Phylogenetic tree constructed using alignments of gag sequence from subtype A reference strains (denoted by prefix 'Ref'), additional subtype A1 isolates, A3 isolates from Senegal, CRF02_AG isolates and subtype A gag sequence from isolates with subtype J-like env regions. Gambian isolates are in red, which includes an older isolate GMB22. Sequence from the non-Gambian gagA/envJ recombinants 98BW21.17 and MTBT4 are highlighted in purple. The cluster formed by gag A sequence from isolates with J-like env regions is boxed. One Gambian isolate (N5284_GM) falls outside this cluster. The tree was reconstructed as in Fig. 1 and bootstrap percentiles above 70% from 1000 replications (using the neighbour-joining method) are shown. The trees are rooted by outgroups formed by subtype J and C reference isolates from the Los Alamos HIV Database (2005) subtype reference set (SE7887 and 95IN21068). Branch lengths represent the number of substitutions per nucleotide sites. The tree includes the DRC isolates MTBT4, KCC2, KTBT13 and KTB035 which required the sequences to be trimmed to 623 bp. A similar tree lacking these sequences but reconstructed with a 951 bp length alignment confirmed the clustering (for the remaining sequences) although with higher bootstrap support.