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Huang C, Yu L, Xu Y, Huang J, Qin Y, Guo X, Zeng Y, Qin Y, Ouyang K, Wei Z, Huang W, García-Sastre A, Chen Y. Long-term co-circulation of multiple influenza A viruses in pigs, Guangxi, China. Emerg Microbes Infect 2024; 13:2337673. [PMID: 38572517 PMCID: PMC11005871 DOI: 10.1080/22221751.2024.2337673] [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: 12/14/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Influenza A viruses (IAVs) pose a persistent potential threat to human health because of the spillover from avian and swine infections. Extensive surveillance was performed in 12 cities of Guangxi, China, during 2018 and 2023. A total of 2540 samples (including 2353 nasal swabs and 187 lung tissues) were collected from 18 pig farms with outbreaks of respiratory disease. From these, 192 IAV-positive samples and 19 genomic sequences were obtained. We found that the H1 and H3 swine influenza A viruses (swIAVs) of multiple lineages and genotypes have continued to co-circulate during that time in this region. Genomic analysis revealed the Eurasian avian-like H1N1 swIAVs (G4) still remained predominant in pig populations. Strikingly, the novel multiple H3N2 genotypes were found to have been generated through the repeated introduction of the early H3N2 North American triple reassortant viruses (TR H3N2 lineage) that emerged in USA and Canada in 1998 and 2005, respectively. Notably, when the matrix gene segment derived from the H9N2 avian influenza virus was introduced into endemic swIAVs, this produced a novel quadruple reassortant H1N2 swIAV that could pose a potential risk for zoonotic infection.
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Affiliation(s)
- Chongqiang Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Liangzheng Yu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Yi Xu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Jiamo Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Yibin Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Institute of Veterinary Medicine, Nanning, People’s Republic of China
| | - Xuan Guo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Nongken Yongxin Animal Husbandry Group Co. Ltd., Nanning, People’s Republic of China
| | - Yongfang Zeng
- Nanning Zhufulai Animal Health Management Co. Ltd., Nanning, People’s Republic of China
| | - Yifeng Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Kang Ouyang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Zuzhang Wei
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Weijian Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ying Chen
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
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Bai Y, Lei H, Song W, Shin SC, Wang J, Xiao B, Koçer ZA, Song MS, Webster R, Webby RJ, Wong SS, Zanin M. Amino acids in the polymerase complex of shorebird-isolated H1N1 influenza virus impact replication and host-virus interactions in mammalian models. Emerg Microbes Infect 2024; 13:2332652. [PMID: 38517705 PMCID: PMC11018082 DOI: 10.1080/22221751.2024.2332652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/15/2024] [Indexed: 03/24/2024]
Abstract
A diverse population of avian influenza A viruses (AIVs) are maintained in wild birds and ducks yet the zoonotic potential of AIVs in these environmental reservoirs and the host-virus interactions involved in mammalian infection are not well understood. In studies of a group of subtype H1N1 AIVs isolated from migratory wild birds during surveillance in North America, we previously identified eight amino acids in the polymerase genes PB2 and PB1 that were important for the transmissibility of these AIVs in a ferret model of human influenza virus transmission. In this current study we found that PB2 containing amino acids associated with transmissibility at 67, 152, 199, 508, and 649 and PB1 at 298, 642, and 667 were associated with more rapid viral replication kinetics, greater infectivity, more active polymerase complexes and greater kinetics of viral genome replication and transcription. Pathogenicity in the mouse model was also impacted, evident as greater weight loss and lung pathology associated with greater inflammatory lung cytokine expression. Further, these AIVs all contained the avian-type amino acids of PB2-E627, D701, G590, Q591 and T271. Therefore, our study provides novel insights into the role of the AIV polymerase complex in the zoonotic transmission of AIVs in mammals.
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Affiliation(s)
- Yaqin Bai
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Guangzhou Medical University, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Diseases, Guangzhou, People’s Republic of China
| | - Hui Lei
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Centre for Immunology & Infection, Hong Kong SAR, People's Republic of China
| | - Wenjun Song
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, People’s Republic of China
| | | | - Jiaqi Wang
- Guangzhou Medical University, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Diseases, Guangzhou, People’s Republic of China
| | - Biying Xiao
- Guangzhou Medical University, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Diseases, Guangzhou, People’s Republic of China
| | - Zeynep A. Koçer
- Emerging Viral Diseases Laboratory, Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Department of Biomedicine and Health Technologies, Izmir International Biomedicine and Genome Institute, Izmir, Türkiye
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University Medical School, Chungbuk, Korea
| | - Robert Webster
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard J. Webby
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Sook-San Wong
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Mark Zanin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Centre for Immunology & Infection, Hong Kong SAR, People's Republic of China
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Briggs K, Chrzastek K, Segovia K, Mo J, Kapczynski DR. Genetic insertion of mouse Myxovirus-resistance gene 1 increases innate resistance against both high and low pathogenic avian influenza virus by significantly decreasing replication in chicken DF1 cell line. Virology 2024; 595:110066. [PMID: 38574415 DOI: 10.1016/j.virol.2024.110066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/01/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
Avian influenza virus (AIV) is a constant threat to animal health with recent global outbreaks resulting in the death of hundreds of millions of birds with spillover into mammals. Myxovirus-resistance (Mx) proteins are key mediators of the antiviral response that block virus replication. Mouse (Mu) Mx (Mx1) is a strong antiviral protein that interacts with the viral nucleoprotein to inhibit polymerase function. The ability of avian Mx1 to inhibit AIV is unclear. In these studies, Mu Mx1 was stably introduced into chicken DF1 cells to enhance the immune response against AIV. Following infection, titers of AIV were significantly decreased in cells expressing Mu Mx1. In addition, considerably less cytopathic effect (CPE) and matrix protein staining was observed in gene-edited cells expressing Mu Mx1, suggesting Mu Mx1 is broadly effective against multiple AIV subtypes. This work provides foundational studies for use of gene-editing to enhance innate disease resistance against AIV.
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Affiliation(s)
- Kelsey Briggs
- Exotic and Emerging Avian Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, Georgia
| | - Klaudia Chrzastek
- Exotic and Emerging Avian Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, Georgia
| | - Karen Segovia
- Exotic and Emerging Avian Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, Georgia
| | - Jongsuk Mo
- Exotic and Emerging Avian Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, Georgia
| | - Darrell R Kapczynski
- Exotic and Emerging Avian Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, Georgia.
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Adlhoch C, Alm E, Enkirch T, Lamb F, Melidou A, Willgert K, Marangon S, Monne I, Stegeman JA, Delacourt R, Baldinelli F, Broglia A. Drivers for a pandemic due to avian influenza and options for One Health mitigation measures. EFSA J 2024; 22:e8735. [PMID: 38576537 PMCID: PMC10988447 DOI: 10.2903/j.efsa.2024.8735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
Avian influenza viruses (AIV) remain prevalent among wild bird populations in the European Union and European Economic Area (EU/EEA), leading to significant illness in and death of birds. Transmission between bird and mammal species has been observed, particularly in fur animal farms, where outbreaks have been reported. While transmission from infected birds to humans is rare, there have been instances of exposure to these viruses since 2020 without any symptomatic infections reported in the EU/EEA. However, these viruses continue to evolve globally, and with the migration of wild birds, new strains carrying potential mutations for mammalian adaptation could be selected. If avian A(H5N1) influenza viruses acquire the ability to spread efficiently among humans, large-scale transmission could occur due to the lack of immune defences against H5 viruses in humans. The emergence of AIV capable of infecting mammals, including humans, can be facilitated by various drivers. Some intrinsic drivers are related to virus characteristics or host susceptibility. Other drivers are extrinsic and may increase exposure of mammals and humans to AIV thereby stimulating mutation and adaptation to mammals. Extrinsic drivers include the ecology of host species, such as including wildlife, human activities like farming practices and the use of natural resources, climatic and environmental factors. One Health measures to mitigate the risk of AIV adapting to mammals and humans focus on limiting exposure and preventing spread. Key options for actions include enhancing surveillance targeting humans and animals, ensuring access to rapid diagnostics, promoting collaboration between animal and human sectors, and implementing preventive measures such as vaccination. Effective communication to different involved target audiences should be emphasised, as well as strengthening veterinary infrastructure, enforcing biosecurity measures at farms, and reducing wildlife contact with domestic animals. Careful planning of poultry and fur animal farming, especially in areas with high waterfowl density, is highlighted for effective risk reduction.
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Lin S, Zhang Y, Yang J, Yang L, Li X, Bo H, Liu J, Tan M, Zhu W, Wang D, Shu Y. Cross-Species Transmission Potential of H4 Avian Influenza Viruses in China: Epidemiological and Evolutionary Study. Viruses 2024; 16:353. [PMID: 38543719 PMCID: PMC10974465 DOI: 10.3390/v16030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 05/23/2024] Open
Abstract
H4 avian influenza viruses (AIVs) have been widely detected in live poultry markets in China. However, the potential public health impact of H4 AIVs remains largely uncertain. Here, we fully analyzed the distribution and phylogenetic relationship of H4 AIVs in China. We obtained 31 isolates of H4 viruses in China during 2009-2022 through surveillance in poultry-associated environments, such as live poultry markets and poultry farms. Genomic sequence analysis together with publicly available data revealed that frequent reassortment and introduction of H4 AIV from wild birds to poultry may have occurred. We identified 62 genotypes among 127 whole genome sequences of H4 viruses in China, indicating that H4 AIVs had great genetic diversity in China. We also investigated molecular markers and found that drug resistance mutations frequently occurred in the M2 protein and a few mutations related to receptor binding and the host signature in H4 AIVs. Our study demonstrates the cross-species transmission potential of H4 AIVs in China and provides some reference significance for its risk assessment.
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Affiliation(s)
- Shuxia Lin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (S.L.)
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Ye Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Jiaying Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (S.L.)
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Hong Bo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Jia Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Min Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (S.L.)
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, China
- Key Laboratory of Pathogen Infection Prevention and Control (MOE), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
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Vora NM, Hassan L, Plowright RK, Horton R, Cook S, Sizer N, Bernstein A. The Lancet-PPATS Commission on Prevention of Viral Spillover: reducing the risk of pandemics through primary prevention. Lancet 2024; 403:597-599. [PMID: 37837991 DOI: 10.1016/s0140-6736(23)01064-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 10/16/2023]
Affiliation(s)
- Neil M Vora
- Conservation International, Arlington, VA 22202, USA; Department of Medicine, Columbia University, New York, NY, USA.
| | | | - Raina K Plowright
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY, USA
| | | | - Sonila Cook
- Preventing Pandemics at the Source, Washington, DC, USA
| | - Nigel Sizer
- Preventing Pandemics at the Source, Washington, DC, USA
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Xu X, Chen Q, Tan M, Liu J, Li X, Yang L, Shu Y, Wang D, Zhu W. Epidemiology, evolution, and biological characteristics of H6 avian influenza viruses in China. Emerg Microbes Infect 2023; 12:2151380. [PMID: 36440484 PMCID: PMC9788695 DOI: 10.1080/22221751.2022.2151380] [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] [Indexed: 11/29/2022]
Abstract
H6 avian influenza virus (AIV) is one of the most prevalent AIV subtypes in birds globally. To investigate the current situation and characteristics of H6 AIVs circulating in China, we analysed the epidemiology, genetic evolution and pathogenic features of this subtype. During 2000-2021, H6 subtype AIVs spread widely through Southern China and presented high host diversity. On analysing 171 H6 viruses isolated during 2009-2021, dynamic reassortments were observed among H6 and other co-circulating AIV subtypes, and these generated a total of 16 different genotypes. A few H6N6 strains possessed L226 and S228 mutations of hemagglutinin (H3 numbering), which may enhance the affinity of H6 viruses to human receptors. H6N6 viruses also exhibited divergent pathogenicity and growth profiles in vivo and in vitro. Some of the H6N6 viruses could infect mice without mammalian adaptation, and even caused death in this species. Therefore, our study demonstrated that the H6 AIVs posed a potential threat to human health and highlighted the urgent need for continued surveillance and evaluation of the H6 influenza viruses circulating in the field.
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Affiliation(s)
- Xiaohao Xu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People’s Republic of China,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Qi Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People’s Republic of China,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Min Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Jia Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People’s Republic of China,Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China, Yuelong Shu School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People’s Republic of China; Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China,Dayan Wang National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China,Wenfei Zhu National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
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8
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Gilbertson B, Duncan M, Subbarao K. Role of the viral polymerase during adaptation of influenza A viruses to new hosts. Curr Opin Virol 2023; 62:101363. [PMID: 37672875 DOI: 10.1016/j.coviro.2023.101363] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 09/08/2023]
Abstract
As a group, influenza-A viruses (IAV) infect a wide range of animal hosts, however, they are constrained to infecting selected host species by species-specific interactions between the host and virus, that are required for efficient replication of the viral RNA genome. When IAV cross the species barrier, they acquire mutations in the viral genome to enable interactions with the new host factors, or to compensate for their loss. The viral polymerase genes polymerase basic 1, polymerase basic 2, and polymerase-acidic are important sites of host adaptation. In this review, we discuss why the viral polymerase is so vital to the process of host adaptation, look at some of the known viral mutations, and host factors involved in adaptation, particularly of avian IAV to mammalian hosts.
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Affiliation(s)
- Brad Gilbertson
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Melanie Duncan
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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9
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Gilbertson B, Subbarao K. What Have We Learned by Resurrecting the 1918 Influenza Virus? Annu Rev Virol 2023; 10:25-47. [PMID: 37774132 DOI: 10.1146/annurev-virology-111821-104408] [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: 10/01/2023]
Abstract
The 1918 Spanish influenza pandemic was one of the deadliest infectious disease events in recorded history, resulting in approximately 50-100 million deaths worldwide. The origins of the 1918 virus and the molecular basis for its exceptional virulence remained a mystery for much of the 20th century because the pandemic predated virologic techniques to isolate, passage, and store influenza viruses. In the late 1990s, overlapping fragments of influenza viral RNA preserved in the tissues of several 1918 victims were amplified and sequenced. The use of influenza reverse genetics then permitted scientists to reconstruct the 1918 virus entirely from cloned complementary DNA, leading to new insights into the origin of the virus and its pathogenicity. Here, we discuss some of the advances made by resurrection of the 1918 virus, including the rise of innovative molecular research, which is a topic in the dual use debate.
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Affiliation(s)
- Brad Gilbertson
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia;
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10
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Griffin EF, Tompkins SM. Fitness Determinants of Influenza A Viruses. Viruses 2023; 15:1959. [PMID: 37766365 PMCID: PMC10535923 DOI: 10.3390/v15091959] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A (IAV) is a major human respiratory pathogen that causes illness, hospitalizations, and mortality annually worldwide. IAV is also a zoonotic pathogen with a multitude of hosts, allowing for interspecies transmission, reassortment events, and the emergence of novel pandemics, as was seen in 2009 with the emergence of a swine-origin H1N1 (pdmH1N1) virus into humans, causing the first influenza pandemic of the 21st century. While the 2009 pandemic was considered to have high morbidity and low mortality, studies have linked the pdmH1N1 virus and its gene segments to increased disease in humans and animal models. Genetic components of the pdmH1N1 virus currently circulate in the swine population, reassorting with endemic swine viruses that co-circulate and occasionally spillover into humans. This is evidenced by the regular detection of variant swine IAVs in humans associated with state fairs and other intersections of humans and swine. Defining genetic changes that support species adaptation, virulence, and cross-species transmission, as well as mutations that enhance or attenuate these features, will improve our understanding of influenza biology. It aids in surveillance and virus risk assessment and guides the establishment of counter measures for emerging viruses. Here, we review the current understanding of the determinants of specific IAV phenotypes, focusing on the fitness, transmission, and virulence determinants that have been identified in swine IAVs and/or in relation to the 2009 pdmH1N1 virus.
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Affiliation(s)
- Emily Fate Griffin
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - Stephen Mark Tompkins
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Center for Influenza Disease and Emergence Response (CIDER), Athens, GA 30602, USA
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11
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Sun H, Li H, Tong Q, Han Q, Liu J, Yu H, Song H, Qi J, Li J, Yang J, Lan R, Deng G, Chang H, Qu Y, Pu J, Sun Y, Lan Y, Wang D, Shi Y, Liu WJ, Chang KC, Gao GF, Liu J. Airborne transmission of human-isolated avian H3N8 influenza virus between ferrets. Cell 2023; 186:4074-4084.e11. [PMID: 37669665 DOI: 10.1016/j.cell.2023.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/08/2023] [Accepted: 08/08/2023] [Indexed: 09/07/2023]
Abstract
H3N8 avian influenza viruses (AIVs) in China caused two confirmed human infections in 2022, followed by a fatal case reported in 2023. H3N8 viruses are widespread in chicken flocks; however, the zoonotic features of H3N8 viruses are poorly understood. Here, we demonstrate that H3N8 viruses were able to infect and replicate efficiently in organotypic normal human bronchial epithelial (NHBE) cells and lung epithelial (Calu-3) cells. Human isolates of H3N8 virus were more virulent and caused severe pathology in mice and ferrets, relative to chicken isolates. Importantly, H3N8 virus isolated from a patient with severe pneumonia was transmissible between ferrets through respiratory droplets; it had acquired human-receptor-binding preference and amino acid substitution PB2-E627K necessary for airborne transmission. Human populations, even when vaccinated against human H3N2 virus, appear immunologically naive to emerging mammalian-adapted H3N8 AIVs and could be vulnerable to infection at epidemic or pandemic proportion.
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Affiliation(s)
- Honglei Sun
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Han Li
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qi Tong
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qiqi Han
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jiyu Liu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Haili Yu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaqi Li
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jizhe Yang
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Riguo Lan
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Guojing Deng
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Haoyu Chang
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yajin Qu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Juan Pu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yipeng Sun
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yu Lan
- Chinese National Influenza Center (CNIC), NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dayan Wang
- Chinese National Influenza Center (CNIC), NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yi Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - William J Liu
- Chinese National Influenza Center (CNIC), NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Kin-Chow Chang
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Chinese National Influenza Center (CNIC), NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Jinhua Liu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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12
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Piepenbrink M, Oladunni F, Nogales A, Khalil AM, Fitzgerald T, Basu M, Fucile C, Topham DJ, Rosenberg AF, Martinez-Sobrido L, Kobie JJ. Highly Cross-Reactive and Protective Influenza A Virus H3N2 Hemagglutinin- and Neuraminidase-Specific Human Monoclonal Antibodies. Microbiol Spectr 2023; 11:e0472822. [PMID: 37318331 PMCID: PMC10433997 DOI: 10.1128/spectrum.04728-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/29/2023] [Indexed: 06/16/2023] Open
Abstract
Due to antigenic drift and shift of influenza A viruses (IAV) and the tendency to elicit predominantly strain-specific antibodies, humanity remains susceptible to new strains of seasonal IAV and is at risk from viruses with pandemic potential for which limited or no immunity may exist. The genetic drift of H3N2 IAV is specifically pronounced, resulting in two distinct clades since 2014. Here, we demonstrate that immunization with a seasonal inactivated influenza vaccine (IIV) results in increased levels of H3N2 IAV-specific serum antibodies against hemagglutinin (HA) and neuraminidase (NA). Detailed analysis of the H3N2 B cell response indicated expansion of H3N2-specific peripheral blood plasmablasts 7 days after IIV immunization which expressed monoclonal antibodies (MAbs) with broad and potent antiviral activity against many H3N2 IAV strains as well as prophylactic and therapeutic activity in mice. These H3N2-specific B cell clonal lineages persisted in CD138+ long-lived bone marrow plasma cells. These results demonstrate that IIV-induced H3N2 human MAbs can protect and treat influenza virus infection in vivo and suggest that IIV can induce a subset of IAV H3N2-specific B cells with broad protective potential, a feature that warrants further study for universal influenza vaccine development. IMPORTANCE Influenza A virus (IAV) infections continue to cause substantial morbidity and mortality despite the availability of seasonal vaccines. The extensive genetic variability in seasonal and potentially pandemic influenza strains necessitates new vaccine strategies that can induce universal protection by focusing the immune response on generating protective antibodies against conserved targets within the influenza virus hemagglutinin and neuraminidase proteins. We have demonstrated that seasonal immunization with inactivated influenza vaccine (IIV) stimulates H3N2-specific monoclonal antibodies in humans that are broad and potent in their neutralization of virus in vitro. These antibodies also provide protection from H3N2 IAV in a mouse model of infection. Furthermore, they persist in the bone marrow, where they are expressed by long-lived antibody-producing plasma cells. This significantly demonstrates that seasonal IIV can induce a subset of H3N2-specific B cells with broad protective potential, a process that if further studied and enhanced could aid in the development of a universal influenza vaccine.
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Affiliation(s)
- Michael Piepenbrink
- Heersink School of Medicine, Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Medicine, Infectious Diseases Division, University of Rochester, Rochester, New York, USA
| | - Fatai Oladunni
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - Ahmed M. Khalil
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Theresa Fitzgerald
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - Madhubanti Basu
- Heersink School of Medicine, Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christopher Fucile
- Heersink School of Medicine, Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David J. Topham
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - Alexander F. Rosenberg
- Heersink School of Medicine, Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Luis Martinez-Sobrido
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - James J. Kobie
- Heersink School of Medicine, Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Medicine, Infectious Diseases Division, University of Rochester, Rochester, New York, USA
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13
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Chen P, Jin Z, Peng L, Zheng Z, Cheung YM, Guan J, Chen L, Huang Y, Fan X, Zhang Z, Shi D, Xie J, Chen R, Xiao B, Yip CH, Smith DK, Hong W, Liu Y, Li L, Wang J, Holmes EC, Lam TTY, Zhu H, Guan Y. Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health. J Virol 2023; 97:e0043423. [PMID: 37289052 PMCID: PMC10308888 DOI: 10.1128/jvi.00434-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/08/2023] [Indexed: 06/09/2023] Open
Abstract
Although influenza A viruses of several subtypes have occasionally infected humans, to date only those of the H1, H2, and H3 subtypes have led to pandemics and become established in humans. The detection of two human infections by avian H3N8 viruses in April and May of 2022 raised pandemic concerns. Recent studies have shown the H3N8 viruses were introduced into humans from poultry, although their genesis, prevalence, and transmissibility in mammals have not been fully elucidated. Findings generated from our systematic influenza surveillance showed that this H3N8 influenza virus was first detected in chickens in July 2021 and then disseminated and became established in chickens over wider regions of China. Phylogenetic analyses revealed that the H3 HA and N8 NA were derived from avian viruses prevalent in domestic ducks in the Guangxi-Guangdong region, while all internal genes were from enzootic poultry H9N2 viruses. The novel H3N8 viruses form independent lineages in the glycoprotein gene trees, but their internal genes are mixed with those of H9N2 viruses, indicating continuous gene exchange among these viruses. Experimental infection of ferrets with three chicken H3N8 viruses showed transmission through direct contact and inefficient transmission by airborne exposure. Examination of contemporary human sera detected only very limited antibody cross-reaction to these viruses. The continuing evolution of these viruses in poultry could pose an ongoing pandemic threat. IMPORTANCE A novel H3N8 virus with demonstrated zoonotic potential has emerged and disseminated in chickens in China. It was generated by reassortment between avian H3 and N8 virus(es) and long-term enzootic H9N2 viruses present in southern China. This H3N8 virus has maintained independent H3 and N8 gene lineages but continues to exchange internal genes with other H9N2 viruses to form novel variants. Our experimental studies showed that these H3N8 viruses were transmissible in ferrets, and serological data suggest that the human population lacks effective immunological protection against it. With its wide geographical distribution and continuing evolution in chickens, other spillovers to humans can be expected and might lead to more efficient transmission in humans.
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Affiliation(s)
- Peiwen Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Ziying Jin
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Liuxia Peng
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Zuoyi Zheng
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Jing Guan
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Liming Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Yiteng Huang
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, Guangxi, China
| | - Zengfeng Zhang
- Department of Microbiology, Guangxi Medical University, Nanning, Guangxi, China
| | - Dongmei Shi
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Jin Xie
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Rirong Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Boheng Xiao
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Chun Hung Yip
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - David K. Smith
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Wenshan Hong
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Yongmei Liu
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lifeng Li
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Jia Wang
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Edward C. Holmes
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tommy Tsan-Yuk Lam
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Huachen Zhu
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Yi Guan
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
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14
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Arcos S, Han AX, te Velthuis AJW, Russell CA, Lauring AS. Mutual information networks reveal evolutionary relationships within the influenza A virus polymerase. Virus Evol 2023; 9:vead037. [PMID: 37325086 PMCID: PMC10263469 DOI: 10.1093/ve/vead037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Abstract
The influenza A virus (IAV) RNA polymerase is an essential driver of IAV evolution. Mutations that the polymerase introduces into viral genome segments during replication are the ultimate source of genetic variation, including within the three subunits of the IAV polymerase (polymerase basic protein 2, polymerase basic protein 1, and polymerase acidic protein). Evolutionary analysis of the IAV polymerase is complicated, because changes in mutation rate, replication speed, and drug resistance involve epistatic interactions among its subunits. In order to study the evolution of the human seasonal H3N2 polymerase since the 1968 pandemic, we identified pairwise evolutionary relationships among ∼7000 H3N2 polymerase sequences using mutual information (MI), which measures the information gained about the identity of one residue when a second residue is known. To account for uneven sampling of viral sequences over time, we developed a weighted MI (wMI) metric and demonstrate that wMI outperforms raw MI through simulations using a well-sampled severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) dataset. We then constructed wMI networks of the H3N2 polymerase to extend the inherently pairwise wMI statistic to encompass relationships among larger groups of residues. We included hemagglutinin (HA) in the wMI network to distinguish between functional wMI relationships within the polymerase and those potentially due to hitch-hiking on antigenic changes in HA. The wMI networks reveal coevolutionary relationships among residues with roles in replication and encapsidation. Inclusion of HA highlighted polymerase-only subgraphs containing residues with roles in the enzymatic functions of the polymerase and host adaptability. This work provides insight into the factors that drive and constrain the rapid evolution of influenza viruses.
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15
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Yan S, Yang F, Yao H, Dong D, Wu D, Wu N, Ye C, Wu H. A multiplex real-time RT-PCR assay for the detection of H1, H2 and H3 subtype avian influenza viruses. Virus Genes 2023; 59:333-337. [PMID: 36515804 DOI: 10.1007/s11262-022-01963-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Avian influenza viruses (AIVs) are influenza A viruses, of which subtypes H1, H2 and H3 are highly transmissible in poultry and have the risk of transmission to human as well. It is important to establish an accurate, sensitive and convenient means of virus detection. In this study, we developed a multiplex real-time RT-PCR assay based on conserved sequences of the virus hemagglutinin and matrix, and designed primers and probes for the simultaneous and rapid detection of AIV subtypes H1, H2 and H3. We used different subtypes of AIVs and other avian respiratory viruses for evaluation of the specificity of this method. The results showed good sensitivity, specificity and reproducibility. The detection limit was 10-100 copies per reaction. The method also achieved good concordance with the virus isolation method when compared to 81 poultry samples evaluated. It provides a new method for detecting mixed infections of AIVs.
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Affiliation(s)
- Sijing Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Fan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China
| | - Dalu Dong
- Hangzhou Biotest Biotech Co.,Ltd, 27 Tuyi Road, Cangqian Street, Yuhang District, Hangzhou, 311121, Zhejiang, China
| | - Danna Wu
- Hangzhou Biotest Biotech Co.,Ltd, 27 Tuyi Road, Cangqian Street, Yuhang District, Hangzhou, 311121, Zhejiang, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China
| | - Chunsheng Ye
- Hangzhou Biotest Biotech Co.,Ltd, 27 Tuyi Road, Cangqian Street, Yuhang District, Hangzhou, 311121, Zhejiang, China.
| | - Haibo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China.
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16
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López-Valiñas Á, Valle M, Wang M, Darji A, Cantero G, Chiapponi C, Segalés J, Ganges L, Núñez JI. Vaccination against swine influenza in pigs causes different drift evolutionary patterns upon swine influenza virus experimental infection and reduces the likelihood of genomic reassortments. Front Cell Infect Microbiol 2023; 13:1111143. [PMID: 36992684 PMCID: PMC10040791 DOI: 10.3389/fcimb.2023.1111143] [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: 11/29/2022] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
Influenza A viruses (IAVs) can infect a wide variety of bird and mammal species. Their genome is characterized by 8 RNA single stranded segments. The low proofreading activity of their polymerases and the genomic reassortment between different IAVs subtypes allow them to continuously evolve, constituting a constant threat to human and animal health. In 2009, a pandemic of an IAV highlighted the importance of the swine host in IAVs adaptation between humans and birds. The swine population and the incidence of swine IAV is constantly growing. In previous studies, despite vaccination, swine IAV growth and evolution were proven in vaccinated and challenged animals. However, how vaccination can drive the evolutionary dynamics of swine IAV after coinfection with two subtypes is poorly studied. In the present study, vaccinated and nonvaccinated pigs were challenged by direct contact with H1N1 and H3N2 independent swine IAVs seeder pigs. Nasal swab samples were daily recovered and broncho-alveolar lavage fluid (BALF) was also collected at necropsy day from each pig for swine IAV detection and whole genome sequencing. In total, 39 swine IAV whole genome sequences were obtained by next generation sequencing from samples collected from both experimental groups. Subsequently, genomic, and evolutionary analyses were carried out to detect both, genomic reassortments and single nucleotide variants (SNV). Regarding the segments found per sample, the simultaneous presence of segments from both subtypes was much lower in vaccinated animals, indicating that the vaccine reduced the likelihood of genomic reassortment events. In relation to swine IAV intra-host diversity, a total of 239 and 74 SNV were detected within H1N1 and H3N2 subtypes, respectively. Different proportions of synonymous and nonsynonymous substitutions were found, indicating that vaccine may be influencing the main mechanism that shape swine IAV evolution, detecting natural, neutral, and purifying selection in the different analyzed scenarios. SNV were detected along the whole swine IAV genome with important nonsynonymous substitutions on polymerases, surface glycoproteins and nonstructural proteins, which may have an impact on virus replication, immune system escaping and virulence of virus, respectively. The present study further emphasized the vast evolutionary capacity of swine IAV, under natural infection and vaccination pressure scenarios.
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Affiliation(s)
- Álvaro López-Valiñas
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la 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
- *Correspondence: José I. Núñez, ; Álvaro López-Valiñas,
| | - Marta Valle
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la 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
| | - Miaomiao Wang
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la 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), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la 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
| | - Guillermo Cantero
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la 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
| | - Joaquim Segalés
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la 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
| | - Llilianne Ganges
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la 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
| | - José I. Núñez
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la 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
- *Correspondence: José I. Núñez, ; Álvaro López-Valiñas,
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Arcos S, Han AX, Te Velthuis AJW, Russell CA, Lauring AS. Mutual information networks reveal evolutionary relationships within the influenza A virus polymerase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528850. [PMID: 36824962 PMCID: PMC9949103 DOI: 10.1101/2023.02.16.528850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The influenza A (IAV) RNA polymerase is an essential driver of IAV evolution. Mutations that the polymerase introduces into viral genome segments during replication are the ultimate source of genetic variation, including within the three subunits of the IAV polymerase (PB2, PB1, and PA). Evolutionary analysis of the IAV polymerase is complicated, because changes in mutation rate, replication speed, and drug resistance involve epistatic interactions among its subunits. In order to study the evolution of the human seasonal H3N2 polymerase since the 1968 pandemic, we identified pairwise evolutionary relationships among ∼7000 H3N2 polymerase sequences using mutual information (MI), which measures the information gained about the identity of one residue when a second residue is known. To account for uneven sampling of viral sequences over time, we developed a weighted MI metric (wMI) and demonstrate that wMI outperforms raw MI through simulations using a well-sampled SARS-CoV-2 dataset. We then constructed wMI networks of the H3N2 polymerase to extend the inherently pairwise wMI statistic to encompass relationships among larger groups of residues. We included HA in the wMI network to distinguish between functional wMI relationships within the polymerase and those potentially due to hitchhiking on antigenic changes in HA. The wMI networks reveal coevolutionary relationships among residues with roles in replication and encapsidation. Inclusion of HA highlighted polymerase-only subgraphs containing residues with roles in the enzymatic functions of the polymerase and host adaptability. This work provides insight into the factors that drive and constrain the rapid evolution of influenza viruses.
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Han YJ, Lee KM, Wu GH, Gong YN, Dutta A, Shih SR. Targeting influenza A virus by splicing inhibitor herboxidiene reveals the importance of subtype-specific signatures around splice sites. J Biomed Sci 2023; 30:10. [PMID: 36737756 PMCID: PMC9895974 DOI: 10.1186/s12929-023-00897-4] [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: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The association between M segment splicing and pathogenicity remains ambiguous in human influenza A viruses. In this study, we aimed to investigate M splicing in various human influenza A viruses and characterize its physiological roles by applying the splicing inhibitor, herboxidiene. METHODS We examined the M splicing of human H1N1 and H3N2 viruses by comparing three H1N1 and H3N2 strains, respectively, through reverse transcriptase-polymerase chain reaction (RT-PCR) analyses. We randomly selected M sequences of human H1N1, H2N2, and H3N2 viruses isolated from 1933 to 2020 and examined their phylogenetic relationships. Next, we determined the effects of single nucleotide variations on M splicing by generating mutant viruses harboring the 55C/T variant through reverse genetics. To confirm the importance of M2 splicing in the replication of H1N1 and H3N2, we treated infected cells with splicing inhibitor herboxidiene and analyzed the viral growth using plaque assay. To explore the physiological role of the various levels of M2 protein in pathogenicity, we challenged C57BL/6 mice with the H1N1 WSN wild-type strain, mutant H1N1 (55T), and chimeric viruses including H1N1 + H3wt and H1N1 + H3mut. One-tailed paired t-test was used for virus titer calculation and multiple comparisons between groups were performed using two-way analysis of variance. RESULTS M sequence splice site analysis revealed an evolutionarily conserved single nucleotide variant C55T in H3N2, which impaired M2 expression and was accompanied by collinear M1 and mRNA3 production. Aberrant M2 splicing resulted from splice-site selection rather than a general defect in the splicing process. The C55T substitution significantly reduced both M2 mRNA and protein levels regardless of the virus subtype. Consequently, herboxidiene treatment dramatically decreased both the H1N1 and H3N2 virus titers. However, a lower M2 expression only attenuated H1N1 virus replication and in vivo pathogenicity. This attenuated phenotype was restored by M replacement of H3N2 M in a chimeric H1N1 virus, despite low M2 levels. CONCLUSIONS The discrepancy in M2-dependence emphasizes the importance of M2 in human influenza A virus pathogenicity, which leads to subtype-specific evolution. Our findings provide insights into virus adaptation processes in humans and highlights splicing regulation as a potential antiviral target.
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Affiliation(s)
- Yi-Ju Han
- grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDivision of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Guan-Hong Wu
- grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Nong Gong
- grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDivision of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDepartment of Laboratory Science, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Avijit Dutta
- grid.454211.70000 0004 1756 999XDivision of Infectious Diseases, Department of Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Department of Laboratory Science, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. .,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan, Taiwan. .,Research Center for Food and Cosmetic Safety, Chang Gung University of Science and Technology, Taoyuan, Taiwan. .,Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan.
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19
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Singh K, Mehta D, Dumka S, Chauhan AS, Kumar S. Quasispecies Nature of RNA Viruses: Lessons from the Past. Vaccines (Basel) 2023; 11:vaccines11020308. [PMID: 36851186 PMCID: PMC9963406 DOI: 10.3390/vaccines11020308] [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: 11/24/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Viral quasispecies are distinct but closely related mutants formed by the disparity in viral genomes due to recombination, mutations, competition, and selection pressure. Theoretical derivation for the origin of a quasispecies is owed to the error-prone replication by polymerase and mutants of RNA replicators. Here, we briefly addressed the theoretical and mathematical origin of quasispecies and their dynamics. The impact of quasispecies for major salient human pathogens is reviewed. In the current global scenario, rapid changes in geographical landscapes favor the origin and selection of mutants. It comes as no surprise that a cauldron of mutants poses a significant risk to public health, capable of causing pandemics. Mutation rates in RNA viruses are magnitudes higher than in DNA organisms, explaining their enhanced virulence and evolvability. RNA viruses cause the most devastating pandemics; for example, members of the Orthomyxoviridae family caused the great influenza pandemic (1918 flu or Spanish flu), the SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory syndrome) outbreak, and the human immunodeficiency viruses (HIV), lentiviruses of the Retroviridae family, caused worldwide devastation. Rapidly evolving RNA virus populations are a daunting challenge for the designing of effective control measures like vaccines. Developing awareness of the evolutionary dispositions of RNA viral mutant spectra and what influences their adaptation and virulence will help curtail outbreaks of past and future pathogens.
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20
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Mettier J, Prompt C, Bruder E, Da Costa B, Chevalier C, Le Goffic R. Comparison of PB1-F2 Proximity Interactomes Reveals Functional Differences between a Human and an Avian Influenza Virus. Viruses 2023; 15:v15020328. [PMID: 36851542 PMCID: PMC9961899 DOI: 10.3390/v15020328] [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: 12/02/2022] [Revised: 01/13/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Most influenza viruses express the PB1-F2 protein which is regarded as a virulence factor. However, PB1-F2 behaves differently in avian and mammalian hosts, suggesting that this protein may be involved in the species barrier crossings regularly observed in influenza viruses. To better understand the functions associated with this viral protein, we decided to compare the BioID2-derived proximity interactome of a human PB1-F2 from an H3N2 virus with that of an avian PB1-F2 from an H7N1 strain. The results obtained reveal that the two proteins share only a few interactors and thus common functions. The human virus protein is mainly involved in signaling by Rho GTPases while the avian virus protein is mainly involved in ribonucleoprotein complex biogenesis. PB1-F2 H3N2 interactors include several members of the 14-3-3 protein family, a family of regulatory proteins involved in many signaling pathways. We then validated the interaction with 14-3-3 proteins and were able to show that the association of H3N2-PB1-F2 with YWHAH increased the activity of the antiviral sensor MDA5, while H7N1-PB1-F2 had no effect. Collectively, these results show that PB1-F2 can associate with a large range of protein complexes and exert a wide variety of functions. Furthermore, PB1-F2 interactome differs according to the avian or human origin of the protein.
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21
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Neumann G, Kawaoka Y. Which Virus Will Cause the Next Pandemic? Viruses 2023; 15:199. [PMID: 36680238 PMCID: PMC9864092 DOI: 10.3390/v15010199] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
One of the most pressing and consequential problems in infectious disease research is to better understand the potential of viruses to cause a pandemic, or, in simple terms, determine which virus will cause the next pandemic. We here define pandemics as WHO-declared pandemics, or disease outbreaks commonly referred to as pandemics that predate the WHO pandemic framework. Despite extensive research in the field of infectious diseases in recent decades, all pandemics have found us unprepared, with enormous losses of human lives, tremendous costs for public health, and vast and potentially long-lasting economic losses. Here, we discuss viruses that may cause a pandemic in the future.
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Affiliation(s)
- Gabriele Neumann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
- Department of Virology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Pandemic Preparedness, Infection and Advanced Research Center, The University of Tokyo, Tokyo 108-8639, Japan
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Understanding the Role of HLA Class I Molecules in the Immune Response to Influenza Infection and Rational Design of a Peptide-Based Vaccine. Viruses 2022; 14:v14112578. [PMID: 36423187 PMCID: PMC9695287 DOI: 10.3390/v14112578] [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: 10/08/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Influenza A virus is a respiratory pathogen that is responsible for regular epidemics and occasional pandemics that result in substantial damage to life and the economy. The yearly reformulation of trivalent or quadrivalent flu vaccines encompassing surface glycoproteins derived from the current circulating strains of the virus does not provide sufficient cross-protection against mismatched strains. Unlike the current vaccines that elicit a predominant humoral response, vaccines that induce CD8+ T cells have demonstrated a capacity to provide cross-protection against different influenza strains, including novel influenza viruses. Immunopeptidomics, the mass spectrometric identification of human-leukocyte-antigen (HLA)-bound peptides isolated from infected cells, has recently provided key insights into viral peptides that can serve as potential T cell epitopes. The critical elements required for a strong and long-living CD8+ T cell response are related to both HLA restriction and the immunogenicity of the viral peptide. This review examines the importance of HLA and the viral immunopeptidome for the design of a universal influenza T-cell-based vaccine.
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Thoner TW, Meloy MM, Long JM, Diller JR, Slaughter JC, Ogden KM. Reovirus Efficiently Reassorts Genome Segments during Coinfection and Superinfection. J Virol 2022; 96:e0091022. [PMID: 36094315 PMCID: PMC9517712 DOI: 10.1128/jvi.00910-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/21/2022] [Indexed: 11/20/2022] Open
Abstract
Reassortment, or genome segment exchange, increases diversity among viruses with segmented genomes. Previous studies on the limitations of reassortment have largely focused on parental incompatibilities that restrict generation of viable progeny. However, less is known about whether factors intrinsic to virus replication influence reassortment. Mammalian orthoreovirus (reovirus) encapsidates a segmented, double-stranded RNA (dsRNA) genome, replicates within cytoplasmic factories, and is susceptible to host antiviral responses. We sought to elucidate the influence of infection multiplicity, timing, and compartmentalized replication on reovirus reassortment in the absence of parental incompatibilities. We used an established post-PCR genotyping method to quantify reassortment frequency between wild-type and genetically barcoded type 3 reoviruses. Consistent with published findings, we found that reassortment increased with infection multiplicity until reaching a peak of efficient genome segment exchange during simultaneous coinfection. However, reassortment frequency exhibited a substantial decease with increasing time to superinfection, which strongly correlated with viral transcript abundance. We hypothesized that physical sequestration of viral transcripts within distinct virus factories or superinfection exclusion also could influence reassortment frequency during superinfection. Imaging revealed that transcripts from both wild-type and barcoded viruses frequently co-occupied factories, with superinfection time delays up to 16 h. Additionally, primary infection progressively dampened superinfecting virus transcript levels with greater time delay to superinfection. Thus, in the absence of parental incompatibilities and with short times to superinfection, reovirus reassortment proceeds efficiently and is largely unaffected by compartmentalization of replication and superinfection exclusion. However, reassortment may be limited by superinfection exclusion with greater time delays to superinfection. IMPORTANCE Reassortment, or genome segment exchange between viruses, can generate novel virus genotypes and pandemic virus strains. For viruses to reassort their genome segments, they must replicate within the same physical space by coinfecting the same host cell. Even after entry into the host cell, many viruses with segmented genomes synthesize new virus transcripts and assemble and package their genomes within cytoplasmic replication compartments. Additionally, some viruses can interfere with subsequent infection of the same host or cell. However, spatial and temporal influences on reassortment are only beginning to be explored. We found that infection multiplicity and transcript abundance are important drivers of reassortment during coinfection and superinfection, respectively, for reovirus, which has a segmented, double-stranded RNA genome. We also provide evidence that compartmentalization of transcription and packaging is unlikely to influence reassortment, but the length of time between primary and subsequent reovirus infection can alter reassortment frequency.
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Affiliation(s)
- Timothy W. Thoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Madeline M. Meloy
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jacob M. Long
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Julia R. Diller
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James C. Slaughter
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kristen M. Ogden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Kuroda M, Usui T, Shibata C, Nishigaki H, Yamaguchi T. Possible bidirectional human-swine and subsequent human-human transmission of influenza virus A(H1N1)/2009 in Japan. Zoonoses Public Health 2022; 69:721-728. [PMID: 35538641 DOI: 10.1111/zph.12960] [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: 08/05/2021] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 11/27/2022]
Abstract
In 2019, sows at a swine farm in Japan showed influenza-like illness (ILI) shortly after contact with an employee that exhibited ILI. Subsequently, a veterinarian became sick shortly after examining the sows and was diagnosed with influenza A virus (IAV) infection. Then, her family also contracted the infection. Subsequently, Pandemic A(H1N1)2009 viruses were isolated from all samples obtained from the sows, veterinarian and her family. Whole-genome analysis of the isolates confirmed that the viruses belonged to the same lineage (6B.1A) and the genome sequences obtained from all of the isolates were almost identical to each other. Furthermore, an epidemiological survey revealed no contact between veterinarians or their families and influenza patients prior to the onset of illness. These results strongly indicated a case of bidirectional infection between humans and sows. At the same time, we found a few unique mutations in the IAV genomes corresponding to the host species. The mutations that occurred in the virus after it was transferred from the farm worker to the sows were not observed in the humans infected from the sows, probably as a result of the mutations reverting to the original nucleotides. These results demonstrate that the bidirectional transmission of IAV is a potential risk for the next pandemic outbreak due to the emergence of new mutant strains.
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Affiliation(s)
- Moegi Kuroda
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Tatsufumi Usui
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
- Laboratory of Veterinary Hygiene, Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Chiharu Shibata
- Laboratory of Veterinary Hygiene, Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Haruka Nishigaki
- Laboratory of Veterinary Hygiene, Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Tsuyoshi Yamaguchi
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
- Laboratory of Veterinary Hygiene, Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Japan
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Wille M, Tolf C, Latorre-Margalef N, Fouchier RAM, Halpin RA, Wentworth DE, Ragwani J, Pybus OG, Olsen B, Waldenström J. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl. Virus Evol 2022; 8:veac074. [PMID: 36128050 PMCID: PMC9477075 DOI: 10.1093/ve/veac074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/12/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
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Affiliation(s)
- Michelle Wille
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Conny Tolf
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | - Jayna Ragwani
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London AL9 7TA, UK
| | - Björn Olsen
- Section of Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala SE751 85, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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27
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Varying Viral Replication and Disease Profiles of H2N2 Influenza in Ferrets Is Associated with Virus Isolate and Inoculation Route. J Virol 2022; 96:e0073222. [PMID: 35862678 PMCID: PMC9327684 DOI: 10.1128/jvi.00732-22] [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] [Indexed: 11/20/2022] Open
Abstract
In 1957 the world was subjected to a pandemic caused by an influenza A virus of the subtype H2N2. Although the virus disappeared in 1968, H2 viruses continue to circulate in avian reservoirs.
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Sun T, Guo Y, Zhao L, Fan M, Huang N, Tian M, Liu Q, Huang J, Liu Z, Zhao Y, Ji Z, Ping J. Evolution of the PB1 gene of human influenza A (H3N2) viruses circulating between 1968 and 2019. Transbound Emerg Dis 2022; 69:1824-1836. [PMID: 34033262 DOI: 10.1111/tbed.14161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/19/2021] [Indexed: 11/29/2022]
Abstract
One avian H3N2 influenza virus, providing its PB1 and HA segments, reassorted with one human H2N2 virus and caused a pandemic outbreak in 1968, killing over 1 million people. After its introduction to humanity, the pandemic H3N2 virus continued adapting to humans and has resulted in epidemic outbreaks every influenza season. To understand the functional roles of the originally avian PB1 gene in the circulating strains of human H3N2 influenza viruses, we analyzed the evolution of the PB1 gene in all human H3N2 isolates from 1968 to 2019. We found several specific residues dramatically changed around 2002-2009 and remained stable through to 2019. Then, we verified the functions of these PB1 mutations in the genetic background of the early pandemic virus, A/Hong Kong/1/1968(HK/68), as well as a recent seasonal strain, A/Jiangsu/34/2016 (JS/16). The PB1 V709I or PB1 V113A/K586R/D619N/V709I induced higher polymerase activity of HK/68 in human cells. And the four mutations acted cooperatively that had an increased replication capacity in vitro and in vivo at an early stage of infection. In contrast, the backward mutant, A113V/R586K/N619D/I709V, reduced polymerase activity in human cells. The PB1 I709V decreased viral replication in vitro, but this mutant only showed less effect on mice infection experiment, which suggested influenza A virus evolved in human host was not always consisted with highly replication efficiency and pathogenicity in other mammalian host. Overall, our results demonstrated that the identified PB1 mutations contributed to the viral evolution of human influenza A (H3N2) viruses.
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Affiliation(s)
- Tongtong Sun
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yanna Guo
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Lingcai Zhao
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Menglu Fan
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Nan Huang
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Miao Tian
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qingzheng Liu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jingjin Huang
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhiyuan Liu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yongzhen Zhao
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhiwei Ji
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, China
| | - Jihui Ping
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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29
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Chauhan RP, Gordon ML. An overview of influenza A virus genes, protein functions, and replication cycle highlighting important updates. Virus Genes 2022; 58:255-269. [PMID: 35471490 DOI: 10.1007/s11262-022-01904-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
Abstract
The recent research findings on influenza A virus (IAV) genome biology prompted us to present a comprehensive overview of IAV genes, protein functions, and replication cycle. The eight gene segments of the IAV genome encode 17 proteins, each having unique functions contributing to virus fitness in the host. The polymerase genes are essential determinants of IAV pathogenicity and virulence; however, other viral components also play crucial roles in the IAV replication, transmission, and adaptation. Specific adaptive mutations within polymerase (PB2, PB1, and PA) and glycoprotein-hemagglutinin (HA) and neuraminidase (NA) genes, may facilitate interspecies transmission and adaptation of IAV. The HA-NA interplay is essential for establishing the IAV infection; the low pH triggers the inactivation of HA-receptor binding, leading to significantly lower NA activities, indicating that the enzymatic function of NA is dependent on HA binding. While the HA and NA glycoproteins are required to initiate infection, M1, M2, NS1, and NEP proteins are essential for cytoplasmic trafficking of viral ribonucleoproteins (vRNPs) and the assembly of the IAV virions. The mechanisms that enable IAV to exploit the host cell resources to advance the infection are discussed. A comprehensive understanding of IAV genome biology is essential for developing antivirals to combat the IAV disease burden.
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Affiliation(s)
- Ravendra P Chauhan
- School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001, South Africa
| | - Michelle L Gordon
- School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001, South Africa.
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30
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Cheng C, Holyoak M, Xu L, Li J, Liu W, Stenseth NC, Zhang Z. Host and geographic barriers shape the competition, coexistence, and extinction patterns of influenza A (H1N1) viruses. Ecol Evol 2022; 12:e8732. [PMID: 35356566 PMCID: PMC8938227 DOI: 10.1002/ece3.8732] [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: 07/17/2021] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 12/29/2022] Open
Abstract
The influenza virus mutates and spreads rapidly, making it suitable for studying evolutionary and ecological processes. The ecological factors and processes by which different lineages of influenza compete or coexist within hosts through time and across geographical space are poorly known. We hypothesized that competition would be stronger for influenza viruses infecting the same host compared to different hosts (the Host Barrier Hypothesis), and for those with a higher cross‐region transmission intensity (the Geographic Barrier Hypothesis). Using available sequences of the influenza A (H1N1) virus in GenBank, we identified six lineages, twelve clades, and several replacement events. We found that human‐hosted lineages had a higher cross‐region transmission intensity than swine‐hosted lineages. Co‐occurrence probabilities of lineages infecting the same host were lower than those infecting different hosts, and human‐hosted lineages had lower co‐occurrence probabilities and genetic diversity than swine‐hosted lineages. These results show that H1N1 lineages infecting the same host or with high cross‐region transmission rates experienced stronger competition and extinction pressures than those infecting different hosts or with low cross‐region transmission. Our study highlights how host and geographic barriers shape the competition, extinction, and coexistence patterns of H1N1 lineages and clades.
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Affiliation(s)
- Chaoyuan Cheng
- State Key Laboratory of Integrated Management on Pest Insects and Rodents in Agriculture Institute of Zoology Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
| | - Marcel Holyoak
- Department of Environmental Science and Policy University of California Davis California USA
| | - Lei Xu
- Ministry of Education Key Laboratory for Earth System Modeling Department of Earth System Science Tsinghua University Beijing China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences Beijing China
- Savaid Medical School University of Chinese Academy of Sciences Beijing China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences Beijing China
- Savaid Medical School University of Chinese Academy of Sciences Beijing China
| | - Nils Chr. Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management on Pest Insects and Rodents in Agriculture Institute of Zoology Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
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31
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Abstract
Horses are the third major mammalian species, along with humans and swine, long known to be subject to acute upper respiratory disease from influenza A virus infection. The viruses responsible are subtype H7N7, which is believed extinct, and H3N8, which circulates worldwide. The equine influenza lineages are clearly divergent from avian influenza lineages of the same subtypes. Their genetic evolution and potential for interspecies transmission, as well as clinical features and epidemiology, are discussed. Equine influenza is spread internationally and vaccination is central to control efforts. The current mechanism of international surveillance and virus strain recommendations for vaccines is described.
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Affiliation(s)
- Thomas M Chambers
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
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32
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Kessler S, Harder TC, Schwemmle M, Ciminski K. Influenza A Viruses and Zoonotic Events-Are We Creating Our Own Reservoirs? Viruses 2021; 13:v13112250. [PMID: 34835056 PMCID: PMC8624301 DOI: 10.3390/v13112250] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 01/16/2023] Open
Abstract
Zoonotic infections of humans with influenza A viruses (IAVs) from animal reservoirs can result in severe disease in individuals and, in rare cases, lead to pandemic outbreaks; this is exemplified by numerous cases of human infection with avian IAVs (AIVs) and the 2009 swine influenza pandemic. In fact, zoonotic transmissions are strongly facilitated by manmade reservoirs that were created through the intensification and industrialization of livestock farming. This can be witnessed by the repeated introduction of IAVs from natural reservoirs of aquatic wild bird metapopulations into swine and poultry, and the accompanied emergence of partially- or fully-adapted human pathogenic viruses. On the other side, human adapted IAV have been (and still are) introduced into livestock by reverse zoonotic transmission. This link to manmade reservoirs was also observed before the 20th century, when horses seemed to have been an important reservoir for IAVs but lost relevance when the populations declined due to increasing industrialization. Therefore, to reduce zoonotic events, it is important to control the spread of IAV within these animal reservoirs, for example with efficient vaccination strategies, but also to critically surveil the different manmade reservoirs to evaluate the emergence of new IAV strains with pandemic potential.
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Affiliation(s)
- Susanne Kessler
- Medical Center, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany; (S.K.); (M.S.)
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Timm C. Harder
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, 17493 Greifswald-Insel Riems, Germany;
| | - Martin Schwemmle
- Medical Center, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany; (S.K.); (M.S.)
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Kevin Ciminski
- Medical Center, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany; (S.K.); (M.S.)
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Correspondence:
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33
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Berry I, Rahman M, Flora MS, Greer AL, Morris SK, Khan IA, Sarkar S, Naureen T, Fisman DN, Mangtani P. Frequency and patterns of exposure to live poultry and the potential risk of avian influenza transmission to humans in urban Bangladesh. Sci Rep 2021; 11:21880. [PMID: 34750452 PMCID: PMC8575886 DOI: 10.1038/s41598-021-01327-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022] Open
Abstract
Avian influenza is endemic in Bangladesh, where greater than 90% of poultry are marketed through live poultry markets (LPMs). We conducted a population-based cross-sectional mobile telephone survey in urban Dhaka, Bangladesh to investigate the frequency and patterns of human exposure to live poultry in LPMs and at home. Among 1047 urban residents surveyed, 74.2% (95% CI 70.9-77.2) reported exposure to live poultry in the past year, with the majority of exposure occurring on a weekly basis. While visiting LPMs was less common amongst females (40.3%, 95% CI 35.0-45.8) than males (58.9%, 95% CI 54.0-63.5), females reported greater poultry exposure through food preparation, including defeathering (13.2%, 95% CI 9.5-17.9) and eviscerating (14.8%, 95% CI 11.2-19.4) (p < 0.001). A large proportion of the urban population is frequently exposed to live poultry in a setting where avian influenza viruses are endemic in LPMs. There is thus not only ample opportunity for spillover of avian influenza infections into humans in Dhaka, Bangladesh, but also greater potential for viral reassortment which could generate novel strains with pandemic potential.
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Affiliation(s)
- Isha Berry
- Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON, M5T 3M7, Canada.
| | - Mahbubur Rahman
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | | | - Amy L Greer
- Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON, M5T 3M7, Canada
- Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Shaun K Morris
- Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON, M5T 3M7, Canada
- Division of Infectious Disease and Center for Global Child Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - Iqbal Ansary Khan
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Sudipta Sarkar
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Tanzila Naureen
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - David N Fisman
- Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON, M5T 3M7, Canada
| | - Punam Mangtani
- London School of Hygiene and Tropical Medicine, London, UK
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34
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Waters K, Gao C, Ykema M, Han L, Voth L, Tao YJ, Wan XF. Triple reassortment increases compatibility among viral ribonucleoprotein genes of contemporary avian and human influenza A viruses. PLoS Pathog 2021; 17:e1009962. [PMID: 34618879 PMCID: PMC8525756 DOI: 10.1371/journal.ppat.1009962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 10/19/2021] [Accepted: 09/20/2021] [Indexed: 12/21/2022] Open
Abstract
Compatibility among the influenza A virus (IAV) ribonucleoprotein (RNP) genes affects viral replication efficiency and can limit the emergence of novel reassortants, including those with potential pandemic risks. In this study, we determined the polymerase activities of 2,451 RNP reassortants among three seasonal and eight enzootic IAVs by using a minigenome assay. Results showed that the 2009 H1N1 RNP are more compatible with the tested enzootic RNP than seasonal H3N2 RNP and that triple reassortment increased such compatibility. The RNP reassortants among 2009 H1N1, canine H3N8, and avian H4N6 IAVs had the highest polymerase activities. Residues in the RNA binding motifs and the contact regions among RNP proteins affected polymerase activities. Our data indicates that compatibility among seasonal and enzootic RNPs are selective, and enzoosis of multiple strains in the animal-human interface can facilitate emergence of an RNP with increased replication efficiency in mammals, including humans.
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Affiliation(s)
- Kaitlyn Waters
- Missouri University Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
| | - Cheng Gao
- Missouri University Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, United States of America
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, United States of America
| | - Matthew Ykema
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Lei Han
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
| | - Lynden Voth
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Xiu-Feng Wan
- Missouri University Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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35
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Review of Influenza Virus Vaccines: The Qualitative Nature of Immune Responses to Infection and Vaccination Is a Critical Consideration. Vaccines (Basel) 2021; 9:vaccines9090979. [PMID: 34579216 PMCID: PMC8471734 DOI: 10.3390/vaccines9090979] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 01/06/2023] Open
Abstract
Influenza viruses have affected the world for over a century, causing multiple pandemics. Throughout the years, many prophylactic vaccines have been developed for influenza; however, these viruses are still a global issue and take many lives. In this paper, we review influenza viruses, associated immunological mechanisms, current influenza vaccine platforms, and influenza infection, in the context of immunocompromised populations. This review focuses on the qualitative nature of immune responses against influenza viruses, with an emphasis on trained immunity and an assessment of the characteristics of the host–pathogen that compromise the effectiveness of immunization. We also highlight innovative immunological concepts that are important considerations for the development of the next generation of vaccines against influenza viruses.
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36
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Fiorino S, Tateo F, Biase DD, Gallo CG, Orlandi PE, Corazza I, Budriesi R, Micucci M, Visani M, Loggi E, Hong W, Pica R, Lari F, Zippi M. SARS-CoV-2: lessons from both the history of medicine and from the biological behavior of other well-known viruses. Future Microbiol 2021; 16:1105-1133. [PMID: 34468163 PMCID: PMC8412036 DOI: 10.2217/fmb-2021-0064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is the etiological agent of the current pandemic worldwide and its associated disease COVID-19. In this review, we have analyzed SARS-CoV-2 characteristics and those ones of other well-known RNA viruses viz. HIV, HCV and Influenza viruses, collecting their historical data, clinical manifestations and pathogenetic mechanisms. The aim of the work is obtaining useful insights and lessons for a better understanding of SARS-CoV-2. These pathogens present a distinct mode of transmission, as SARS-CoV-2 and Influenza viruses are airborne, whereas HIV and HCV are bloodborne. However, these viruses exhibit some potential similar clinical manifestations and pathogenetic mechanisms and their understanding may contribute to establishing preventive measures and new therapies against SARS-CoV-2.
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Affiliation(s)
- Sirio Fiorino
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Fabio Tateo
- Institute of Geosciences & Earth Resources, CNR, c/o Department of Geosciences, Padova University, 35127, Italy
| | - Dario De Biase
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Claudio G Gallo
- Fisiolaserterapico Emiliano, Castel San Pietro Terme, Bologna, 40024, Italy
| | | | - Ivan Corazza
- Department of Experimental, Diagnostic & Specialty Medicine, University of Bologna, Bologna, 40126, Italy
| | - Roberta Budriesi
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Matteo Micucci
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Michela Visani
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Elisabetta Loggi
- Hepatology Unit, Department of Medical & Surgical Sciences, University of Bologna, Bologna, 40126, Italy
| | - Wandong Hong
- Department of Gastroenterology & Hepatology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang, 325035, PR China
| | - Roberta Pica
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
| | - Federico Lari
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Maddalena Zippi
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
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37
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Sun H, Li F, Liu Q, Du J, Liu L, Sun H, Li C, Liu J, Zhang X, Yang J, Duan Y, Bi Y, Pu J, Sun Y, Tong Q, Wang Y, Du X, Shu Y, Chang KC, Liu J. Mink is a highly susceptible host species to circulating human and avian influenza viruses. Emerg Microbes Infect 2021; 10:472-480. [PMID: 33657971 PMCID: PMC7993395 DOI: 10.1080/22221751.2021.1899058] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Pandemic influenza, typically caused by the reassortment of human and avian influenza viruses, can result in severe or fatal infections in humans. Timely identification of potential pandemic viruses must be a priority in influenza virus surveillance. However, the range of host species responsible for the generation of novel pandemic influenza viruses remains unclear. In this study, we conducted serological surveys for avian and human influenza virus infections in farmed mink and determined the susceptibility of mink to prevailing avian and human virus subtypes. The results showed that farmed mink were commonly infected with human (H3N2 and H1N1/pdm) and avian (H7N9, H5N6, and H9N2) influenza A viruses. Correlational analysis indicated that transmission of human influenza viruses occurred from humans to mink, and that feed source was a probable route of avian influenza virus transmission to farmed mink. Animal experiments showed that mink were susceptible and permissive to circulating avian and human influenza viruses, and that human influenza viruses (H3N2 and H1N1/pdm), but not avian viruses, were capable of aerosol transmission among mink. These results indicate that farmed mink could be highly permissive “mixing vessels” for the reassortment of circulating human and avian influenza viruses. Therefore, to reduce the risk of emergence of novel pandemic viruses, feeding mink with raw poultry by-products should not be permitted, and epidemiological surveillance of influenza viruses in mink farms should be urgently implemented.
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Affiliation(s)
- Honglei Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Fangtao Li
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Qingzhi Liu
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jianyong Du
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Litao Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Haoran Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Chong Li
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Jiyu Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Xin Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Jizhe Yang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yuhong Duan
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yuhai Bi
- Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Center for Influenza Research and Early-Warning (CASCIRE), Institute of Microbiology, Beijing, People's Republic of China
| | - Juan Pu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yipeng Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Qi Tong
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yongqiang Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People's Republic of China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People's Republic of China
| | - Kin-Chow Chang
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
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Waters K, Wan HJ, Han L, Xue J, Ykema M, Tao YJ, Wan XF. Variations outside the conserved motifs of PB1 catalytic active site may affect replication efficiency of the RNP complex of influenza A virus. Virology 2021; 559:145-155. [PMID: 33887645 PMCID: PMC8579824 DOI: 10.1016/j.virol.2021.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 12/24/2022]
Abstract
PB1 functions as the catalytic subunit of influenza virus RNA polymerase complex and plays an essential role in viral RNA transcription and replication. To determine plasticity in the PB1 enzymatic site and map catalytically important residues, 658 mutants were constructed, each with one to seven mutations in the enzymatic site of PB1. The polymerase activities of these mutants were quantified using a minigenome assay, and polymerase activity-associated residues were identified using sparse learning. Results showed that polymerase activities are affected by the residues not only within the conserved motifs, but also across the inter-motif regions of PB1, and the latter are primarily located at the base of the palm domain, a region that is conserved in avian PB1 but with high sequence diversity in swine PB1. Our results suggest that mutations outside the PB1 conserved motifs may affect RNA replication and could be associated with influenza virus host adaptation.
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Affiliation(s)
- Kaitlyn Waters
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Hamilton J Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Lei Han
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Jianli Xue
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Matthew Ykema
- Department of BioSciences, Rice University, Houston, TX, 77251, USA
| | - Yizhi J Tao
- Department of BioSciences, Rice University, Houston, TX, 77251, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39762, USA; Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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39
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Mettier J, Marc D, Sedano L, Da Costa B, Chevalier C, Le Goffic R. Study of the host specificity of PB1-F2-associated virulence. Virulence 2021; 12:1647-1660. [PMID: 34125653 PMCID: PMC8205076 DOI: 10.1080/21505594.2021.1933848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Influenza A viruses cause important diseases in both human and animal. The PB1-F2 protein is a virulence factor expressed by some influenza viruses. Its deleterious action for the infected host is mostly described in mammals, while the available information is scarce in avian hosts. In this work, we compared the effects of PB1-F2 in avian and mammalian hosts by taking advantage of the zoonotic capabilities of an avian H7N1 virus. In vitro, the H7N1 virus did not behave differently when PB1-F2 was deficient while a H3N2 virus devoid of PB1-F2 was clearly less inflammatory. Likewise, when performing in vivo challenges of either chickens or embryonated eggs, with the wild-type or the PB1-F2 deficient virus, no difference could be observed in terms of mortality, host response or tropism. PB1-F2 therefore does not appear to play a major role as a virulence factor in the avian host. However, when infecting NF-κB-luciferase reporter mice with the H7N1 viruses, a massive PB1-F2-dependent inflammation was quantified, highlighting the host specificity of PB1-F2 virulence. Surprisingly, a chimeric 7:1 H3N2 virus harboring an H7N1-origin segment 2 (i.e. expressing the avian PB1-F2) induced a milder inflammatory response than its PB1-F2-deficient counterpart. This result shows that the pro-inflammatory activity of PB1-F2 is governed by complex mechanisms involving components from both the virus and its infected host. Thus, a mere exchange of segment 2 between strains is not sufficient to transmit the deleterious character of PB1-F2.
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Affiliation(s)
- Joëlle Mettier
- Université Paris-Saclay, INRAE, UVSQ, UMR892 VIM, Jouy-en-Josas, France
| | - Daniel Marc
- UMR1282 Infectiologie Et Santé Publique, INRAE, Nouzilly, France
| | - Laura Sedano
- Université Paris-Saclay, INRAE, UVSQ, UMR892 VIM, Jouy-en-Josas, France
| | - Bruno Da Costa
- Université Paris-Saclay, INRAE, UVSQ, UMR892 VIM, Jouy-en-Josas, France
| | | | - Ronan Le Goffic
- Université Paris-Saclay, INRAE, UVSQ, UMR892 VIM, Jouy-en-Josas, France
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Ding X, Qin L, Meng J, Peng Y, Wu A, Jiang T. Progress and Challenge in Computational Identification of Influenza Virus Reassortment. Virol Sin 2021; 36:1273-1283. [PMID: 34037948 DOI: 10.1007/s12250-021-00392-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
Genomic reassortment is an important evolutionary mechanism for influenza viruses. In this process, the novel viruses acquire new characteristics by the exchange of the intact gene segments among multiple influenza virus genomes, which may cause flu endemics and epidemics within or even across hosts. Due to the safety and ethical limitations of the experimental studies on influenza virus reassortment, numerous computational researches on the influenza virus reassortment have been done with the explosion of the influenza virus genomic data. A great amount of computational methods and bioinformatics databases were developed to facilitate the identification of influenza virus reassortments. In this review, we summarized the progress and challenge of the bioinformatics research on influenza virus reassortment, which can guide the researchers to investigate the influenza virus reassortment events reasonably and provide valuable insight to develop the related computational identification tools.
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Affiliation(s)
- Xiao Ding
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Luyao Qin
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Jing Meng
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Yousong Peng
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China. .,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China.
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41
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Avian Influenza in Wild Birds and Poultry: Dissemination Pathways, Monitoring Methods, and Virus Ecology. Pathogens 2021; 10:pathogens10050630. [PMID: 34065291 PMCID: PMC8161317 DOI: 10.3390/pathogens10050630] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/21/2022] Open
Abstract
Avian influenza is one of the largest known threats to domestic poultry. Influenza outbreaks on poultry farms typically lead to the complete slaughter of the entire domestic bird population, causing severe economic losses worldwide. Moreover, there are highly pathogenic avian influenza (HPAI) strains that are able to infect the swine or human population in addition to their primary avian host and, as such, have the potential of being a global zoonotic and pandemic threat. Migratory birds, especially waterfowl, are a natural reservoir of the avian influenza virus; they carry and exchange different virus strains along their migration routes, leading to antigenic drift and antigenic shift, which results in the emergence of novel HPAI viruses. This requires monitoring over time and in different locations to allow for the upkeep of relevant knowledge on avian influenza virus evolution and the prevention of novel epizootic and epidemic outbreaks. In this review, we assess the role of migratory birds in the spread and introduction of influenza strains on a global level, based on recent data. Our analysis sheds light on the details of viral dissemination linked to avian migration, the viral exchange between migratory waterfowl and domestic poultry, virus ecology in general, and viral evolution as a process tightly linked to bird migration. We also provide insight into methods used to detect and quantify avian influenza in the wild. This review may be beneficial for the influenza research community and may pave the way to novel strategies of avian influenza and HPAI zoonosis outbreak monitoring and prevention.
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42
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Mercan Y, Atim G, Kayed AE, Azbazdar ME, Kandeil A, Ali MA, Rubrum A, McKenzie P, Webby RJ, Erima B, Wabwire-Mangen F, Ukuli QA, Tugume T, Byarugaba DK, Kayali G, Ducatez MF, Koçer ZA. Molecular Characterization of Closely Related H6N2 Avian Influenza Viruses Isolated from Turkey, Egypt, and Uganda. Viruses 2021; 13:v13040607. [PMID: 33918166 PMCID: PMC8065897 DOI: 10.3390/v13040607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 01/22/2023] Open
Abstract
Genetic analysis of circulating avian influenza viruses (AIVs) in wild birds at different geographical regions during the same period could improve our knowledge about virus transmission dynamics in natural hosts, virus evolution as well as zoonotic potential. Here, we report the genetic and molecular characterization of H6N2 influenza viruses isolated from migratory birds in Turkey, Egypt, and Uganda during 2017–2018. The Egyptian and Turkish isolates were genetically closer to each other than they were to the virus isolated from Uganda. Our results also suggest that multiple reassortment events were involved in the genesis of the isolated viruses. All viruses contained molecular markers previously associated with increased replication and/or pathogenicity in mammals. The results of this study indicate that H6N2 viruses carried by migratory birds on the West Asian/East African and Mediterranean/Black Sea flyways have the potential to transmit to mammals including humans. Additionally, adaptation markers in these viruses indicate the potential risk for poultry, which also increases the possibility of human exposure to these viruses.
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Affiliation(s)
- Yavuz Mercan
- Emerging Viral Diseases Laboratory, Izmir Biomedicine and Genome Center, 35340 Izmir, Turkey; (Y.M.); (M.E.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Gladys Atim
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
| | - Ahmed E. Kayed
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12311, Egypt; (A.E.K.); (A.K.); (M.A.A.)
| | - M. Ekin Azbazdar
- Emerging Viral Diseases Laboratory, Izmir Biomedicine and Genome Center, 35340 Izmir, Turkey; (Y.M.); (M.E.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12311, Egypt; (A.E.K.); (A.K.); (M.A.A.)
| | - Mohamed A. Ali
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12311, Egypt; (A.E.K.); (A.K.); (M.A.A.)
| | - Adam Rubrum
- St Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (P.M.); (R.J.W.)
| | - Pamela McKenzie
- St Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (P.M.); (R.J.W.)
| | - Richard J. Webby
- St Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (P.M.); (R.J.W.)
| | - Bernard Erima
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
| | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
- School of Public Health, Makerere University, P.O. Box 7062 Kampala, Uganda
| | - Qouilazoni A. Ukuli
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
| | - Titus Tugume
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
| | - Denis K. Byarugaba
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
- College of Veterinary Medicine, Makerere University, P.O. Box 7062 Kampala, Uganda
| | - Ghazi Kayali
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas, Houston, TX 77030, USA;
- Human Link, Dubai, United Arab Emirates
| | | | - Zeynep A. Koçer
- Emerging Viral Diseases Laboratory, Izmir Biomedicine and Genome Center, 35340 Izmir, Turkey; (Y.M.); (M.E.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
- Correspondence: ; Tel.: +90-232-299-4165
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Zhu J, Jiang Z, Liu J. The matrix gene of pdm/09 H1N1 contributes to the pathogenicity and transmissibility of SIV in mammals. Vet Microbiol 2021; 255:109039. [PMID: 33740730 DOI: 10.1016/j.vetmic.2021.109039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/10/2021] [Indexed: 01/07/2023]
Abstract
The H1N1 influenza virus of swine-origin was responsible for the H1N1 pandemic in 2009 (pdm/09 H1N1), where the virus was transmitted to humans and then spread between people, and its continued circulation has resulted in it becoming a seasonal human flu virus. Since 2016, the matrix (M) gene of pdm/09 H1N1 has been involved in the reassortment of swine influenza viruses (SIVs) in China and has gradually become a dominant genotype in pigs. However, whether M gene substitution will influence the fitness of emerging SIVs remains unclear. Here, we analyzed the biological characteristics of SIVs with the M gene from Eurasian avian-like (EA) SIV or pdm/09 H1N1 in mammals and found that SIVs containing the pdm/09-M gene exhibit stronger virulence in mice, more efficient respiratory droplet transmission between ferrets, and increased transcription of viral genes in A549 cells compared with those containing EA-M. We also determined the functional significance of the pdm/09-M gene in conferring an elevated release of progeny viruses comprised of largely filamentous virions rather than spherical virions. Our study suggests that pdm/09-M plays a crucial role in the genesis of emerging SIVs in terms of the potential prevalence in the population.
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Affiliation(s)
- Junda Zhu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100094, China
| | - Zhimin Jiang
- Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100094, China.
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Nomura N, Matsuno K, Shingai M, Ohno M, Sekiya T, Omori R, Sakoda Y, Webster RG, Kida H. Updating the influenza virus library at Hokkaido University -It's potential for the use of pandemic vaccine strain candidates and diagnosis. Virology 2021; 557:55-61. [PMID: 33667751 DOI: 10.1016/j.virol.2021.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/04/2020] [Accepted: 02/16/2021] [Indexed: 11/25/2022]
Abstract
Genetic reassortment of influenza A viruses through cross-species transmission contributes to the generation of pandemic influenza viruses. To provide information on the ecology of influenza viruses, we have been conducting a global surveillance of zoonotic influenza and establishing an influenza virus library. Of 4580 influenza virus strains in the library, 3891 have been isolated from over 70 different bird species. The remaining 689 strains were isolated from humans, pigs, horses, seal, whale, and the environment. Phylogenetic analyses of the HA genes of the library isolates demonstrate that the library strains are distributed to all major known clusters of the H1, H2 and H3 subtypes of HA genes that are prevalent in humans. Since past pandemic influenza viruses are most likely genetic reassortants of zoonotic and seasonal influenza viruses, a vast collection of influenza A virus strains from various hosts should be useful for vaccine preparation and diagnosis for future pandemics.
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Affiliation(s)
- Naoki Nomura
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Keita Matsuno
- Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Masashi Shingai
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE) Hokkaido University, Sapporo, Japan
| | - Marumi Ohno
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Toshiki Sekiya
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE) Hokkaido University, Sapporo, Japan; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Ryosuke Omori
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Sakoda
- Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE) Hokkaido University, Sapporo, Japan
| | | | - Hiroshi Kida
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE) Hokkaido University, Sapporo, Japan; Collaborating Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan.
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45
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McBride DS, Lauterbach SE, Li YT, Smith GJD, Killian ML, Nolting JM, Su YCF, Bowman AS. Genomic Evidence for Sequestration of Influenza A Virus Lineages in Sea Duck Host Species. Viruses 2021; 13:v13020172. [PMID: 33498851 PMCID: PMC7911388 DOI: 10.3390/v13020172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/29/2022] Open
Abstract
Wild birds are considered the natural reservoir of influenza A viruses (IAVs) making them critical for IAV surveillance efforts. While sea ducks have played a role in novel IAV emergence events that threatened food security and public health, very few surveillance samples have been collected from sea duck hosts. From 2014–2018, we conducted surveillance focused in the Mississippi flyway, USA at locations where sea duck harvest has been relatively successful compared to our other sampling locations. Our surveillance yielded 1662 samples from sea ducks, from which we recovered 77 IAV isolates. Our analyses identified persistence of sea duck specific IAV lineages across multiple years. We also recovered sea duck origin IAVs containing an H4 gene highly divergent from the majority of North American H4-HA with clade node age of over 65 years. Identification of IAVs with long branch lengths is indicative of substantial genomic change consistent with persistence without detection by surveillance efforts. Sea ducks play a role in the movement and long-term persistence of IAVs and are likely harboring more undetected IAV diversity. Sea ducks should be a point of emphasis for future North American wild bird IAV surveillance efforts.
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Affiliation(s)
- Dillon S. McBride
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (D.S.M.); (S.E.L.); (J.M.N.)
| | - Sarah E. Lauterbach
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (D.S.M.); (S.E.L.); (J.M.N.)
| | - Yao-Tsun Li
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (Y.-T.L.); (G.J.D.S.); (Y.C.F.S.)
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (Y.-T.L.); (G.J.D.S.); (Y.C.F.S.)
| | - Mary Lea Killian
- Diagnostic Virology Laboratory, National Veterinary Services Laboratories, APHIS, USDA, 1920 Dayton Avenue, Ames, IA 50010, USA;
| | - Jacqueline M. Nolting
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (D.S.M.); (S.E.L.); (J.M.N.)
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (Y.-T.L.); (G.J.D.S.); (Y.C.F.S.)
| | - Andrew S. Bowman
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (D.S.M.); (S.E.L.); (J.M.N.)
- Correspondence: ; Tel.: +1-(614)-292-6923; Fax: +1-(614)-292-4142
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Abstract
The emergence and spread of infectious diseases with pandemic potential occurred regularly throughout history. Major pandemics and epidemics such as plague, cholera, flu, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have already afflicted humanity. The world is now facing the new coronavirus disease 2019 (COVID-19) pandemic. Many infectious diseases leading to pandemics are caused by zoonotic pathogens that were transmitted to humans due to increased contacts with animals through breeding, hunting and global trade activities. The understanding of the mechanisms of transmission of pathogens to humans allowed the establishment of methods to prevent and control infections. During centuries, implementation of public health measures such as isolation, quarantine and border control helped to contain the spread of infectious diseases and maintain the structure of the society. In the absence of pharmaceutical interventions, these containment methods have still been used nowadays to control COVID-19 pandemic. Global surveillance programs of water-borne pathogens, vector-borne diseases and zoonotic spillovers at the animal-human interface are of prime importance to rapidly detect the emergence of infectious threats. Novel technologies for rapid diagnostic testing, contact tracing, drug repurposing, biomarkers of disease severity as well as new platforms for the development and production of vaccines are needed for an effective response in case of pandemics.
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Affiliation(s)
- Jocelyne Piret
- CHU de Québec - Laval University, Quebec City, QC, Canada
| | - Guy Boivin
- CHU de Québec - Laval University, Quebec City, QC, Canada
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Monto AS, Fukuda K. Lessons From Influenza Pandemics of the Last 100 Years. Clin Infect Dis 2021; 70:951-957. [PMID: 31420670 PMCID: PMC7314237 DOI: 10.1093/cid/ciz803] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/14/2019] [Indexed: 01/15/2023] Open
Abstract
Seasonal influenza is an annual occurrence, but it is the threat of pandemics that produces universal concern. Recurring reports of avian influenza viruses severely affecting humans have served as constant reminders of the potential for another pandemic. Review of features of the 1918 influenza pandemic and subsequent ones helps in identifying areas where attention in planning is critical. Key among such issues are likely risk groups and which interventions to employ. Past pandemics have repeatedly underscored, for example, the vulnerability of groups such as pregnant women and taught other lessons valuable for future preparedness. While a fundamental difficulty in planning for the next pandemic remains their unpredictability and infrequency, this uncertainty can be mitigated, in part, by optimizing the handling of the much more predictable occurrence of seasonal influenza. Improvements in antivirals and novel vaccine formulations are critical in lessening the impact of both pandemic and seasonal influenza.
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Affiliation(s)
- Arnold S Monto
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor
| | - Keiji Fukuda
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam
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48
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PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. J Virol 2020; 95:JVI.01582-20. [PMID: 33028722 PMCID: PMC7737735 DOI: 10.1128/jvi.01582-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/04/2020] [Indexed: 12/12/2022] Open
Abstract
Clade 2.2.1 avian influenza viruses (H5N1) are unique to Egypt and have caused the highest number of human H5N1 influenza cases worldwide, presenting a serious global public health threat. These viruses may have the greatest evolutionary potential for adaptation from avian hosts to human hosts. Using a comprehensive phylogenetic approach, we identified several novel clade 2.2.1 virus polymerase mutations that increased viral replication in vitro in human cells and in vivo in mice. These mutations were in the polymerase PA subunit and acted cooperatively with the E627K mutation in the PB2 polymerase subunit to provide higher replication in contemporary clade 2.2.1.2 viruses than in ancestral clade 2.2.1 viruses. These data indicated that ongoing clade 2.2.1 dissemination in the field has driven PA mutations to modify viral replication to enable host range expansion, with a higher public health risk for humans. Adaptive mutations and/or reassortments in avian influenza virus polymerase subunits PA, PB1, and PB2 are one of the major factors enabling the virus to overcome the species barrier to infect humans. The majority of human adaptation polymerase mutations have been identified in PB2; fewer adaptation mutations have been characterized in PA and PB1. Clade 2.2.1 avian influenza viruses (H5N1) are unique to Egypt and generally carry the human adaptation PB2-E627K substitution during their dissemination in nature. In this study, we identified other human adaptation polymerase mutations by analyzing phylogeny-associated PA mutations that H5N1 clade 2.2.1 viruses have accumulated during their evolution in the field. This analysis identified several PA mutations that produced increased replication by contemporary clade 2.2.1.2 viruses in vitro in human cells and in vivo in mice compared to ancestral clade 2.2.1 viruses. The PA mutations acted cooperatively to increase viral polymerase activity and replication in both avian and human cells, with the effect being more prominent in human cells at 33°C than at 37°C. These results indicated that PA mutations have a role in establishing contemporary clade 2.2.1.2 virus infections in poultry and in adaptation to infect mammals. Our study provided data on the mechanism for PA mutations to accumulate during avian influenza virus evolution and extend the viral host range. IMPORTANCE Clade 2.2.1 avian influenza viruses (H5N1) are unique to Egypt and have caused the highest number of human H5N1 influenza cases worldwide, presenting a serious global public health threat. These viruses may have the greatest evolutionary potential for adaptation from avian hosts to human hosts. Using a comprehensive phylogenetic approach, we identified several novel clade 2.2.1 virus polymerase mutations that increased viral replication in vitro in human cells and in vivo in mice. These mutations were in the polymerase PA subunit and acted cooperatively with the E627K mutation in the PB2 polymerase subunit to provide higher replication in contemporary clade 2.2.1.2 viruses than in ancestral clade 2.2.1 viruses. These data indicated that ongoing clade 2.2.1 dissemination in the field has driven PA mutations to modify viral replication to enable host range expansion, with a higher public health risk for humans.
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49
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Mujica G, Sternberg Z, Solis J, Wand T, Carrasco P, Henao-Martínez AF, Franco-Paredes C. Defusing COVID-19: Lessons Learned from a Century of Pandemics. Trop Med Infect Dis 2020; 5:E182. [PMID: 33266051 PMCID: PMC7709642 DOI: 10.3390/tropicalmed5040182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/21/2022] Open
Abstract
Amidst the COVID-19 global pandemic of 2020, identifying and applying lessons learned from previous influenza and coronavirus pandemics may offer important insight into its interruption. Herein, we conducted a review of the literature of the influenza pandemics of the 20th century; and of the coronavirus and influenza pandemics of the 21st century. Influenza and coronavirus pandemics are zoonoses that spread rapidly in consistent seasonal patterns during an initial wave of infection and subsequent waves of spread. For all of their differences in the state of available medical technologies, global population changes, and social and geopolitical factors surrounding each pandemic, there are remarkable similarities among them. While vaccination of high-risk groups is advocated as an instrumental mode of interrupting pandemics, non-pharmacological interventions including avoidance of mass gatherings, school closings, case isolation, contact tracing, and the implementation of infection prevention strategies in healthcare settings represent the cornerstone to halting transmission. In conjunction with lessons learned from previous pandemics, the public health response to the COVID-19 pandemic constitutes the basis for delineating best practices to confront future pandemics.
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Affiliation(s)
- Graciela Mujica
- School of Medicine, University of Colorado, 13001 E 17th Pl, Aurora, CO 80045, USA; (G.M.); (Z.S.); (J.S.); (T.W.)
| | - Zane Sternberg
- School of Medicine, University of Colorado, 13001 E 17th Pl, Aurora, CO 80045, USA; (G.M.); (Z.S.); (J.S.); (T.W.)
| | - Jamie Solis
- School of Medicine, University of Colorado, 13001 E 17th Pl, Aurora, CO 80045, USA; (G.M.); (Z.S.); (J.S.); (T.W.)
| | - Taylor Wand
- School of Medicine, University of Colorado, 13001 E 17th Pl, Aurora, CO 80045, USA; (G.M.); (Z.S.); (J.S.); (T.W.)
| | - Peter Carrasco
- International Association for Immunization Managers, Washington, DC 20037, USA;
- Department of Immunization and Vaccines, World Health Organization, 1202 Geneva, Switzerland
| | - Andrés F. Henao-Martínez
- Department of Medicine, Division of Infectious Diseases, Anschutz Medical Center, University of Colorado, Aurora, CO 80045, USA;
| | - Carlos Franco-Paredes
- Department of Medicine, Division of Infectious Diseases, Anschutz Medical Center, University of Colorado, Aurora, CO 80045, USA;
- Hospital Infantil de México, Federico Gomez, México City 06720, Mexico
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50
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Thompson AJ, Paulson JC. Adaptation of influenza viruses to human airway receptors. J Biol Chem 2020; 296:100017. [PMID: 33144323 PMCID: PMC7948470 DOI: 10.1074/jbc.rev120.013309] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/19/2022] Open
Abstract
Through annual epidemics and global pandemics, influenza A viruses (IAVs) remain a significant threat to human health as the leading cause of severe respiratory disease. Within the last century, four global pandemics have resulted from the introduction of novel IAVs into humans, with components of each originating from avian viruses. IAVs infect many avian species wherein they maintain a diverse natural reservoir, posing a risk to humans through the occasional emergence of novel strains with enhanced zoonotic potential. One natural barrier for transmission of avian IAVs into humans is the specificity of the receptor-binding protein, hemagglutinin (HA), which recognizes sialic-acid-containing glycans on host cells. HAs from human IAVs exhibit “human-type” receptor specificity, binding exclusively to glycans on cells lining the human airway where terminal sialic acids are attached in the α2-6 configuration (NeuAcα2-6Gal). In contrast, HAs from avian viruses exhibit specificity for “avian-type” α2-3-linked (NeuAcα2-3Gal) receptors and thus require adaptive mutations to bind human-type receptors. Since all human IAV pandemics can be traced to avian origins, there remains ever-present concern over emerging IAVs with human-adaptive potential that might lead to the next pandemic. This concern has been brought into focus through emergence of SARS-CoV-2, aligning both scientific and public attention to the threat of novel respiratory viruses from animal sources. In this review, we summarize receptor-binding adaptations underlying the emergence of all prior IAV pandemics in humans, maintenance and evolution of human-type receptor specificity in subsequent seasonal IAVs, and potential for future human-type receptor adaptation in novel avian HAs.
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Affiliation(s)
- Andrew J Thompson
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA.
| | - James C Paulson
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA; Department of Immunology & Microbiology, Scripps Research, La Jolla, California, USA.
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