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 and ORF 1a/b sequences of PDCoV were obtained from GenBank (n=23) for phylogenetic analysis. For analysis based on S gene, we also included those from Mexico (n = 27). General information of nucleotide sequences used is listed in Table 1.