Molecular Variation in Porcine Circovirus Type 2 in Jalisco, Mexico, and Its Potential Impact on Vaccine Efficacy

Background/Objectives: Porcine circovirus type 2 (PCV2) remains a major viral agent in pig production worldwide due to its association with economically relevant diseases and productivity losses. Nine genotypes (PCV2a–PCV2i) have been reported, with successive genotype shifts characterized by the historical predominance of PCV2a, the expansion of PCV2b, and the emergence of PCV2d as the predominant genotype in several swine-producing countries. The aim of this study was to characterize the ORF2 gene of PCV2 circulating in Jalisco, Mexico, to provide updated information for regional surveillance and control strategies. Methods: Samples were collected from 80 pig farms located in four regions of Jalisco with different pig density levels and production systems. PCV2-positive samples were subjected to ORF2 amplification and sequencing. Genotype assignment, phylogenetic analysis, and in silico recombination screening using multiple detection methods were performed. All sequences were deposited in GenBank. Results: A total of 70 ORF2-PCV2 sequences were obtained and assigned to two genotypes: PCV2d (51/70, 72.9%) and PCV2a (19/70, 27.1%). The sequences were submitted to GenBank under accession numbers PV235521–PV235590. Recombination analysis identified seven recombinant sequences, and unusual ORF2 extensions were detected in some sequences, evidencing the presence of genetic variants circulating in the region. Conclusions: These findings confirm the predominance of PCV2d in Jalisco while highlighting the continued circulation of PCV2a. The coexistence of both genotypes, together with recombinant sequences and ORF2 extensions, indicates ongoing PCV2 genetic diversification in the region. Continuous molecular surveillance remains essential to monitor viral evolution, support genotype-informed control strategies, and strengthen swine health programs.