Genomic Characterizations of Porcine Epidemic Diarrhea Viruses (PEDV) in Diarrheic Piglets and Clinically Healthy Adult Pigs from 2019 to 2022 in China

SIMPLE SUMMARY: Diarrhea causes huge economic losses in the global swine industry. Porcine epidemic diarrhea virus (PEDV) has been identified as a direct causative pathogen of diarrheic diseases in piglets. PEDV can infect all ages of pigs; however, little is known about the prevalence and evolution of PEDV in adult pigs. Here, we explored the genomic characteristics of PEDV in both diarrheic piglets and clinically healthy adult pigs from 2019 to 2022 in China. We found that PEDV variants are not only prevalent in diseased piglets but are also circulating in adult pigs. In addition, intra- and inter-subgroup recombinants were detected in adult pigs, indicating that adult pigs may also serve as the host of viral reservoirs for rapid PEDV evolution. This study provides up-to-date information on PEDV’s prevalence and evolution in both diseased piglets and healthy adult pigs in China. ABSTRACT: Porcine epidemic diarrhea virus (PEDV) is a major causative pathogen of diarrheic disease. In this study, the prevalence and evolution of PEDV was evaluated using intestinal samples collected from six provinces of China in 2019–2022. PEDV could not only be detected in diarrheic piglets but also in adult pigs without enteric diseases. The complete genomes of five temporal and geographical representative PEDV strains were determined. Genome-based phylogenetic analysis indicated that XJ1904-700 belongs to the G2-a subgroup, while the other strains are clustered within the S-INDEL subgroup. Recombination analyses supported that JSNJ2004-919 is an inter-subgroup recombinant from SD2014-like (G2-b), CHZ-2013-like (G2-b) and CV777-like (G1-b) isolates, while FJFZ2004-1017 is an intra-subgroup recombinant from XM1-2-like (S-INDEL) and LYG-2014-like (S-INDEL) isolates. Both JSNJ2004-919 and FJFZ2004-1017 were from adult pigs, providing evidence that adult pigs may also serve as the host of PEDV reservoirs for virus evolution. Overall, this study provides new insights into PEDV’s prevalence and evolution in both diseased piglets and clinically healthy adult pigs.