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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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Cui X, Ma J, Pang Z, Chi L, Mai C, Liu H, Liao M, Sun H. The evolution, pathogenicity and transmissibility of quadruple reassortant H1N2 swine influenza virus in China: A potential threat to public health. Virol Sin 2024; 39:205-217. [PMID: 38346538 DOI: 10.1016/j.virs.2024.02.002] [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: 10/03/2023] [Accepted: 02/06/2024] [Indexed: 04/30/2024] Open
Abstract
Swine are regarded as "intermediate hosts" or "mixing vessels" of influenza viruses, capable of generating strains with pandemic potential. From 2020 to 2021, we conducted surveillance on swine H1N2 influenza (swH1N2) viruses in swine farms located in Guangdong, Yunnan, and Guizhou provinces in southern China, as well as Henan and Shandong provinces in northern China. We systematically analyzed the evolution and pathogenicity of swH1N2 isolates, and characterized their replication and transmission abilities. The isolated viruses are quadruple reassortant H1N2 viruses containing genes from pdm/09 H1N1 (PB2, PB1, PA and NP genes), triple-reassortant swine (NS gene), Eurasian Avian-like (HA and M genes), and recent human H3N2 (NA gene) lineages. The NA, PB2, and NP of SW/188/20 and SW/198/20 show high gene similarities to A/Guangdong/Yue Fang277/2017 (H3N2). The HA gene of swH1N2 exhibits a high evolutionary rate. The five swH1N2 isolates replicate efficiently in human, canine, and swine cells, as well as in the turbinate, trachea, and lungs of mice. A/swine/Shandong/198/2020 strain efficiently replicates in the respiratory tract of pigs and effectively transmitted among them. Collectively, these current swH1N2 viruses possess zoonotic potential, highlighting the need for strengthened surveillance of swH1N2 viruses.
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MESH Headings
- Animals
- Swine
- Reassortant Viruses/genetics
- Reassortant Viruses/pathogenicity
- Reassortant Viruses/isolation & purification
- China/epidemiology
- Orthomyxoviridae Infections/virology
- Orthomyxoviridae Infections/transmission
- Orthomyxoviridae Infections/veterinary
- Swine Diseases/virology
- Swine Diseases/transmission
- Influenza A Virus, H1N2 Subtype/genetics
- Influenza A Virus, H1N2 Subtype/pathogenicity
- Influenza A Virus, H1N2 Subtype/isolation & purification
- Humans
- Mice
- Dogs
- Evolution, Molecular
- Phylogeny
- Virus Replication
- Public Health
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza, Human/virology
- Influenza, Human/transmission
- Mice, Inbred BALB C
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/pathogenicity
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Virulence
- Female
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Affiliation(s)
- Xinxin Cui
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Jinhuan Ma
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Zifeng Pang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Lingzhi Chi
- Shandong Vocational Animal Science and Veterinary College, Weifang, 261061, China
| | - Cuishan Mai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Hanlin Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China; Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Hailiang Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China.
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Wang Q, Liu Z, Zeng X, Zheng Y, Lan L, Wang X, Lai Z, Hou X, Gao L, Liang L, Tang S, Zhang Z, Leng J, Fan X. Integrated analysis of miRNA-mRNA expression of newly emerging swine H3N2 influenza virus cross-species infection with tree shrews. Virol J 2024; 21:4. [PMID: 38178220 PMCID: PMC10768296 DOI: 10.1186/s12985-023-02260-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Cross-species transmission of zoonotic IAVs to humans is potentially widespread and lethal, posing a great threat to human health, and their cross-species transmission mechanism has attracted much attention. miRNAs have been shown to be involved in the regulation of IAVs infection and immunity, however, few studies have focused on the molecular mechanisms underlying miRNAs and mRNAs expression after IAVs cross-species infection. METHODS We used tree shrews, a close relative of primates, as a model and used RNA-Seq and bioinformatics tools to analyze the expression profiles of DEMs and DEGs in the nasal turbinate tissue at different time points after the newly emerged swine influenza A virus SW2783 cross-species infection with tree shrews, and miRNA-mRNA interaction maps were constructed and verified by RT-qPCR, miRNA transfection and luciferase reporter assay. RESULTS 14 DEMs were screened based on functional analysis and interaction map, miR-760-3p, miR-449b-2, miR-30e-3p, and miR-429 were involved in the signal transduction process of replication and proliferation after infection, miR-324-3p, miR-1301-1, miR-103-1, miR-134-5p, miR-29a, miR-31, miR-16b, miR-34a, and miR-125b participate in negative feedback regulation of genes related to the immune function of the body to activate the antiviral immune response, and miR-106b-3p may be related to the cross-species infection potential of SW2783, and the expression level of these miRNAs varies in different days after infection. CONCLUSIONS The miRNA regulatory networks were constructed and 14 DEMs were identified, some of them can affect the replication and proliferation of viruses by regulating signal transduction, while others can play an antiviral role by regulating the immune response. It indicates that abnormal expression of miRNAs plays a crucial role in the regulation of cross-species IAVs infection, which lays a solid foundation for further exploration of the molecular regulatory mechanism of miRNAs in IAVs cross-species infection and anti-influenza virus targets.
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Affiliation(s)
- Qihui Wang
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China.
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
| | - Zihe Liu
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Xia Zeng
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Yu Zheng
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Li Lan
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Xinhang Wang
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Zhenping Lai
- Department of Microbiology, Guangxi Medical University, Nanning, 530021, China
| | - Xiaoqiong Hou
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Lingxi Gao
- Department of Microbiology, Guangxi Medical University, Nanning, 530021, China
| | - Liang Liang
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Shen Tang
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Zengfeng Zhang
- Department of Microbiology, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Jing Leng
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, 530200, China.
- Key Laboratory of Characteristic Experimental Animal Models of Guangxi, Guangxi University of Chinese Medicine, Nanning, 530200, China.
| | - Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, 530021, China.
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
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Jallow MM, Barry MA, Fall A, Ndiaye NK, Kiori D, Sy S, Goudiaby D, Niang MN, Fall G, Fall M, Dia N. Influenza A Virus in Pigs in Senegal and Risk Assessment of Avian Influenza Virus (AIV) Emergence and Transmission to Human. Microorganisms 2023; 11:1961. [PMID: 37630521 PMCID: PMC10459748 DOI: 10.3390/microorganisms11081961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
We conducted an active influenza surveillance in the single pig slaughterhouse in Dakar to investigate the epidemiology and genetic characteristics of influenza A viruses (IAVs) and to provide serologic evidence of avian influenza virus (AIV) infection in pigs at interfaces with human populations in Senegal. Nasal swab and blood samples were collected on a weekly basis from the same animal immediately after slaughter. Influenza A viruses were diagnosed using RT-qPCR and a subset of positive samples for H3 and H1 subtypes were selected for full genome amplification and NGS sequencing. Serum samples were tested by HI assay for the detection of antibodies recognizing four AIVs, including H9N2, H5N1, H7N7 and H5N2. Between September 2018 and December 2019, 1691 swine nasal swabs were collected and tested. Influenza A virus was detected in 30.7% (520/1691), and A/H1N1pdm09 virus was the most commonly identified subtype with 38.07% (198/520), followed by A/H1N2 (16.3%) and A/H3N2 (5.2%). Year-round influenza activity was noted in pigs, with the highest incidence between June and September. Phylogenetic analyses revealed that the IAVs were closely related to human IAV strains belonging to A/H1N1pdm09 and seasonal H3N2 lineages. Genetic analysis revealed that Senegalese strains possessed several key amino acid changes, including D204 and N241D in the receptor binding site, S31N in the M2 gene and P560S in the PA protein. Serological analyses revealed that 83.5% (95%CI = 81.6-85.3) of the 1636 sera tested were positive for the presence of antibodies against either H9N2, H5N1, H7N7 or H5N2. Influenza H7N7 (54.3%) and H9N2 (53.6%) were the dominant avian subtypes detected in Senegalese pigs. Given the co-circulation of multiple subtypes of influenza viruses among Senegalese pigs, the potential exists for the emergence of new hybrid viruses of unpredictable zoonotic and pandemic potential in the future.
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Affiliation(s)
- Mamadou Malado Jallow
- Institut Pasteur de Dakar, Département de Virologie, Dakar BP 220, Senegal; (M.M.J.); (A.F.); (N.K.N.); (D.K.); (S.S.); (D.G.); (M.N.N.); (G.F.)
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar BP 206, Senegal;
| | - Mamadou Aliou Barry
- Institut Pasteur de Dakar, Unité d’Epidémiologie des Maladies Infectieuses, Dakar BP 220, Senegal;
| | - Amary Fall
- Institut Pasteur de Dakar, Département de Virologie, Dakar BP 220, Senegal; (M.M.J.); (A.F.); (N.K.N.); (D.K.); (S.S.); (D.G.); (M.N.N.); (G.F.)
| | - Ndiendé Koba Ndiaye
- Institut Pasteur de Dakar, Département de Virologie, Dakar BP 220, Senegal; (M.M.J.); (A.F.); (N.K.N.); (D.K.); (S.S.); (D.G.); (M.N.N.); (G.F.)
| | - Davy Kiori
- Institut Pasteur de Dakar, Département de Virologie, Dakar BP 220, Senegal; (M.M.J.); (A.F.); (N.K.N.); (D.K.); (S.S.); (D.G.); (M.N.N.); (G.F.)
| | - Sara Sy
- Institut Pasteur de Dakar, Département de Virologie, Dakar BP 220, Senegal; (M.M.J.); (A.F.); (N.K.N.); (D.K.); (S.S.); (D.G.); (M.N.N.); (G.F.)
| | - Déborah Goudiaby
- Institut Pasteur de Dakar, Département de Virologie, Dakar BP 220, Senegal; (M.M.J.); (A.F.); (N.K.N.); (D.K.); (S.S.); (D.G.); (M.N.N.); (G.F.)
| | - Mbayame Ndiaye Niang
- Institut Pasteur de Dakar, Département de Virologie, Dakar BP 220, Senegal; (M.M.J.); (A.F.); (N.K.N.); (D.K.); (S.S.); (D.G.); (M.N.N.); (G.F.)
| | - Gamou Fall
- Institut Pasteur de Dakar, Département de Virologie, Dakar BP 220, Senegal; (M.M.J.); (A.F.); (N.K.N.); (D.K.); (S.S.); (D.G.); (M.N.N.); (G.F.)
| | - Malick Fall
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar BP 206, Senegal;
| | - Ndongo Dia
- Institut Pasteur de Dakar, Département de Virologie, Dakar BP 220, Senegal; (M.M.J.); (A.F.); (N.K.N.); (D.K.); (S.S.); (D.G.); (M.N.N.); (G.F.)
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Genetic Diversity of the Hemagglutinin Genes of Influenza a Virus in Asian Swine Populations. Viruses 2022; 14:v14040747. [PMID: 35458477 PMCID: PMC9032595 DOI: 10.3390/v14040747] [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: 02/02/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 01/04/2023] Open
Abstract
Swine influenza (SI) is a major respiratory disease of swine; SI is due to the influenza A virus of swine (IAV-S), a highly contagious virus with zoonotic potential. The intensity of IAV-S surveillance varies among countries because it is not a reportable disease and causes limited mortality in swine. Although Asia accounts for half of all pig production worldwide, SI is not well managed in those countries. Rigorously managing SI on pig farms could markedly reduce the economic losses, the likelihood of novel reassortants among IAV-S, and the zoonotic IAV-S infections in humans. Vaccination of pigs is a key control measure for SI, but its efficacy relies on the optimal antigenic matching of vaccine strains with the viral strains circulating in the field. Here, we phylogenetically reviewed the genetic diversity of the hemagglutinin gene among IAVs-S that have circulated in Asia during the last decade. This analysis revealed the existence of country-specific clades in both the H1 and H3 subtypes and cross-border transmission of IAVs-S. Our findings underscore the importance of choosing vaccine antigens for each geographic region according to both genetic and antigenic analyses of the circulating IAV-S to effectively manage SI in Asia.
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