Abstract:
PEDV and PDCoV are recognized as important pathogens causing enteric disease in swine herds worldwide. During 2014-2015, several outbreaks of PEDV occurred in many provinces in Thailand, and the clinical signs were more severe than those of classical PEDV in Thailand during 2008-2012. Therefore, the new introduction of PEDV or mutated virus strains was suspected. In 2015, PDCoV was also reported in Thailand, making the situation of enteric disease in the Thai swine industry worse. Since genetic classification studies of PEDV and PDCoV had never been done in Thailand before, this study aimed to investigate the genetic diversity of PEDV and PDCoV in the swine population in Thailand. PEDV in Thailand can be classified into seven subgroups based on the spike gene. Subgroups TH2, TH1, and TH4 were the predominant strains during 2008-2013, 2014-2016, and 2016-2018, respectively. The substitution rate of TH1 was higher during 2008-2015 compared to other strains in Thailand. After 2018, the incidence of PEDV decreased, and sporadic cases of new recombinants could be observed. For PDCoV, the origin of the virus is still unclear, although the study demonstrated that Thai and SEA PDCoV are closer to those of the Chinese PDCoV. Using full-length sequences, PDCoV could be classified into three different genogroups, including SEA, China, and the US, while SEA PDCoV could be further classified into three different subgroups. Subgroup SEA-1, or the SEA pandemic variants, responded to the outbreak in Thailand, Lao PDR, and Vietnam, during 2013-2016. The results also suggested that recombination was an important mechanism in the PDCoV evolution of the SEA genogroups. This study provided insight into the circulating strains of PEDV and PDCoV that can be used to develop effective preventive strategies. The information on the evolutionary dynamics of the virus and genetic information of the present variants in the field can also be applied for vaccine development.
