Genetic Variation Analysis of Porcine Circovirus Type 4 in South China in 2019 to 2021

Figures

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  Figure 1. Geographical distribution map of the domestic PCV4 strains collected (The different colors in the figure have no special meaning, only to distinguish between the adjacent regions). The abbreviation indicates the name of the region, and the numbers indicate the number of PCV4 strains collected in China (41).

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  Figure 2. Phylogenetic tree of the 50 PCV strains. The red triangle is the representative strain of cluster 1 (PCV4a-1); the green triangle is the representative strain of cluster 2 (PCV4a-2); the blue circle is the PCV4 strain isolated from raccoon dogs; the black circle is the PCV4 strain isolated from foxes; the black triangle represents the Korean PCV4 strain; the red square is the PCV4 representative strain.

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  Figure 3. Comparative amino acid analysis of the Cap proteins of PCV4. Strain MK986820 was the standard strain, and three strains annotated with a pentagram were the representative sequences screened in this study. Residues are indicated by dots if fully consistent.

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  Figure 4. Prediction results for the B-cell epitopes, secondary structure, and surface position of some species’ genes. Epitope: Position above the epitope threshold. Prediction: Future protein sequences are shown in an orange gradient, indicating the BepiPred-2.0 prediction. Structure: helix (H-pink probability gradient), prediction table (E-blue probability gradient), and coil (C-orange probability gradient). Surface: buried (B)/exposure (E) and orange gradient illustrate the predicted relative surface accessibility. Three representative domestic strains are shown.

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  Figure 5. Identification of the recombination events. MT882344 is the most representative recombinant, and it is reconstituted between MT193105 and NC_055580. The window size is 30, the y axis indicates the base position, the x-axis indicates the position of the information site, and the left and right bounds of the pink box indicate the breakpoint position.