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Large-Scale Surveillance and In-Depth Evolutionary Analyses of H7N9 Avian Influenza Virus


Su-Chun Wang, Shuo Liu, Wen-Ming Jiang, Qing-Ye Zhuang, Kai-Cheng Wang, Guang-Yu Hou, Jin-Ping Li, Jian-Min Yu, Xiang Du, Zhi-Yuan Yang, Yue-Huan Liu, Ji-Wang Chen, Ji-Ming Chen
Author Affiliation(s)
China Animal Health and Epidemiology Center, Qingdao, 210095, China (Su-Chun Wang, Shuo Liu, Wen-Ming Jiang, Qing-Ye Zhuang, Kai-Cheng Wang, Guang-Yu Hou, Jin-Ping Li, Jian-Min Yu, Xiang Du, Ji-Ming Chen); Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China (Zhi-Yuan Yang, Yue-Huan Liu); Department of Medicine, Section of Pulmonary, Critical Care, Sleep and Allergy Medicine, University of Illinois at Chicago, Chicago, IL60612, USA (Ji-Wang Chen)

Corresponding Author(s)
Ji-Ming Chen (E-mail:;

Subject Areas
Ecology; Epidemiology; Evolution; Genetics; Infectious diseases; Microbiology; Molecular & cellular biology; Public health; Theoretical biology; Veterinary medicine; Virology

The novel H7N9 subtype avian influenza virus (AIV) has caused hundreds of human deaths in China since its emergence in 2013. In this study, we conducted large-scale surveillance of AIVs, which demonstrated the prevalence and distribution of the H7N9 AIV and its potential gene-donor viruses (H9N2 subtype AIV) in different species of poultry. We also conducted in-depth phylogenetic analyses of AIVs, which suggested that one genotype of the H9N2 subtype AIV circulating in chickens, pigeons and bramblings could donate six internal genes to the H7N9 AIV, and multiple genotypes of the H7N9 AIV circulated in Henan province. Moreover, by calculating the distribution of the mutations and the nonsynonymous/synonymous rate ratios, we identified five mutations in the viral HA gene specific to the H7N9 AIV, and one of the specific mutations, Q226L (H3 numbering) that confers increased binding to human-like receptors, was probably fixed by positive selection. These results are important for the design of evidence-based measures to control this zoonotic virus, as well as providing novel insights into the distribution, risk and evolution of H7N9 AIVs. Additionally, we proposed a novel hypothesis that the H7N9 AIV may have originated in pigeons through natural selection.

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  • Comments #1      2016-02-02 13:48:37    
    The article is timely and of great impact on surveillance, prevention and management of this potentially emerging zoonotic disease.
  • Comments #3      2016-01-11 18:52:45    
    Newpubli Editorial Team did not invite peer reviewers to rate the value rank of this preprint until this website was optimized adequately.
  • Comments #2      2016-01-11 18:51:39    
    This preprint is being proofread in grammar by International Science Editing.

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