Figure 2

Phylogenetic tree with all available subtype J-like env Gambian isolates (red), including the three older isolates GM4, GM22 and GM24, and other subtype J env sequences from the Los Alamos HIV Database. MBTB4 and 98BW21.17 (in purple) are subtype A gag /J env recombinants described from outside the Gambia (DRC and Botswana respectively). The Gambian subtype J-like env monophyletic cluster is boxed. SE92809 and SE9173 are the two subtype J reference strains (From DRC, isolated in Sweden). The phylogenetic tree was reconstructed as in Fig. 1 and bootstrap percentiles above 70% from 1000 replications (using the neighbour-joining method) are shown. The tree is rooted by outgroups formed by subtype A1 and CRF02_AG env fragments from the Gambia (N75698A1_GM and N16805_GM). Branch lengths are expressed as the number of substitutions per nucleotide sites.