Spatiotemporal distribution and molecular characteristics of porcine diarrhea-associated viruses detected in Chinese pigs.xlsx

Recent large-scale outbreaks of diarrhea in pigs in China have been attributed to viral pathogens. The most frequently detected viruses in affected pigs include Porcine Epidemic Diarrhea Virus (PEDV), Porcine Rotavirus (PoRV), Transmissible Gastroenteritis Virus (TGEV), and Porcine Deltacoronavirus (PDCoV). To investigate the primary viral causes of diarrhea, we collected 1,328 fecal samples from 84 pig farms across 20 provinces. PEDV showed the highest positivity rate at 50.90% (684/1,328), with a positive farm rate of 66.67% (54/84). PoRVA had a positive rate of 33.80% (454/1,328) and a positive farm rate of 40.48% (34/84). TGEV and PDCoV exhibited lower positivity rates of 3.10% (41/1,328) and 6.00% (81/1,328), respectively, with positive farm rates of 14.29% (12/84) and 16.67% (14/84). Co-infections, primarily involving PEDV and PoRVA, accounted for 19.05% (253/1,328) of cases. Additionally, an analysis of the spatiotemporal distribution of viruses from 2022 to 2024 was conducted. This study also included phylogenetic and amino acid analyses focusing on PEDV and PoRVA. Among them, PEDV predominantly belongs to GⅡa and GⅡc, while PoRVA predominantly belongs to G4 and G9. We analyzed neutralizing epitopes and functional sites of the PEDV S protein, revealing that the SS2 and SS6 epitopes are relatively conserved, while various mutations were observed in other functional sites. Additionally, significant variability in the VP7 protein of PoRVA was noted among different genotypes, with several conserved amino acid sequences identified, including aa 106-115 (FLTKGWPTGS), aa 159-170 (ILNEWLCNPMDI), and aa 251-259 (KLGPRENVA), primarily located in the loop regions of the VP7 protein. The study investigates the epidemiology and spatiotemporal distribution of viral diarrhea in China from 2022 to 2024, which helps identify high-risk areas and peak periods, thereby providing guidance for epidemic early warning and resource allocation. Additionally, the study conducted a further analysis of the antigenic epitopes of PEDV and PoRVA, providing important information for vaccine design and the formulation of immunization strategies.