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

Luke Elizabeth Hanna, Ujjwal Neogi, Udaykumar Ranga, Soumya Swaminathan, Vinayaka R. Prasad

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1 Scopus citations


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 coreceptor tropism for gp120 of three of the proviral sequences.

Original languageEnglish (US)
Pages (from-to)586-591
Number of pages6
JournalAIDS Research and Human Retroviruses
Issue number6
StatePublished - Jun 1 2014


ASJC Scopus subject areas

  • Immunology
  • Virology
  • Infectious Diseases

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