Fig. 1

Phylogenetic inference of HIV-1 protease and partial reverse transcriptase sequences from antiretroviral-naïve patients in Senegal. Maximum likelihood analysis, implemented with the PhyML standalone package v3.1, involved 89 nucleotide sequences covering 1026 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. The “Cx” clade indicates a possible transmission network between two men (self-reported homosexual and heterosexual). Some clades were collapsed for clarity. Diamond triangles are study field isolates (right panel), of which those with three stars*** are unique recombinant forms (URFs). The left panel depicts 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, F1, F2, B, D, CRF06_CPX, A1, K, C, H. Genomic splits or breakpoints were confirmed by reconstruction of phylogenetic trees focused on those unbroken regions (not shown). Boot-scanning was generated in SimPlot v3.5.1 under the Neighbor-Joining algorithm, modelled with the Kimura two-parameter and 100 bootstrap replicates (percentage of permuted trees on the y-axis). Boot-scanning was run with parameters of 50% consensus sequences, 300 base-pair window size, 10 base-pair step size (nucleotides position on the x-axis), and a nucleotide transition/transversion ratio of 2.0