Alpha-7 phylogenetic tree showing representative types and variant lineages.

<p>A maximum likelihood (ML) tree was constructed using RAxML MPI v 7.2.8.27 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072565#B42" target="_blank">42</a>] and PhyML MPI v 1.4.3 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072565#B43" target="_blank">43</a>] inferred from the global alignment of complete circular genome nucleotide sequences linearized at the first ATG of the E1 ORF. Numbers on or near branches indicate support indices < 100% by RAxML and PhyML, respectively. The shaded areas represent groupings of lineages and sublineages of HPV18, HPV39, HPV45, HPV59, HPV68 and HPV70; the prototype sequences of HPV85 and HPV97 are also included as indicated, although no variant lineages are distinguished due to the limited number of isolates of these types. The length of broken and solid lines represent distance between clades, although the number of changes is different for these two lines, as indicated in the upper left corner of the figure. HPV51, an alpha-5 type, was set as the outgroup.