Recombination analysis of the complete genome of EV71. Similarity plot (upper panel) and bootscan analysis (lower panel) were conducted with SimPlot version 3.5.1 (Kimura distance model; window size, 500 bp; step, 20 bp) on a gapless nucleotide alignment, generated with ClustalX, with the genome sequence of the EV71 “genotype D” strain V10-2234054 as the query sequence. The yellow line denotes EV71 genotype A strain BrCr, the blue line denotes EV71 genotype B strain Nagoya, the red line denotes EV71 genotype C strain 4643-TW98, and the grey line denotes CVA16 prototype strain G-10. Arrows indicate the gene regions in which potential recombination breakpoints are located.
Yip et al. Virology Journal 2013 10:222 doi:10.1186/1743-422X-10-222