Evaluation of VP4-VP2 sequencing for molecular typing of human enteroviruses

Figures

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  Fig 1. Relationship between 249 EV and RV prototypes based on the VP4-pVP2 amino acid sequence. The assigned species of Enterovirus alphacoxsackie, E. betacoxsackie, E. coxsackiepol, E. deconjuncti, E. alpharhino, E. betarhino, and E. cerhino prototypes are labeled EV-A, -B, -C, -D, RV-A, -B, and -C, respectively. (A) Phylogenetic analysis. Sequences were aligned using the MUSCLE algorithm. The phylogenetic tree was constructed using the neighbor-joining method with Poisson correction. (B) (left) Matrix of pairwise identity comparison among 249 prototypes. Identity percent is indicated using color-coded boxes; (right) Mean, min, and max values of identity percent for inter- and intra-species comparisons.

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  Fig 2. Histogram of pairwise identity frequency based on the VP4-pVP2 amino acid sequence. (A) Comparisons among total EV prototypes. (B) Intra-species comparisons for EVs and RVs are separately presented (EV-A, -B, -C, -D, RV-A, -B, and -C). The proposed 95% threshold is indicated as a dotted line. EV pairs showing >95% identity are listed in Table 1.

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  Fig 3. Distribution of identities between prototype and matched strains. Box plots represent the identity percent between the indicated prototypes as a query in the blastp analysis and the top 100 matched references with assigned types. (A) E. alphacoxsackie, (B) E. betacoxsackie, (C) E. coxsackiepol, and (D) E. deconjuncti. Untyped or mislabeled references were excluded from the blastp analysis results.