ML phylogenetic tree of HIV-1 subtype B pol (∼1000 pb) sequences circulating in Cuba (n = 322), US (n = 525), France (n = 348), and other Caribbean countries (n = 418).

The branches are colored according to the origin of each sequence, as indicated at the legend (bottom left). The circular brackets highlight the position of the pandemic (B_PANDEMIC, green line) and non-pandemic (B_CARIBBEAN, blue line) HIV-1 subtype B clades. Shaded boxes highlight the position of the two major HIV-1 subtype B Cuban clades (B_CU-I and B_CU-II). The number of Cuban sequences distributed accordingly to the clade size is shown (top left). Key nodes with aLRT support values >0.80 (*) and ≥0.90 (**) are indicated. The tree was rooted using HIV-1 subtype D reference sequences (gray branches). The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site.