A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfillment of the requirements for the degree of Master of Dentistry. Johannesburg, 2018. / Background: Accurate HIV diagnosis is critical and can be life-saving. A Rapid Test (RT) is considered key to HIV prevention and management. Some studies have found RT to be comparable with ELISA whilst others have reported on lower sensitivity. Aim and study design: The aim of this retrospective comparative descriptive study was to evaluate the sensitivity and specificity of the Tri-line HIV rapid test device in comparison to ELISA on patient records from Wits Oral Health Centre (WOHC) between 2014 and 2016 Method: The study population comprised records of patients older than18 months who had Tri-Line HIV RT and blood drawn for ELISA on the same day. Descriptive analysis of the data was carried out. Results: The sensitivity of Tri-line was 80% (CI: 59-93%) and specificity was 100% (CI: 83-100%). The PPV was 100% (CI: 83-100%) and NPV was 80% (CI: 65-90%). ROC area of 0.9 at 95% CI was determined. Conclusion: Due to a low sample size in this study a definitive conclusion could not be drawn. However on the basis of the results obtained, although the tri-line RT showed lower sensitivity it was shown to be a clinically useful test. / LG2018

Human immunodeficiency virus reverse transcriptase (HIV RT) is a virally encoded polymerase responsible for replicating the HIV genome. Most HIV treatments include nucleotide RT inhibitors (NRTIs) which inhibit HIV RT replication by serving as a substrate for the polymerase reaction but then blocks subsequent polymerization after incorporation. However, resistance to these NRTIs may occur through specific mutations in HIV RT that increase the discrimination of HIV RT for natural nucleotides over NRTIs. The role of enzyme conformational dynamics in specificity and substrate selection was studied using transient kinetic methods on HIV RT enzymes that have been site-specifically labeled with a conformationally sensitive fluorophore, to measure the rates of binding and catalysis. First, HIV RT with the mutation of lysine to arginine at the residue position 65 (K65R) was examined for its resistance against the NRTI tenofovir diphosphate (TFV), an acyclic deoxyadenosine triphosphate (dATP) analog. It was found that HIV RT K65R resistance to TFV was achieved through decreased rates of catalysis and increased rates of dissociation for TFV over dATP when compared with the kinetics of wild-type HIV RT. Moreover, global fitting analysis confirmed a mechanism where a large conformational change, after initial ground state binding of the substrate, contributed significantly to enzyme specificity. This led to our investigation of the molecular basis for enzyme specificity using HIV RT as a model system. Again, transient kinetic methods were applied with the addition of molecular dynamics simulations. The simulated results were substantiated by the corroborating experimental results. It was found that a substrate-induced conformational change in the transition of HIV RT from an open nucleotide-bound state to a closed nucleotide-bound state was the major determinant in enzyme specificity. The molecular basis for substrate selection resulted from the molecular alignments of the substrate in the active-site, which induced the conformational change. When the correct nucleotide was bound, optimal molecular interactions in the active-site yielded a stably closed complex, which promoted nucleotide incorporation. In contrast, when an incorrect nucleotide was bound, the molecular interactions at the active-site were not ideal, which yielded an unstable closed complex, which promoted substrate dissociation rather than incorporation. / text