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).