To determine the genetic characteristics of these viruses, all eight gene segments of the viruses grown in MDCKs were sequenced and phylogenetic analyses were performed. Phylogenetic analysis of the hemagglutinin (HA) reveals that the 11 H1 HA genes are separated into EA-like H1N1 lineage and H1N1/2009 pandemic lineage (Fig. 1a). All ten H1 HA genes clustered into the EA H1N1 lineage share 95.9–100% identity at the nucleotide level, whereas the interlineage homology is <74%. All the three H3 HA genes share over 98.6% of identity and are clustered into HL H3N2 lineage (Fig. 1c). Similar to the HA genes, ten N1 NA genes and one N1 NA gene are clustered into the EA H1N1 lineage and H1N1/2009 pandemic lineage, respectively (Fig. 1b). The N1 intralineage virus homology is over 94.7%, while the homology between the lineages is <89.4%. Three N2 NA genes are clustered into HL H3N2 lineage, which share over 98.7% of homology within the lineage (Fig. 1d).Fig. 1Phylogenetic trees of the HA H1 (a), NA N1 (b), HA H3 (c), NA N2 (d), M (e), NS (f), PB2 (g), PB1 (h), PA (i), and NP (j) genes of the H1N1 and H3N2 influenza lineages. The unrooted trees were generated with the MEGA 7.0 program by using neighbor-joining analysis and reliability of the tree was assessed by bootstrap analysis with 1000 replications. Neighbor-joining bootstrap values ≥70 are shown at the major branches of the trees. The 12 trees were rooted to A/Brevig_Mission/1/18(H1N1). Viruses shown in black were downloaded from available databases. The isolates in our study were marked in different color, consistent with Fig. 2