Megalign program of 7

Sequence similarity analyses were performed using the MegAlign program of DNASTAR 7.0 software (DNASTAR Inc.). MEGA v.7.0.21 was used to perform a multiple sequence alignment and the aa p-distance was calculated using the p-distance model. Phylogenetic analysis of the genomes, ORF1a, ORF1b, and ORF2 genes were also performed using MEGA v.7.0.21. Branch statistics were calculated by bootstrap analysis of 1,000 replicates. The accession numbers of the nucleotide sequences obtained in this study and reference sequences were shown in Table S3. Recombination analysis was performed using RDP 4.0 (version 4.96) with the RDP, GeneConv, Chimaera, MaxChi, BootScan, SiScan, and 3Seq methods. Briefly, the sequences with significant recombination event (P < 0.05) derived from at least five methods were presented.

Sequence homology analyses were performed using the MegAlign program of DNASTAR 7.0 software (Version 7.0, DNA Star, Madison, WI, USA). MEGA v.7.0.21 (DNA Star, Madison, WI, USA) was used to perform multiple sequence alignment and to build a neighbor-joining phylogenetic tree with 1000 bootstrap support. The recombination event was assessed using RDP 4.97 and SimPlot software (version 3.5.1, DNA Star, Madison, WI, USA).