2.5. Phylogenetic analysis
The PDCoV whole genome, ORF 1a/b and S nucleotide sequences in this study, were aligned using ClustalW from MegaX software (Kumar et al., 2018). We used PDCoV genome sequences obtained from GenBank isolated in the US (n = 13), China (n = 5), Japan (n = 1), Vietnam (n = 2) and Thailand (n = 2). We included sequences from Mexico (n = 4) for phylogenetic analysis of S gene. A general time reversible (GTR) nucleotide substitution model with gamma distribution among site rate variation was used, with a maximum likelihood estimation model for phylogenetic reconstruction. Bootstrap analysis was carried out on 1000 data sets. The percentage of nucleotide sequence identity was also calculated.
Results