Research Article: High level of HIV-1 drug resistance mutations in patients with unsuppressed viral loads in rural northern South Africa

Date Published: July 27, 2017

Publisher: BioMed Central

Author(s): Elizabeth M. Etta, Lufuno Mavhandu, Cecile Manhaeve, Keanan McGonigle, Patrick Jackson, David Rekosh, Marie-Louise Hammarskjold, Pascal O. Bessong, Denis M. Tebit.


Combination antiretroviral therapy (cART) has significantly reduced HIV morbidity and mortality in both developed and developing countries. However, the sustainability of cART may be compromised by the emergence of viral drug resistance mutations (DRM) and the cellular persistence of proviruses carrying these DRM. This is potentially a more serious problem in resource limited settings.

DRM were evaluated in individuals with unsuppressed viral loads after first or multiple lines of cART at two sites in rural Limpopo, South Africa. Seventy-two patients with viral loads of >1000 copies/ml were recruited between March 2014 and December 2015. Complete protease (PR) and partial Reverse Transcriptase (RT) sequences were amplified from both plasma RNA and paired proviral DNA from 35 of these subjects. Amplicons were directly sequenced to determine subtype and DRM using the Stanford HIV Drug Resistance Interpretation algorithm.

Among the 72 samples, 69 could be PCR amplified from RNA and 35 from both RNA and DNA. Sixty-five (94.2%) viruses were subtype C, while one was subtype B (1.4%), one recombinant K/C, one recombinant C/B and one unclassified. Fifty-eight (84%) sequences carried at least one DRM, while 11 (15.9%) displayed no DRM. DRM prevalence according to drug class was: NRTI 60.8% NNRTI 65.2%, and PI 5.8%. The most common DRMs were; M184V (51.7%), K103N (50%), V106M (20.6%), D67N (13.3%), K65R (12%). The frequency of the DRM tracked well with the frequency of use of medications to which the mutations were predicted to confer resistance. Interestingly, a significant number of subjects showed predicted resistance to the newer NNRTIs, etravirine (33%) and rilpivirine (42%), both of which are not yet available in this setting. The proportion of DRM in RNA and DNA were mostly similar with the exception of the thymidine analogue mutations (TAMs) D67N, K70R, K219QE; and K103N which were slightly more prevalent in DNA than RNA. Subjects who had received cART for at least 5 years were more likely to harbour >2 DRM (p < 0.05) compared to those treated for a shorter period. DRM were more prevalent in this rural setting compared to a neighbouring urban setting. We found a very high prevalence of NRTI and NNRTI DRM in patients from rural Limpopo settings with different durations of treatment. The prevalence was significantly higher than those reported in urban settings in South Africa. The dominance of NNRTI based mutations late in treatment supports the use of PI based regimens for second line treatment in this setting. The slight dominance of TAMs in DNA from infected PBMCs compared to plasma virus requires further studies that should include cART subjects with suppressed virus. Such studies will improve our understanding of the pattern of drug resistance and dynamics of viral persistence in these rural settings.

Partial Text

HIV drug resistance remains a major threat to the success of scaling up of combination antiretroviral therapy (cART) in developing countries, especially in Africa where about 60% of HIV-infected individuals were on cART in 2012 [1]. The increased availability of cART has led to remarkable treatment results in most programs in sub-Saharan Africa (SSA), leading to a significant reduction of new infections [2]. Despite this success, some patients with incomplete adherence to treatment protocols might fail therapy and develop resistant viruses [3]. One challenge of cART in SSA has been the inability to routinely monitor virological parameters such as viral load (VL) and drug resistance, which are important to guide patient management and choose the right salvage treatments [4, 5]. Recent WHO recommendations stipulate that VL monitoring be utilized as the preferred method to determine treatment failure in SSA [6]. Within the past years, VL monitoring has in fact been successfully implemented as part of care in South Africa [6].

This study was performed among patients failing treatment in two treatment centres in rural South Africa: the HAPG Wellness Clinic which started cART administration in 2000, 4 years before the roll-out of antiretroviral therapy in the public health sector in South Africa; and the Donald Fraser Clinic which started providing treatment in 2004. Although both sites have been implementing VL and CD4+ T-cell count monitoring, according to national guidelines, and as part of HIV management for several years, the prevalence of DRM was still high. The M184V mutation was the most prevalent DRM, observed in 52% of study subjects. This coincided with the extensive use of 3TC, surpassed only by the use of TDF and EFV in the population. Interestingly, TDF mutations were one of the least common DRM in the study despite its frequent usage, supporting its inclusion as the main backbone during first line treatment.




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