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Phylogenetic Analysis of the Hemagglutinin Genes of 36 H9N2 Subtype Avian Influenza Viruses Isolated from Poultry in China during 2009–2015

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Preprint abstract
Qing-Xiu Cai, Bo Wei, Yuan-Yuan Zhang, Yi-Hai Jiang, Hong-Li Ling
Author Affiliation(s)
Qingdao Vland Biotech Incorporation, Qingdao, 26000, China
Corresponding Author(s)
Hong-Li Ling (E-mail:
Subject Areas
Epidemiology; Infectious diseases; Medicine; Microbiology; Veterinary medicine; Virology

H9N2 subtype avian influenza viruses are prevalent in China, and have aroused increasing concerns for their impact in poultry and risk to public health. Vaccination has played an effective role in controlling the viruses, while more knowledge is still needed on the epidemiology of the viruses for development of more effective vaccines. In this study, 36 H9N2 strains were isolated from vaccinated flocks during 2009–2015. Their hemaglutinin (HA) genes were sequenced and phyologenetically analyzed. The results showed that all the 36 viral strains belonged to the Y280 lineage, and their HA gene sequence identities were 91.5%–99.5% for nucleotide sequences and 90.6%–99.5% for amino acid sequences. The HA gene sequence identities between the 36 viruses and H9N2 vaccine strains were 83.8%–92.8% for nucleotide sequences and 82.3%–93.3% for amino acid sequences. The cleavage sites in the viral HA genes of 34 out of the 36 strains were of the motif of PSRSSR↓GL, and the other two were of the motif of PASSR↓GL. Furthermore, at position 216 (H3 numbering) in the receptor-binding site of the viral HA gene, 34 out of 36 the strains had the substitution of Q216L, which indicated that these viruses had increased binding to human-like receptors. Therefore, this study provided novel data regarding the epidemiology of H9N2 subtype avian influenza viruses in China.

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