Nucleotide and deduced amino acid sequences of the 33 PEDV isolates were aligned, edited, and analyzed with ClustalX version 1.83, Bioedit version 7.0.5.2, and MegAlign software (DNAStar Inc., Madison, WI, USA), respectively. Phylogenetic trees were generated by using partial S and full-length M genes, including the deduced amino acid sequences with selected reference PEDV strains, by applying the Jotun Hein method in the MegAlign software. To assess the relative support for each clade, bootstrap values were calculated from 1,000 replicate analyses.