Recombination analysis of S-INDEL like strains
A recombination analysis of the 91 strains detected in this study and
178 reference strains were performed by using RDP4 software. The results
derived from seven recombination methods indicated that six S-INDEL like
strains (CH/HNBR/01/2021, CH/JSXZ/12/2020, CH/SCYB/12/2020,
CH/SCGA/202103, CH/SCST/04/2020, and CH/HNSQ/02/2021) were recombinant
strains originated from FR/001/2014 strain detected in France and
vaccine strain AJ1102 (Figure 3). Further similarity comparisons were
made using SimPlot among six S-INDEL like strains and their parental
strains, the recombination breakpoint hot plots were found to be located
within the 720–1220 bp, 743–1204 bp or 743–1201 bp of S genes.