This project investigates the Prevalence of HIV-1 minor drug resistance variants in antiretroviral naive individuals in Botswana. Maruapula uses one of the cheaper, more sensitive assays, PAN Degenerate Amplification and Adaptation (PANDAA qPCR) to quantify minor HIV-1 drug resistant variants. The rationale for this project is that several studies have shown possible associations between minority HIV-1 drug resistant variants and ART treatment failure while other studies have found no association between NRTI-resistant minority variants and ART treatment failure. Moreover, the detection of low frequency HIV minor variants might be increased by using sensitive assays such as PANDAA. Testing for HIV-1 minority variants is not yet used routinely in the clinical set up for patient management.
The objective of this project is to optimise PANDAA qPCR assay to detect the following HIV-1 RT resistance mutations: K65R, K103N, Y181C, M184V, V106M and G190A. She then aims to determine the prevalence of minor drug resistance variants in antiretroviral naïve people in Botswana by detecting the six reverse transcriptase resistance mutations (K65R, K103N, Y181C, M184V, V106M and G190A).
The population for this project includes recently diagnosed antiretroviral naïve pregnant women aged between 18-25years. Patient samples will be extracted from plasma using EZ1 extraction machine, followed by cDNA synthesis then amplifying pol gene to generate 1.8kb amplicon. The generated amplicon will be used for both qPCR and population sequencing.
Results of highly sensitive PANDAA qPCR and population sequencing data will be compared for concordance and presence of additional mutations.