Whole-genome sequencing and assembly
The whole-genome sequence of each influenza virus isolate was obtained by using the Genome Sequencer Junior (Roche 454) or ABI 3730 genetic analyzer (Applied Biosystems) as previously described (Vijaykrishna, 2011, Liang, 2014). Original reads that shared >90% sequence identity in a 40-nucleotide overlapping region were assembled into contigs using Lasergene, version 9.0 (DNAStar).