The Emergence and Evolution of Porcine Sapelovirus: Insights from Genomic Surveillance and Recombination Analysis in China

Figures

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  Figure 1. Epidemiological survey of Porcine Sapelovirus (PSV) in China. (A) Geographic distribution of PSV infection rates across Chinese provinces based on the available literature. (B) Trends in PSV prevalence across different sampling periods. (C) PSV infection rates stratified by pig age. (D) Comparison of PSV prevalence between herds with healthy pigs and herds with diarrhea.

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  Figure 2. Profile of PSV co-infections in China. (A) Comparison of trends in single infections and co-infections. (B) Annual analysis of the PSV infection patterns. (C) Analysis of the PSV co-infection combinations.

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  Figure 3. Genetic relatedness analysis of epidemic PSV strains in China. (A) Nucleotide identity heatmap. Seventy-four Chinese PSV sequences and seven foreign strains were obtained from GenBank (https://www.ncbi.nlm.nih.gov/) (accessed on 9 September 2025). Sequence alignment and pairwise identity analyses were performed using the DNASTER Lasergene (7.1). The percentage identity is shown using the color scale on the right. (B) Phylogenetic analysis. It was reconstructed using full-length nucleotide sequences with the Neighbor-Joining method in MEGA X. The Kimura 2-parameter model and 1000 bootstrap replicates were used. Strains from the same region are marked with the same font color, and foreign strains are indicated by different background colors.

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  Figure 4. Prediction and analysis of recombination trends in the PSV. Full-length genome sequences from 74 Chinese PSV isolates were analyzed for recombination using the RDP 4.0 software. The proportions of recombination events are shown in (A,B). Significant recombination breakpoints identified from these events are summarized and shown in a scatter plot (top panel, (B)). Twenty-one high-confidence recombination events, consistently detected by seven algorithms (RDP, GENECONV, BootScan, MaxChi, Chimaera, SiScan, and 3Seq), were selected for detailed analysis. Their recombination maps are shown in the bottom panel, aligned with the PSV genome schematic and the breakpoint scatter plot for comparison. The dashed frame indicates a region with dense clustering of recombination breakpoints.

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  Figure 5. Temporal origin and evolutionary analysis of PSV. A time-scaled phylogenetic tree was reconstructed using MEGA X software with the RelTime with Dated Tips method based on the full-length genome sequences of 54 viruses, including 42 porcine sapeloviruses, nine porcine enteroviruses (PEV), two marmot sapeloviruses, and one avian sapelovirus. The sampling year for each sequence was used as a calibration constraint. The estimated divergence time for each major branch is shown.