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

Date Published: October 13, 2011

Publisher: BioMed Central

Author(s): Vijay B Bansode, Simon AA Travers, Amelia C Crampin, Bagrey Ngwira, Neil French, Judith R Glynn, Grace P McCormack.


Drug 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.

Fifteen 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.

Despite 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

Partial Text

It has been estimated that in sub-Saharan Africa, approximately 3.9 million people have started antiretroviral treatment (ART) since its introduction (UNAIDS, 2010). Given the large population on treatment, viral diversity coupled with low adherence could lead to the emergence and large-scale transmission of drug resistant strains. Rates of drug resistance among patients who received ART in sub-Saharan Africa range from 3.7%-49% after 24-163 weeks of HAART [1]. Various factors contribute to this large range in resistance among African cohorts such as variation in available healthcare systems and practices, adherence, and access to monitoring [2]. Development of DRMs to Trioimmune®, the drug combination used as first line therapy in Karonga District, Malawi, has been reported in Zambia [3], South Africa [4], Cameroon [5], Kenya [6] and Uganda [7]. Previous studies on drug resistance in Malawi showed various DRMs to both NRTIs and NNRTIs in both drug naïve individuals [8] and those failing therapy [9]. However, very little data is yet available on the emergence of drug resistance to ongoing treatment and the transmission of drug resistant variants in subtype C infected countries [3,5-7,10].

One hundred and forty nine subtype C sequences were generated from 75 individuals, 65 of which were from blood samples collected at baseline (and reported to be ART naïve). DRMs were found in sequences from 15 individuals (20%) overall, and for 10 individuals (15.4%) the mutations were found in sequences from baseline samples (drug naïve). Details of observed drug resistance mutations are summarized in Table 1. Seven individuals showed DRMs (or ambiguities that suggest the presence of DRMs) to NRTIs used in Karonga with 6/7 showing the mutation V118I. While ten individuals showed the presence of DRMs to NNRTIs only five showed DRMs against therapies used in Karonga, the most common being Y181C and G190AE.

Through genotyping RT from HIV-1 subtype C infected individuals on ART using a consensus sequencing approach, we have shown the presence of mutations associated with drug resistance to the therapy used in Karonga District. Drug resistance to Trioimmune® occurred at an overall rate of 20% of individuals (both drug naïve and drug exposed, which is comparable to rates found in other African countries [4-7,16-18] but, as expected, greater than that described in our previous study (7.5%) [8] which did not include individuals currently on therapy.

The authors declare that they have no competing interests.

VB carried out the molecular biology work and subsequent analysis; AC, BN, NF and JG participated in design of the study; ST and GM conceived and supervised the study. All authors have read and approved the final manuscript.