Genetic Analysis of the Nonstructural (NS) Genes of H9N2 Chicken Influenza Viruses Isolated in China During 1998–2002

H9N2 subtype avian influenza viruses are widespread in domestic poultry. Genetic analysis indicated that three lineages of H9N2 viruses have been established in Eurasia and only one lineage is present on chicken farms in mainland China. Here, NS1 genes of eight H9N2 chicken influenza viruses, isolated in mainland China during 1998–2002, were completely sequenced and phylogenetically analyzed. By comparison, the homology of the NS1 of the A/chicken/Neimenggu/ZH/02 (Ck/NM/ZH/02) strain had a high identity (93.8%) with that of A/chicken/Korea/323/96 (Ck/Kor/323/96), which is an A/duck/Hong Kong/Y439/97 (Dk/HK/Y439/97)-like virus. NS1 peptides of seven strains possessed 217 amino acids, while that of the strain Ck/NM/ZH/02 coded 230 amino acids. Except for the amino acid at position 225, the additional amino acid sequence (13 AAs) of NS1 of Ck/NM/Zh/02 at the carboxy-terminus is identical with that of Ck/Kor/323/96. Phylogenetic analysis showed that seven of the tested strains belong to the A/duck/Hong Kong/Y280/97 (DK/HK/Y280/97)-like lineage, while the NS1 gene of Ck/NM/Zh/02 belongs to the Dk/HK/Y439/97-like lineage and has a close relationship with that of the Ck/Kor/323/96-like viruses. Therefore, although most of the H9N2 influenza viruses circulating on chicken farms in mainland China belong to the DK/HK/Y280/97-like lineage, the present results indicate that the other two of the three H9N2 lineage viruses also circulate in the chicken population in mainland China.