FIG. 1.

The profiles of the sequence insertion in the HIV-1 subtype C LTR. The top panel depicts a schematic representation of a typical HIV-1 LTR showing important transcription factor binding sites including the RBEIII, NF-κB, Sp1, and TATA box. The USF-1 site is inactive in subtype C, indicated using a crossed box. The arrow indicates the transcriptional start site. Multiple sequence alignment of the viral enhancer and the upstream region derived from 25 Indian and 4 African viral strains has been presented with the Indie-C1 sequence at the top for comparison. The viral strains have been classified into four categories based on the nature of the transcription factor binding sites in the inserted sequences. The inserted transcription factor binding sites NF-κB, κB like, and RBEIII have been highlighted in red, pink, and green background colors, respectively, while the original sites are shaded gray. The asterisk represents sequences previously published. With the exception of the Indian D24, the rest of the published sequences belong to Africa. Dots and dashes represent sequence identity and deletions, respectively.