Integrated Genomic Analysis Uncovers the Evolutionary Landscape and Global Dissemination of Senecavirus A

Figures

• 

  Figure 1. Global sampling distribution and phylogenetic structure of SVA. (A) Geographic distribution and sampling density of SVA sequences. Darker shading represents countries with more submitted sequences and therefore greater sampling density. (B) Maximum-likelihood phylogeny of complete SVA genomes. Outer colored ranges indicate viral lineages, while inner colored nodes represent the countries of origin.

• 

  Figure 2. SplitsTree network and genome-wide mapping of recombination. (A) Phylogenetic network analysis reveals recombination events among SVA strains. Recombinant strains are indicated by their GenBank accession numbers, and nodes correspond to putative parental sequences. Intersecting boxes in the network represent conflicting phylogenetic signals, indicating potential recombination events among these sequences. (B) Genome-wide recombination patterns of SVA. Each horizontal bar corresponds to a complete genome, and colored segments indicate regions inferred to be derived from different parental lineages. Genome coordinates (nt) are shown along the x-axis, with the annotated genomic organization of SVA displayed at the bottom for reference.

• 

  Figure 3. Haplotype network and geographic distribution of the SVA 3AB gene. (A) Haplotype network of the SVA 3AB gene colored by country. Each node represents a distinct haplotype, with node size proportional to the number of sequences sharing that haplotype. Connections between nodes represent mutational steps, and node colors indicate the country of origin. (B) Global and country-level distribution of SVA 3AB haplotypes. The outer circular chart represents the distribution of haplotypes across different continents, with colors indicating different continents. The inner pie chart shows the distribution of haplotypes among different countries, with colors corresponding to different countries.

• 

  Figure 4. Purifying selection across SVA genes. (A) Scatter plot of negatively selected sites in SVA genes. In each plot, the y-axis represents the posterior probability that a site is under negative selection (dN/dS < 1), as inferred from sites consistently detected by three complementary methods (MEME, FEL, and FUBAR), and the x-axis represents the positions of negatively selected sites within each gene. (B) Relative positions of negatively selected sites across SVA genes. The x-axis represents the relative positions of negatively selected sites, and the y-axis corresponds to gene names. The color intensity of each point reflects the magnitude of the posterior probability.

• 

  Figure 5. Time-scaled phylogeny and effective population size dynamics of SVA. (A) Time-scaled phylogeny of SVA. Branch lengths are proportional to time, with the x-axis representing years. The tree highlights two major SVA lineages, and branch colors correspond to the countries of origin. (B) Bayesian skyline plot of SVA. Bayesian skyline analysis illustrating temporal changes in the effective population size of SVA. The y-axis represents the effective population size (Ne), and the x-axis represents time (years).

• 

  Figure 6. Phylogeographic reconstruction of SVA dissemination. Arrows indicate the direction of viral spread between countries or regions, with arrow thickness proportional to the posterior probability of the inferred transmission routes and arrow color reflecting the strength of support (Bayes factor).