Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains

Guo, Jiahui; Fang, Liurong; Ye, Xu; Chen, Jiyao; Xu, Shangen; Zhu, Xinyu; Miao, Yimin; Wang, Dang; Xiao, Shaobo

Porcine epidemic diarrhea virus (PEDV), which re‐emerged in China in October 2010, has spread rapidly worldwide. Detailed analyses of the complete genomes of different PEDV strains are essential to understand the relationships among re‐emerging and historic strains worldwide. Here, we analysed the complete genomes of 409 strains from different countries, which were classified into five subgroup strains (i.e., GI‐a, GI‐b, GII‐a, GII‐b, and GII‐c). Phylogenetic study of different genes in the PEDV strains revealed that the newly discovered subgroup GII‐c exhibited inconsistent topologies between the spike gene and other genes. Furthermore, recombination analysis indicated that GII‐c viruses evolved from a recombinant virus that acquired the 5′ part of the spike gene from the GI‐a subgroup and the remaining genomic regions from the GII‐a subgroup. Molecular clock analysis showed that divergence of the GII‐c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re‐emergence outbreaks. Interestingly, Ascaris suum, a large roundworm occurring in pigs, was found to be an unusual PEDV host, providing potential support for cross‐host transmission. This study has significant implications for understanding ongoing global PEDV outbreaks and will guide future efforts to develop effective preventative measures against PEDV.