Abstract
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.