BACKGROUND : Although the use of highly active antiretroviral therapy in HIV positive individuals has proved to be
effective in suppressing the virus to below detection limits of commonly used assays, virological failure associated
with drug resistance is still a major challenge in some settings. The prevalence and effect of pre-treatment resistance
associated variants on virological outcomes may also be underestimated because of reliance on conventional
population sequencing data which excludes minority species. We investigated long term virological outcomes
and the prevalence and pattern of pre-treatment minority drug resistance mutations in individuals initiating
HAART at a local HIV clinic.
METHODS : Patient’s records of viral load results and CD4 cell counts from routine treatment monitoring were
used and additional pre-treatment blood samples for Sanger sequencing were obtained. A selection of pretreatment
samples from individuals who experienced virological failure were evaluated for minority resistance
associated mutations to 1 % prevalence and compared to individuals who achieved viral suppression.
RESULTS : At least one viral load result after 6 months or more of treatment was available for 65 out of 78
individuals followed for up to 33 months. Twenty (30.8 %) of the 65 individuals had detectable viremia and
eight (12.3 %) of them had virological failure (viral load > 1000 RNA copies/ml) after at least 6 months of
HAART. Viral suppression, achieved by month 8 to month 13, was followed by low level viremia in 10.8 % of
patients and virological failure in one patient after month 20. There was potentially reduced activity to Emtricitabine or
Tenofovir in three out of the eight cases in which minority drug resistance associated variants were investigated but
detectable viremia occurred in one of these cases while the activity of Efavirenz was generally reduced in all
the eight cases.
CONCLUSIONS : Early viral suppression was followed by low level viremia for some patients which may be an
indication of failure to sustain viral suppression over time. The low level viremia may also be representing
early stages of resistance development. The mutation patterns detected in the minority variants showed
potential reduced drug sensitivity which highlights their potential to dominate after treatment initiation.
TRIAL REGISTRATION : Not applicable.
Additional file 1: Figure S1. Deep sequencing coverage. C – E shows
sequencing coverage for samples with virologicalfailure (L031, L054 and
L064 respectively), F shows coverage for a sample with detectable
viremia (L009)and G and H show coverage for virally suppressed samples
(L074 and L075 respectively). Mutations wereexcluded from analysis for
any of the following: noisy mutations filtering, coverage filtering, forward/
reverse unbalanced frequency and forward/reverse unbalanced coverage.