FIG. 2.

Phylogenetic analysis of the LTR and V3 env sequences. Phylogenetic analysis of (A) the LTR and (B) V3 env sequences derived from the 25 Indian viral isolates containing the promoter insertions. The reference sequences have been downloaded from the Los Alamos HIV sequence database. After gap-stripping of the sequences, 321 and 57 positions were used in the analysis of the LTR and V3 env regions, respectively. The trees are mid-point rooted. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The individual sequences have been highlighted with different shapes based on the nature of the sequence insertion. Square, diamond, circle and pentagon shapes represent sequence insertions containing the NF-κB, κB-like, RBEIII and RBEIII+κB-like motifs, respectively.