title: Diversity, evolution and population dynamics of avian influenza viruses circulating in the live poultry markets in China.
abstract: Live poultry markets (LPMs) are an important source of novel avian influenza viruses (AIV). During 2015-2016 we surveyed AIV diversity in ten LPMs in Hubei, Zhejiang and Jiangxi provinces, China. A high diversity and prevalence of AIVs (totaling 12 subtypes) was observed in LPMs in these provinces. Strikingly, however, the subtypes discovered during 2015-2016 were markedly different to those reported by us in these same localities one year previously, suggesting a dynamic shift in viral genetic diversity over the course of a single year. Phylogenetic analyses revealed frequent reassortment, including between high and low pathogenic AIV subtypes and among those that circulate in domestic and wild birds. Notably, the novel H5N6 reassortant virus, which contains a set of H9N2-like internal genes, was prevalent in all three regions surveyed. Overall, these data highlight the profound changes in genetic diversity and in patterns of reassortment in those AIVs that circulate in LPMs.
authors.affiliation: State Key Laboratory of Virology/Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206 Beijing, China.
authors.forename: Liang-Jun
authors.initials: LJ
authors.lastname: Chen
authors.affiliation: Wenzhou Center for Disease Control and Prevention, Wenzhou 325001, Zhejiang Province, China.
authors.forename: Xian-Dan
authors.initials: XD
authors.lastname: Lin
authors.affiliation: Wuhan Center for Disease Control and Prevention, Wuhan 430015, Hubei Province, China.
authors.forename: Jun-Hua
authors.initials: JH
authors.lastname: Tian
authors.affiliation: Ganzhou Center for Disease Control and Prevention, Ganzhou 341000, Jiangxi Province, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Liao
authors.affiliation: Yuhuan Center for Disease Control and Prevention, Yuhuan 317600, Zhejiang Province, China.
authors.forename: Xu-Hua
authors.initials: XH
authors.lastname: Ying
authors.affiliation: State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206 Beijing, China.
authors.forename: Jian-Wei
authors.initials: JW
authors.lastname: Shao
authors.affiliation: Wuhan Center for Disease Control and Prevention, Wuhan 430015, Hubei Province, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Virology/Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206 Beijing, China.
authors.forename: Jing-Jing
authors.initials: JJ
authors.lastname: Guo
authors.affiliation: Longquan Center for Disease Control and Prevention, Longquan, Zhejiang Province, China.
authors.forename: Miao-Ruo
authors.initials: MR
authors.lastname: Wang
authors.affiliation: Wuhan Center for Disease Control and Prevention, Wuhan 430015, Hubei Province, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Peng
authors.affiliation: State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206 Beijing, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
authors.forename: Mang
authors.initials: M
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206 Beijing, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.affiliation: State Key Laboratory of Virology/Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China. Electronic address: zqyang@whu.edu.cn.
authors.forename: Zhan-Qiu
authors.initials: ZQ
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Virology/Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206 Beijing, China. Electronic address: zhangyongzhen@icdc.cn.
authors.forename: Yong-Zhen
authors.initials: YZ
authors.lastname: Zhang
mesh_terms: D000818:Animals; D002645:Chickens / Q000821:virology; D002681:China / Q000453:epidemiology; D010856:Columbidae / Q000821:virology; D004372:Ducks / Q000821:virology; D014644:Genetic Variation / Q000235:genetics*; D057221:Influenza A Virus, H1N2 Subtype / Q000235:genetics*; D000071225:Influenza A Virus, H5N8 Subtype / Q000235:genetics*; D053127:Influenza A Virus, H9N2 Subtype / Q000235:genetics*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000821:virology; D010802:Phylogeny; D011157:Population Dynamics
keywords: Avian influenza virus; Evolution; H5N6 virus; Live poultry markets; Reassortant