title: Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China.
abstract: The wide circulation of novel avian influenza viruses (AIVs) highlights the risk of pandemic influenza emergence in China. To investigate the prevalence and genetic diversity of AIVs in different ecological contexts, we surveyed AIVs in live poultry markets (LPMs), free-range poultry and the wetland habitats of wild birds in Zhejiang and Hubei provinces. Notably, LPMs contained the highest frequency of AIV infection, and the greatest number of subtypes (n = 9) and subtype co-infections (n = 14), as well as frequent reassortment, suggesting that they play an active role in fuelling AIV transmission. AIV-positive samples were also identified in wild birds in both provinces and free-range poultry in one sampling site close to a wetland region in Hubei. H9N2, H7N9 and H5N1 were the most commonly sampled subtypes in the LPMs from Zhejiang, whilst H5N6 and H9N2 were the dominant subtypes in the LPMs from Hubei. Phylogenetic analyses of the whole-genome sequences of 43 AIVs revealed that three reassortant H5 subtypes were circulating in LMPs in both geographical regions. Notably, the viruses sampled from the wetland regions and free-range poultry contained complex reassortants, for which the origins of some segments were unclear. Overall, our study highlights the extent of AIV genetic diversity in two highly populated parts of central and south-eastern China, particularly in LPMs, and emphasizes the need for continual surveillance.
authors.affiliation: State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206, Beijing, PRChina.|School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PRChina.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, PRChina.
authors.forename: Liang-Jun
authors.initials: LJ
authors.lastname: Chen
authors.affiliation: Wenzhou Center for Disease Control and Prevention, Wenzhou, 325001, Zhejiang Province, PRChina.
authors.forename: Xian-Dan
authors.initials: XD
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206, Beijing, PRChina.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, PRChina.
authors.forename: Wen-Ping
authors.initials: WP
authors.lastname: Guo
authors.affiliation: Wenzhou Center for Disease Control and Prevention, Wuhan, 430015, Hubei Province, PRChina.
authors.forename: Jun-Hua
authors.initials: JH
authors.lastname: Tian
authors.affiliation: State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206, Beijing, PRChina.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, PRChina.
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.affiliation: Yuhuan Center for Disease Control and Prevention, Yuhuan, 317600, Zhejiang Province, PRChina.
authors.forename: Xu-Hua
authors.initials: XH
authors.lastname: Ying
authors.affiliation: Longquan Center for Disease Control and Prevention, Longquan, Zhejiang Province, PRChina.
authors.forename: Miao-Ruo
authors.initials: MR
authors.lastname: Wang
authors.affiliation: Wenzhou Center for Disease Control and Prevention, Wuhan, 430015, Hubei Province, PRChina.
authors.forename: Bin
authors.initials: B
authors.lastname: Yu
authors.affiliation: School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PRChina.
authors.forename: Zhan-Qiu
authors.initials: ZQ
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206, Beijing, PRChina.|Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological 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, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206, Beijing, PRChina.|Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological 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 Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206, Beijing, PRChina.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, PRChina.|School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PRChina.
authors.forename: Yong-Zhen
authors.initials: YZ
authors.lastname: Zhang
mesh_terms: D000818:Animals; D000835:Animals, Wild; D005075:Biological Evolution; D002681:China / Q000453:epidemiology; D014644:Genetic Variation; D016679:Genome, Viral; D007157:Immunologic Surveillance; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification / Q000235:genetics*; D064766:Influenza A Virus, H7N9 Subtype / Q000145:classification / Q000235:genetics*; D053127:Influenza A Virus, H9N2 Subtype / Q000145:classification / Q000235:genetics*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000635:transmission / Q000821:virology; D010802:Phylogeny; D058974:Phylogeography; D011200:Poultry; D012367:RNA, Viral / Q000235:genetics; D016865:Reassortant Viruses / Q000145:classification / Q000235:genetics*; D017423:Sequence Analysis, RNA; D053833:Wetlands
chemical_list: D012367:RNA, Viral