OmniVira

Genetic diversity of H9N2 avian influenza viruses in poultry across China and implications for zoonotic transmission.

Jing Yang1,2,3 Juan Li4,5 Ju Sun1,3,6 Jiaming Li1,3 Guanghua Fu7 Tian Tian1,6 Yongchun Yang8 Xuancheng Lu9 Shan Li4,5 Lixia Wang1,6 Jia Dong1 Mingjia Wu1,2 Yun Liu1,6 Delong Li10 Dongfang Hu11 Hui Dong4 Ruoyu Shang1,5 Yanqing Wang1,2 Kunpeng Yuan1,6 Lin Ran1,2 Honglei Sun12 Wenxia Tian6 Yu Huang7 Jinhua Liu12 Wenjun Liu1,2 Weifeng Shi13,14 George F Gao15,16,17 Yuhai Bi18,19,20,21,22
Affiliations 22 institutions
  1. Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, China.
  2. University of Chinese Academy of Sciences, Beijing, China.
  3. Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, Beijing, China.
  4. Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, China.
  5. School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, China.
  6. College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China.
  7. Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China.
  8. Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology and College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China.
  9. National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), Laboratory Animal Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.
  10. College of Veterinary Medicine, Southwest University, Chongqing, China.
  11. College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China.
  12. National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China.
  13. Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [email protected].
  14. Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [email protected].
  15. Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, China. [email protected].
  16. University of Chinese Academy of Sciences, Beijing, China. [email protected].
  17. The D. H. Chen School of Universal Health, Zhejiang University, Hangzhou, China. [email protected].
  18. Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, China. [email protected].
  19. University of Chinese Academy of Sciences, Beijing, China. [email protected].
  20. Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, Beijing, China. [email protected].
  21. College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China. [email protected].
  22. Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, China. [email protected].
PMID40461649 DOI10.1038/s41564-025-02002-x Year2025 Journal Nature microbiology Nat Microbiol Languageeng Statusppublish

Abstract

Nationwide surveillance of avian influenza viruses (AIVs) in live poultry markets across China has occurred since 2014, providing a resource for AIV prevalence and genetic diversity studies. Here we report that 3,237 of 18,425 samples from poultry were AIV positive (17.57%) between 2019 and 2023, with H9N2 being the dominant subtype. We developed an automated phylogeny-based nomenclature system to classify genetic clades of the dominant H9N2 lineage, the BJ94 lineage. Using this model, we found that ten haemagglutinin (HA) sub-subclades cocirculated in poultry and showed antigenic variation. In addition, 99.46% and 96.17% of H9N2 AIVs in 2021-2023 possessed human-receptor binding-related HA-L226 and human MxA-resistance-related NP-N52 mutations, respectively. H9N2 strains with these two mutations preferred human-type receptors and increased replication in human cells in vitro, regardless of the presence of PB2-V/K/E627. Moreover, H9N2 AIVs containing HA-L226, PB2-V/K627 and NP-N52 were transmitted from infected to naive guinea pigs and ferrets through direct contact and respiratory droplet. This highlights the potential zoonotic risks of H9N2 AIVs.

Supporting text Virus Host Location
Genetic Variation 127 Influenza A Virus, H9N2 Subtype 71 Influenza in Birds 341 Poultry 112 Poultry Diseases 74 Viral Zoonoses 65 Zoonoses 397 Animals 1948 Chickens 146 China 229 Ferrets 79 Guinea Pigs 21 Hemagglutinin Glycoproteins, Influenza Virus 180 Humans 1440 Influenza, Human 286 Mutation 209 Phylogeny 805

Evidence records

3 total
Zoonotic Surveillance
1 records · 1 evidence types
Evidence type Viral Detection
1 records
OVE9376 Viral Detection
Key finding

H9N2 avian influenza virus was detected in poultry samples collected across China between 2019 and 2023, with 17.57% positivity among 18,425 specimens.

Virus
Influenza A virus H9N2
Host
birds Aves Natural host
Location
China
Supporting text

We report that 3,237 of 18,425 samples from poultry were AIV positive (17.57%) between 2019 and 2023, with H9N2 being the dominant subtype.

Method
surveillance | viral RNA detection
Sample type
poultry samples
Geographic raw
China
Country inferred
CHN
Experimental Infection
1 records · 1 evidence types
Evidence type Experimental Transmission
1 records
OVE9378 Experimental Transmission
Key finding

H9N2 avian influenza viruses containing HA-L226, PB2-V/K627, and NP-N52 mutations transmitted via direct contact and respiratory droplets from infected to naïve guinea pigs and ferrets under controlled experimental conditions.

Virus
Influenza A virus H9N2
Host
domestic guinea pig Cavia porcellus Experimental system domestic ferret Mustela putorius furo Experimental system
Location
Not specified
Supporting text

H9N2 AIVs containing HA-L226, PB2-V/K627 and NP-N52 were transmitted from infected to naive guinea pigs and ferrets through direct contact and respiratory droplet.

Method
controlled co-housing experiment | respiratory droplet exposure assay | virological detection of infection in recipients
Experimental system
animal transmission model using direct-contact and respiratory-droplet exposure between infected and naïve individuals
Functional Mechanism
1 records · 1 evidence types
Evidence type Molecular Adaptation
1 records
OVE9377 Molecular Adaptation
Key finding

The HA-L226 and NP-N52 mutations in H9N2 avian influenza viruses confer human-type receptor binding preference and enhanced replication in human cells, indicating molecular adaptation toward humans.

Virus
Influenza A virus H9N2
Host
Not specified
Location
Not specified
Supporting text

99.46% and 96.17% of H9N2 AIVs in 2021-2023 possessed human-receptor binding-related HA-L226 and human MxA-resistance-related NP-N52 mutations, respectively. H9N2 strains with these two mutations preferred human-type receptors and increased replication in human cells in vitro.

Genes or proteins
HA | NP
Receptors
human-type receptors
Host factors
MxA
Mutations
HA-L226 | NP-N52
Mechanism types
receptor binding | replication adaptation | host-range expansion