Dominant subtype switch in avian influenza viruses during 2016–2019 in China

Yuhai Bi (), Juan Li, Shanqin Li, Guanghua Fu, Tao Jin, Cheng Zhang, Yongchun Yang, Zhenghai Ma, Wenxia Tian, Jida Li, Shuqi Xiao, Liqiang Li, Renfu Yin, Yi Zhang, Lixin Wang, Yantao Qin, Zhongzi Yao, Fanyu Meng, Dongfang Hu, Delong Li, Gary Wong, Fei Liu, Na Lv, Liang Wang, Lifeng Fu, Yang Yang, Yun Peng, Jinmin Ma, Kirill Sharshov, Alexander Shestopalov, Marina Gulyaeva, George F. Gao, Jianjun Chen, Yi Shi, William J. Liu, Dong Chu, Yu Huang, Yingxia Liu, Lei Liu, Wenjun Liu, Quanjiao Chen () and Weifeng Shi ()
Additional contact information
Yuhai Bi: Chinese Academy of Sciences
Juan Li: Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences
Shanqin Li: University of Chinese Academy of Sciences
Guanghua Fu: Fujian Academy of Agricultural Sciences
Tao Jin: China National Genebank-Shenzhen, BGI-Shenzhen
Cheng Zhang: Chinese Academy of Sciences
Yongchun Yang: College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University
Zhenghai Ma: Xinjiang University
Wenxia Tian: Shanxi Agricultural University
Jida Li: Zunyi Medical University
Shuqi Xiao: Northwest A&F University
Liqiang Li: China National Genebank-Shenzhen, BGI-Shenzhen
Renfu Yin: Jilin University
Yi Zhang: Zunyi Medical University
Lixin Wang: Hainan Medical University
Yantao Qin: Diqing Tibetan Autonomous Prefecture Centers for Disease Control and Prevention
Zhongzi Yao: CASCIRE, Chinese Academy of Sciences
Fanyu Meng: Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences
Dongfang Hu: Henan Institute of Science and Technology
Delong Li: Southwest University
Gary Wong: Chinese Academy of Sciences
Fei Liu: Chinese Academy of Sciences
Na Lv: Chinese Academy of Sciences
Liang Wang: Chinese Academy of Sciences
Lifeng Fu: Chinese Academy of Sciences
Yang Yang: University of Chinese Academy of Sciences
Yun Peng: University of Chinese Academy of Sciences
Jinmin Ma: China National Genebank-Shenzhen, BGI-Shenzhen
Kirill Sharshov: Novosibirsk State University
Alexander Shestopalov: Novosibirsk State University
Marina Gulyaeva: Novosibirsk State University
George F. Gao: Chinese Academy of Sciences
Jianjun Chen: CASCIRE, Chinese Academy of Sciences
Yi Shi: Chinese Academy of Sciences
William J. Liu: Chinese Center for Disease Control and Prevention (China CDC)
Dong Chu: State Forestry and Grassland Administration
Yu Huang: Fujian Academy of Agricultural Sciences
Yingxia Liu: Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People’s Hospital
Lei Liu: Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People’s Hospital
Wenjun Liu: Chinese Academy of Sciences
Quanjiao Chen: CASCIRE, Chinese Academy of Sciences
Weifeng Shi: Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: Abstract We have surveyed avian influenza virus (AIV) genomes from live poultry markets within China since 2014. Here we present a total of 16,091 samples that were collected from May 2016 to February 2019 in 23 provinces and municipalities in China. We identify 2048 AIV-positive samples and perform next generation sequencing. AIV-positive rates (12.73%) from samples had decreased substantially since 2016, compared to that during 2014–2016 (26.90%). Additionally, H9N2 has replaced H5N6 and H7N9 as the dominant AIV subtype in both chickens and ducks. Notably, novel reassortants and variants continually emerged and disseminated in avian populations, including H7N3, H9N9, H9N6 and H5N6 variants. Importantly, almost all of the H9 AIVs and many H7N9 and H6N2 strains prefer human-type receptors, posing an increased risk for human infections. In summary, our nation-wide surveillance highlights substantial changes in the circulation of AIVs since 2016, which greatly impacts the prevention and control of AIVs in China and worldwide.

Date: 2020
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DOI: 10.1038/s41467-020-19671-3

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