Genetic and Evolutionary Analysis of Porcine Kobuvirus in Guangxi Province, Southern China, Between 2021 and 2025

Kobuvirus is a new genus of viruses in the <i>Picornaviridae</i> family causing diarrhea in animals. Porcine kobuvirus (PKV) is an important pathogen with a high rate of infection in pig herds. In this study, a total of 10,990 fecal swabs and tissue samples were collected from different areas of Guangxi province in southern China during 2021-2025 and then tested for PKV using RT-qPCR. The results showed a 19.19% (2109/10,990) PKV positivity rate. Sixty-two PKV-positive samples, which were selected according to sampling regions, sampling seasons, and detection Ct values, were used for PCR amplification and gene sequencing. A sequence comparison showed that the nucleotide and amino acid identities of <i>VP1</i>, <i>2B</i>, and <i>3D</i> genes were 78.6-99.5% and 83.5-100%, 77.7-99.8% and 80.9-100%, and 90.9-99.8% and 94.9-99.9%, respectively, indicating that the <i>3D</i> gene was more conserved than the <i>VP1</i> and <i>2B</i> genes. The phylogenetic trees based on these three genes revealed that the PKV <i>VP1</i> gene sequences from different countries could be classified into two groups (Groups I and II), and the PKV <i>VP1</i> gene sequences obtained from Guangxi province were distributed in Groups I and II and formed independent clades. The <i>2B</i> and <i>3D</i> gene sequences could also be classified into two groups (Groups I and II). Bayesian analysis indicated a state of population growth for PKV strains from the time of their discovery until 2009, at which point it began to decline. Amino acid sequence analysis of the <i>VP1</i> gene identified mutations and insertions in the obtained PKV strains. Recombinant analysis showed that no recombinant event was found in the <i>VP1</i>, <i>2B</i>, and <i>3D</i> genes of the obtained strains. The results indicated the geographically specific inheritance and variation in PKV, provided more information on the prevalence and genetic evolution of PKV in Guangxi province, Southern China, and emphasized the importance of regularly monitoring genetic variation in PKV for better comprehension of PKV.