A novel subgenotype C6 Enterovirus A71 originating from the recombination between subgenotypes C4 and C2 strains in mainland China

Figures

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  Figure 1. Phylogenetic tree based on the VP1 sequences of EV-A71. The evolutionary tree was constructed using the maximum likelihood method with the General Time Reversible (GTR) model by MEGAX. Bootstrap values were calculated by 1000 replicates. Bootstrap values lower than 60% are hidden. The branch of subgenotype C4 is compressed to save space. The solid square (black filled square) indicates the new subgenotype C6 EV-A71 strain DL71. CVA16 G-10 was used as the out-group strain. The scale bar indicates the number of nucleotide substitutions per site.

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  Figure 2. Phylogenetic trees based on the complete genomes and individual genes of DL71 and EV-A71 reference strains. The evolutionary trees based on (a) the complete genomes and individual genes (b) 5′UTR, (c) VP4, (d) VP2, (e) VP3, (f) VP1, (g) 2A, (h) 2B, (i) 2C, (j) 3A, (k) 3B, (l) 3C, (m) 3D and (n) 3′UTR were constructed using the maximum likelihood method with the GTR model by MEGAX. Bootstrap values lower than 60% are hidden. DL71 is labeled with a solid square (black filled square). The asterisk (*) indicates that DL71 is located within the branch of subgenotype C4 in the phylogenetic trees based on (d) VP2, (e) VP3, (j) 3A, (k) 3B, and (l) 3C.

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  Figure 3. Recombination analyses of DL71. (a) Graphical representation of EV-A71 genome. (b) A schematic map of recombination within DL71 genome. DL71 genome is shown as a red rectangle. The backbone of DL71 is derived from the major parent (green rectangles), while other genetic components of DL71 is derived from the minor parent (brown rectangles). (c) The plot display of 9 recombination events in DL71 genome identified by RDP4. (d) The genome of DL71 was used as the query sequence in the Similarity plot analysis. (e) The genome of DL71 was used as the query sequence in the BootScan analysis. The vertical red line indicates the breakpoint regions.

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  Figure 4. Phylogenetic trees based on the non-recombination regions of DL71. The regions (a) 1–309 bp, (b) 608–837 bp, (c) 1141–2329 bp, (d) 2701–2948 bp, (e) 3297–3685 bp, (f) 4039–4365 bp, (g) 4668–5813 bp, (h) 6187–6553 bp, and (i) 6915–7215 bp of DL71 and other reference strains were used to construct the phylogenetic trees by the maximum likelihood method with 1000 bootstrap replicates. The recombinant strain DL71 is labeled with a solid square (black filled square), the major parental strain with a solid regular triangle (black filled upward triangle), and the minor parental strain with a solid inverted triangle (black filled downward triangle).

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  Figure 5. Phylogenetic trees based on the recombination regions of DL71. The regions (a) 310–607 bp, (b) 838–1140 bp, (c) 2330–2700 bp, (d) 2949–3296 bp, (e) 3686–4038 bp, (f) 4366–4667 bp, (g) 5814–6186 bp, (h) 6554–6914 bp, and (i) 7216–7460 bp of DL71 and other reference strains were used to construct the phylogenetic trees by the maximum likelihood method with 1000 bootstrap replicates. The recombinant strain DL71, the major parental strain and the minor parental strain are indicated with “black filled square”, “black filled upward triangle” and “black filled downward triangle”, respectively.