Epidemiology and phylogeny of spike gene of porcine epidemic diarrhea virus from Yunnan, China

Porcine epidemic diarrhea (PED) causes acute enteric disease and yellowish watery diarrhea, making piglets fast dehydration to death. PED threatens pig industry and leads to substantial economic losses. After the first reports, PED in Yunnan province, China was again identified in 2013 during an epidemiological survey, with follow-up data showing an overall positive rate of 17.47% during 2013–2017, lower than that in other provinces in China. The complete S gene of porcine epidemic diarrhea virus (PEDV) is 4149–4158 bp long. Phylogenetic analysis of S gene was performed using 9 new isolates from Yunnan province, China, together with 225 full-length S genes available in GenBank. The nine Yunnan isolates were clustered into classical G1b and pandemic G2a groups, indicating new variants have been emerging in Yunnan province. When taking the previously submitted 3 isolates from China into consideration, all the 12 isolates were clustered into 4 groups, i.e., G1a, G1b, G2a and G2b, suggesting that a highly diverse and complex clustering might result from co-infections in more than 13 provinces in China, as well in South Korea, Japan, Vietnam, Thai and USA. Identification of new types of PEDV strains would stimulate the development of effective vaccines for the prevention and control of PED in a more precise manner.