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Novel HIV-1 long terminal repeat (LTR) sequences of subtype B and mosaic intersubtype B/C recombinants in North India

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Abstract

Although the HIV-1 epidemic in India is mainly due to subtype C, other subtypes have also been reported from different parts of India. HIV-1 LTR sequence analysis from six HIV-1 infected individuals from North India was carried out to determine the nature and extent of variations. Four out of six samples formed a unique phylogenetic cluster which was close to subtype B. The other two samples (A3 and S3) turned out to be novel mosaic recombinants showing resemblance to subtypes B, B/C-India and B/C-Myanmar gene segments. All four subtype B LTR samples and the two B/C recombinants showed conserved as well as unique polymorphisms in all of the putative transcription factor binding sites (TFBS). These changes may potentially alter basal as well as Tat-mediated HIV-1 LTR promoter activation. The two recombinants possessed three copies of the NF-κB TFBS as seen with the majority of subtype C and recombinant B/C isolates reported earlier, but the other four non-recombinant B-LTRs showed only two copies of the NF-κB site. This is the first study to show a dominance of unique subtype B-LTRs and strongly suggests that this region could also be a hot spot for the formation of highly complex inter subtype B/C recombinants.

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Acknowledgments

This work was supported by a grant from the Department of Biotechnology, Government of India, to the corresponding author (A.C.B) and to the National Institute of Immunology, New Delhi, India. We thank our Director, Dr. Avadesh Surolia, for support and encouragement. Support received from PGIMER, Chandigarh, is gratefully acknowledged.

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Authors and Affiliations

  1. Division of Virology, National Institute of Immunology, JNU Campus, New Delhi, 110067, India

    Ujjwal Neogi, Vikas Sood & Akhil C. Banerjea

  2. Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India

    Nidhi Goel & Ajay Wanchu

Authors
  1. Ujjwal Neogi
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  2. Vikas Sood
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  3. Nidhi Goel
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  4. Ajay Wanchu
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  5. Akhil C. Banerjea
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Corresponding author

Correspondence to Akhil C. Banerjea.

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Ujjwal Neogi and Vikas Sood contributed equally to this work.

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Neogi, U., Sood, V., Goel, N. et al. Novel HIV-1 long terminal repeat (LTR) sequences of subtype B and mosaic intersubtype B/C recombinants in North India. Arch Virol 153, 1961–1966 (2008). https://doi.org/10.1007/s00705-008-0210-y

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  • DOI: https://doi.org/10.1007/s00705-008-0210-y

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