Fig. 3

A phylogenetic tree of the L1 region (~ 450 bp) covering nucleotide positions (5722-6162) numbered to NC001526 HPV-16 reference genome) used to assign HPV types to sequences in this study. Trees were constructed using BEAST method. Strains from Botswana sequenced in the present study are shown in the tree (left), while Kenya sequences are shown in the tree (right). Reference strains are designated by their accession number. All positions with less than 95% site coverage were eliminated, i.e., fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position (partial deletion option). There were a total of 339 positions in the final dataset. Evolutionary analyses were conducted in BEAST v1.2