Genetic evolution of avian influenza A (H9N2) virus in a live poultry market in central Jiangsu, China, 2019–2020

Abstract:

[Background] Since the 1990s, H9N2 avian influenza virus has become a major threat to human and animal health. [Objective] To understand the molecular evolutionary characteristics of H9N2 avian influenza virus in a live poultry market in central Jiangsu, 2019–2020. [Methods] The specimens were detected by real-time quantitative PCR method, and SPF chicken embryos were used for the isolation of virus strains from the specimens. The whole genome of each isolate was sequenced with specific primers. Blast, ClustalX and Mega 6 were used for sequence alignments and phylogenetic analysis. [Results] A total of 231 environmental and poultry specimens were collected from a farmers’ market from 2019 to 2020, from which of 34 influenza A virus strains were detected, including 33 strains of H9N2 subtype. Twenty strains of H9N2 virus were isolated with SPF chicken embryos, and the whole genomes of 11 strains were sequenced and aligned. The HA and NA gene sequences indicated that the 11 strains belonged to G57 genotype of Y280-like lineage. According to the evolutionary characteristics of HA and NA, the 11 strains can be divided into 5 gene constellations (A, B, C, D and E), of which constellation A (n=5) was dominant. The cleavage site of HA1 and HA2 subunits of HA protein of the 11 strains was a basic amino acid R, which indicated low pathogenicity. Four mutations (including I155T, H183N, A190T/V and Q226L) were occurred in the receptor-binding region of HA protein, indicating that these viruses had enhanced ability of binding to human SAα2-6Gal receptor. [Conclusion] The H9N2 avian influenza virus in the live poultry market in central Jiangsu is characterized by active evolution and has a risk of transmission to people. Efforts should be made to strengthen the monitoring and the research on cross-species transmission of avian influenza virus in the live poultry market.