title: Genesis, Evolution and Prevalence of H5N6 Avian Influenza Viruses in China.
abstract: Constant surveillance of live poultry markets (LPMs) is currently the best way to predict and identify emerging avian influenza viruses (AIVs) that pose a potential threat to public health. Through surveillance of LPMs from 16 provinces and municipalities in China during 2014-2016, we identified 3,174 AIV-positive samples and isolated and sequenced 1,135 AIVs covering 31 subtypes. Our analysis shows that H5N6 has replaced H5N1 as one of the dominant AIV subtypes in southern China, especially in ducks. Phylogenetic analysis reveals that H5N6 arose from reassortments of H5 and H6N6 viruses, with the hemagglutinin and neuraminidase combinations being strongly lineage specific. H5N6 viruses constitute at least 34 distinct genotypes derived from various evolutionary pathways. Notably, genotype G1.2 virus, with internal genes from the chicken H9N2/H7N9 gene pool, was responsible for at least five human H5N6 infections. Our findings highlight H5N6 AIVs as potential threats to public health and agriculture.
authors.affiliation: Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China; Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yuhai
authors.initials: Y
authors.lastname: Bi
authors.affiliation: Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei 430071, China.
authors.forename: Quanjiao
authors.initials: Q
authors.lastname: Chen
authors.affiliation: Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Qianli
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei 430071, China.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Chen
authors.affiliation: China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Jin
authors.affiliation: CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Gary
authors.initials: G
authors.lastname: Wong
authors.affiliation: National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
authors.forename: Chuansong
authors.initials: C
authors.lastname: Quan
authors.affiliation: National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.affiliation: Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
authors.affiliation: Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin University, Jilin 130062, China.
authors.forename: Renfu
authors.initials: R
authors.lastname: Yin
authors.affiliation: Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei 430071, China.
authors.forename: Lihua
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei 430071, China.
authors.forename: Mingxin
authors.initials: M
authors.lastname: Li
authors.affiliation: Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin University, Jilin 130062, China.
authors.forename: Zhuang
authors.initials: Z
authors.lastname: Ding
authors.affiliation: Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China.
authors.forename: Rongrong
authors.initials: R
authors.lastname: Zou
authors.affiliation: Yunnan Center for Disease Control and Prevention, Kunming 650022, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Xu
authors.affiliation: Yunnan Center for Disease Control and Prevention, Kunming 650022, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Li
authors.affiliation: Diqing Tibetan Autonomous Prefecture Centers for Disease Control and Prevention, Shangri-la 674400, China.
authors.forename: Huijun
authors.initials: H
authors.lastname: Wang
authors.affiliation: National Research Center for Veterinary Medicine, Luoyang 471003, China.
authors.forename: Kegong
authors.initials: K
authors.lastname: Tian
authors.affiliation: Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China.
authors.forename: Guanghua
authors.initials: G
authors.lastname: Fu
authors.affiliation: Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Research Institute of Experimental and Clinical Medicine, Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Alexander
authors.initials: A
authors.lastname: Shestopalov
authors.affiliation: College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
authors.forename: Shoujun
authors.initials: S
authors.lastname: Li
authors.affiliation: Ministry of Education Key Laboratory for Earth System Modelling, Center for Earth System Science, Tsinghua University, Beijing 100084, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Xu
authors.affiliation: Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
authors.forename: Hongjie
authors.initials: H
authors.lastname: Yu
authors.affiliation: Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, China.
authors.forename: Tingrong
authors.initials: T
authors.lastname: Luo
authors.affiliation: Yunnan Center for Disease Control and Prevention, Kunming 650022, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Lu
authors.affiliation: China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China. Electronic address: yingxialiu@hotmail.com.
authors.forename: Yingxia
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Institute of Pathogen Biology, Taishan Medical College, Taian 271016, China. Electronic address: shiwf@ioz.ac.cn.
authors.forename: Weifeng
authors.initials: W
authors.lastname: Shi
authors.affiliation: Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: liud@im.ac.cn.
authors.forename: Di
authors.initials: D
authors.lastname: Liu
authors.affiliation: Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China; Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: gaof@im.ac.cn.
authors.forename: George Fu
authors.initials: GF
authors.lastname: Gao
mesh_terms: D000383:Agriculture; D000818:Animals; D001483:Base Sequence; D002645:Chickens / Q000821:virology; D002681:China / Q000453:epidemiology; D002947:Cities; D010856:Columbidae / Q000821:virology; D004372:Ducks / Q000821:virology; D062665:Epidemiological Monitoring; D019143:Evolution, Molecular; D005777:Geese / Q000821:virology; D005814:Genes, Viral / Q000235:genetics; D016679:Genome, Viral; D005838:Genotype; D062305:Geographic Mapping; D006388:Hemagglutinins; D006801:Humans; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics / Q000472:pathogenicity; D000071225:Influenza A Virus, H5N8 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity*; D064766:Influenza A Virus, H7N9 Subtype / Q000235:genetics / Q000472:pathogenicity; D053127:Influenza A Virus, H9N2 Subtype / Q000235:genetics / Q000472:pathogenicity; D005585:Influenza in Birds / Q000453:epidemiology* / Q000821:virology*; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology; D009439:Neuraminidase; D010802:Phylogeny; D011200:Poultry / Q000821:virology; D015995:Prevalence; D011634:Public Health; D012367:RNA, Viral / Q000235:genetics; D016865:Reassortant Viruses
chemical_list: D006388:Hemagglutinins; D012367:RNA, Viral; D009439:Neuraminidase
keywords: H5N6 avian influenza; birds; evolution; genesis; human infection; live poultry markets; prevalence; resassortment