ML phylogenetic tree of HIV-1 subtype C <i>pol</i> (∼1000 pb) sequences circulating in Cuba (<i>n</i> = 49), and in central (<i>n</i> = 53), eastern (<i>n</i> = 330) and southern (<i>n</i> = 545) African countries.

<p>Branches are colored according to the origin of each sequence, as indicated at the legend (bottom left). The circular bracket highlights the position of the subtype C east African clade (C_EA). Shaded boxes highlight the position of the two major HIV-1 subtype C Cuban clades (C_CU-I and C_CU-II). Key nodes with <i>a</i>LRT support values >0.80 (*) and ≥0.90 (**) are indicated. The tree was rooted using HIV-1 subtype A1 and D reference sequences (gray branches). The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site.