title: Influenza H7N9 and H9N2 viruses: coexistence in poultry linked to human H7N9 infection and genome characteristics.
abstract: Avian influenza virus A of the novel H7N9 reassortant subtype was recently found to cause severe human respiratory infections in China. Live poultry markets were suspected locations of the human H7N9 infection sources, based on the cases' exposure histories and sequence similarities between viral isolates. To explore the role of live poultry markets in the origin of the novel H7N9 virus, we systematically examined poultry and environmental specimens from local markets and farms in Hangzhou, using real-time reverse transcription-PCR (RT-PCR) as well as high-throughput next-generation sequencing (NGS). RT-PCR identified specimens positive for the H7 and N9 genomic segments in all of the 12 poultry markets epidemiologically linked to 10 human H7N9 cases. Chickens, ducks, and environmental specimens from the markets contained heavily mixed subtypes, including H7, N9, H9, and N2 and sometimes H5 and N1. The idea of the coexistence of H7N9 and H9N2 subtypes in chickens was further supported by metagenomic sequencing. In contrast, human H7N9 infection cases (n = 31) were all negative for H9N2 virus according to real-time RT-PCR. The six internal segments were indistinguishable for the H7N9 and H9N2 viruses. The H9, N2, and internal-segment sequences were very close to the sequence of the H9N2 virus circulating in chickens in China recently. Our results provide direct evidence that H9N2 strains coexisted with the novel human-pathogenic H7N9 influenza virus in epidemiologically linked live poultry markets. Avian influenza A virus of the H9N2 subtype likely made a recent contribution to the evolution of the H7N9 virus and continues to do so.
  
  
  OBJECTIVE
  Our results suggest that avian influenza A virus of the H9N2 subtype likely made a recent contribution to the evolution of the H7N9 virus, a novel reassortant avian influenza virus A subtype, and continues to do so. The finding helps shed light on how the H7N9 virus emerged, spread, and transmitted to humans. It is of considerable interest for assessing the risk of the possible emergence of novel reassortant viruses with enhanced transmissibility to humans.
authors.affiliation: Hangzhou Center for Disease Control and Prevention, Zhejiang, China.
authors.forename: Xinfen
authors.initials: X
authors.lastname: Yu
authors.forename: Tao
authors.initials: T
authors.lastname: Jin
authors.forename: Yujun
authors.initials: Y
authors.lastname: Cui
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Pu
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Jin
authors.initials: J
authors.lastname: Xu
authors.forename: Guang
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authors.lastname: Liu
authors.forename: Huijue
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authors.lastname: Jia
authors.forename: Dan
authors.initials: D
authors.lastname: Liu
authors.forename: Shili
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authors.lastname: Song
authors.forename: Yang
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authors.lastname: Yu
authors.forename: Li
authors.initials: L
authors.lastname: Xie
authors.forename: Renjie
authors.initials: R
authors.lastname: Huang
authors.forename: Hua
authors.initials: H
authors.lastname: Ding
authors.forename: Yu
authors.initials: Y
authors.lastname: Kou
authors.forename: Yinyan
authors.initials: Y
authors.lastname: Zhou
authors.forename: Yayu
authors.initials: Y
authors.lastname: Wang
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.forename: Ye
authors.initials: Y
authors.lastname: Yin
authors.forename: Jian
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authors.lastname: Wang
authors.forename: Chenyi
authors.initials: C
authors.lastname: Guo
authors.forename: Xianwei
authors.initials: X
authors.lastname: Yang
authors.forename: Liangping
authors.initials: L
authors.lastname: Hu
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Wu
authors.forename: Hailong
authors.initials: H
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.forename: Guoqiu
authors.initials: G
authors.lastname: Zhao
authors.forename: Jiyong
authors.initials: J
authors.lastname: Zhou
authors.forename: Jingcao
authors.initials: J
authors.lastname: Pan
authors.forename: George F
authors.initials: GF
authors.lastname: Gao
authors.forename: Ruifu
authors.initials: R
authors.lastname: Yang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002645:Chickens; D002681:China; D060085:Coinfection / Q000662:veterinary* / Q000821:virology; D004372:Ducks; D016679:Genome, Viral; D006801:Humans; D064766:Influenza A Virus, H7N9 Subtype / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D053127:Influenza A Virus, H9N2 Subtype / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000821:virology*; D007251:Influenza, Human / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny