Additional file 2: Figure S1.

Comparative sequence analysis of the 2A-2B junction (A). Multiple alignment of the nucleotide sequences of EV71 “genotype D” strain V10-2234054, EV71 genotype B strain Nagoya and genotype C strain 4643-TW98. In EV71 genotype B and EV71 genotype C, only the nucleotides different from those in EV71 strain V10-2234054 are depicted. The nucleotides in EV71 genotype C that are the same as those in EV71 strain V10-2234054 but different from those in EV71 genotype B are highlighted in grey, and those in EV71 genotype B that are the same as those in V10-2234054 but different from those in EV71 genotype C are highlighted in black. Comparative sequence analysis of the 3C region (B). Multiple alignment of the nucleotide sequences of EV71 strain V10-2234054, EV71 genotype B strain Nagoya and CVA16 strain G-10. In EV71 genotype B and CVA16 strain G-10, only the nucleotides different from those in EV71 strain V10-2234054 are depicted. The nucleotides in EV71 genotype B that are the same as those in EV71 strain V10-2234054 but different from those in CVA16 strain G-10 are highlighted in grey, and those in CVA16 strain G-10 that are the same as those in V10-2234054 but different from those in EV71 genotype B are highlighted in black. The predicted breakpoint position by bootscan analysis is indicated by an arrow.

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Yip et al. Virology Journal 2013 10:222   doi:10.1186/1743-422X-10-222