title: Occurrence and reassortment of avian influenza A (H7N9) viruses derived from coinfected birds in China.
abstract: Over the course of two waves of infection, H7N9 avian influenza A virus has caused 436 human infections and claimed 170 lives in China as of July 2014. To investigate the prevalence and genetic diversity of H7N9, we surveyed avian influenza viruses in poultry in Jiangsu province within the outbreak epicenter. We found frequent occurrence of H7N9/H9N2 coinfection in chickens. Molecular clock phylogenetic analysis confirms coinfection by H7N9/H9N2 viruses and also reveals that the identity of the H7N9 outbreak lineage is confounded by ongoing reassortment between outbreak viruses and diverse H9N2 viruses in domestic birds. Experimental inoculation of a coinfected sample in cell culture yielded two reassortant H7N9 strains with polymerase segments from the original H9N2 strain. Ongoing reassortment between the H7N9 outbreak lineage and diverse H9N2 viruses may generate new strains with the potential to infect humans, highlighting the need for continued viral surveillance in poultry and humans.
  
  
  OBJECTIVE
  We found frequent occurrence of H7N9/H9N2 coinfection in chickens. The H7N9 outbreak lineage is confounded by ongoing reassortment between H7N9 and H9N2 viruses. The importance of H9N2 viruses as the source of novel avian influenza virus infections in humans requires continuous attention.
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Hang
authors.initials: H
authors.lastname: Fan
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Jayna
authors.initials: J
authors.lastname: Raghwani
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
authors.forename: Tommy Tsan-Yuk
authors.initials: TT
authors.lastname: Lam
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Hong-Wu
authors.initials: HW
authors.lastname: Yao
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wo
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Kun
authors.initials: K
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Xiao-Ping
authors.initials: XP
authors.lastname: An
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Guang-Qian
authors.initials: GQ
authors.lastname: Pei
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Hao
authors.initials: H
authors.lastname: Li
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Hong-Yu
authors.initials: HY
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Jian-Jun
authors.initials: JJ
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Tao
authors.initials: T
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Mai-Juan
authors.initials: MJ
authors.lastname: Ma
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Xian
authors.initials: X
authors.lastname: Xia
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Yan-De
authors.initials: YD
authors.lastname: Dong
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Tong-Yan
authors.initials: TY
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Jia-Fu
authors.initials: JF
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
authors.forename: Yin-Hui
authors.initials: YH
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Guan
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China tong.yigang@gmail.com caowc@bmi.ac.cn.
authors.forename: Yigang
authors.initials: Y
authors.lastname: Tong
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China tong.yigang@gmail.com caowc@bmi.ac.cn.
authors.forename: Wu-Chun
authors.initials: WC
authors.lastname: Cao
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D060085:Coinfection / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D019143:Evolution, Molecular; D064766:Influenza A Virus, H7N9 Subtype / Q000235:genetics / Q000302:isolation & purification*; D053127:Influenza A Virus, H9N2 Subtype / Q000235:genetics / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology / Q000821:virology*; D017720:Molecular Epidemiology; D011200:Poultry; D016865:Reassortant Viruses / Q000235:genetics / Q000302:isolation & purification*