Table 1.
Primers used to amplify VP1 and 3Dpol regions of the Coxsackievirus B1.
Table 2.
Background data for each sequence used in this work.
Fig 1.
Maximum clade credibility (MCC) phylogeny of coxsackievirus B1 VP1.
The full VP1 region was compared in 77 strains with prototype coxsackievirus B3 strains used as the outgroup. The tree shows the proportional relationship between branch length and time, with the time scale in years given in the bottom line. The dashed line in the time scale is the scale bar for nucleotide genetic distance. The support values for key nodes are indicated by bootstrap (BS) or posterior probability (PP) according to neighbor-joining (NJ), maximum likelihood (ML), or BEAST method and are indicated as BS-NJ/BS-ML/PP-BMCMC. Each branch thickness is also indicated as PP-BEAST. Genotypes, clusters and nucleotide/amino acid similarity within genotype are shown on the right. For each strain name, VP1 genotypes are differentiated by color (Genotype I: purple, Genotype II: green, Genotype III: orange, Genotype IV: blue), and 3Dpol genotypes are differentiated by shading (Genotype A: blue, Genotype B: green, Genotype C: orange).
Fig 2.
Maximum clade credibility (MCC) tree summarizing the inferred geophylogeny of 76 coxsackievirus B1 VP1 sequences.
Branch thickness indicates the location probability and is colored to indicate the most probable location. The support values for key nodes are indicated by posterior probability values. The time scale in years is given in the bottom line. The dashed line above the time scale is the scale bar for genetic distance. For each strain name, VP1 genotypes are differentiated by color (Genotype I: purple, Genotype II: green, Genotype III: orange, Genotype IV: blue), and 3Dpol genotypes are differentiated by shading (Genotype A: blue, Genotype B: green, Genotype C: orange).
Fig 3.
Effect of VP1 genetic diversity on virus population.
A Bayesian Skyline Plot (BSP) was used to plot changes in the effective population size over time for coxsackievirus B1 and for subgenotypes II and IV. The x-axis is the time scale (years), and the y-axis is the logarithmic scale (where Ne is the effective population size and t is the generation time). The thick solid line indicates the median estimates, and the grey area shows the 95% highest probability density (HPD).
Fig 4.
Phylogenies of enterovirus B by 3Dpol region.
The RNA polymerase 3Dpol regions (nt 6682–7092) of 133 strains were compared. Branch thickness indicates the support values. The dashed line below is the scale bar for nucleotide genetic distance. (A) Maximum clade credibility tree. The support values for key nodes are indicated by bootstrap (BS) or posterior probability (PP) according to neighbor-joining (NJ), maximum likelihood (ML), or BEAST method and are indicated as BS-NJ/BS-ML/PP-BMCMC. The time scale in years is given in the bottom line. Genotypes and nucleotide/amino acid similarity within genotype are shown on the right. For each strain name, 3Dpol genotypes are differentiated by shading (Genotype A: blue, Genotype B: green, Genotype C: orange), and VP1 genotypes are differentiated by color (Genotype I: purple, Genotype II: green, Genotype III: orange, Genotype IV: blue). (B) Maximum likelihood tree. (C) Neighbor-joining tree. Branch is colored to indicate the genotype.
Fig 5.
Distribution of 3Dpol genotypes of enterovirus B by isolation year and location.
Timelines (horizontal lines) for each sampling sequence in each serotype (left vertical lines). Isolation locations for Genotypes A (left), B (middle), and C (right) are differentiated by color. The isolation countries are colored as shown on the right.
Fig 6.
Analysis of recombination events in 76 VP1 coxsackievirus B1 and 133 3Dpol enterovirus B sequences.
The left figures (A–C) show the results for the VP1 region while the right figures (D–F) show the results for the 3Dpol region. The relationships between query strains (potential recombination strains) and reference strains (major parent, minor parent, or non-donor strains) are depicted by phylogenetic distance and genetic distance in bootscan plots (A, D) and SimPlots (B, E), respectively. In both plots, which were generated with the Simplot program, potential recombination breakpoints defined where sequence crossover occurs. (C, F) Phylogenetic comparison. The trees of the fragments flanking the breakpoint showed that the recombinant strains were located in different cluster with high bootstrap value. Strain names are color coded as follows: potential recombination strains (black), major donor strains (red), minor donor strains (blue), and non-donor strain(s) (green).