Phylogenetic Analysis of Eight Genes of H9N2 Subtype Influenza Virus: A Mainland China Strain Possessing Early Isolates’ Genes that have been Circulating

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Abstract
H9N2 subtype influenza virus has become worldwide and prevalent in China. Previous studies illustrated that at least three sublineages had been established in terrestrial poultry of Eurasian avian. In this presentation, eight full-length genes of an H9N2 strain, A/Chicken/Shanghai/F/98 (Ck/SH/F/98) were obtained. Sequence analysis and phylogenetic studies were conducted by comparing eight genes with those of all the available H9N2 strains from the GenBank. The results showed that four genes (HA, NA, M and NS genes) of Ck/SH/F/98 were incorporated into the sublineage represented by the early mainland China strain, Ck/BJ/1/94. However, the other four of RNP genes of Ck/SH/F/98 did not show close relationship with those of the three known sublineages’ viruses. Therefore, Ck/SH/F/98 was a natural reassortant between different sublineages. In addition, comparison showed that Ck/SH/F/98 could be a putative precursor of a later isolate from southern China, Dk/ST/1605/01, with at least six genes of both closely related, indicating genes of Ck/SH/F/98 and early isolates had ever been circulating. Further comparison in terms of molecular markers of species specificity of HA1 revealed that DK/ST/1605/01 also resembled Ck/SH/F/98 more than a common earlier duck strain. The results supported the idea of two-way transmission between terrestrial and aquatic birds that emphasized the importance to raise concerns on the natural evolution of all the eight genes of H9N2 avian influenza viruses.