Host-driven evolution of PCV2: insights into genetic diversity and adaptation

Figure 1. Structured coalescent-based phylogenetic tree of PCV-2a, b, d and abd dataset. Branch colors, as from the legend, mark the inferred animal category where the ancestral strain was circulating, while node size represents the posterior confidence of the inference. The network on the upper left of each panel depicts the migration rate between animal categories. Arrows and circle sizes are proportional to the inferred migration rate and population size, respectively.

Figure 2. In the upper panel, the amino acid positions under statistically significant diversifying selection, as identified by MEME, are mapped onto the tertiary structure of PCV2 capsid protein. Different figures are used to represent the various datasets analyzed. Host species (or combinations of hosts) are color-coded. In the lower panel, a summary of the distribution of the same amino acid positions along the Cap sequences is presented, alongside the epitopic regions identified in previous experimental studies (36–41).

Figure 3. Depiction of the contrast-FEL results. Sites with a higher non-synonymous substitution rate (β) in wild boars and domestic pigs are depicted in blue and red, respectively. Both statistically significant and non-significant sites are reported.

Figure 4. In the upper panel, the amino acid positions under statistically significant directional selection, as identified by FADE, are mapped onto the tertiary structure of PCV2 capsid protein. Different figures are used to represent the various datasets analyzed. In the lower panel, a summary of the distribution of the same amino acid positions along the Cap sequences is presented, alongside the epitopic regions identified in previous experimental studies (36–41).

Figure 5. In the left panel, sites with a tendency toward radical changes in amino acid charge, as detected using PRIME in the PCV2abd dataset, are depicted in red. The pentameric and trimeric organization of the PCV2 capsid structure are highlighted in darker gray. In the right panel, positions reported by Dhindwal et al., 2019 (42) as involved in heparan sulfate binding are colored in blue. Dotted red circles emphasize regions identified by Ouyang et al. (2023) (43) as affected by charge modifications, while blue circles highlight additional areas where a comparable distribution of heparan sulfate binding sites and sites under selective pressure were observed in the present study.

Figure 6. In the left panel, sites with a tendency toward radical changes in amino acid charge, as detected using PRIME in the PCV2d dataset, are depicted in red. The pentameric and trimeric organization of the PCV2 capsid structure are highlighted in darker gray. In the right panel, positions reported by Dhindwal et al., 2019 (42) as involved in heparan sulfate binding are colored in blue. Dotted red circles emphasize regions identified by Ouyang et al. (2023) (43) as affected by charge modifications, while blue circles highlight additional areas where a comparable distribution of heparan sulfate binding sites and sites under selective pressure were observed in the present study.