Genetic variation and phylogenetic analysis of hemagglutinin genes of H9 avian influenza viruses isolated in China during 2010–2012

Abstract Genetic variation and phylogenetic relationships of H9 avian influenza viruses (AIVs) were analyzed based on hemagglutinin (HA) gene sequences of 84 Chinese H9 reference viruses recently available in GenBank, 3 widely used vaccine strains and 29 novel isolates. The novel isolates were obtained from vaccinated poultry flocks in 11 provinces of China during 2010 to 2012. The nucleotide homologies of HA genes of these isolates ranged from 87.8–99.8%, and from 89.8–93.2% as compared with the vaccine strains. Among the 29 novel isolates and the 84 reference viruses, 69.9% of the them belonged to the lineage h9.4.2.5 and had the dominant PSRSSR↓GLF motifs in the HA cleavage sites, while 27.4% of the them belonged to the newly emerging lineage h9.4.2.6 and had the dominant PARSSR↓GLF motifs, no consecutive basic amino acids insertion, showing the characteristic feature of low-pathogenic AIV. All the lineage h9.4.2.5 viruses and 75% of the lineage h9.4.2.6 viruses had the substitution Q226L (in H3 numbering). Additional potential glycosylation site at residues 313–315 (NCS) were found merely in all the lineage h9.4.2.5 viruses. Our results demonstrated that lineage h9.4.2.5 was more dominant than other lineages as it harbored more viruses that widely distributed in China in recent years. New lineage h9.4.2.6 previously existed mainly in South China had emerged in North China. Updated vaccine and increased veterinary biosecurity on poultry farms and trade markets are needed to prevent and control avian influenza.