Molecular evolution of porcine epidemic diarrhea virus and porcine deltacoronavirus strains in Central China

Porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) are epizootic swine viruses. To detect and study the evolution of PEDV and PDCoV in central China (Shanxi, Henan, Hubei province), 70 clinical intestinal and fecal samples from piglets with severe watery diarrhea during August 2015 and June 2016 were collected, tested and analyzed. PEDV was more frequently detected by PCR than PDCoV. Phylogenetic analysis of S genes showed that the 10 PEDV strains from this study clustered into G2a (n = 7) and G2b (n = 3) groups. Additionally, the three G2b strains (PEDV S2△) contained the same specific 3 nt deletion in S2 as other reference strains in G2b. Interestingly, complete genome analysis indicated that CH/hubei/2016 was closer to the US INDEL strain and G2a group. CH/hubei/2016 had one recombination event in S2 gene which may have resulted from AH2012-12 (from G2b group) and CH-ZMDZY-11 (from G2a group). Furthermore, 10 purifying selection sites in S gene indicated an adaptive evolution of PEDV in central China swine herds. These results suggested that Pandemic G2a and G2b are predominant PEDV genotype circulating in central China. In addition, the deletion and recombination identified in S gene suggested PEDV strains of central exhibited an evolutionary variety. However, whether these changes affect the pathogenicity and antigenicity of wild PEDV is unknown and is worth for further investigation.