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An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings
Published on: March 30, 2014
Genomic signatures of protease and reverse transcriptase genes from HIV-1 subtype C isolated from first-line ART
Sushanta Kumar Barik1, Keshar Kunja Mohanty1, Shripad A Patil1
1ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar-Pradesh, India.
Insights
Genomic analysis of HIV-1 subtype C in North Indian patients revealed drug resistance mutations in the protease and reverse transcriptase genes. This study highlights the importance of monitoring viral evolution in patients undergoing antiretroviral therapy.
Area of Science:
- Virology
- Genetics
- Molecular Biology
Background:
- Antiretroviral therapy (ART) is crucial for managing HIV-1 infection.
- Monitoring drug resistance mutations is essential for effective HIV treatment.
- HIV-1 subtype C is prevalent in many regions, including North India.
Purpose of the Study:
- To analyze genomic signatures of HIV-1 protease and reverse transcriptase genes in North Indian patients.
- To identify drug resistance mutation patterns in patients undergoing ART for 1 to 7 years.
- To investigate viral evolution and genetic diversity using computational tools.
Main Methods:
- Isolation and amplification of HIV-1 protease and reverse transcriptase genes from patient plasma samples (DNA and RNA).
- Sequencing using the WHO dried blood spot protocol.
- Analysis of drug resistance mutations via the HIV Drug Resistance Database (Stanford University).
- Utilized computational tools (VESPA, SNAP) for signature pattern, hypermutation, selection pressure, and entropy analysis.
Main Results:
- Observed lamivudine-, nevirapine-, and efavirenz-associated drug resistance mutations (e.g., M184V/I, Y181C, H221Y, M230I) in the reverse transcriptase gene of two patients.
- No mutations were detected in the remaining seven patients.
- Identified signature amino acid sequences and calculated synonymous to non-synonymous nucleotide ratios.
- Found no evidence of hypermutation but noted highest entropy at specific amino acid positions.
Conclusions:
- Specific drug resistance mutations were identified in a subset of ART-treated HIV-1 subtype C patients in North India.
- Genomic analysis revealed insights into viral evolution and selection pressures.
- Continuous surveillance of HIV-1 genetic diversity and resistance patterns is vital for optimizing treatment strategies.
Abstract:
Genomic signatures of the protease and reverse transcriptase gene of HIV-1 from HIV infected North Indian patients who were under ART from 1 to ≤ 7 years were analyzed. The DNA from plasma samples of 9 patients and RNA from 57 patients were isolated and subjected to amplification for the protease and reverse transcriptase gene of HIV-1 subtype C. Then sequencing was carried out following the WHO dried blood spot protocol. The drug resistance mutation patterns were analyzed using the HIV Drug Resistance Database, Stanford University, USA. Lamivudine-associated drug-resistance mutations such as M184V/M184I, nevirapine-associated drug resistance mutations Y181C and H221Y, and efavirenz-associated drug resistance mutations M230I were observed in reverse transcriptase gene of archived DNA of two HIV-1 infected patients. No mutation was observed in the remaining 7 patients. Various computational tools and websites like viral epidemiological signature pattern analysis (VESPA), hyper mutation, SNAP version 2.1.1, and entropy were utilized for the analysis of the signature pattern of amino acids, hyper mutation, selection pressure, and Shannon entropy in the protease and reverse transcriptase gene sequences of the 9 archived DNA, 56 protease gene and 51 reverse transcriptase gene from the HIV-1 DNA amplified sequences of RNA. The HIV-1 Subtype-C (Gene bank accession number: AB023804) and first isolate HXB2 (Gene bank accession number: K03455.1) was taken as reference sequence. The signature amino acid sequences were identified in the protease and reverse transcriptase gene, no hyper mutation, highest entropy was marked in the amino acid positions and synonymous to non-synonymous nucleotide ratio was calculated in the protease and reverse transcriptase gene of 9 archived DNA sequences, 56 protease and 51 reverse transcriptase gene sequences of HIV-1 Subtype C isolates.
