Figure 1.
Alpha-7 phylogenetic tree showing representative types and variant lineages.
A maximum likelihood (ML) tree was constructed using RAxML MPI v 7.2.8.27 [42] and PhyML MPI v 1.4.3 [43] 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.
Figure 2.
HPV18 tree topology and pairwise comparisons of individual complete genomes.
Phylogenetic trees were inferred from global alignment of complete genome nucleotide sequences (the other alpha-7 HPV reference prototypes were set as the outgroup). Numbers on or near branches indicate support indices in the following order: maximum likelihood (ML) bootstrap percentages using RAxML MPI v 7.2.8.27 [42] and PhyML MPI v 1.4.3 [43], and Bayesian credibility value percentage using MrBayes v 3.1.2 [44]. An asterisk (*) indicates 100% agreement between methods. “NA” indicates disagreement between a method and the reference RAxML tree at a given node. Thus, one tree is shown, but three different methods of tree construction were used to estimate the support of the provided tree, as explained above. Distinct variant lineages (i.e., termed A, B, and C) are classified according to the topology and nucleotide sequence differences from > 1% to < 10%; distinct sublineages (e.g., termed A1 and A2) were also inferred from the tree topology and nucleotide sequence differences in the > 0.5% to < 1% range. The percent nucleotide differences for each isolate compared to all other isolates (i.e., 1 x 1 comparisons) are shown in the panel to the right of the phylogeny. Values for each comparison of a given isolate are connected by lines and the comparison to self is indicated by the 0% difference point. Symbols and colored lines are used to distinguish each isolate.
Figure 3.
HPV39 variant tree topology and pairwise comparisons of individual complete genomes.
The phylogenetic tree was constructed as described in Figure 2. Distinct variant lineages and sublineages were determined as described in Figure 2. The percent nucleotide sequence differences are shown in the panel to the right of the phylogenetic tree as described in Figure 2.
Figure 4.
HPV45 variant tree topology and pairwise comparisons of individual complete genomes.
The phylogenetic tree was constructed as described in Figure 2. Distinct variant lineages and sublineages were determined as described in Figure 2. The percent nucleotide sequence differences are shown in the panel to the right of the phylogenetic tree as described in Figure 2.
Figure 5.
HPV59 variant tree topology and pairwise comparisons of individual complete genomes.
The phylogenetic tree was constructed as described in Figure 2. Distinct variant lineages and sublineages were determined as described in Figure 2. The percent nucleotide sequence differences are shown in the panel to the right of the phylogenetic tree as described in Figure 2.
Figure 6.
HPV68 variant tree topology and pairwise comparisons of individual complete genomes.
The phylogenetic tree was constructed as described in Figure 2. Distinct variant lineages and sublineages were determined as described in Figure 2. The percent nucleotide sequence differences are shown in the panel to the right of the phylogenetic tree as described in Figure 2.
Figure 7.
HPV70 variant tree topology and pairwise comparisons of individual complete genomes.
The phylogenetic tree was constructed as described in Figure 2. Distinct variant lineages and sublineages were determined as described in Figure 2. The percent nucleotide sequence differences are shown in the panel to the right of the phylogenetic tree as described in Figure 2.
Figure 8.
Phylogenetic tree and pairwise comparisons of representative Alpha-7 lineages and sublineage complete genomes.
The phylogenetic tree was constructed as described in Figure 2. Representative genomes for each variant lineage and sublineage described in this report are used and the names of the isolates are shown to the right of the tree branches. The percent nucleotide sequence differences are shown in the panel to the right of the phylogenetic tree as described in Figure 2.