[Show abstract][Hide abstract] ABSTRACT: Background
HIV-1 is capable of evading the CTL immune response
by introducing mutations in residues both within the
epitopes and in sequences flanking the epitopes. The
present study aims at identifying the mechanisms of
CTL immune escape primarily in the asymptomatic
phase of HIV-1 subtype C in drug naive patients from
an Indian clinical cohort.
In a prospective study, a cohort of select seropositive drug
naive subjects is being monitored at YRG CARE, Chennai
for a period of two years with repeated sampling at
6-month intervals. The viral RNA was extracted from
plasma and Gag was amplified, followed by Sanger
sequencing. The samples of interest were further subjected
to next-generation sequencing using Illumina MiSeq and
analyzed using the CLC Genomics Workbench software.
Twenty plasmid clones of gag were sequenced from one
of the subjects at four different time-points. We observed
multiple viral strains that did or did not contain an insertion
of 14 amino acid residues in the PTAP domain of
p6 gag. The PTAP duplication was further confirmed in
6 other subjects using the next- generation sequencing.
The preliminary data suggest that subtype C is capable
of causing sequence insertions of longer length in the
PTAP domain of the p6 gag, unlike other viral subtypes
that insert sequences of shorter length at this location.
The bio informatics analysis is suggestive of the role of the
amino acid insertions in immune escape in the chronic
phase of the HIV-1 infection.
[Show abstract][Hide abstract] ABSTRACT: Conclusions: 1. HIV-1 subtype C is endowed with a unique capability to duplicate longer sequence insertions at specific locations. 2. The PTAP domain duplication in p6-gag enhances viral replication fitness possibly by enhancing the viral budding.
International conference on Cellular and Molecular Mechanisms of Disease Processes-2014, University of Kashmir, Srinagar, Kashmir.; 04/2014
[Show abstract][Hide abstract] ABSTRACT: Commercial HIV-1 genotypic resistance assays are very expensive, particularly for use in resource-constrained settings like India. Hence a cost effective in-house assay for drug resistance was validated against the standard ViroSeq HIV-1 Genotyping System 2.0 (Celera Diagnostics, CA, USA). A total of 50 samples were used for this evaluation (21 proficiency panels and 29 clinical isolates). Known resistance positions within HIV-1 protease (PR) region (1-99 codons) and HIV-1 reverse-transcriptase (RT) region (1-240 codons) were included. The results were analysed for each codon as follows: (i) concordant; (ii) partially concordant; (iii) indeterminate and (iv) discordant. A total of 2750 codons (55 codons per patient samplex50 samples) associated with drug resistance (1050 PR and 1700 RT) were analysed. For PR, 99% of the codon results were concordant and 1% were partially concordant. For RT, 99% of the codon results were concordant, 0.9% were partially concordant and 0.1% were discordant. No indeterminate results were observed and the results were reproducible. Overall, the in-house assay provided comparable results to those of US FDA approved ViroSeq, which costs about a half of the commercial assay ($ 100 vs. $ 230), making it suitable for resource-limited settings.
[Show abstract][Hide abstract] ABSTRACT: Continuation of failed highly active antiretroviral therapy regimens can lead to the accumulation of mutations that may limit options for second-line treatment. We studied the pattern of drug resistance mutations among 138 Indian patients who experienced failure of nonnucleotide reverse-transcriptase-containing first-line highly active antiretroviral therapy. This study demonstrates a high frequency of drug resistance mutations in human immunodeficiency virus-infected Indians who experience immunologic treatment failure and suggests the need for viral load monitoring.