Emergence of EV-71 subgenotypes by recombination with other HEV-A viruses. Similarity plot analyses were performed using the full genome sequence of all EV-71 genotypes and subgenotypes. The sequences were queried against all other available HEV-A viruses. The nucleotide sequence of BrCr, genotype A (a), nucleotide sequence of MS87, subgenotype B2 (b), consensus nucleotide sequence of subgenotype B3 (c), consensus nucleotide sequence of subgenotype B4 (d), consensus nucleotide sequence of subgenotype C2 (e) SHZH98, subgenotype C4 (f) and SHZH03, subgenotype C4 (g) were used in the similarity plot analyses. Results from the bootscan analyses indicate the likelihood of clustering of subgenotype B2 isolate, MS87 (h), subgenotype B4 (i) and subgenotype C2 (j) isolates with their respective potential parental isolates. A sliding window of 1000 nucleotides was moved in increments of 20 nucleotides at a time. All gaps were stripped and the sequences were corrected for multiple substitutions. A transition to tranversion ratio of ten was used and 50% consensus files were used to exclude the poorly conserved sites. The subgenotype C2 isolates (k) were also queried against other HEV-A viruses using a window size of 400 nucleotides in increments of 20 nucleotides per slide. Bootstrap values of > 70% were used to indicate robust support for the tree topology . The different HEV-A viruses and EV-71 genotypes are represented by the different line colors.