TY - JOUR
T1 - Phylogenetic characterization of six full-length HIV-1 subtype C molecular clones from three patients
T2 - Identification of rare subtype C strains containing two NF-κB motifs in the long terminal repeat
AU - Hanna, Luke Elizabeth
AU - Neogi, Ujjwal
AU - Ranga, Udaykumar
AU - Swaminathan, Soumya
AU - Prasad, Vinayaka R.
PY - 2014/6/1
Y1 - 2014/6/1
N2 - 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.
AB - 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.
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U2 - 10.1089/aid.2013.0275
DO - 10.1089/aid.2013.0275
M3 - Article
C2 - 24387762
AN - SCOPUS:84902145926
SN - 0889-2229
VL - 30
SP - 586
EP - 591
JO - AIDS Research and Human Retroviruses
JF - AIDS Research and Human Retroviruses
IS - 6
ER -