The Decade of Porcine Circovirus Type 2 (PCV2) in Thailand: Phylodynamic and Molecular Epidemiology

Porcine circovirus type 2 (PCV2) is a major swine pathogen causing significant economic losses in the swine industry worldwide. Continual monitoring of genetic and antigenic diversity is essential for the early detection of emerging variants. This study investigates the evolutionary dynamics and genetic variation of PCV2 circulating in Thailand and across Asia from 2007 to 2024, using integrated phylogenetic and phylodynamic analyses. Analysis of 2739 PCV2 genomes, after excluding 0.99% recombinant strains, revealed four main groups circulating in Asia, with PCV2d as the predominant genotype. PCV2d has diversified into several distinct clades, including a recently identified variant with the ¹³³HDAM¹³⁶ amino acid motif, which likely originated from earlier variants, the ¹³³ANAL¹³⁶ and ¹³³ATAL¹³⁶ motifs. Recombination analysis detected intragenotypic recombination events within PCV2d strains circulating in Thailand, emphasizing the role of genetic recombination in driving the evolutionary changes of the virus. Phylodynamic analysis demonstrated significant fluctuations in the virus population size, correlating with changes in genotype dominance over time. Selective pressure analysis identified positively selected sites in the capsid protein (codons 63, 131, 134, 169, and 190), indicating ongoing adaptation under host immune pressures. Structural modeling and epitope analyses revealed mutations affecting antigenic sites and immune recognition, suggesting concerns for vaccine efficacy. This integrated approach enhances our understanding of PCV2 evolution, informing strategies for effective vaccine development and disease control.