Phylogenetic characterization of six full-length HIV-1 subtype C molecular clones from three patients: Identification of rare subtype C strains containing two NF-κB motifs in the long terminal repeat.

Hanna, L.E.; Neogi, U.; Ranga, U.; Swaminathan, S.; Prasad, V.R.

AIDS Research and Human Retroviruses ; 2014; 30; 586-591.

Abstract: Molecular surveillance is the backbone of HIV-1 vaccinology. Full-length HIV-1 sequences are useful tools that can provide a better understanding of the epidemiology in a given region. A limited number of full-length HIV-1 sequences are available from India, where > 95% of the HIV infections are due to HIV-1 subtype C (HIV-1C), which is distinct from the prototype African HIV-1C. In this study, we sequenced six full-length clones isolated from three patients. Extensive phylogenetic analyses of the full-length viral sequences using bioinformatic tools identified a separate cluster of Indian strains, thus confirming the distinct phylogenetic identity of the Indian HIV-1C. Notably, the long terminal repeat (LTR) of two of the six molecular clones contained only two NF-κB binding sites. The sequences also displayed features characteristic of HIV-1C including a Tat dicysteine motif, a shortened Rev open reading frame, and a predicted CCR5 co-receptor tropism for gp120 of three of the proviral sequences.

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