Fig. 5

Evolutionary relationships of HPV E6/E7 sequences derived from LSIL and HSIL samples. a Prototypical HPV genome based on the genetic information of HPV-16. The contiguous E6 (477 bp) and E7 (297 bp) gene segment of each sample was the target used for sequencing, genotyping, and phylogenetic analysis. b Phylogenetic tree of 28 representative E6/E7 nucleotide sequences (one from each genotype) revealed two distinct clades: high-risk [black bracket] and low-risk [green bracket] that cluster respective species (α-5, 6, 7, 9, 11) and (α-3, 8, 10, 13, 15) within the α-genus. The evolutionary distances between species also correlate with the level of IARC-defined carcinogenicity. This finding is consistent with phylogenetic trees constructed traditionally from L1 ORF sequences [8]. The tree was inferred by the Neighbor-Joining method with the Maximum Composite Likelihood nucleotide substitution model using MEGA6 [29]. The scale bar indicates nucleotide substitutions per site. The bootstrap values are displayed for the primary and secondary nodes. The full tree is shown in Additional file 5: Figure S3. Carc, carcinogenic; Not Class, not classifiable; Poss Carc, possibly carcinogenic; Prob Not Carc, probably not carcinogenic