Genetic characteristics of porcine epidemic diarrhea virus in Chinese mainland, revealing genetic markers of classical and variant virulent parental/attenuated strains

• The subgroup-Va was the dominant subgroup in PEDV and eight novel variant PEDV strains were identified in Chinese mainland
• The variant PEDV in China seemed spread from the southeast coastal districts to other coastal and interior districts
• The 1-750 bp of S could represent S1 or S for genetic characteristics and protein property analysis to some extent
• Three genetic markers were identified to differentiate the classical and variant virulent parental/attenuated PEDV strains

Since October 2010, porcine epidemic diarrhea (PED) caused by variant porcine epidemic diarrhea virus (PEDV) has led great economic losses to the global pig industry, especially in China. To study the genetic characteristics of PEDV strains in Chinese mainland, a total of 603 clinical samples from nine provinces/districts of Chinese mainland from January 2014 to December 2015 were collected for RT-PCR detection and 1-1323 bp of S gene of 91 isolates and ORF3 gene of 46 isolates were sequenced. The results showed that the variant PEDV were the dominant pathogens of viral diarrhea diseases in these areas. Six novel variant PEDV strains (FJAX1, FJAX2, HeNPDS1, HeNPDS2, HeNPY3, and HeNPY4) with two amino acids (aa) deletion at the 56–57 aa of S protein were identified. A total of 405 Chinese PEDV strains were subjected to phylogenetic and phylogeographic analysis. The results revealed that the subgroup Va in variant PEDV group were the dominant subgroup and the spread trend of variant PEDV strains seemed to be from the southeast coastal districts to other coastal districts and interior districts. The N-terminal of S gene (1–750 bp), to some extent, could represent S1 or full length S gene for phylogenetic, similarity, antigen index, hydrophilicity plot, and differentiation analyses. The 404–472 bp of S gene contained the three genetic markers, i.e., “TAA” insertion at 404–405 bp, “ACAGGT” deletion at 430–435 bp, and “ATA” deletion at 455–457 bp can be used to differentiate the classical and variant virulent parental/attenuated PEDV strains and help us to learn the infectious and genetic characteristics of PEDV strains more convenient and cheaper. This study has important implication for understanding the infectious, genetic, and evolutionary aspects of PEDV strains in Chinese mainland.