Recombination analysis
In order to investigate the recombination events occurred in the detected variant strains, especially the S-INDEL, all of the detected strains and 178 reference strains obtained from Genbank were analyzed using program RDP4 (Martin et al., 2010). Potential recombinant strains, parental strains, and possible recombination breakpoints were identified by a series of methods including RDP, GeneConv, SiScan, 3Seq, BootScan, MaxChi, and Chimaera. Recombination events were examined by at least three of the methods mentioned above with a cutoff of p < 0.05. Based on the fragment size of genome that contributed to the recombinants, the original sequences were defined as major parents (contributing the larger fragment) and the minor parents (contributing the small fragment).