Genetic evolution and identification of an unclassified cluster of porcine circovirus type 2 in southern China.

Porcine Circovirus type 2 (PCV2) is an important pathogen that threatens China's swine industry, and the continuous mutation and evolution of its genotypes pose serious challenges for disease prevention and control. Although southern China is a crucial production area for pig farming, systematic analyses of the genetic and evolutionary characteristics of the circulating PCV2 strains in this region are lacking. To elucidate the epidemiological status and biological characteristics of PCV2 variants in southern China, we analyzed 339 full-genome sequences of PCV2 isolates collected from the region between 2015 and 2024, along with 38 reference strains. Using bioinformatics software, we constructed a phylogenetic tree and performed nucleotide homology alignment, amino acid sequence alignment, selection pressure analysis, and antigenic epitope prediction to providing the first comprehensive overview of the genetic evolution of PCV2 in this region over the past decade. Our results demonstrate that the PCV2d genotype predominated at 56.5%, whereas PCV2b at 23.9% and PCV2a at 8.0% exhibited subdominant distributions, indicative of the co-circulation of multiple genotypes. The ORF2 gene is primarily under purifying selection; however, signals of genotype-specific positive selection are also present. Key amino acid variation sites are mainly located on the surface of the capsid protein and within antigenic epitope regions, suggesting that these sites may be subjected to host immune selection pressure. The predictions of B-cell epitopes indicate that the amino acid regions at positions 175-180 are highly conserved, providing targets for subunit vaccine design. Notably, we identified an independent lineage comprising two strains, which occupies a unique phylogenetic position and exhibits a specific amino acid mutation pattern, potentially representing an unclassified genetic cluster of PCV2. Furthermore, this study indicated that PCV2 in southern China exhibits characteristics of both genotype turnover and polymorphism. Persistent variation in the ORF2 gene drives viral evolution, and the discovery of the unclassified genetic cluster further enhances our understanding of the genetic diversity of PCV2, providing an important theoretical basis for formulating targeted prevention and control strategies as well as vaccine updates.