Figure 1

Phylogenetic classification of 38 new Gambian HIV-1 full-length env sequences (highlighted in red), along with reference subtypes and additional subtype A sequences (CRF02_AG and Senegalese A3 variants). The full Los Alamos HIV Database (2005) subtype reference set was initially used to construct the tree, but all CRFs other than CRF02_AG have been omitted here for clarity. The phylogenetic tree was constructed using a maximum likelihood method [18], under the General Time Reversible model of nucleotide substitution [19], with proportion of invariable sites and substitution rate heterogeneity. Bootstrap percentiles above 70% from 1000 replications (using the neighbor-joining method) are shown at the corresponding branches defining major grouping of sequences. Five of the new Gambian sequences cluster with the Senegalese A3 variant sequences with a bootstrap support of 81 (∞). Branch lengths represent the number of substitutions per nucleotide sites.