title: High genetic diversity and frequent genetic reassortment of avian influenza A(H9N2) viruses along the East Asian-Australian migratory flyway.
abstract: To understand the molecular epidemiology and evolution of avian influenza viruses (AIV) along the East Asian-Australian migration flyway, we collected faecal samples (n=2859) between November 2014 and March 2015 from poultry, environmental sources and wild birds in Dongying, Shandong province and Yancheng, Jiangsu province in eastern China. The presence of AIV RNA was evaluated by real-time PCR and the positivity rate ranged from 0 to 29.3%. In both Dongying and Yancheng, samples collected from live poultry markets had the highest positivity rate for AIV RNA. AIV whole genomes were generated and phylogenetically analysed. Our results demonstrate that most of the viruses belonged to the H9N2 subtype, and could be classified into nine novel genotypes based on the phylogenetic analysis of the eight gene segments of the AIV genomes. This revealed a high genetic diversity of H9N2 in this region and suggested that they might have undergone frequent genetic reassortment. In addition, the internal genes (PB2, etc.) of two viruses from wild birds and several viruses from poultry belonged to the same gene constellation, suggesting a potential inter-host transmission of AIV between wild birds and poultry in live markets along routes of migratory flyways. Our results highlight the high genetic diversity of AIV along the East Asian-Australian migration flyway and the need for more extensive AIV surveillance in eastern China.
authors.affiliation: College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China; Institute of Pathogen Biology, Taishan Medical College, Tai'an, Shandong 271000, China. Electronic address: haiming0110@163.com.
authors.forename: Haiming
authors.initials: H
authors.lastname: Wang
authors.affiliation: Institute of Pathogen Biology, Taishan Medical College, Tai'an, Shandong 271000, China. Electronic address: zhangzhenjie213@163.com.
authors.forename: Zhenjie
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Dongying Forest and Plant Protection Station, Dongying, Shandong 257091, China. Electronic address: chenzhanqiang0546@126.com.
authors.forename: Zhanqiang
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Dongying Forest and Plant Protection Station, Dongying, Shandong 257091, China. Electronic address: dysbzzyr@163.com.
authors.forename: Yanru
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Institute of Pathogen Biology, Taishan Medical College, Tai'an, Shandong 271000, China. Electronic address: lvqiang7759@163.com.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Lv
authors.affiliation: Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China. Electronic address: wsws66948407@163.com.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: An
authors.affiliation: Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China. Electronic address: tong.yigang@gmai.com.
authors.forename: Yigang
authors.initials: Y
authors.lastname: Tong
authors.affiliation: National Virus Reference Laboratory, University College Dublin, Dublin, Ireland. Electronic address: micheal.carr@ucd.ie.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Carr
authors.affiliation: College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China. Electronic address: ssh6811@163.com.
authors.forename: Shuhong
authors.initials: S
authors.lastname: Sun
authors.affiliation: Institute of Pathogen Biology, Taishan Medical College, Tai'an, Shandong 271000, China. Electronic address: shiwf@ioz.ac.cn.
authors.forename: Weifeng
authors.initials: W
authors.lastname: Shi
mesh_terms: D025041:Animal Migration; D000818:Animals; D000835:Animals, Wild; D001315:Australia; D001717:Birds; D005202:Asia, Eastern; D005814:Genes, Viral; D014644:Genetic Variation; D053127:Influenza A Virus, H9N2 Subtype / Q000145:classification / Q000235:genetics*; D005585:Influenza in Birds / Q000453:epidemiology / Q000821:virology*; D010802:Phylogeny; D016865:Reassortant Viruses / Q000235:genetics*
keywords: Avian influenza virus; East Asian–Australian migration flyway; Genetic diversity; H9N2; Reassortment