Intra-Clade C signature polymorphisms in HIV-1 LTR region: The Indian and African lookout.

Supriya Singh, Arbind Kumar, Megha Brijwal, Aashish Choudhary, Kriti Singh, Rishabh Singh, Mohammad Husain, Lalit Dar

Virus research 2021 May

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Polymorphisms occurring in LTR (Long Terminal Repeat) region can profoundly impact pathogenicity, transmission and biology of Human Immunodeficiency Virus Type 1 (HIV-1). We investigated intra-clade polymorphisms, associated with HIV-1 clade-C infections that occur in India and Africa. Plasma samples were obtained from 24 HIV-infected ART-experienced individuals. Next Generation Sequencing was performed on Illumina Hi Seq X system. Sequence analysis was done using MEGA v7. Transcription factor binding sites (TFBS) were investigated to unveil signature sequences. Signature nucleotides in Indian sequences were observed at 19 positions, of which 7 nucleotide signatures occurred in transcription binding sites (TFBS), namely NF-AT-II, NF-AT-III, USF, TCF- 1alpha, Sp1-I and TAR. Intra-clade C variations in HIV-1 LTR that inscribe signature nucleotides in Indian sequences lead to formation monophyletic cluster of Indian sequences. Moreover, occurrence of intra-clade signature nucleotides was observed at the key positions in the transcription factor binding sites in Indian and African clade-C sequences. Copyright © 2021 Elsevier B.V. All rights reserved.

Citation

Supriya Singh, Arbind Kumar, Megha Brijwal, Aashish Choudhary, Kriti Singh, Rishabh Singh, Mohammad Husain, Lalit Dar. Intra-Clade C signature polymorphisms in HIV-1 LTR region: The Indian and African lookout. Virus research. 2021 May;297:198370