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.

In this study, the authors present a genomic surveillance of avian influenza genomes sampled from live poultry markets in China. They report that a number of variants have emerged since 2016 that pose an increased risk to humans. They highlight the importance of continuous genome surveillance of circulating influenza strains.

Details

Title
Dominant subtype switch in avian influenza viruses during 2016–2019 in China
Author
Bi Yuhai 1   VIAFID ORCID Logo  ; Li, Juan 2   VIAFID ORCID Logo  ; Li, Shanqin 3 ; Fu Guanghua 4 ; Jin, Tao 5   VIAFID ORCID Logo  ; Zhang, Cheng 6 ; Yang, Yongchun 7 ; Ma Zhenghai 8 ; Tian Wenxia 9   VIAFID ORCID Logo  ; Li, Jida 10 ; Xiao Shuqi 11 ; Li, Liqiang 5 ; Yin Renfu 12   VIAFID ORCID Logo  ; Zhang, Yi 10 ; Wang, Lixin 13 ; Qin Yantao 14 ; Yao Zhongzi 15 ; Meng Fanyu 16 ; Hu, Dongfang 17 ; Delong, Li 18 ; Wong, Gary 19 ; Liu, Fei 20 ; Lv Na 20 ; Wang, Liang 20 ; Fu Lifeng 20   VIAFID ORCID Logo  ; Yang, Yang 3 ; Peng, Yun 3 ; Ma Jinmin 5   VIAFID ORCID Logo  ; Sharshov Kirill 21 ; Shestopalov, Alexander 21 ; Gulyaeva Marina 21   VIAFID ORCID Logo  ; Gao, George F 22   VIAFID ORCID Logo  ; Chen, Jianjun 15   VIAFID ORCID Logo  ; Shi, Yi 23   VIAFID ORCID Logo  ; Liu, William J 24   VIAFID ORCID Logo  ; Chu, Dong 25 ; Huang, Yu 4 ; Liu Yingxia 26 ; Liu, Lei 26 ; Liu, Wenjun 23 ; Chen Quanjiao 15 ; Shi, Weifeng 27   VIAFID ORCID Logo 

1  Chinese Academy of Sciences, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309); University of Chinese Academy of Sciences, Beijing, China (GRID:grid.410726.6) (ISNI:0000 0004 1797 8419); Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People’s Hospital, Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Shenzhen, China (GRID:grid.410741.7) 
2  Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China (GRID:grid.410741.7) 
3  University of Chinese Academy of Sciences, Beijing, China (GRID:grid.410726.6) (ISNI:0000 0004 1797 8419) 
4  Fujian Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Medicine, Fuzhou, China (GRID:grid.418033.d) (ISNI:0000 0001 2229 4212) 
5  China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China (GRID:grid.21155.32) (ISNI:0000 0001 2034 1839) 
6  Chinese Academy of Sciences, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309); Xinjiang University, College of Life Science and Technology, Urumchi, China (GRID:grid.413254.5) (ISNI:0000 0000 9544 7024) 
7  College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China (GRID:grid.443483.c) (ISNI:0000 0000 9152 7385) 
8  Xinjiang University, College of Life Science and Technology, Urumchi, China (GRID:grid.413254.5) (ISNI:0000 0000 9544 7024) 
9  Shanxi Agricultural University, College of Animal Science and Veterinary Medicine, Taigu, China (GRID:grid.412545.3) (ISNI:0000 0004 1798 1300) 
10  Zunyi Medical University, Institute of Zoonosis, College of Public Hygiene, Zunyi, China (GRID:grid.417409.f) (ISNI:0000 0001 0240 6969) 
11  Northwest A&F University, College of Veterinary Medicine, Yangling, China (GRID:grid.144022.1) (ISNI:0000 0004 1760 4150) 
12  Jilin University, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin, China (GRID:grid.64924.3d) (ISNI:0000 0004 1760 5735) 
13  Hainan Medical University, School of Basic Medicine and Life Science, Haikou, China (GRID:grid.443397.e) (ISNI:0000 0004 0368 7493) 
14  Diqing Tibetan Autonomous Prefecture Centers for Disease Control and Prevention, Shangri-la, China (GRID:grid.443397.e) 
15  CASCIRE, Chinese Academy of Sciences, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan, China (GRID:grid.9227.e) (ISNI:0000000119573309) 
16  Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China (GRID:grid.9227.e) 
17  Henan Institute of Science and Technology, College of Animal Science and Technology, Xinxiang, China (GRID:grid.503006.0) (ISNI:0000 0004 1761 7808) 
18  Southwest University, College of Animal Science, Chongqing, China (GRID:grid.263906.8) 
19  Chinese Academy of Sciences, Institut Pasteur of Shanghai, Shanghai, China (GRID:grid.9227.e) (ISNI:0000000119573309); Université Laval, Département de microbiologie-infectiologie et d’immunologie, Québec City, Canada (GRID:grid.23856.3a) (ISNI:0000 0004 1936 8390) 
20  Chinese Academy of Sciences, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309) 
21  Novosibirsk State University, Federal Research Center of Fundamental and Translational Medicine, Federal State Budget Scientific Institution, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia (GRID:grid.4605.7) (ISNI:0000000121896553) 
22  Chinese Academy of Sciences, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309); University of Chinese Academy of Sciences, Beijing, China (GRID:grid.410726.6) (ISNI:0000 0004 1797 8419); Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People’s Hospital, Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Shenzhen, China (GRID:grid.410741.7); Chinese Center for Disease Control and Prevention (China CDC), National Institute for Viral Disease Control and Prevention, Beijing, China (GRID:grid.198530.6) (ISNI:0000 0000 8803 2373) 
23  Chinese Academy of Sciences, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309); University of Chinese Academy of Sciences, Beijing, China (GRID:grid.410726.6) (ISNI:0000 0004 1797 8419) 
24  Chinese Center for Disease Control and Prevention (China CDC), National Institute for Viral Disease Control and Prevention, Beijing, China (GRID:grid.198530.6) (ISNI:0000 0000 8803 2373) 
25  State Forestry and Grassland Administration, General Station for Surveillance of Wildlife-borne Infectious Diseases, Shenyang, PR China (GRID:grid.198530.6) 
26  Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People’s Hospital, Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Shenzhen, China (GRID:grid.410741.7) 
27  Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China (GRID:grid.9227.e); Shandong First Medical University & Shandong Academy of Medical Sciences, School of Public Health, Taian, China (GRID:grid.9227.e) 
Publication year
2020
Publication date
2020
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41467-020-19671-3
ProQuest document ID
2473210830
Copyright
© The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.