2.4. Whole genome sequencing
Viral RNA was purified from one sample and processed for next generation
sequencing (Illumina, Inc), following manufacturer’s specifications.
Reads were imported into CLC genomics and assembled de novo.Whole genome sequences of PDCoV were obtained from GenBank (n=23) for
phylogenetic analysis. For phylogenetic analysis based on S gene, we
also included those from Mexico (n = 27). General information of
nucleotide sequences used is listed in Table 1.