influenza virus adaptation, including viral fitness, interspecies transmission, and virulence. Our findings provide evidence that significant selection pressures have shaped the evolution of the H5N1 clade 2.3.4.4b viruses, facilitating their expanded host tropism and the potential for further adaptation to mammalian hosts. We discuss how exogenous factors, such as altered bird migration patterns and increased host susceptibility, may have contributed to the expanded host range. As H5N1 viruses continue to infect new hosts, there is a greater risk of emergent novel variants with increased pathogenicity in humans and animals. Thus, comprehensive One Health surveillance is critical to monitor transmission among avian and mammalian hosts.
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4
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Ryder R, Smith E, Borthwick D, Elder J, Panditrao M, Morales C, Wadford DA. Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022. Viruses 2024; 16:1209. [PMID: 39205183 PMCID: PMC11359944 DOI: 10.3390/v16081209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants constitute a challenge for public health authorities worldwide. Recombinant variants, composed of two or more SARS-CoV-2 lineages, often have unknown impacts on transmission, immune escape, and virulence in the early stages of emergence. We examined 4213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 in California to describe regional and statewide trends in prevalence. Many of these recombinant genomes, such as those belonging to the XZ lineage or novel recombinant lineages, likely originated within the state of California. We discuss the challenges and limitations surrounding Pango lineage assignments, the use of publicly available sequence data, and adequate sample sizes for epidemiologic analyses. Although these challenges will continue as SARS-CoV-2 sequencing volumes decrease globally, this study enhances our understanding of SARS-CoV-2 recombinant genomes to date while providing a foundation for future insights into emerging recombinant lineages.
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Affiliation(s)
- Rahil Ryder
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Emily Smith
- Theiagen Genomics, Highlands Ranch, CO 80129, USA;
| | - Deva Borthwick
- COVID Control Branch, Division of Communicable Disease Control, CDPH, Richmond, CA 94804, USA
| | - Jesse Elder
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Mayuri Panditrao
- COVID Control Branch, Division of Communicable Disease Control, CDPH, Richmond, CA 94804, USA
| | - Christina Morales
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Debra A. Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
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5
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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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6
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He CQ, Kong C, He M, Chen GX, Liu SM, Ding NZ. Intrasegmental recombination as an evolutionary force of Lassa fever virus. Front Microbiol 2024; 15:1411537. [PMID: 38832113 PMCID: PMC11144899 DOI: 10.3389/fmicb.2024.1411537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
Lassa fever (LF), caused by Lassa virus (LASV), is one of the most dangerous diseases to public health. Homologous recombination (HR) is a basic genetic power driving biological evolution. However, as a negative-stranded RNA virus, it is unknown whether HR occurs between LASVs and its influence on the outbreak of LF. In this study, after analyzing 575 S and 433 L segments of LASV collected in Africa, we found that LASV can achieve HR in both of its segments. Interestingly, although the length of S segment is less than half of the L segment, the proportion of LASVs with S recombinants is significantly higher than that with L recombinants. These results suggest that HR may be a feature of LASV, which can be set by natural selection to produce beneficial or eliminate harmful mutations for the virus, so it plays a role in LASV evolution during the outbreak of LF.
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Affiliation(s)
- Cheng-Qiang He
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Science, Shandong Normal University, Jinan, China
| | | | | | | | | | - Nai-Zheng Ding
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Science, Shandong Normal University, Jinan, China
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7
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Yang C, Chen J, Zhou H, Zeng D, Wan H, Yang J. Therapeutic effect of Yinhuapinggan granules mediated through the intestinal flora in mice infected with the H1N1 influenza virus. Front Microbiol 2024; 15:1394304. [PMID: 38741735 PMCID: PMC11089240 DOI: 10.3389/fmicb.2024.1394304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 05/16/2024] Open
Abstract
Objective In this study, we examined the therapeutic effects of Yinhuapinggan granules (YHPGs) in influenza-infected mice. We also examined how YHPGs affect the composition of the intestinal flora and associated metabolites. Methods We used the nasal drip method to administer the influenza A virus (IAV) H1N1 to ICR mice. Following successful model construction, the mice were injected with 0.9% sterile saline and low (5.5 g/kg), medium (11 g/kg), and high (22 g/kg) doses of YHPGs. The pathological changes in the lungs and intestines were evaluated by gavage for 5 consecutive days. Detection of sIgA, IL-6, TNF-α, INF-γ, and TGF-β cytokine levels in serum by enzyme-linked immunosorbent assay. Real-time fluorescence quantitative polymerase chain reaction and Western blot were used to measure the mRNA and protein expression of the tight junction proteins claudin-1, occludin, and zonula occludens-1 (ZO-1) in the colon. To assess the influence of YHPGs on the intestinal microbiota, feces were obtained from the mice for 16s rRNA sequencing, and short-chain fatty acids (SCFAs) were measured in the feces. Results By reducing the production of pro-inflammatory cytokines and increasing the relative expression of claudin-1, occludin, and ZO-1 in colon tissues, YHPGs had a protective effect in tissues from the lungs and colon. When YHPGs were administered to mice with IAV infection, the relative abundance of Lactobacillus, Coprobacillus, Akkermansia, Prevotella, Oscillospira, and Ruminococcus increased, whereas the relative abundance of Desulfovibrio decreased. Conclusion The therapeutic mechanism of YHPGs against IAV infection in mice may be underpinned by modulation of the structural composition of colonic bacteria and regulation of SCFA production.
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Affiliation(s)
- Can Yang
- School of Basic Medical Sciences, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Jing Chen
- School of Life Sciences, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Huifen Zhou
- School of Life Sciences, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Di Zeng
- School of Life Sciences, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Haitong Wan
- School of Basic Medical Sciences, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Jiehong Yang
- School of Basic Medical Sciences, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
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8
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Ranum JN, Ledwith MP, Alnaji FG, Diefenbacher M, Orton R, Sloan E, Güereca M, Feltman E, Smollett K, da Silva Filipe A, Conley M, Russell A, Brooke C, Hutchinson E, Mehle A. Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome. Nucleic Acids Res 2024; 52:3199-3212. [PMID: 38407436 PMCID: PMC11014358 DOI: 10.1093/nar/gkae133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/27/2024] Open
Abstract
Productive infections by RNA viruses require faithful replication of the entire genome. Yet many RNA viruses also produce deletion-containing viral genomes (DelVGs), aberrant replication products with large internal deletions. DelVGs interfere with the replication of wild-type virus and their presence in patients is associated with better clinical outcomes. The DelVG RNA itself is hypothesized to confer this interfering activity. DelVGs antagonize replication by out-competing the full-length genome and triggering innate immune responses. Here, we identify an additionally inhibitory mechanism mediated by a new class of viral proteins encoded by DelVGs. We identified hundreds of cryptic viral proteins translated from DelVGs. These DelVG-encoded proteins (DPRs) include canonical viral proteins with large internal deletions, as well as proteins with novel C-termini translated from alternative reading frames. Many DPRs retain functional domains shared with their full-length counterparts, suggesting they may have activity during infection. Mechanistic studies of DPRs derived from the influenza virus protein PB2 showed that they poison replication of wild-type virus by acting as dominant-negative inhibitors of the viral polymerase. These findings reveal that DelVGs have a dual inhibitory mechanism, acting at both the RNA and protein level. They further show that DPRs have the potential to dramatically expand the functional proteomes of diverse RNA viruses.
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Affiliation(s)
- Jordan N Ranum
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mitchell P Ledwith
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fadi G Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Meghan Diefenbacher
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Elizabeth Sloan
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Melissa Güereca
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth M Feltman
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | | | - Michaela Conley
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alistair B Russell
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Edward Hutchinson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Andrew Mehle
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
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9
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Lou J, Liang W, Cao L, Hu I, Zhao S, Chen Z, Chan RWY, Cheung PPH, Zheng H, Liu C, Li Q, Chong MKC, Zhang Y, Yeoh EK, Chan PKS, Zee BCY, Mok CKP, Wang MH. Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations. Nat Commun 2024; 15:2546. [PMID: 38514647 PMCID: PMC10958014 DOI: 10.1038/s41467-024-46918-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/12/2024] [Indexed: 03/23/2024] Open
Abstract
Influenza virus continuously evolves to escape human adaptive immunity and generates seasonal epidemics. Therefore, influenza vaccine strains need to be updated annually for the upcoming flu season to ensure vaccine effectiveness. We develop a computational approach, beth-1, to forecast virus evolution and select representative virus for influenza vaccine. The method involves modelling site-wise mutation fitness. Informed by virus genome and population sero-positivity, we calibrate transition time of mutations and project the fitness landscape to future time, based on which beth-1 selects the optimal vaccine strain. In season-to-season prediction in historical data for the influenza A pH1N1 and H3N2 viruses, beth-1 demonstrates superior genetic matching compared to existing approaches. In prospective validations, the model shows superior or non-inferior genetic matching and neutralization against circulating virus in mice immunization experiments compared to the current vaccine. The method offers a promising and ready-to-use tool to facilitate vaccine strain selection for the influenza virus through capturing heterogeneous evolutionary dynamics over genome space-time and linking molecular variants to population immune response.
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Affiliation(s)
- Jingzhi Lou
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- Beth Bioinformatics Co. Ltd, Hong Kong SAR, China
| | - Weiwen Liang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lirong Cao
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Inchi Hu
- Department of Statistics, George Mason University, Fairfax, VA, USA
| | - Shi Zhao
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- School of Public Health, Tianjin Medical University, Tianjin, China
| | - Zigui Chen
- Department of Microbiology, CUHK, Hong Kong SAR, China
| | - Renee Wan Yi Chan
- Department of Paediatrics, CUHK, Hong Kong SAR, China
- Hong Kong Hub of Paediatric Excellence, CUHK, Hong Kong SAR, China
| | | | - Hong Zheng
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
| | - Caiqi Liu
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
| | - Qi Li
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
| | - Marc Ka Chun Chong
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Yexian Zhang
- Beth Bioinformatics Co. Ltd, Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Eng-Kiong Yeoh
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- Centre for Health Systems and Policy Research, CUHK, Hong Kong SAR, China
| | - Paul Kay-Sheung Chan
- Department of Microbiology, CUHK, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, CUHK, Hong Kong SAR, China
| | - Benny Chung Ying Zee
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Chris Ka Pun Mok
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, CUHK, Hong Kong SAR, China.
| | - Maggie Haitian Wang
- JC School of Public Health and Primary Care (JCSPHPC), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China.
- CUHK Shenzhen Research Institute, Shenzhen, China.
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10
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Ranum JN, Ledwith MP, Alnaji FG, Diefenbacher M, Orton R, Sloan E, Guereca M, Feltman EM, Smollett K, da Silva Filipe A, Conley M, Russell AB, Brooke CB, Hutchinson E, Mehle A. Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.570638. [PMID: 38168266 PMCID: PMC10760031 DOI: 10.1101/2023.12.12.570638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Productive infections by RNA viruses require faithful replication of the entire genome. Yet many RNA viruses also produce deletion-containing viral genomes (DelVGs), aberrant replication products with large internal deletions. DelVGs interfere with the replication of wild-type virus and their presence in patients is associated with better clinical outcomes as they. The DelVG RNA itself is hypothesized to confer this interfering activity. DelVGs antagonize replication by out-competing the full-length genome and triggering innate immune responses. Here, we identify an additionally inhibitory mechanism mediated by a new class of viral proteins encoded by DelVGs. We identified hundreds of cryptic viral proteins translated from DelVGs. These DelVG-encoded proteins (DPRs) include canonical viral proteins with large internal deletions, as well as proteins with novel C-termini translated from alternative reading frames. Many DPRs retain functional domains shared with their full-length counterparts, suggesting they may have activity during infection. Mechanistic studies of DPRs derived from the influenza virus protein PB2 showed that they poison replication of wild-type virus by acting as dominant-negative inhibitors of the viral polymerase. These findings reveal that DelVGs have a dual inhibitory mechanism, acting at both the RNA and protein level. They further show that DPRs have the potential to dramatically expand the functional proteomes of diverse RNA viruses.
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Affiliation(s)
- Jordan N Ranum
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison WI 53706 USA
| | - Mitchell P Ledwith
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison WI 53706 USA
| | - Fadi G Alnaji
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | | | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Elisabeth Sloan
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Melissa Guereca
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 USA
| | - Elizabeth M Feltman
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison WI 53706 USA
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | | | - Michaela Conley
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alistair B Russell
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Edward Hutchinson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Andrew Mehle
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison WI 53706 USA
- Lead contact
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11
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Carpenter MJ, Rodgers CR, Torchetti MK, Fox KA, Burton M, Sherman TJ, Mayo CE. Recovery of multireassortant bluetongue virus serotype 6 sequences from a mule deer (Odocoileus hemionus) and Dorset sheep (Ovis aries) in Colorado. Vet Microbiol 2024; 289:109944. [PMID: 38141398 DOI: 10.1016/j.vetmic.2023.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 12/25/2023]
Abstract
We report the discovery of two bluetongue virus serotype 6 (BTV-6) reassortants recovered from a domestic sheep and a free-ranging mule deer in northern Colorado. At the time of this publication, whole-genome sequencing of BTV-6 isolates in the Western U.S. have not been undertaken. These findings reflect the incursive movement of geographically distinct BTV serotypes into important agricultural areas of the U.S. and demonstrate reassortment with regionally circulating serotypes.
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Affiliation(s)
- Molly J Carpenter
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA.
| | - Case R Rodgers
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA.
| | - Mia K Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, US Department of Agriculture, 1800 Dayton Ave, Ames, IA 50010, USA.
| | - Karen A Fox
- Colorado Division of Parks and Wildlife, 4330 Laporte Avenue, Fort Collins, CO 80521, USA.
| | - Mollie Burton
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA.
| | - Tyler J Sherman
- Diagnostic Medicine Center, Colorado State University, 2450 Gillette Drive, Fort Collins, CO 80526, USA.
| | - Christie E Mayo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA.
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12
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Li X, Li Y, Shang X, Kong H. A sequence-based machine learning model for predicting antigenic distance for H3N2 influenza virus. Front Microbiol 2024; 15:1345794. [PMID: 38314434 PMCID: PMC10834737 DOI: 10.3389/fmicb.2024.1345794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Introduction Seasonal influenza A H3N2 viruses are constantly changing, reducing the effectiveness of existing vaccines. As a result, the World Health Organization (WHO) needs to frequently update the vaccine strains to match the antigenicity of emerged H3N2 variants. Traditional assessments of antigenicity rely on serological methods, which are both labor-intensive and time-consuming. Although numerous computational models aim to simplify antigenicity determination, they either lack a robust quantitative linkage between antigenicity and viral sequences or focus restrictively on selected features. Methods Here, we propose a novel computational method to predict antigenic distances using multiple features, including not only viral sequence attributes but also integrating four distinct categories of features that significantly affect viral antigenicity in sequences. Results This method exhibits low error in virus antigenicity prediction and achieves superior accuracy in discerning antigenic drift. Utilizing this method, we investigated the evolution process of the H3N2 influenza viruses and identified a total of 21 major antigenic clusters from 1968 to 2022. Discussion Interestingly, our predicted antigenic map aligns closely with the antigenic map generated with serological data. Thus, our method is a promising tool for detecting antigenic variants and guiding the selection of vaccine candidates.
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Affiliation(s)
- Xingyi Li
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Big Data Storage and Management MIIT Lab, Xi'an, Shaanxi, China
| | - Yanyan Li
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Big Data Storage and Management MIIT Lab, Xi'an, Shaanxi, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Big Data Storage and Management MIIT Lab, Xi'an, Shaanxi, China
| | - Huihui Kong
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, China
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13
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Trovão NS, Khan SM, Lemey P, Nelson MI, Cherry JL. Comparative evolution of influenza A virus H1 and H3 head and stalk domains across host species. mBio 2024; 15:e0264923. [PMID: 38078770 PMCID: PMC10886446 DOI: 10.1128/mbio.02649-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE For decades, researchers have studied the rapid evolution of influenza A viruses for vaccine design and as a useful model system for the study of host/parasite evolution. By performing an exhaustive analysis of hemagglutinin protein (HA) sequences from 49 lineages independently evolving in birds, swine, canines, equines, and humans over the last century, our work uncovers surprising features of HA evolution. In particular, the canine H3 stalk, unlike human H3 and H1 stalk domains, is not evolving slowly, suggesting that evolution in the stalk domain is not universally constrained across all host species. Therefore, a broader multi-host perspective on HA evolution may be useful during the evaluation and design of stalk-targeted vaccine candidates.
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Affiliation(s)
- Nidia S Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Sairah M Khan
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Martha I Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Joshua L Cherry
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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14
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Taniguchi K, Noshi T, Omoto S, Sato A, Shishido T, Matsuno K, Okamatsu M, Krauss S, Webby RJ, Sakoda Y, Kida H. The impact of PA/I38 substitutions and PA polymorphisms on the susceptibility of zoonotic influenza A viruses to baloxavir. Arch Virol 2024; 169:29. [PMID: 38216710 PMCID: PMC10786730 DOI: 10.1007/s00705-023-05958-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/28/2023] [Indexed: 01/14/2024]
Abstract
Genetic reassortment of avian, swine, and human influenza A viruses (IAVs) poses potential pandemic risks. Surveillance is important for influenza pandemic preparedness, but the susceptibility of zoonotic IAVs to the cap-dependent endonuclease inhibitor baloxavir acid (BXA) has not been thoroughly researched. Although an amino acid substitution at position 38 in the polymerase acidic protein (PA/I38) in seasonal IAVs reduces BXA susceptibility, PA polymorphisms at position 38 are rarely seen in zoonotic IAVs. Here, we examined the impact of PA/I38 substitutions on the BXA susceptibility of recombinant A(H5N1) viruses. PA mutants that harbored I38T, F, and M were 48.2-, 24.0-, and 15.5-fold less susceptible, respectively, to BXA than wild-type A(H5N1) but were susceptible to the neuraminidase inhibitor oseltamivir acid and the RNA polymerase inhibitor favipiravir. PA mutants exhibited significantly impaired replicative fitness in Madin-Darby canine kidney cells at 24 h postinfection. In addition, in order to investigate new genetic markers for BXA susceptibility, we screened geographically and temporally distinct IAVs isolated worldwide from birds and pigs. The results showed that BXA exhibited antiviral activity against avian and swine viruses with similar levels to seasonal isolates. All viruses tested in the study lacked the PA/I38 substitution and were susceptible to BXA. Isolates harboring amino acid polymorphisms at positions 20, 24, and 37, which have been implicated in the binding of BXA to the PA endonuclease domain, were also susceptible to BXA. These results suggest that monitoring of the PA/I38 substitution in animal-derived influenza viruses is important for preparedness against zoonotic influenza virus outbreaks.
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Affiliation(s)
- Keiichi Taniguchi
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Takeshi Noshi
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Shinya Omoto
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Akihiko Sato
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Takao Shishido
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan.
| | - Keita Matsuno
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Masatoshi Okamatsu
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Scott Krauss
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Richard J Webby
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Yoshihiro Sakoda
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroshi Kida
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
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15
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Holmes KE, VanInsberghe D, Ferreri LM, Elie B, Ganti K, Lee CY, Lowen AC. Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567585. [PMID: 38014182 PMCID: PMC10680852 DOI: 10.1101/2023.11.19.567585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
For many viruses, narrow bottlenecks acting during transmission sharply reduce genetic diversity in a recipient host relative to the donor. Since genetic diversity represents adaptive potential, such losses of diversity are though to limit the opportunity for viral populations to undergo antigenic change and other adaptive processes. Thus, a detailed picture of evolutionary dynamics during transmission is critical to understanding the forces driving viral evolution at an epidemiologic scale. To advance this understanding, we used a novel barcoded virus library and a guinea pig model of transmission to decipher where in the transmission process diversity is lost for influenza A viruses. In inoculated guinea pigs, we show that a high level of viral genetic diversity is maintained across time. Continuity in the barcodes detected furthermore indicates that stochastic effects are not pronounced within inoculated hosts. Importantly, in both aerosol-exposed and direct contact-exposed animals, we observed many barcodes at the earliest time point(s) positive for infectious virus, indicating robust transfer of diversity through the environment. This high viral diversity is short-lived, however, with a sharp decline seen 1-2 days after initiation of infection. Although major losses of diversity at transmission are well described for influenza A virus, our data indicate that events that occur following viral transfer and during the earliest stages of natural infection have a predominant role in this process. This finding suggests that immune selection may have greater opportunity to operate during influenza A transmission than previously recognized.
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Affiliation(s)
- Katie E. Holmes
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - David VanInsberghe
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lucas M. Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Baptiste Elie
- MIVEGEC, CNRS, IRD, Université de Montpellier, Montpellier, France
| | - Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Jung-gu, Daegu, Republic of Korea
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Emory Center of Excellence for Influenza Research and Response (CEIRR), Atlanta, GA, USA
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16
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Mai G, Zhang C, Lan C, Zhang J, Wang Y, Tang K, Tang J, Zeng J, Chen Y, Cheng P, Liu S, Long H, Wen Q, Li A, Liu X, Zhang R, Xu S, Liu L, Niu Y, Yang L, Wang Y, Yin D, Sun C, Chen YQ, Shen W, Zhang Z, Du X. Characterizing the dynamics of BCR repertoire from repeated influenza vaccination. Emerg Microbes Infect 2023; 12:2245931. [PMID: 37542407 PMCID: PMC10438862 DOI: 10.1080/22221751.2023.2245931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/12/2023] [Accepted: 08/03/2023] [Indexed: 08/06/2023]
Abstract
Yearly epidemics of seasonal influenza cause an enormous disease burden around the globe. An understanding of the rules behind the immune response with repeated vaccination still presents a significant challenge, which would be helpful for optimizing the vaccination strategy. In this study, 34 healthy volunteers with 16 vaccinated were recruited, and the dynamics of the BCR repertoire for consecutive vaccinations in two seasons were tracked. In terms of diversity, length, network, V and J gene segments usage, somatic hypermutation (SHM) rate and isotype, it was found that the overall changes were stronger in the acute phase of the first vaccination than the second vaccination. However, the V gene segments of IGHV4-39, IGHV3-9, IGHV3-7 and IGHV1-69 were amplified in the acute phase of the first vaccination, with IGHV3-7 dominant. On the other hand, for the second vaccination, the changes were dominated by IGHV1-69, with potential for coding broad neutralizing antibody. Additional analysis indicates that the application of V gene segment for IGHV3-7 in the acute phase of the first vaccination was due to the elevated usage of isotypes IgM and IgG3. While for IGHV1-69 in the second vaccination, it was contributed by isotypes IgG1 and IgG2. Finally, 41 public BCR clusters were identified in the vaccine group, with both IGHV3-7 and IGHV1-69 were involved and representative complementarity determining region 3 (CDR3) motifs were characterized. This study provides insights into the immune response dynamics following repeated influenza vaccination in humans and can inform universal vaccine design and vaccine strategies in the future.
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Affiliation(s)
- Guoqin Mai
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Chi Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Chunhong Lan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People’s Republic of China
- Center for Precision Medicine, Guangdong Academy of Medical Sciences, Medical Research Institute, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, People’s Republic of China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, People’s Republic of China
| | - Jie Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Kang Tang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jing Tang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jinfeng Zeng
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yilin Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Peiwen Cheng
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shuning Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Haoyu Long
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Qilan Wen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Aqin Li
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Xuan Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Ruitong Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shuyang Xu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Lin Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yanlan Niu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Lan Yang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yihan Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Di Yin
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Caijun Sun
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Wei Shen
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Zhenhai Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People’s Republic of China
- Center for Precision Medicine, Guangdong Academy of Medical Sciences, Medical Research Institute, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, People’s Republic of China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, People’s Republic of China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, People’s Republic of China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, People’s Republic of China
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17
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Han AX, de Jong SPJ, Russell CA. Co-evolution of immunity and seasonal influenza viruses. Nat Rev Microbiol 2023; 21:805-817. [PMID: 37532870 DOI: 10.1038/s41579-023-00945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
Seasonal influenza viruses cause recurring global epidemics by continually evolving to escape host immunity. The viral constraints and host immune responses that limit and drive the evolution of these viruses are increasingly well understood. However, it remains unclear how most of these advances improve the capacity to reduce the impact of seasonal influenza viruses on human health. In this Review, we synthesize recent progress made in understanding the interplay between the evolution of immunity induced by previous infections or vaccination and the evolution of seasonal influenza viruses driven by the heterogeneous accumulation of antibody-mediated immunity in humans. We discuss the functional constraints that limit the evolution of the viruses, the within-host evolutionary processes that drive the emergence of new virus variants, as well as current and prospective options for influenza virus control, including the viral and immunological barriers that must be overcome to improve the effectiveness of vaccines and antiviral drugs.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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18
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Gao R, Pascua PNQ, Nguyen HT, Chesnokov A, Champion C, Mishin VP, Wentworth DE, Gubareva LV. New insights into the neuraminidase-mediated hemagglutination activity of influenza A(H3N2) viruses. Antiviral Res 2023; 218:105719. [PMID: 37717821 PMCID: PMC10549826 DOI: 10.1016/j.antiviral.2023.105719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/07/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
Influenza virus neuraminidase (NA) can act as a receptor-binding protein, a role commonly attributed to hemagglutinin (HA). In influenza A(H3N2) viruses, three NA amino acid residues have previously been associated with NA-mediated hemagglutination: T148, D151, and more recently, H150. These residues are part of the 150-loop of the NA monomer. Substitutions at 148 and 151 arise from virus propagation in laboratory cell cultures, whereas changes at 150 occurred during virus evolution in the human host. In this study, we examined the effect of natural amino acid polymorphism at position 150 on NA-mediated hemagglutination. Using the A/Puerto Rico/8/34 backbone, we generated a comprehensive panel of recombinant A(H3N2) viruses that have different NAs but shared an HA that displays poor binding to red blood cells (RBCs). None of the tested substitutions at 150 (C, H, L, R, and S) promoted NA-binding. However, we identified two new determinants of NA-binding, Q136K and T439R, that emerged during virus culturing. Similar to T148I, both Q136K and T439R reduced NA enzyme activity by 48-86% and inhibition (14- to 173-fold) by the NA inhibitor zanamivir. NA-binding was observed when a virus preparation contained approximately 10% of NA variants with either T148I or T439R, highlighting the benefit of using deep sequencing in virus characterization. Taken together, our findings provide new insights into the molecular mechanisms underlying the ability of NA to function as a binding protein. Information gained may aid in the design of new and improved NA-targeting antivirals.
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Affiliation(s)
- Rongyuan Gao
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | | | - Ha T Nguyen
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Anton Chesnokov
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Chloe Champion
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA; Chippewa Government Solutions, Sault Sainte Marie, MI, USA
| | - Vasiliy P Mishin
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Dave E Wentworth
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Larisa V Gubareva
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA.
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19
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Liu X, Peng Y, Chen Z, Jiang F, Ni F, Tang Z, Yang X, Song C, Yuan M, Tao Z, Xu J, Wang Y, Qian Q, Ewing RM, Yin P, Hu Y, Wang W, Wang Y. Impact of non-pharmaceutical interventions during COVID-19 on future influenza trends in Mainland China. BMC Infect Dis 2023; 23:632. [PMID: 37759271 PMCID: PMC10523625 DOI: 10.1186/s12879-023-08594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Influenza is a common illness for its high rates of morbidity and transmission. The implementation of non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic to manage its dissemination could affect the transmission of influenza. METHODS A retrospective analysis, between 2018 and 2023, was conducted to examine the incidence of influenza virus types A and B among patients in sentinel cities located in North or South China as well as in Wuhan City. For validations, data on the total count of influenza patients from 2018 to 2023 were collected at the Central Hospital of Wuhan, which is not included in the sentinel hospital network. Time series methods were utilized to examine seasonal patterns and to forecast future influenza trends. RESULTS Northern and southern cities in China had earlier outbreaks during the NPIs period by about 8 weeks compared to the 2018-2019. The implementation of NPIs significantly reduced the influenza-like illness (ILI) rate and infection durations. Influenza B Victoria and H3N2 were the first circulating strains detected after the relaxation of NPIs, followed by H1N1 across mainland China. The SARIMA model predicted synchronized H1N1 outbreak cycles in North and South China, with H3N2 expected to occur in the summer in southern cities and in the winter in northern cities over the next 3 years. The ILI burden is expected to rise in both North and South China over the next 3 years, with higher ILI% levels in southern cities throughout the year, especially in winter, and in northern cities mainly during winter. In Wuhan City and the Central Hospital of Wuhan, influenza levels are projected to peak in the winter of 2024, with 2 smaller peaks expected during the summer of 2023. CONCLUSIONS In this study, we report the impact of NPIs on future influenza trends in mainland China. We recommend that local governments encourage vaccination during the transition period between summer and winter to mitigate economic losses and mortality associated with influenza.
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Affiliation(s)
- Xiaofan Liu
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Ying Peng
- Wuhan Centers for Disease Control and Prevention, Wuhan, 430024, Hubei, China
| | - Zhe Chen
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Fangfang Jiang
- Department of Biostatistics, University of Iowa, Iowa City, IA, 52242, USA
| | - Fang Ni
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Zhiyong Tang
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Xun Yang
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Cheng Song
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Mingli Yuan
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Zhaowu Tao
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Junjie Xu
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Ying Wang
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Qiong Qian
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Rob M Ewing
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Ping Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China.
| | - Yi Hu
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China.
| | - Weihua Wang
- Department of Pulmonary and Critical Care Medicine, Tongji Medical College, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China.
| | - Yihua Wang
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK.
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20
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López-Valiñas Á, Valle M, Pérez M, Darji A, Chiapponi C, Ganges L, Segalés J, Núñez JI. Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals. Front Cell Infect Microbiol 2023; 13:1258321. [PMID: 37780850 PMCID: PMC10540852 DOI: 10.3389/fcimb.2023.1258321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023] Open
Abstract
Influenza A viruses (IAVs) are characterized by having a segmented genome, low proofreading polymerases, and a wide host range. Consequently, IAVs are constantly evolving in nature causing a threat to animal and human health. In 2009 a new human pandemic IAV strain arose in Mexico because of a reassortment between two strains previously circulating in pigs; Eurasian "avian-like" (EA) swine H1N1 and "human-like" H1N2, highlighting the importance of swine as adaptation host of avian to human IAVs. Nowadays, although of limited use, a trivalent vaccine, which include in its formulation H1N1, H3N2, and, H1N2 swine IAV (SIAV) subtypes, is one of the most applied strategies to reduce SIAV circulation in farms. Protection provided by vaccines is not complete, allowing virus circulation, potentially favoring viral evolution. The evolutionary dynamics of SIAV quasispecies were studied in samples collected at different times from 8 vaccinated and 8 nonvaccinated pigs, challenged with H1N2 SIAV. In total, 32 SIAV genomes were sequenced by next-generation sequencing, and subsequent variant-calling genomic analysis was carried out. Herein, a total of 364 de novo single nucleotide variants (SNV) were found along all genetic segments in both experimental groups. The nonsynonymous substitutions proportion found was greater in vaccinated animals suggesting that H1N2 SIAV was under positive selection in this scenario. The impact of each substitution with an allele frequency greater than 5% was hypothesized according to previous literature, particularly in the surface glycoproteins hemagglutinin and neuraminidase. The H1N2 SIAV quasispecies evolution capacity was evidenced, observing different evolutionary trends in vaccinated and nonvaccinated animals.
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Affiliation(s)
- Álvaro López-Valiñas
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Marta Valle
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Marta Pérez
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Ayub Darji
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Chiara Chiapponi
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia-Romagna, Brescia, Italy
| | - Llilianne Ganges
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
- WOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain
| | - Joaquim. Segalés
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José I. Núñez
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
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21
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Hamede R, Fountain‐Jones NM, Arce F, Jones M, Storfer A, Hohenlohe PA, McCallum H, Roche B, Ujvari B, Thomas F. The tumour is in the detail: Local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils. Evol Appl 2023; 16:1316-1327. [PMID: 37492149 PMCID: PMC10363845 DOI: 10.1111/eva.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/27/2023] Open
Abstract
Infectious diseases are a major threat for biodiversity conservation and can exert strong influence on wildlife population dynamics. Understanding the mechanisms driving infection rates and epidemic outcomes requires empirical data on the evolutionary trajectory of pathogens and host selective processes. Phylodynamics is a robust framework to understand the interaction of pathogen evolutionary processes with epidemiological dynamics, providing a powerful tool to evaluate disease control strategies. Tasmanian devils have been threatened by a fatal transmissible cancer, devil facial tumour disease (DFTD), for more than two decades. Here we employ a phylodynamic approach using tumour mitochondrial genomes to assess the role of tumour genetic diversity in epidemiological and population dynamics in a devil population subject to 12 years of intensive monitoring, since the beginning of the epidemic outbreak. DFTD molecular clock estimates of disease introduction mirrored observed estimates in the field, and DFTD genetic diversity was positively correlated with estimates of devil population size. However, prevalence and force of infection were the lowest when devil population size and tumour genetic diversity was the highest. This could be due to either differential virulence or transmissibility in tumour lineages or the development of host defence strategies against infection. Our results support the view that evolutionary processes and epidemiological trade-offs can drive host-pathogen coexistence, even when disease-induced mortality is extremely high. We highlight the importance of integrating pathogen and population evolutionary interactions to better understand long-term epidemic dynamics and evaluating disease control strategies.
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Affiliation(s)
- Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
| | | | - Fernando Arce
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Menna Jones
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Andrew Storfer
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | - Hamish McCallum
- Centre for Planetary Health and Food SecurityGriffith University, Nathan CampusNathanQueenslandAustralia
| | - Benjamin Roche
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
| | - Beata Ujvari
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Frédéric Thomas
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
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22
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Peng F, Xia Y, Li W. Prediction of Antigenic Distance in Influenza A Using Attribute Network Embedding. Viruses 2023; 15:1478. [PMID: 37515165 PMCID: PMC10385503 DOI: 10.3390/v15071478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Owing to the rapid changes in the antigenicity of influenza viruses, it is difficult for humans to obtain lasting immunity through antiviral therapy. Hence, tracking the dynamic changes in the antigenicity of influenza viruses can provide a basis for vaccines and drug treatments to cope with the spread of influenza viruses. In this paper, we developed a novel quantitative prediction method to predict the antigenic distance between virus strains using attribute network embedding techniques. An antigenic network is built to model and combine the genetic and antigenic characteristics of the influenza A virus H3N2, using the continuous distributed representation of the virus strain protein sequence (ProtVec) as a node attribute and the antigenic distance between virus strains as an edge weight. The results show a strong positive correlation between supplementing genetic features and antigenic distance prediction accuracy. Further analysis indicates that our prediction model can comprehensively and accurately track the differences in antigenic distances between vaccines and influenza virus strains, and it outperforms existing methods in predicting antigenic distances between strains.
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Affiliation(s)
- Fujun Peng
- School of Information Science and Engineering, Yunnan University, Kunming 650500, China
| | - Yuanling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Weihua Li
- School of Information Science and Engineering, Yunnan University, Kunming 650500, China
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23
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Qin L, Ding S, He Z. Compositional biases and evolution of the largest plant RNA virus order Patatavirales. Int J Biol Macromol 2023; 240:124403. [PMID: 37076075 DOI: 10.1016/j.ijbiomac.2023.124403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/13/2023] [Accepted: 03/25/2023] [Indexed: 04/21/2023]
Abstract
Patatavirales is the largest order of plant RNA viruses and exclusively contains the family Potyviridae, accounting for 30 % of all known plant viruses. The composition bias of animal RNA viruses and several plant RNA viruses has been determined. However, the comprehensive nucleic acid composition, codon pair usage patterns, dinucleotide preference and codon pair preference of plant RNA viruses have not been investigated to date. In this study, integrated analysis and discussion of the nucleic acid composition, codon usage patterns, dinucleotide composition and codon pair bias of potyvirids were performed using 3732 complete genome coding sequences. The nucleic acid composition of potyvirids was significantly enriched in A/U. Interestingly, the A/U-rich nucleotide composition of Patatavirales is essential for determining the preferred A-ended and U-ended codons and the overexpression of UpG and CpA dinucleotides. The codon usage patterns and codon pair bias of potyvirids were significantly correlated with their nucleic acid composition. Additionally, the codon usage pattern, dinucleotide composition and codon-pair bias of potyvirids are more dependent on the classification of the virus compared with their hosts. Our analysis provides a better understanding of future research on the origin and evolution patterns of the order Patatavirales.
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Affiliation(s)
- Lang Qin
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China
| | - Zhen He
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China.
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24
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Pushan SS, Samantaray M, Rajagopalan M, Ramaswamy A. Evolution of Indian Influenza A (H1N1) Hemagglutinin Strains: A Comparative Analysis of the Pandemic Californian HA Strain. Front Mol Biosci 2023; 10:1111869. [PMID: 37006623 PMCID: PMC10061220 DOI: 10.3389/fmolb.2023.1111869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
The need for a vaccine/inhibitor design has become inevitable concerning the emerging epidemic and pandemic viral infections, and the recent outbreak of the influenza A (H1N1) virus is one such example. From 2009 to 2018, India faced severe fatalities due to the outbreak of the influenza A (H1N1) virus. In this study, the potential features of reported Indian H1N1 strains are analyzed in comparison with their evolutionarily closest pandemic strain, A/California/04/2009. The focus is laid on one of its surface proteins, hemagglutinin (HA), which imparts a significant role in attacking the host cell surface and its entry. The extensive analysis performed, in comparison with the A/California/04/2009 strain, revealed significant point mutations in all Indian strains reported from 2009 to 2018. Due to these mutations, all Indian strains disclosed altered features at the sequence and structural levels, which are further presumed to be associated with their functional diversity as well. The mutations observed with the 2018 HA sequence such as S91R, S181T, S200P, I312V, K319T, I419M, and E523D might improve the fitness of the virus in a new host and environment. The higher fitness and decreased sequence similarity of mutated strains may compromise therapeutic efficacy. In particular, the mutations observed commonly, such as serine-to-threonine, alanine-to-threonine, and lysine-to-glutamine at various regions, alter the physico-chemical features of receptor-binding domains, N-glycosylation, and epitope-binding sites when compared with the reference strain. Such mutations render diversity among all Indian strains, and the structural and functional characterization of these strains becomes inevitable. In this study, we observed that mutational drift results in the alteration of the receptor-binding domain, the generation of new variant N-glycosylation along with novel epitope-binding sites, and modifications at the structural level. Eventually, the pressing need to develop potentially distinct next-generation therapeutic inhibitors against the HA strains of the Indian influenza A (H1N1) virus is also highlighted here.
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Affiliation(s)
- Shilpa Sri Pushan
- Department of Bioinformatics, Pondicherry University, Puducherry, India
| | - Mahesh Samantaray
- Department of Bioinformatics, Pondicherry University, Puducherry, India
| | - Muthukumaran Rajagopalan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Amutha Ramaswamy
- Department of Bioinformatics, Pondicherry University, Puducherry, India
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25
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The Functions of TRIM56 in Antiviral Innate Immunity and Tumorigenesis. Int J Mol Sci 2023; 24:ijms24055046. [PMID: 36902478 PMCID: PMC10003129 DOI: 10.3390/ijms24055046] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
As a member of the TRIM (tripartite motif) protein family, TRIM56 can function as an E3 ubiquitin ligase. In addition, TRIM56 has been shown to possess deubiquitinase activity and the ability to bind RNA. This adds to the complexity of the regulatory mechanism of TRIM56. TRIM56 was initially found to be able to regulate the innate immune response. In recent years, its role in direct antiviral and tumor development has also attracted the interest of researchers, but there is no systematic review on TRIM56. Here, we first summarize the structural features and expression of TRIM56. Then, we review the functions of TRIM56 in TLR and cGAS-STING pathways of innate immune response, the mechanisms and structural specificity of TRIM56 against different types of viruses, and the dual roles of TRIM56 in tumorigenesis. Finally, we discuss the future research directions regarding TRIM56.
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Taylor KY, Agu I, José I, Mäntynen S, Campbell AJ, Mattson C, Chou TW, Zhou B, Gresham D, Ghedin E, Díaz Muñoz SL. Influenza A virus reassortment is strain dependent. PLoS Pathog 2023; 19:e1011155. [PMID: 36857394 PMCID: PMC10010518 DOI: 10.1371/journal.ppat.1011155] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/13/2023] [Accepted: 01/26/2023] [Indexed: 03/02/2023] Open
Abstract
RNA viruses can exchange genetic material during coinfection, an interaction that creates novel strains with implications for viral evolution and public health. Influenza A viral genetic exchange can occur when genome segments from distinct strains reassort in coinfected cells. Predicting potential genomic reassortment between influenza strains has been a long-standing goal. Experimental coinfection studies have shed light on factors that limit or promote reassortment. However, determining the reassortment potential between diverse Influenza A strains has remained elusive. To address this challenge, we developed a high throughput genotyping approach to quantify reassortment among a diverse panel of human influenza virus strains encompassing two pandemics (swine and avian origin), three specific epidemics, and both circulating human subtypes A/H1N1 and A/H3N2. We found that reassortment frequency (the proportion of reassortants generated) is an emergent property of specific pairs of strains where strain identity is a predictor of reassortment frequency. We detect little evidence that antigenic subtype drives reassortment as intersubtype (H1N1xH3N2) and intrasubtype reassortment frequencies were, on average, similar. Instead, our data suggest that certain strains bias the reassortment frequency up or down, independently of the coinfecting partner. We observe that viral productivity is also an emergent property of coinfections, but uncorrelated to reassortment frequency; thus viral productivity is a separate factor affecting the total number of reassortants produced. Assortment of individual segments among progeny and pairwise segment combinations within progeny generally favored homologous combinations. These outcomes were not related to strain similarity or shared subtype but reassortment frequency was closely correlated to the proportion of both unique genotypes and of progeny with heterologous pairwise segment combinations. We provide experimental evidence that viral genetic exchange is potentially an individual social trait subject to natural selection, which implies the propensity for reassortment is not evenly shared among strains. This study highlights the need for research incorporating diverse strains to discover the traits that shift the reassortment potential to realize the goal of predicting influenza virus evolution resulting from segment exchange.
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Affiliation(s)
- Kishana Y. Taylor
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Ilechukwu Agu
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Ivy José
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Sari Mäntynen
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - A. J. Campbell
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Courtney Mattson
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Tsui-Wen Chou
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
| | - Bin Zhou
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
| | - Elodie Ghedin
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States of America
| | - Samuel L. Díaz Muñoz
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
- Genome Center University of California, Davis Davis, California
- * E-mail:
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Chu JT, Gu H, Sun W, Fan RL, Nicholls JM, Valkenburg SA, Poon LL. Heterosubtypic immune pressure accelerates emergence of influenza A virus escape phenotypes in mice. Virus Res 2023; 323:198991. [PMID: 36302472 PMCID: PMC10194115 DOI: 10.1016/j.virusres.2022.198991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2022]
Abstract
Rapid antigenic evolution of the influenza A virus surface antigen hemagglutinin undermines protection conferred by seasonal vaccines. Protective correlates targeted by universal vaccines such as cytotoxic T cells or HA stem directed broadly neutralizing antibodies have been shown to select for immune escape mutants during infection. We developed an in vivo serial passage mouse model for viral adaptation and used next generation sequencing to evaluate full genome viral evolution in the context of broadly protective immunity. Heterosubtypic immune pressure increased the incidence of genome-wide single nucleotide variants, though mutations found in early adapted populations were predominantly stochastic in nature. Prolonged adaptation under heterosubtypic immune selection resulted in the manifestation of highly virulent phenotypes that ablated vaccine mediated protection from mortality. High frequency mutations unique to escape phenotypes were identified within the polymerase encoding segments. These findings suggest that a suboptimial usage of population-wide universal influenza vaccine may drive formation of escape variants attributed to polygenic changes.
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Affiliation(s)
- Julie Ts Chu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wanying Sun
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Rebecca Ly Fan
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - John M Nicholls
- Department of Pathology, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sophie A Valkenburg
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Leo Lm Poon
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong Special Administrative Region, China.
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Ye Q, Liu H, Mao J, Shu Q. Nonpharmaceutical interventions for COVID-19 disrupt the dynamic balance between influenza A virus and human immunity. J Med Virol 2023; 95:e28292. [PMID: 36367115 PMCID: PMC9877879 DOI: 10.1002/jmv.28292] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
During the COVID-19 epidemic, nonpharmaceutical interventions (NPIs) blocked the transmission route of respiratory diseases. This study aimed to investigate the impact of NPIs on the influenza A virus (IAV) outbreak. The present study enrolled all children with respiratory tract infections who came to the Children's Hospital of Zhejiang University between January 2019 and July 2022. A direct immunofluorescence assay kit detected IAV. Virus isolation and Sanger sequencing were performed. From June to July 2022, in Hangzhou, China, the positive rate of IAV infection in children has increased rapidly, reaching 30.41%, and children over 3 years old are the main infected population, accounting for 75% of the total number of infected children. Influenza A (H3N2) viruses are representative strains during this period. In this outbreak, H3N2 was isolated from a cluster of its own and is highly homologous with A/South_Dakota/22/2022 (2021-2022 Northern Hemisphere). Between isolated influenza A (H3N2) viruses and A/South_Dakota/22/2022, the nucleotide homology of the HA gene ranged from 97.3% to 97.5%; the amino acid homology was 97%-97.2%, and the genetic distance of nucleotides ranged from 0.05 to 0.052. Compared with A/South_Dakota/22/2022, the isolated H3N2 showed S156H, N159Y, I160T, D186S, S198P, I48T, S53D, and K171N mutations. There was no variation in 13 key amino acid sites associated with neuraminidase inhibitor resistance in NA protein. Long-term NPIs have significantly affected the evolution and transmission of the influenza virus and human immunity, breaking the dynamic balance between the IAV and human immunity.
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Affiliation(s)
- Qing Ye
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Huihui Liu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Jianhua Mao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Qiang Shu
- Department of Thoracic & Cardiovascular Surgery, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
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Bao Y, Shi Y, Zhou L, Gao S, Yao R, Guo S, Geng Z, Bao L, Zhao R, Cui X. MicroRNA-205-5p: A potential therapeutic target for influenza A. J Cell Mol Med 2022; 26:5917-5928. [PMID: 36403222 PMCID: PMC9716220 DOI: 10.1111/jcmm.17615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 02/11/2024] Open
Abstract
We are committed to finding host targets for influenza A therapeutics. The nucleoprotein (NP) plays an important role in influenza A virus replication and is an indispensable part of viral transcription and replication. Exploring endogenous substances that can modulate NP is critical for finding host targets. MicroRNAs (miRNAs, miR) are a novel class of powerful, endogenous gene expression regulators. Herein, we used miRanda to analyse the base complementarity between the NP gene and the 14 host miRNAs reported previously by us. MiRanda predicted that miR-431-5p, miR-744-3p and miR-205-5p could complement the NP gene. To understand the effect of these miRNAs on NP expression, we co-transfected 293 T cells with NP gene sequence containing above miRNAs binding site or full sequence of NP gene (transfected into pmirGlo or pcDNA3.1 vectors, respectively), and mimics of miR-205-5p, miR-431-5p and miR-744-3p. Dual luciferase reporter gene or Western blotting assays confirmed that miR-205-5p and miR-431-5p inhibit NP expression by binding with the miRNA binding site of NP gene. Further, we infected Mouse Lung Epithelial (MLE-12) cells overexpressing miR-205-5p and miR-431-5p with influenza A virus and performed Western blotting to examine NP expression. We found that NP expression was significantly reduced in MLE-12 cells overexpressing miR-205-5p during influenza A infection. The miR-205-5p overexpression-induced inhibition of influenza A replication could be attributed to the inhibition of NP expression. Further, we administered oseltamivir and Jinchai Antiviral Capsules (JC, an anti-influenza Chinese medicine) to influenza A virus-infected MLE-12 cells and mice. We found that miR-205-5p was significantly decreased increased in infected cells and lung tissues, and oseltamivir and JC could up-regulate miR-205-5p. In conclusion, we provide new evidence that miR-205-5p plays a role in regulating viral NP protein expression in combating influenza A and may be a potential target for influenza A therapy.
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Affiliation(s)
- Yanyan Bao
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Yujing Shi
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Lirun Zhou
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Shuangrong Gao
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Rongmei Yao
- Institute of Traditional Chinese MedicineTianjin University of Traditional Chinese MedicineTianjinChina
| | - Shanshan Guo
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Zihan Geng
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Lei Bao
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Ronghua Zhao
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Xiaolan Cui
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
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30
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Assessment of Fcγ receptor-dependent binding of influenza hemagglutinin vaccine-induced antibodies in a non-human primate model. iScience 2022; 25:105085. [PMID: 36147947 PMCID: PMC9486051 DOI: 10.1016/j.isci.2022.105085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/09/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Several cross-protective antibodies that recognize a broad range of influenza A virus (IAV) strains are known to have functions in virus elimination such as Fcγ receptor (FcγR)-effector function and neutralizing activity against the head region. Although few studies have used primary cells as effector cells, the FcγR-effector function was evaluated after isolating each cell subset. Herein, we established an original assay system to evaluate purified FI6 IgG-mediated binding to hemagglutinin (HA)-expressing cells by flow cytometry using peripheral blood mononuclear cells from cynomolgus macaques. In addition, we evaluated the FcγR-effector function of IAV vaccine-induced anti-HA antibodies in cynomolgus macaques after administering the split vaccine. We found several cell types, mainly classical monocytes, bound to HA-expressing target cells in an FcγR-dependent manner, that were dominant in the binding of the cell population. Thus, this assay system could facilitate the development of a universal influenza vaccine.
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31
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Prada LSD, Sanz-Muñoz I, de Lejarazu RO, Eiros JM, García-Sastre A, Aydillo T. Immunodominance hierarchy after seasonal influenza vaccination. Emerg Microbes Infect 2022; 11:2670-2679. [PMID: 36219456 DOI: 10.1080/22221751.2022.2135460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Current influenza vaccines elicit humoral immune responses against the hemagglutinin (HA) protein of influenza viruses. Different antigenic sites have been identified in the HA head as the main target of hemagglutination inhibition (HAI) antibodies (Sb, Sa, Cb, Ca1 and Ca2). To determine immunodominance (ID) of each site, we performed HAI assays against a panel of mutant viruses, each one lacking one of the classically defined antigenic sites and compared it to wild type (Wt). Agglutinating antibodies were measured before and after vaccination in two different regimens: Quadrivalent Influenza Vaccine (QIV) in young adults; or Adjuvanted Trivalent influenza Vaccine (ATIV) in elderly. Our results showed abs before vaccination were significantly reduced against all antigenic sites in the elderly and only against Sb and Ca2 in young adults compared to the Wt. Humoral response to vaccination was significantly reduced against all viruses compared to the Wt for the ATIV and only against Sb and Ca2 for the QIV. The strongest reduction was observed in all cases against Sb followed by Ca2. We concluded that ID profile was clearly dominated by Sb followed by Ca2. Additionally, the antibody response evolved with age, increasing the response towards less immunodominant epitopes of HA head. Adjuvants can positively influence ID hierarchy broadening responses towards multiple antigenic sites of HA head.
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Affiliation(s)
- Laura Sánchez-de Prada
- National Influenza Centre of Valladolid, 47010, Spain.,Hospital Clínico Universitario de Valladolid, 47003, Spain
| | | | | | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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32
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Cavany SM, Barbera C, Carpenter M, Rodgers C, Sherman T, Stenglein M, Mayo C, Perkins TA. Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges. Virus Evol 2022; 8:veac094. [PMID: 36381232 PMCID: PMC9662319 DOI: 10.1093/ve/veac094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 10/10/2023] Open
Abstract
When related segmented RNA viruses co-infect a single cell, viral reassortment can occur, potentially leading to new strains with pandemic potential. One virus capable of reassortment is bluetongue virus (BTV), which causes substantial health impacts in ruminants and is transmitted via Culicoides midges. Because midges can become co-infected by feeding on multiple different host species and remain infected for their entire life span, there is a high potential for reassortment to occur. Once a midge is co-infected, additional barriers must be crossed for a reassortant virus to emerge, such as cellular co-infection and dissemination of reassortant viruses to the salivary glands. We developed three mathematical models of within-midge BTV dynamics of increasing complexity, allowing us to explore the conditions leading to the emergence of reassortant viruses. In confronting the simplest model with published data, we estimate that the average life span of a bluetongue virion in the midge midgut is about 6 h, a key determinant of establishing a successful infection. Examination of the full model, which permits cellular co-infection and reassortment, shows that small differences in fitness of the two infecting strains can have a large impact on the frequency with which reassortant virions are observed. This is consistent with experimental co-infection studies with BTV strains with different relative fitnesses that did not produce reassortant progeny. Our models also highlight several gaps in existing data that would allow us to elucidate these dynamics in more detail, in particular the times it takes the virus to disseminate to different tissues, and measurements of viral load and reassortant frequency at different temperatures.
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Affiliation(s)
- Sean M Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Carly Barbera
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Molly Carpenter
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Case Rodgers
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Tyler Sherman
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Mark Stenglein
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Christie Mayo
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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Liu Y, Chen H, Duan W, Zhang X, He X, Nielsen R, Ma L, Zhai W. Predicting Egg Passage Adaptations to Design Better Vaccines for the H3N2 Influenza Virus. Viruses 2022; 14:v14092065. [PMID: 36146872 PMCID: PMC9501976 DOI: 10.3390/v14092065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Seasonal H3N2 influenza evolves rapidly, leading to an extremely poor vaccine efficacy. Substitutions employed during vaccine production using embryonated eggs (i.e., egg passage adaptation) contribute to the poor vaccine efficacy (VE), but the evolutionary mechanism remains elusive. Using an unprecedented number of hemagglutinin sequences (n = 89,853), we found that the fitness landscape of passage adaptation is dominated by pervasive epistasis between two leading residues (186 and 194) and multiple other positions. Convergent evolutionary paths driven by strong epistasis explain most of the variation in VE, which has resulted in extremely poor vaccines for the past decade. Leveraging the unique fitness landscape, we developed a novel machine learning model that can predict egg passage substitutions for any candidate vaccine strain before the passage experiment, providing a unique opportunity for the selection of optimal vaccine viruses. Our study presents one of the most comprehensive characterizations of the fitness landscape of a virus and demonstrates that evolutionary trajectories can be harnessed for improved influenza vaccines.
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Affiliation(s)
- Yunsong Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Chen
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Wenyuan Duan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xionglei He
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94707, USA
- Department of Statistics, University of California-Berkeley, Berkeley, CA 94707, USA
- Globe Institute, University of Copenhagen, 1350 København, Copenhagen, Denmark
| | - Liang Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Correspondence:
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Li C, Culhane MR, Schroeder DC, Cheeran MCJ, Galina Pantoja L, Jansen ML, Torremorell M. Vaccination decreases the risk of influenza A virus reassortment but not genetic variation in pigs. eLife 2022; 11:78618. [PMID: 36052992 PMCID: PMC9439680 DOI: 10.7554/elife.78618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Although vaccination is broadly used in North American swine breeding herds, managing swine influenza is challenging primarily due to the continuous evolution of influenza A virus (IAV) and the ability of the virus to transmit among vaccinated pigs. Studies that have simultaneously assessed the impact of vaccination on the emergence of IAV reassortment and genetic variation in pigs are limited. Here, we directly sequenced 28 bronchoalveolar lavage fluid (BALF) samples collected from vaccinated and unvaccinated pigs co-infected with H1N1 and H3N2 IAV strains, and characterized 202 individual viral plaques recovered from 13 BALF samples. We identified 54 reassortant viruses that were grouped in 17 single and 16 mixed genotypes. Notably, we found that prime-boost vaccinated pigs had less reassortant viruses than nonvaccinated pigs, likely due to a reduction in the number of days pigs were co-infected with both challenge viruses. However, direct sequencing from BALF samples revealed limited impact of vaccination on viral variant frequency, evolutionary rates, and nucleotide diversity in any IAV coding regions. Overall, our results highlight the value of IAV vaccination not only at limiting virus replication in pigs but also at protecting public health by restricting the generation of novel reassortants with zoonotic and/or pandemic potential. Swine influenza A viruses cause severe illness among pigs and financial losses on pig farms worldwide. These viruses can also infect humans and have caused deadly human pandemics in the past. Influenza A viruses are dangerous because viruses can be transferred between humans, birds and pigs. These co-infections can allow the viruses to swap genetic material. Viral genetic exchanges can result in new virus strains that are more dangerous or that can infect other types of animals more easily. Farmers vaccinate their pigs to control the swine influenza A virus. The vaccines are regularly updated to match circulating virus strains. But the virus evolves rapidly to escape vaccine-induced immunity, and infections are common even in vaccinated pigs. Learning about how vaccination affects the evolution of influenza A viruses in pigs could help scientists prevent outbreaks on pig farms and avoid spillover pandemics in humans. Li et al. show that influenza A viruses are less likely to swap genetic material in vaccinated and boosted pigs than in unvaccinated animals. In the experiments, Li et al. collected swine influenza A samples from the lungs of pigs that had received different vaccination protocols. Next, Li et al. used next-generation sequencing to identify new mutations in the virus or genetic swaps among different strains. In pigs infected with both the H1N1 and H3N2 strains of influenza, the two viruses began trading genes within a week. But less genetic mixing occurred in vaccinated and boosted pigs because they spent less time infected with both viruses than in unvaccinated pigs. The vaccination status of the pig did not have much effect on how many new mutations occurred in the viruses. The experiments show that vaccinating and boosting pigs against influenza A viruses may protect against genetic swapping among influenza viruses. If future studies on pig farms confirm the results, the information gleaned from the study could help scientists improve farm vaccine protocols to further reduce influenza risks to animals and people.
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Affiliation(s)
- Chong Li
- College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| | - Marie R Culhane
- College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| | - Declan C Schroeder
- College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| | - Maxim C-J Cheeran
- College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
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35
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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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Varghese PM, Kishore U, Rajkumari R. Innate and adaptive immune responses against Influenza A Virus: Immune evasion and vaccination strategies. Immunobiology 2022; 227:152279. [DOI: 10.1016/j.imbio.2022.152279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022]
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Immune Escape Adaptive Mutations in Hemagglutinin Are Responsible for the Antigenic Drift of Eurasian Avian-Like H1N1 Swine Influenza Viruses. J Virol 2022; 96:e0097122. [PMID: 35916512 PMCID: PMC9400474 DOI: 10.1128/jvi.00971-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The continuous antigenic variation of influenza A viruses remains a major hurdle for vaccine selection; however, the molecular determinants and mechanisms of antigenic change remain largely unknown. In this study, two escape mutants were generated by serial passages of the Eurasian avian-like H1N1 swine influenza virus (EA H1N1 SIV) A/swine/Henan/11/2005 (HeN11) in the presence of two neutralizing monoclonal antibodies (mAbs) against the hemagglutinin (HA) protein, which were designated HeN11-2B6-P5 and HeN11-4C7-P8, respectively. The HeN11-2B6-P5 mutant simultaneously harbored the N190D and I230M substitutions in HA, whereas HeN11-4C7-P8 harbored the M269R substitution in HA (H3 numbering). The effects of each of these substitutions on viral antigenicity were determined by measuring the neutralization and hemagglutination inhibition (HI) titers with mAbs and polyclonal sera raised against the representative viruses. The results indicate that residues 190 and 269 are key determinants of viral antigenic variation. In particular, the N190D mutation had the greatest antigenic impact, as determined by the HI assay. Further studies showed that both HeN11-2B6-P5 and HeN11-4C7-P8 maintained the receptor-binding specificity of the parent virus, although the single mutation N190D decreased the binding affinity for the human-type receptor. The replicative ability in vitro of HeN11-2B6-P5 was increased, whereas that of HeN11-4C7-P8 was decreased. These findings extend our understanding of the antigenic evolution of influenza viruses under immune pressure and provide insights into the functional effects of amino acid substitutions near the receptor-binding site and the interplay among receptor binding, viral replication, and antigenic drift. IMPORTANCE The antigenic changes that occur continually in the evolution of influenza A viruses remain a great challenge for the effective control of disease outbreaks. Here, we identified three amino acid substitutions (at positions 190, 230, and 269) in the HA of EA H1N1 SIVs that determine viral antigenicity and result in escape from neutralizing monoclonal antibodies. All three of these substitutions have emerged in nature. Of note, residues 190 and 230 have synergistic effects on receptor binding and antigenicity. Our findings provide a better understanding of the functional effects of amino acid substitutions in HA and their consequences for the antigenic drift of influenza viruses.
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Lofgren E, Naumova EN, Gorski J, Naumov Y, Fefferman NH. How Drivers of Seasonality in Respiratory Infections May Impact Vaccine Strategy: A Case Study in How Coronavirus Disease 2019 (COVID-19) May Help Us Solve One of Influenza's Biggest Challenges. Clin Infect Dis 2022; 75:S121-S129. [PMID: 35607766 PMCID: PMC9213832 DOI: 10.1093/cid/ciac400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Vaccines against seasonal infections like influenza offer a recurring testbed, encompassing challenges in design, implementation, and uptake to combat a both familiar and ever-shifting threat. One of the pervading mysteries of influenza epidemiology is what causes the distinctive seasonal outbreak pattern. Proposed theories each suggest different paths forward in being able to tailor precision vaccines and/or deploy them most effectively. One of the greatest challenges in contrasting and supporting these theories is, of course, that there is no means by which to actually test them. In this communication we revisit theories and explore how the ongoing coronavirus disease 2019 (COVID-19) pandemic might provide a unique opportunity to better understand the global circulation of respiratory infections. We discuss how vaccine strategies may be targeted and improved by both isolating drivers and understanding the immunological consequences of seasonality, and how these insights about influenza vaccines may generalize to vaccines for other seasonal respiratory infections.
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Affiliation(s)
- Eric Lofgren
- WSU Paul G. Allen School for Global Health Allen Center PO Box 647090 240 SE Ott Road Pullman, WA 99164, USA
| | - Elena N. Naumova
- Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy Jaharis Family Center for Biomedical and Nutrition Sciences Tufts University 150 Harrison Avenue Boston, MA 02111, USA
| | - Jack Gorski
- Blood Research Institute Versiti Milwaukee WI, 53226, USA
| | - Yuri Naumov
- Chief Science Officer Back Bay Group 10 Post Office Square – Suite 1300N Boston, MA 02109, USA
| | - Nina H. Fefferman
- Ecology and Evolutionary Biology National Institute for Mathematical and Biological Synthesis University of Tennessee 447 Hesler Biology Building Knoxville, TN, 37966, USA,Corresponding Author: Nina H. Fefferman
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Yang F, Zhu L, Liu F, Cheng L, Yao H, Wu N, Wu H, Li L. Generation and characterization of monoclonal antibodies against the hemagglutinin of H3N2 influenza A viruses. Virus Res 2022; 317:198815. [PMID: 35595011 DOI: 10.1016/j.virusres.2022.198815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 01/01/2023]
Abstract
Seasonal influenza viruses are highly contagious, leading to 290,000-650,000 mortalities every year globally. Among the influenza viruses, influenza A virus (H3N2) has attracted much attention due to its high frequency of antigenic variations, resulting in poor protection by vaccination. We generated a panel of murine neutralizing monoclonal antibodies (mAbs) against A/Texas/50/2012 (H3N2) and identified the relevant epitopes that potentially influence the antigenicity by selecting mAb-resistant mutants. The epitopes were mainly in antigenic site A (1/9, 11.1%), B (6/9, 66.7%), and C (1/9, 11.1%), which is consistent with recent reports on the immunodominance of antigenic site B. The amino acid substitutions at positions 156, 157, 159, 160, and 189 at antigenic site B resulted in decreased mAb capability for blocking receptor binding. In addition, the neutralizing spectra of three mAbs (1F8, 1G9 and 1H5) were different, suggesting that their epitopes may be different but partially overlapping, and it required further study. Further, the mAb 3F9 selected a new substitution, D53G/N, at antigenic site C and showed in vitro neutralizing activity against A/Victoria/361/2011 (H3N2), A/Texas/50/2012 (H3N2), and A/Hong Kong/2671/2019 (H3N2), suggesting a potential epitope on H3 hemagglutinin for inducing broad neutralizing antibody responses. Continuous research and regular monitoring of novel epitopes are of great importance for improving vaccine strain selection.
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Affiliation(s)
- Fan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Linwei Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Fumin Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Linfang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Haibo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
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Hemagglutinin Gene Variation Rate of H9N2 Avian Influenza Virus by Vaccine Intervention in China. Viruses 2022; 14:v14051043. [PMID: 35632783 PMCID: PMC9146883 DOI: 10.3390/v14051043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
H9N2 subtype avian influenza virus (AIV) is widespread globally, with China being the main epidemic center. Inactivated virus vaccination was adopted as the main prevention method in China. In this study, 22 hemagglutinin (HA) sequences were obtained from all inactivated vaccine strains of H9N2 subtype AIVs in China since its introduction. A phylogenetic analysis of the vaccine sequences and HA sequences of all published H9N2 subtype AIVs was conducted to investigate the relationship between vaccine use and the virus genetic diversity of the virus. We found that during 2002–2006, when fewer vaccines were used, annual genetic differences between the HA sequences were mainly distributed between 0.025 and 0.075 and were mainly caused by point mutations. From 2009 to 2013, more vaccines were used, and the genetic distance between sequences was about 10 times greater than between 2002 and 2006, especially in 2013. In addition to the accumulation of point mutations, insertion mutations may be the main reason for the large genetic differences between sequences from 2009 to 2013. These findings suggest that the use of inactivated vaccines affected point mutations in the HA sequences and that the contribution of high-frequency replacement vaccine strains to the rate of virus evolution is greater than that of low-frequency replacement vaccine strains. The selection pressure of the vaccine antibody plays a certain role in regulating the variation of HA sequences in H9N2 subtype AIV.
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He Z, Qin L, Xu X, Ding S. Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases. Comput Struct Biotechnol J 2022; 20:2600-2610. [PMID: 35685354 PMCID: PMC9160401 DOI: 10.1016/j.csbj.2022.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 01/23/2023] Open
Abstract
During recent decades, many new emerging or re-emerging RNA viruses have been found in plants through the development of deep-sequencing technology and big data analysis. These findings largely changed our understanding of the origin, evolution and host range of plant RNA viruses. There is evidence that their genetic composition originates from viruses, and host populations play a key role in the evolution and host adaptability of plant RNA viruses. In this mini-review, we describe the state of our understanding of the evolution of plant RNA viruses in view of compositional biases and explore how they adapt to the host. It appears that adenine rich (A-rich) coding sequences, low CpG and UpA dinucleotide frequencies and lower codon usage patterns were found in the vast majority of plant RNA viruses. The codon usage pattern of plant RNA viruses was influenced by both natural selection and mutation pressure, and natural selection mostly from hosts was the dominant factor. The codon adaptation analyses support that plant RNA viruses probably evolved a dynamic balance between codon adaptation and deoptimization to maintain efficient replication cycles in multiple hosts with various codon usage patterns. In the future, additional combinations of computational and experimental analyses of the nucleotide composition and codon usage of plant RNA viruses should be addressed.
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Affiliation(s)
- Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Corresponding author.
| | - Lang Qin
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Xiaowei Xu
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Shiwen Ding
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
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Generation of Human Lung Organoid Cultures from Healthy and Tumor Tissue to Study Infectious Diseases. J Virol 2022; 96:e0009822. [DOI: 10.1128/jvi.00098-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Three-dimensional (3D) human lung organoids reflect the native cell composition of the lung as well as its physiological properties. Human 3D lung organoids offer ideal conditions, such as timely availability in large quantities and high physiological relevance for reassessment and prediction of disease outbreaks of respiratory pathogens and pathogens that use the lung as a primary entry portal.
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43
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Dong C, Wang BZ. Engineered Nanoparticulate Vaccines to Combat Recurring and Pandemic Influenza Threats. ADVANCED NANOBIOMED RESEARCH 2022; 2:2100122. [PMID: 35754779 PMCID: PMC9231845 DOI: 10.1002/anbr.202100122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Reoccurring seasonal flu epidemics and occasional pandemics are among the most severe threats to public health. Current seasonal influenza vaccines provide limited protection against drifted circulating strains and no protection against influenza pandemics. Next-generation influenza vaccines, designated as universal influenza vaccines, should be safe, affordable, and elicit long-lasting cross-protective influenza immunity. Nanotechnology plays a critical role in the development of such novel vaccines. Engineered nanoparticles can incorporate multiple advantageous properties into the same nanoparticulate platforms to improve vaccine potency and breadth. These immunological properties include virus-like biomimicry, high antigen-load, controlled antigen release, targeted delivery, and induction of innate signaling pathways. Many nanoparticle influenza vaccines have shown promising results in generating potent and broadly protective immune responses. This review will summarize the necessity and characteristics of next-generation influenza vaccines and the immunological correlates of broad influenza immunity and focus on how cutting-edge nanoparticle technology contributes to such vaccine development. The review will give new insights into the rational design of nanoparticle universal vaccines to combat influenza epidemics and pandemics.
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Affiliation(s)
- Chunhong Dong
- Center for Inflammation, Immunity & Infection, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia 30303, USA
| | - Bao-Zhong Wang
- Center for Inflammation, Immunity & Infection, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia 30303, USA
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Hasan A, Sasaki T, Phadungsombat J, Koketsu R, Rahim R, Ara N, Biswas SM, Yonezawa R, Nakayama EE, Rahman M, Shioda T. Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. Trop Med Infect Dis 2022; 7:tropicalmed7030038. [PMID: 35324585 PMCID: PMC8949303 DOI: 10.3390/tropicalmed7030038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 12/10/2022] Open
Abstract
Influenza is one of the most common respiratory virus infections. We analyzed hemagglutinin (HA) and neuraminidase (NA) gene segments of viruses isolated from influenza patients who visited Evercare Hospital Dhaka, Bangladesh, in early 2020 immediately before the coronavirus disease 2019 (COVID-19) pandemic. All of them were influenza virus type A (IAV) H1N1pdm. Sequence analysis of the HA segments of the virus strains isolated from the clinical specimens and the subsequent phylogenic analyses of the obtained sequences revealed that all of the H1N1pdm recent subclades 6B.1A5A + 187V/A, 6B.1A5A + 156K, and 6B.1A5A + 156K with K209M were already present in Bangladesh in January 2020. Molecular clock analysis results suggested that the subclade 6B.1A5A + 156K emerged in Denmark, Australia, or the United States in July 2019, while subclades 6B.1A5A + 187V/A and 6B.1A5A + 156K with K209M emerged in East Asia in April and September 2019, respectively. On the other hand, sequence analysis of NA segments showed that the viruses lacked the H275Y mutation that confers oseltamivir resistance. Since the number of influenza cases in Bangladesh is usually small between November and January, these results indicated that the IAV H1N1pdm had spread extremely rapidly without acquiring oseltamivir resistance during a time of active international flow of people before the COVID-19 pandemic.
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Affiliation(s)
- Abu Hasan
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
| | - Tadahiro Sasaki
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
| | - Juthamas Phadungsombat
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Ritsuko Koketsu
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
| | - Rummana Rahim
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
| | - Nikhat Ara
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
| | - Suma Mita Biswas
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
| | - Riku Yonezawa
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
| | - Emi E. Nakayama
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
| | - Mizanur Rahman
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
- Correspondence: (M.R.); (T.S.)
| | - Tatsuo Shioda
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (M.R.); (T.S.)
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Fox A, Carolan L, Leung V, Phuong HVM, Khvorov A, Auladell M, Tseng YY, Thai PQ, Barr I, Subbarao K, Mai LTQ, van Doorn HR, Sullivan SG. Opposing Effects of Prior Infection versus Prior Vaccination on Vaccine Immunogenicity against Influenza A(H3N2) Viruses. Viruses 2022; 14:470. [PMID: 35336877 PMCID: PMC8949461 DOI: 10.3390/v14030470] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/10/2021] [Accepted: 11/28/2021] [Indexed: 02/05/2023] Open
Abstract
Prior vaccination can alternately enhance or attenuate influenza vaccine immunogenicity and effectiveness. Analogously, we found that vaccine immunogenicity was enhanced by prior A(H3N2) virus infection among participants of the Ha Nam Cohort, Viet Nam, but was attenuated by prior vaccination among Australian Health Care Workers (HCWs) vaccinated in the same year. Here, we combined these studies to directly compare antibody titers against 35 A(H3N2) viruses spanning 1968-2018. Participants received licensed inactivated vaccines containing A/HongKong/4801/2014 (H3N2). The analysis was limited to participants aged 18-65 Y, and compared those exposed to A(H3N2) viruses circulating since 2009 by infection (Ha Nam) or vaccination (HCWs) to a reference group who had no recent A(H3N2) infection or vaccination (Ha Nam). Antibody responses were compared by fitting titer/titer-rise landscapes across strains, and by estimating titer ratios to the reference group of 2009-2018 viruses. Pre-vaccination, titers were lowest against 2009-2014 viruses among the reference (no recent exposure) group. Post-vaccination, titers were, on average, two-fold higher among participants with prior infection and two-fold lower among participants with 3-5 prior vaccinations compared to the reference group. Titer rise was negligible among participants with 3-5 prior vaccinations, poor among participants with 1-2 prior vaccinations, and equivalent or better among those with prior infection compared to the reference group. The enhancing effect of prior infection versus the incrementally attenuating effect of prior vaccinations suggests that these exposures may alternately promote and constrain the generation of memory that can be recalled by a new vaccine strain.
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Affiliation(s)
- Annette Fox
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
| | - Louise Carolan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
| | - Vivian Leung
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
| | - Hoang Vu Mai Phuong
- National Institute of Hygiene and Epidemiology, Ha Noi 100000, Vietnam; (H.V.M.P.); (P.Q.T.); (L.T.Q.M.)
| | - Arseniy Khvorov
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
| | - Maria Auladell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Yeu-Yang Tseng
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
| | - Pham Quang Thai
- National Institute of Hygiene and Epidemiology, Ha Noi 100000, Vietnam; (H.V.M.P.); (P.Q.T.); (L.T.Q.M.)
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Le Thi Quynh Mai
- National Institute of Hygiene and Epidemiology, Ha Noi 100000, Vietnam; (H.V.M.P.); (P.Q.T.); (L.T.Q.M.)
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Africa Asia Programme, National Hospital of Tropical Diseases, Ha Noi 100000, Vietnam;
- Centre of Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Sheena G. Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
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Kim G, Shin HM, Kim HR, Kim Y. Effects of Host and Pathogenicity on Mutation Rates in Avian Influenza A Viruses. Virus Evol 2022; 8:veac013. [PMID: 35295747 PMCID: PMC8922178 DOI: 10.1093/ve/veac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/11/2022] [Accepted: 02/20/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Mutation is the primary determinant of genetic diversity in influenza viruses. The rate of mutation, measured in an absolute time-scale, is likely to be dependent on the rate of errors in copying RNA sequences per replication and the number of replications per unit time. Conditions for viral replication are probably different among host taxa, potentially generating the host-specificity of the viral mutation rate, and possibly between highly and low pathogenic viruses. This study investigated whether mutation rates per year in avian influenza A viruses depend on host taxa and pathogenicity. We inferred mutation rates from the rates of synonymous substitutions, which are assumed to be neutral and thus equal to mutation rates, at four segments that code internal viral proteins (PB2, PB1, PA, NP). On the phylogeny of all avian viral sequences for each segment, multiple distinct subtrees (clades) were identified that represent viral subpopulations, which are likely to have evolved within particular host taxa. Using simple regression analysis, we found that mutation rates were significantly higher in viruses infecting chickens than domestic ducks, and in those infecting wild shorebirds than wild ducks. Host-dependency of the substitution rate was also confirmed by Bayesian phylogenetic analysis. However, we did not find evidence that the mutation rate is higher in highly pathogenic than in low pathogenic viruses. We discuss these results considering viral replication rate as the major determinant of mutation rate per unit time.
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Affiliation(s)
- Gwanghun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hyun Mu Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon 25159, Republic of Korea
| | - Hang-Rae Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon 25159, Republic of Korea
| | - Yuseob Kim
- Division of EcoScience and Department of Life Science, Ewha Womans University, Seoul 03760, Republic of Korea
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Nabakooza G, Pastusiak A, Kateete DP, Lutwama JJ, Kitayimbwa JM, Frost SDW. Whole-genome analysis to determine the rate and patterns of intra-subtype reassortment among influenza type-A viruses in Africa. Virus Evol 2022; 8:veac005. [PMID: 35317349 PMCID: PMC8933723 DOI: 10.1093/ve/veac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/13/2022] [Accepted: 01/28/2022] [Indexed: 12/05/2022] Open
Abstract
Influenza type-A viruses (IAVs) present a global burden of human respiratory infections and mortality. Genome reassortment is an important mechanism through which epidemiologically novel influenza viruses emerge and a core step in the safe reassortment-incompetent live-attenuated influenza vaccine development. Currently, there are no data on the rate, spatial and temporal distribution, and role of reassortment in the evolution and diversification of IAVs circulating in Africa. We aimed to detect intra-subtype reassortment among Africa pandemic H1N1pdm09 (2009-10), seasonal H1N1pdm09 (2011-20), and seasonal H3N2 viruses and characterize the genomic architecture and temporal and spatial distribution patterns of the resulting reassortants. Our study was nested within the Uganda National Influenza Surveillance Programme. Next-generation sequencing was used to generate whole genomes (WGs) from 234 H1N1pdm09 (n = 116) and H3N2 (n = 118) viruses sampled between 2010 and 2018 from seven districts in Uganda. We combined our newly generated WGs with 658 H1N1pdm09 and 1131 H3N2 WGs sampled between 1994 and 2020 across Africa and identified reassortants using an automated Graph Incompatibility Based Reassortment Finder software. Viral reassortment rates were estimated using a coalescent reassortant constant population model. Phylogenetic analysis was used to assess the effect of reassortment on viral genetic evolution. We observed a high frequency of intra-subtype reassortment events, 12 · 4 per cent (94/758) and 20 · 9 per cent (256/1,224), and reassortants, 13 · 3 per cent (101/758) and 38 · 6 per cent (472/1,224), among Africa H1N1pdm09 and H3N2 viruses, respectively. H1N1pdm09 reassorted at higher rates (0.1237-0.4255) than H3N2 viruses (0 · 00912-0.0355 events/lineage/year), a case unique to Uganda. Viral reassortants were sampled in 2009 through 2020, except in 2012. 78 · 2 per cent (79/101) of H1N1pdm09 reassortants acquired new non-structural, while 57 · 8 per cent (273/472) of the H3N2 reassortants had new hemagglutinin (H3) genes. Africa H3N2 viruses underwent more reassortment events involving larger reassortant sets than H1N1pdm09 viruses. Viruses with a specific reassortment architecture circulated for up to five consecutive years in specific countries and regions. The Eastern (Uganda and Kenya) and Western Africa harboured 84 · 2 per cent (85/101) and 55 · 9 per cent (264/472) of the continent's H1N1pdm09 and H3N2 reassortants, respectively. The frequent reassortment involving multi-genes observed among Africa IAVs showed the intracontinental viral evolution and diversification possibly sustained by viral importation from outside Africa and/or local viral genomic mixing and transmission. Novel reassortant viruses emerged every year, and some persisted in different countries and regions, thereby presenting a risk of influenza outbreaks in Africa. Our findings highlight Africa as part of the global influenza ecology and the advantage of implementing routine whole-over partial genome sequencing and analyses to monitor circulating and detect emerging viruses. Furthermore, this study provides evidence and heightens our knowledge on IAV evolution, which is integral in directing vaccine strain selection and the update of master donor viruses used in recombinant vaccine development.
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Affiliation(s)
- Grace Nabakooza
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O Box 7072, Kampala, Uganda
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Rd, P.O BOX 4, Mukono, Uganda
| | | | - David Patrick Kateete
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O Box 7072, Kampala, Uganda
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda
| | - Julius Julian Lutwama
- Department of Arbovirology Emerging & Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Plot No: 51-59, Nakiwogo Road, P.O. Box 49, Entebbe, Uganda
| | - John Mulindwa Kitayimbwa
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Rd, P.O BOX 4, Mukono, Uganda
| | - Simon David William Frost
- Microsoft Research, 14820 NE 36th Street, Redmond, WA 98052, USA
- London School of Hygiene & Tropical Medicine (LSHTM), Keppel St, Bloomsbury, London WC1E 7HT, UK
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Van Goethem N, Danwang C, Bossuyt N, Van Oyen H, Roosens NHC, Robert A. A systematic review and meta-analysis of host genetic factors associated with influenza severity. BMC Genomics 2021; 22:912. [PMID: 34930124 PMCID: PMC8686082 DOI: 10.1186/s12864-021-08240-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The severity of influenza disease can range from mild symptoms to severe respiratory failure and can partly be explained by host genetic factors that predisposes the host to severe influenza. Here, we aimed to summarize the current state of evidence that host genetic variants play a role in the susceptibility to severe influenza infection by conducting a systematic review and performing a meta-analysis for all markers with at least three or more data entries. RESULTS A total of 34 primary human genetic association studies were identified that investigated a total of 20 different genes. The only significant pooled ORs were retrieved for the rs12252 polymorphism: an overall OR of 1.52 (95% CI [1.06-2.17]) for the rs12252-C allele compared to the rs12252-T allele. A stratified analysis by ethnicity revealed opposite effects in different populations. CONCLUSION With exception for the rs12252 polymorphism, we could not identify specific genetic polymorphisms to be associated with severe influenza infection in a pooled meta-analysis. This advocates for the use of large, hypothesis-free, genome-wide association studies that account for the polygenic nature and the interactions with other host, pathogen and environmental factors.
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Affiliation(s)
- Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Brussels, Belgium
| | - Célestin Danwang
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Brussels, Belgium
| | - Nathalie Bossuyt
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Brussels, Belgium
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Moore TC, Fong J, Rosa Hernández AM, Pogreba-Brown K. CAFOs, novel influenza, and the need for One Health approaches. One Health 2021; 13:100246. [PMID: 33997233 PMCID: PMC8091921 DOI: 10.1016/j.onehlt.2021.100246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/02/2021] [Accepted: 04/04/2021] [Indexed: 11/18/2022] Open
Abstract
Concentrated animal feeding operations (CAFOs) present highly efficient means of meeting food demands. CAFOs create unique conditions that can affect the health and environment of animals and humans within and outside operations, leading to potential epidemiological concerns that scale with operational size. One such arena meriting further investigation is their possible contribution to novel influenzas. CAFOs present opportunities for cross-species transmission of influenza as demonstrated by reports of swine flu and avian influenza outbreaks. Conditions and pathways leading to novel influenza strains are complex and require varied prevention and intervention approaches. Current challenges for prevention of respiratory viruses entering or leaving swine and poultry CAFOs are multifaceted and include adherence of personal safety measures, lack of training and safety provisions for personnel, and incomplete standardized federal, state, and/or county regulation and enforcement coverage across agricultural systems. This report acknowledges that any proposed CAFO-associated influenza intervention should be cross-organizational, and no single intervention should be expected to provide full resolution. Proposed interventions affect multiple components of the One Health triad, and include seasonal human influenza immunization, PPE regulation and adherence, alternative waste management, general biosecurity standardization and an industry best practices incentive program. Due to the complexity of this problem, multiple anticipated communication, enforcement, and logistical challenges may hinder the full implementation of proposed solutions. General and operation-specific (swine and poultry) biosecurity practices may mitigate some of the risks associated with influenza virus reassortment across species. Education and advocacy can help protect workers, communities, veterinarians and consumers from CAFO-associated influenza virus. To achieve this, there must be more complete communication between CAFOs, governing agencies, health services, animal services, researchers, and consumers to better explore the potential health outcomes associated with CAFOs.
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Affiliation(s)
- Thomas C. Moore
- The University of Arizona, Mel and Enid Zuckerman College of Public Health, Department of Epidemiology and Biostatistics, USA
| | - Joseph Fong
- The University of Arizona, Mel and Enid Zuckerman College of Public Health, Department of Epidemiology and Biostatistics, USA
| | - Ayeisha M. Rosa Hernández
- The University of Arizona, Mel and Enid Zuckerman College of Public Health, Department of Epidemiology and Biostatistics, USA
| | - Kristen Pogreba-Brown
- The University of Arizona, Mel and Enid Zuckerman College of Public Health, Department of Epidemiology and Biostatistics, USA
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Ghafari M, Simmonds P, Pybus OG, Katzourakis A. A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses. Curr Biol 2021; 31:4689-4696.e5. [PMID: 34478645 PMCID: PMC8585505 DOI: 10.1016/j.cub.2021.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/02/2021] [Accepted: 08/05/2021] [Indexed: 01/16/2023]
Abstract
Estimating viral timescales is fundamental in understanding the evolutionary biology of viruses. Molecular clocks are widely used to reveal the recent evolutionary histories of viruses but may severely underestimate their longer-term origins because of the inverse correlation between inferred rates of evolution and the timescale of their measurement. Here, we provide a predictive mechanistic model that readily explains the rate decay phenomenon over a wide range of timescales and recapitulates the ubiquitous power-law rate decay with a slope of -0.65. We show that standard substitution models fail to correctly estimate divergence times once the most rapidly evolving sites saturate, typically after hundreds of years in RNA viruses and thousands of years in DNA viruses. Our model successfully recreates the observed pattern of decay and explains the evolutionary processes behind the time-dependent rate phenomenon. We then apply our model to re-estimate the date of diversification of genotypes of hepatitis C virus to 423,000 (95% highest posterior density [HPD]: 394,000-454,000) years before present, a time preceding the dispersal of modern humans out of Africa, and show that the most recent common ancestor of sarbecoviruses dates back to 21,000 (95% HPD: 19,000-22,000) years ago, nearly thirty times older than previous estimates. This creates a new perspective for our understanding of the origins of these viruses and also suggests that a substantial revision of evolutionary timescales of other viruses can be similarly achieved.
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Affiliation(s)
- Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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