Genetic Diversity and Evolution of Porcine Rotavirus Species A in Guangxi Province, Southern China, Between 2022 and 2025

Rotaviruses (RVs) are important pathogens which induce gastroenteritis in different kinds of animals, including mammals and birds. Rotaviruses are divided into nine species (RVA-RVD and RVF-RVJ), and RVA-RVC and RVH can infect both humans and pigs. It is vital to understand the genetic diversity and evolution of porcine rotavirus (PoRV) for effective prevention and control of this disease. In this study, 5320 intestinal tissue samples and fecal swabs were collected from different pig farms in Guangxi Province, southern China, from 2022 to 2025. These samples were tested for PoRV species A (PoRVA), PoRVB, PoRVC, and PoRVH using the multiplex RT-qPCR. The positive samples of PoRVA were further selected to amplify and analyze the VP4, VP6, and VP7 gene sequences. The phylogenetic trees were constructed based on the PoRVA VP4, VP6, and VP7 gene sequences. Bayesian time-dynamic analysis and recombination analysis were performed for the PoRVA VP4 gene. The results indicated that the PoRVA, PoRVB, PoRVC, and PoRVH positivity rates were 16.92% (900/5320), 0.51% (27/5320), 12.71% (676/5320), and 6.22% (331/5320), respectively. Fifty-two VP4, VP6, and VP7 gene sequences were obtained from the 52 selected PoRVA-positive clinical samples. The nucleotide and amino acid identity analysis of the obtained PoRVA VP4, VP6, and VP7 genes indicated that the genetic diversity of the VP4 gene was higher than that of the VP6 and VP7 genes. The phylogenetic trees based on the VP4, VP6, and VP7 genes revealed that the predominant strains of PoRVA in Guangxi Province were the G9P[13]I5 genotype. Bayesian analysis indicated that the population size of PoRVA kept steady with no significant expansion from its discovery in the 1970s to approximately 2016, then exhibited gradual growth. Sequence analysis of the PoRVA VP4 gene revealed substitutions and recombination in the PoRVA strains, and one strain was derived from recombination of a porcine-originating strain and a human-originating strain. This study provided useful information on the molecular characteristics and genetic diversity of PoRVA and supplied important clues for in-depth research on the cross-species transmission of PoRVA.