Abstract: ObjectiveTo conduct high-throughput sequencing and phylogenetic analysis of H6N6 subtype avian influenza virus (AIV) isolated from live-poultry markets in Guangdong Province in 2013 to provide experimental data for monitoring the AIV. MethodsHigh-throughput sequencing and phylogenetic analysis of 2 strains of avian H6N6 virus, A/Environment/Guangdong/SW-C12382070/2013(H6N6) and A/Environment/Guangdong/SW-C12382099/2013(H6N6), were conducted by using Ion Torrent. ResultsThe sequence analysis of the hemagglutinin (HA) gene showed that the viruses were low pathogenic AIV, with a typical HA cleavage site of P-Q-I-E-T-R-G. The HA genes of the two strains of AIV were closely related to A/duck/NhaTrang/60/2013(H6N6). The neuramidinase (NA) genes of the two isolates were closely related to A/chicken/Hunan/S4495/2010(H6N6). The phylogenic analysis indicated that the eight genes of the two isolates belonged to the Eurasian avian lineage. Their HA, NA, and NP genes belonged to ST2853-like lineage, ST192-like lineage, and HN573-like lineage, respectively. However, the alkaline polymerase 2 (PB2), alkaline polymerase 1 (PB1), acid polymerase (PA), matrix protein (M), and non structural protein (NS) genes belonged to ST339-like lineage. ConclusionThe two strains of H6N6 subtype AIV were recombinant viruses resulted from different genotype viruses.