Fig. 2

Phylogenetic inference of HIV-1 partial reverse transcriptase sequences from antiretroviral-naïve patients in Senegal and Guinea. Maximum likelihood analysis, implemented with the PhyML standalone package v3.1, involved 98 nucleotide sequences covering 717 positions in the final dataset. Branch lengths are measured in the number of substitutions per site. The percentage of trees (SH-aLRT) in which the associated taxa clustered together is shown and values ≥ 85 were significant. Filled and empty diamond triangles are study field isolates, respectively from Senegal and Guinea. Some clades were collapsed for clarity. Unique recombinant forms (URFs) are indicated in the tree (right panel) with three stars***. The left panel shows Boot-scanning plots for each URF queried against representative HIV-1 reference sequences obtained from the Los Alamos HIV database (https://www.hiv.lanl.gov). These sequences are color coded and included A3, CRF02_AG, B, D, G, K, J. Genomic splits or breakpoints were confirmed by reconstruction of phylogenetic trees focused on those unbroken regions (not shown). Boot-scanning was run with the settings described in Fig. 1 (legends); at the difference that the window size was set at 250 base-pair