Reverse transcriptase drug resistance mutations in HIV-1 subtype C infected patients on ART in Karonga District, Malawi

Abstract

BackgroundDrug resistance testing before initiation of, or during, antiretroviral therapy (ART) is not routinely performed in resource-limited settings. High levels of viral resistance circulating within the population will have impact on treatment programs by increasing the chances of transmission of resistant strains and treatment failure. Here, we investigate Drug Resistance Mutations (DRMs) from blood samples obtained at regular intervals from patients on ART (Baseline-22 months) in Karonga District, Malawi. One hundred and forty nine reverse transcriptase (RT) consensus sequences were obtained via nested PCR and automated sequencing from blood samples collected at three-month intervals from 75 HIV-1 subtype C infected individuals in the ART programme.ResultsFifteen individuals showed DRMs, and in ten individuals DRMs were seen from baseline samples (reported to be ART naïve). Three individuals in whom no DRMs were observed at baseline showed the emergence of DRMs during ART exposure. Four individuals who did show DRMs at baseline showed additional DRMs at subsequent time points, while two individuals showed evidence of DRMs at baseline and either no DRMs, or different DRMs, at later timepoints. Three individuals had immune failure but none appeared to be failing clinically.ConclusionDespite the presence of DRMs to drugs included in the current regimen in some individuals, and immune failure in three, no signs of clinical failure were seen during this study. This cohort will continue to be monitored as part of the Karonga Prevention Study so that the long-term impact of these mutations can be assessed. Documenting proviral population is also important in monitoring the emergence of drug resistance as selective pressure provided by ART compromises the current plasma population, archived viruses can re-emerge

Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing

“…Consensus sequencing of reverse transcriptase from five patients had previously revealed discrepancies in the presence/absence of DRMs [6,7]. Baseline describes the sampling time-point prior to ART initiation with subsequent samples being described as the number of months post ART initiation.…”

“…Recent research on HIV-1 in Karonga District, Malawi has shown that of the 40 HIV-1 subtype C infected individuals on HAART that we tested, 14% contained drug resistance mutations (DRMs) in the reverse transcriptase (RT) gene of viruses stored in the provirus [6] with clonal sequencing of latent viruses showing discrepancies in the presence and prevalence of DRMs in the proviral DNA [7]. These discrepancies further support the limitations of bulk sequencing for determining drug resistance in viruses contained within the proviral DNA.…”