Molecular characterization and phylogenetic analysis of H3 subtype avian influenza viruses isolated from domestic ducks in Zhejiang Province in China

In 2013, 15 avian influenza viruses (AIVs), H3N2 (n = 7), H3N3 (n = 3), H3N6 (n = 3), and H3N8 (n = 2), were isolated from domestic ducks in Zhejiang Province in China. These strains were characterized by whole genome sequencing with subsequent phylogenetic analysis and genetic comparison. Phylogenetic analysis of all eight viral genes showed that these strains clustered in the AIV Eurasian lineage. Analysis of the neuraminidase (NA) gene indicates that a re-assortment event between H3 and H9N2 AIV occurred in these ducks. The molecular markers analyzed over the genome of all viruses indicated that these strains were low-pathogenic AIVs. Although there was no evidence of re-assortment in subtype H3 AIVs among the avian species’ and mammalian hosts in this study, continued surveillance is needed considering the important role of domestic ducks in AIV re-assortment.