Molecular Epidemiological Investigation and Viral Isolation of Porcine Rotavirus in Southwest China During 2024–2025

In 2023, the detection rate of porcine rotavirus (PoRV) surpassed that of porcine epidemic diarrhea virus (PEDV) for the first time, establishing PoRV as the predominant pathogen responsible for viral diarrhea in pigs. To systematically investigate the epidemiology and molecular characteristics of PoRV in Southwest China, a total of 196 diarrheal clinical samples were collected from 29 large-scale pig farms across the region during 2024-2025. RT-qPCR results revealed a high PoRV positivity rate of 57.14% (112/196) with group A porcine rotavirus (PoRVA) being the most prevalent at 46.43%, representing the predominant group. Genotyping and phylogenetic analysis of the VP4 and VP7 genes indicated that the P genotype P[13] was most prevalent (77.78%, 21/27), while the major G genotypes were G4 (39.28%) and G9 (35.71%). The most common G/P combinations were G9P[13] and G4P[13]. Furthermore, a PoRV strain was successfully isolated and identified through whole-genome sequencing, indirect immunofluorescence assay (IFA), and transmission electron microscopy (TEM). The isolate was designated RVA/Pig-wt/SCLS-JW/2024/G1P[7], with a whole-genome constellation of G1-P[7]-I5-R1-C1-M1-A8-N1-T1-E1-H1. The structural proteins VP1-4 and VP6-7, along with nonstructural genes NSP1 and NSP5, shared high sequence identity with porcine strains, whereas the nonstructural genes NSP2-NSP4 clustered more closely with human rotaviruses. These findings indicate a higher prevalence of PoRV in southwestern China compared to other regions; the dominant circulating genotypes have shifted to G9 and G4; the isolated G1P[7] strain is relatively rare in China and might be a genetic recombinant of human and porcine rotaviruses. This study provides valuable data and theoretical support for understanding the current epidemiology of PoRV, and facilitates vaccine development and the formulation of prevention and control strategies.