Temporal evolutionary dynamics of porcine epidemic diarrhea virus in China from 2013 to 2023

Porcine epidemic diarrhea virus (PEDV) is the most dominant virus causing diarrhea in swine, and suckling piglets exhibit extremely high mortality. Continuous surveillance is essential for understanding the evolutionary trajectory of PEDV and for disease control. In this study, we analyzed the temporal evolutionary dynamics of PEDV in China from 2013 to 2023 by integrating newly sequenced genomic data with sequences available in public databases. Phylogenetic reconstruction, evolutionary rate estimation, selective pressure analysis, population dynamics modeling, and prediction of N-glycosylation sites in the Spike gene were performed. Our results revealed dynamic genotype turnover over the past decade, with the G2c subtype in China gradually became the dominant strain. The evolution rate of the S gene of the G2 genotype in China showed variation between time-defined periods. The dN/dS ratio for the Spike gene was consistently below 1 and exhibited a general declining trend. The dN/dS ratio exhibited a transient increase of 25.8% from its lowest point in late 2018 to a peak in 2021. Analysis of N-glycosylation sites showed that, during 2013-2023, the pattern characterized by reduced site diversity but increased site number underwent a shift. However, these observations are based on computational predictions and represent temporal trends. This study highlights the ongoing diversification of PEDV under changing epidemiological, offering a scientific basis for assessing its ongoing threat to the swine sector.