Primary Drug Resistance in South Africa: Data from 10 Years of Surveys

Abstract

HIV-1 transmitted drug resistance (TDR) could reverse the gains of antiretroviral rollout. To ensure that current first-line therapies remain effective, TDR levels in recently infected treatment-naive patients need to be monitored. A literature review and data mining exercise was carried out to determine the temporal trends in TDR in South Africa. In addition, 72 sequences from seroconvertors identified from Africa Centre's 2010 HIV surveillance round were also examined for TDR. Publicly available data on TDR were retrieved from GenBank, curated in RegaDB, and analyzed using the Calibrated Population Resistance Program. There was no evidence of TDR from the 2010 rural KwaZulu Natal samples. Ten datasets with a total of 1618 sequences collected between 2000 and 2010 were pooled to provide a temporal analysis of TDR. The year with the highest TDR rate was 2002 [6.67%, 95% confidence interval (CI): 3.09-13.79%; n = 6/90]. After 2002, TDR levels returned to < 5% (WHO low-level threshold) and showed no statistically significant increase in the interval between 2002 and 2010. The most common mutations were associated with NNRTI resistance, K103N, followed by Y181C and Y188C/L. Five sequences had multiple resistance mutations associated with NNRTI resistance. There is no evidence of TDR in rural KwaZulu-Natal. TDR levels in South Africa have remained low following a downward trend since 2003. Continuous vigilance in monitoring of TDR is needed as more patients are initiated and maintained onto antiretroviral therapy.

Early Warning Indicators for First-Line Virologic Failure Independent of Adherence Measures in a South African Urban Clinic

“…While we did not assess for HIVDR prior to ART initiation, which could be a risk factor for VF within the first 6 months of ART initiation, the rates of transmitted HIVDR have been reportedly low to non-existent in KwaZulu-Natal. 74 Furthermore, baseline HIV genotyping is not routinely available in South Africa and could therefore not be integrated into clinical algorithms at this time. Finally, only one clinical site was examined, which does not permit comparisons across diverse programs or geographic settings (rural or peri-urban).…”

Consequences of Prior Use of Full-dose Ritonavir as Single Protease Inhibitor as Part of Combination Antiretroviral Regimens on the Future Therapy Choices in HIV-1–Infected Children

“…The amplicon was sequenced using 4 primers. 13 Sequencing reactions were run on an automated 3500xl, 24 capillary Genetic Analyzer (Applied Bioscience).…”

RegaDB: community-driven data management and analysis for infectious diseases

“…Under SATuRN, 47000 genotypes with treatment and monitoring data have been collected. Using the built-in customized report and query functionality, data of specific attributes are selected, analysed and used to answer specific clinical and research questions (de Oliveira et al, 2010;Manasa et al, 2012). In addition, members of the SATuRN project recently published a book (Rossouw et al, 2013) containing a series of case studies used for training.…”