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AIDS Res Hum Retroviruses. 2008 Feb;24(2):229-34. doi: 10.1089/aid.2007.0229.

Evidence of a novel B/C recombinant exhibiting unique breakpoints of near full-length HIV type 1 genome from Northeastern India.

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  • 1Division of Molecular Virology, National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune-411026, India.


Despite the predominance of the HIV-1 clade C in India, the presence of other subtypes and recombinants has been reported. Here we report the identification of a novel HIV-1 B/C recombinant isolated from Northeast India and characterized near full length genome of the recombinant virus. Bootscan analysis of the nearly full-length genome showed a unique mosaic structure consisting of a subtype B backbone with three subtype C genome insertions. Breakpoint analyses revealed insertion of fragments belonging to subtype C at positions 1853-2223 in gag and 3025-3759 and 3998-5073 in pol. Phylogenetic analysis revealed that the segments of subtype B clustered with sequences of subtype B viruses reported from Thailand whereas segments of subtype C clustered with sequences of subtype C viruses reported from India. We report the mosaic structure that is distinct to HIV-1 B/C recombinant viruses reported to date.

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