Background: Increased access to antiretroviral therapy (ART) has been associated with significant reductions in AIDS related morbidity and mortality as well as a significant reduction in HIV incidence. As more patients access ART, higher proportions of newly infected patients is expected to be infected with drug resistant viruses in resource limited settings.
Methods: Samples from treatment naïve participants from 3 rounds of an annual population based HIV surveillance programme in rural Kwazulu-Natal were genotyped for drug resistance. The sample types included, EDTA microtubes (2010) and DBS (2011 and 2012). Samples were selected from the population for 2010, 2011 and 2012 with an estimated duration of infection. In addition, we randomly selected samples from chronically infected drug naive individuals with VL > 10,000 copies/ml (2011 and 2012). The quality of sequences was assessed using the Calibrated Population Resistance (CPR) tool and by phylogenetic reconstruction analysis using ML and NJ methods. The 2009 surveillance of drug resistance mutation (SDRM) list was used in the drug resistance analysis. All statistical analyses were undertaken using Stata 10.
Results: We sequenced 701 treatment naïve individuals (success rate 86%); 67 (2010), 381(2011), and 253 (2012). This represents approximately 15% of the surveillance samples for 2011 and 2012. Men constituted 25% of the participants. The average age was 34 years and the median viral load was 116,600 RNA copies/ml. One or more SDRM were identified in 36 (5%) of the 701 participants. Of these, the NNRTI SDRM were the most dominant, being detected in 32 (5%) samples. The most common were K103N, V106M and G190A, in 27 (3.8%), 3 (0.4%) and 2 (0.3%) samples respectively. Only 3 (0.4%) samples had 2 or more NNRTI SDRM. NRTI SDRM were detected in 11 (1.6%) of the participants, 9 of whom had only one NRTI SDRM. Six (1%) of the participants had both NNRTI and NRTI resistance mutations, K103N + M184V being the most common combination. There was no evidence of SDRM from the 2010 participants. The 2011 and 2012 samples both had 18 participants with some SDRM, 5% and 8% respectively.
Conclusions: The NNRTI SDRMs are the major contributors to observed patterns of primary drug resistance. There is an increasing need to identify recently infected participants in order to better understand the trends in primary drug resistance in reponse to changes in treatment coverage and treatment regimens in public sector treatment programmes.