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

Figures

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  Figure 1. Visualization of the top 10 recombination breakpoint hotspots in PCV2 genomes. The gray bar represents the full PCV2 genome (1767 nt). The blue and green arrows indicate the positions and directions of ORF1 and ORF2, respectively. Orange bars represent the top 10 most frequently identified breakpoint positions, as determined from 27 recombinant sequences. Breakpoints are concentrated in the region between ORF1 and ORF2, suggesting a possible recombination hotspot in the intergenic junction.

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  Figure 2. The bootscanning analysis revealed the recombination event of 334TH2023. The recombination breakpoints were identified at nucleotide positions 711 and 1629. Yellow and green shades highlighted the recombination regions.

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  Figure 3. The maximum likelihood phylogenetic tree of 2712 complete genomes sequences (1766–1788 bp) of PCV2 sequences circulating in Asia from 2007 to 2024. Recombinant sequences identified through RDP4 were excluded prior to tree reconstruction. The colored strips around the outer circle represent sequences originating from different countries, as indicated by the labels in the legend. The colors of the internal branches denote the grouping of PCV2 genotypes: blue branches represent PCV2b, purple branches represent PCV2a, green branches represent PCV2h, and red branches represent PCV2d. Bootstrap support values greater than 70 are indicated by gray circles at the corresponding nodes.

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  Figure 4. The time‐scaled phylogenetic tree of ORF2 (702 bp) of 286 PCV2 sequence circulated in Thailand during 2007–2024. This time‐scaled tree depicts the genetic relationships of PCV2 strains sampled over time, grouped into PCV2a, PCV2b, and PCV2d. PCV2d is further divided into three clades based on amino acids 133–136: ATAL, ANAL, and HDAM. The colors of the branches and nodes represent the sampling years, as indicated in the legend.

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  Figure 5. Bayesian skyride plots for complete capsid gene of PCV2 population in Thailand. The x‐axis showed the years before 2024. The y‐axis showed effective viral population size. The thicker bold line represents the median estimate of the effective number of infections over time, while the thinner blue lines depict the 95% HPD interval, showing the upper and lower bounds.

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  Figure 7. T‐cell epitopes of the PCV2 capsid protein. The figure illustrates the sequence alignment of 20 representative capsid proteins from PCV2a, PCV2b, and three clades of PCV2d. Yellow highlights indicate conserved mutation locations, while blue rectangles mark the positions of MHC class I T‐cell epitopes, and red rectangles indicate the positions of MHC class II T‐cell epitopes.

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