Maximum likelihood phylogenetic tree based on 1,981 HIV-1 subtype C <i>pol</i> (∼1,000 pb) sequences.

Sequences were sampled at different countries from the east (n = 352), central (n = 53) and southern (n = 1,576) African regions shown in Table 1. The color of branches represents the geographic region from where the subtype C sequences originated, according to the map given in the figure. The boxes highlight the position of the major east African subtype C lineages. The tree was rooted using HIV-1 subtype A1 and D reference sequences (black branches). Horizontal branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site.