Evidence of Spillover and Recombination Between Domestic Pigs and Wild Boars Provides New Insights into Porcine Circoviruses

Figures

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  Figure 1. Evolutionary analysis of PCV2 inferred in IQ-TREE by using the Maximum Likelihood method and the best-fit model GTR + F + R4 model (General Time Reversible model). The tree with the highest log likelihood (−15,347.224) is shown. The phylogenetic analysis was performed using the full PCV2 genome of 308 sequences, with model selection performed by ModelFinder Plus and branch support assessed with 2000 ultrafast bootstrap replicates and 2000 SH-aLRT replicates. Sequences marked with a star represent samples obtained in the present study. Only the bootstrap values higher than 70% are shown in the tree. The triangular diagram on the left side of the phylogenetic tree represents the quartet puzzling support topology obtained with TREE-PUZZLE for this dataset. The percentage of resolved quartets is 87.6% (corresponding to the sum of the three values at the triangle’s tips).

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  Figure 2. Auspice view of the PCV2 tree generated using the INSaFLU/Nextstrain pipeline and corresponding world map of the estimated transmission pathways. (A)—Phylogenetic tree used for phylogeographic analysis. Colors represent country of origin and branch length represent time; (B)—Map showing transmission lines portraying potential viral dispersion routes; (C)—Expanded view of the tree branch containing sequences PV753264, PV753265 and PV753267; (D)—Expanded view of the tree branch containing sequence PV753266.

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  Figure 3. Graphical outputs of recombination analyses performed in RDP4 concerning PCV2 sequences. (A) 3Seq, (B) Bootscan, and (C) BURT graphics illustrating the recombination event that originated the sequence PV753265. In the 3Seq graphic, the red line represents the Recombinant (PV753265), the green line the Major Parent (KX960917), and the blue line the Minor Parent (KT819170). In the Bootscan and BURT plots, the yellow line represents similarity between the Major and Minor Parents, the blue line between the Recombinant and the Major Parent, and the purple line between the Recombinant and the Minor Parent. The blue-shaded region (positions 1170–1325 nt) indicates the 155 nt segment excluded from analysis by all three methods. (D) Bootscan, (E) BURT, and (F) VisRD Occupancy graphics illustrating the recombinant event that originated the Recombinant sequence (MH465453). In the three graphics, the yellow line represents similarity between the Major (PV753265) and Minor Parents (KC515014), the blue line between the Recombinant and the Major Parent, and the purple line between the Recombinant and the Minor Parent.

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  Figure 4. Evolutionary analysis of PCV3 inferred in IQ-TREE by using the Maximum Likelihood method and TIM + F + R3 model (Transitional model). The tree with the highest log likelihood (–11387.853) is shown. The phylogenetic analysis was performed using the coding regions of the PCV3 genome (in the order Rep + ORF3 + Cap) of 239 sequences, with model selection performed by ModelFinder Plus and branch support assessed with 10,000 ultrafast bootstrap replicates (with NNI correction) and 10,000 SH-aLRT replicates. Sequences marked with a star represent samples obtained in the present study. Only the bootstrap values higher than 70% are shown in the tree. The triangular diagram on the left side of the phylogenetic tree represents the quartet puzzling support topology obtained with TREE-PUZZLE for this dataset (Rep + ORF3 + Cap dataset). The percentage of resolved quartets is 84.3% (corresponding to the sum of the three values at the triangle’s tips).

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  Figure 5. Auspice view of the PCV3 tree generated using the INSaFLU/Nextstrain pipeline and corresponding world map of the estimated transmission pathways. (A)—Phylogenetic tree used for phylogeographic analysis. Colors represent country of origin and branch length represent time; (B)—Map showing transmission lines portraying potential viral dispersion routes; (C)—Expanded view of the tree branch containing sequence OR479851; (D)—Expanded view of the tree branch containing sequence PV753268.

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  Figure 6. Root-to-tip regression analysis performed with TempEst. Gray dots represent sequences, plotted according to its genetic divergence from the inferred root of the tree (y-axis, substitutions per site) against its sampling date (x-axis, in years). The black line represents the best-fit regression of root-to-tip distances over time. In the PCV2 graphic (A) the line’s slope is 4.67 × 10−4 substitutions/site/year, the correlation coefficient is 0.11 and the coefficient of determination R2 equals 0.012. In the PCV3 graphic (B) the line’s slope is 1.21 × 10−4 substitutions/site/year, the correlation coefficient is 0.13 and the coefficient of determination R2 equals 0.016.