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Updated: Jun 5, 2026
10:18
Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
Enhanced strand transfer and mismatch extension by HIV-1C reverse transcriptase promote sequence motif duplication
Arun Panchapakesan1,2, Aditya Pradeepbhai Joshi1, Afzal Amanullah1
1HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, India.
Journal of Virology
|June 4, 2026
Summary
HIV-1C reverse transcriptase (RT) has unique biochemical properties, including enhanced template strand transfer and mismatched end extension, that promote sequence motif duplications. These RT variations contribute to HIV-1 evolution and the emergence of clinically relevant viral variants.
Area of Science:
- Virology
- Molecular Biology
- Genetics
Background:
- Genetic diversification of HIV-1 is driven by reverse transcriptase (RT) errors and template switching.
- Sequence motif duplications, often occurring in HIV-1C, alter viral gene regulation and function.
- The mechanistic basis for higher duplication frequencies in HIV-1C remained unclear.
Purpose of the Study:
- Investigate if intrinsic biochemical properties of HIV-1C RT contribute to elevated sequence motif duplication frequencies.
- Identify specific RT residues and their impact on recombination and duplication events.
- Elucidate the molecular mechanisms driving subtype-specific duplication biases in HIV-1.
Main Methods:
- Bioinformatic analysis of 6,877 full-length HIV-1 genomes to identify duplication hotspots.
- Comparative sequence analysis of RT, focusing on subtype-specific residues like T359.
- Structural modeling to predict T359's interaction with the RT-template complex.
- Biochemical characterization of recombinant RT variants and functional assays for template strand transfer and primer extension.
- Next-generation sequencing-based primer extension assays.
Main Results:
- Identified four duplication hotspots, with highest frequencies in HIV-1C.
- Discovered subtype-specific RT residues, including T359, potentially stabilizing the RT-template complex.
- HIV-1C RT showed enhanced template strand transfer and more efficient extension of mismatched 3' termini compared to HIV-1B RT.
- Residue 359 was shown to modulate polymerase activity and maintain subtype-specific catalytic function.
Conclusions:
- Subtype-specific biochemical properties of HIV-1C RT, mediated by T359, promote nonhomologous recombination leading to sequence motif duplications.
- These duplications have significant biological consequences, affecting viral gene expression and potentially enhancing fitness under antiretroviral pressure.
- The findings provide a mechanistic explanation for HIV-1C's distinct evolutionary patterns and persistence.
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