Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Introduction: Since the South African public sector antiretroviral roll-out programme started in 2004, the success of antiretroviral combination therapy (cART) has been experienced in terms of survival, prevention of mother-to-child transmission (PMTCT) and quality of life. However, as the programme matures, viral resistance to the constituent drugs will increase. Monitoring antiretroviral drug resistance (ARVDR) should therefore be a priority in the public health approach to HIV treatment. Methods: A cross-sectional investigation of genotypic antiretroviral drug resistance in: a) HIV-infected mothers who were exposed to a PMTCT regimen of short course azidothymidine (AZT) with single dose nevirapine (NVP) during labour. b) HIV-infected adults and children who were cART-naïve (transmitted or initial resistance). c) HIV-infected adults and children who were failing cART (drug-induced or acquired resistance). In case of adults, this includes patients on a first-line, non-nucleoside reverse transcriptase (NNRTI)-based regimen, or on a second-line, protease inhibitor (PI)-based regimen, and in case of children, this includes patients on a first-line PI-based regimen. Results: In mothers who received a PMTCT-regimen that combined AZT and NVP the prevalence of NNRTI resistance mutations was 17.1% (95% CI: 8.7-25.6%). The prevalence of transmitted ARVDR in adults was low, as was initial ARVDR in young children (mostly PMTCT-exposed), except for NNRTI resistance in children who had received NVP as part of PMTCT. Drug-induced resistance was found in adults failing first-line NNRTI-based cART, with 83% having resistance to ≥1 drug. In contrast, adult patients failing second-line PI-based cART had a low prevalence of PI resistance; the predominant reason for failure was poor drug exposure, as detected by measuring lopinavir concentrations in blood plasma and hair samples. In contrast, PI resistance in children was not rare, largely due to historic exposure to un-boosted PIs. This resulted in extensive resistance to PIs and reverse transcriptase inhibitors (RTI) in some children. Conclusions: A combined regimen of short course AZT with intrapartum NVP for PMTCT may, in addition to reducing the risk of neonatal infection, also reduce the risk of NVP resistance in the mothers compared to a regimen of NVP only. In South Africa, the prevalence of transmitted ARVDR remains low relative to industrialised countries, probably as comparatively little time has elapsed since the scale-up of cART. Adults failing first-line cART are likely to respond to second-line cART, without failure due to resistance. However some children with PI and RTI resistance cannot be adequately treated with drugs currently available through the roll-out programme. This emphasizes the urgent need for a rational and science-based approach to managing cART-experienced children, including access to additional drugs to form a third-line paediatric cART regimen. / AFRIKAANSE OPSOMMING: Inleiding: Sedert die begin van die Suid Afrikaanse publieke sektor antiretrovirale uitrol program in 2004 is die sukses van antiretrovirale kombinasie-behandeling (k-ARB) ervaar in terme van oorlewing, voorkoming van moeder na kind oordrag (VMKO) en lewenskwaliteit. Nietemin, sal weerstandigheid teen die middels wat in die antiretrovirale program gebruik word toeneem soos wat die program gevestig raak. Die monitoring van antiretrovirale middel-weerstandigheid is derhalwe ‘n prioriteit in gemeenskap-gesondheid benadering tot MIV behandeling. Metodes: ‘n Deursnit ondersoek van genotipiese antiretrovirale middel-weerstandigheid in: a) MIV-geïnfekteerde moeders wat blootgestel is aan VMKO regimen bestaande uit ‘n kort kursus AZT met ‘n enkeldosis nevirapien (NVP) tydens kraam. b) MIV-geïnfekteerde volwassenes en kinders wat komibinasieterapie-naïef (oorgedraagde of inisiële weerstandigheid) is. c) MIV-geïnfekteerde volwassenes en kinders wat k-ARB faal (middel-geïnduseerde weerstandigheid). In geval van volwassenes, sluit dit pasiënte op ‘n eerste-linie, non-nucleosied tru-transkriptase inhibitor (NNRTI)-regimen, en tweede-linie protease inhibitor (PI)-gebaseerde regimen, en in geval van kinders, sluit dit pasiënte in op ‘n eerste-linie PI-gebaseerde regimen. Resultate: In moeders wat ‘n gekombineerde AZT en NVP VMKO-regimen ontvang het, was die voorkoms van NNRTI weerstandigheid 17.1% (95%-vertrouensinterval: 8.7-25.6%). Die voorkoms van oorgedraagde ARVMW in MIV-geïnfekteerde volwassenes en kinders wat kombinasieterapie-naïef is, was laag, so ook ARVMW in jong kinders (meestal VMKO-blootgestel), behalwe vir non-nukleosied tru-transkriptase inhibitor (NNRT) weerstandigheid in kinders wat NVP ontvang het deur VMKO. Middel-geïnduseerde weerstandigheid was gevind in volwassenes wat die eerste-linie NNRTI-gebaseerde k-ARB gefaal het, met 83% wat weerstandigheid teen ≥1 middel het. Volwassenes wat ‘n tweede-linie protease inhibitor (PI) –gebaseerde k-ARB gefaal het , het ‘n lae voorkoms van PI weerstandigheid, met die oorwegenede oorsaak, swak middel-bloostelling, soos bepaal deur van lopinavir-konsentrasies in bloed plasma en hare. In teenstelling hiermee was PI weerstandigheid nie skaars in kinders nie, hoofsaaklik weens historiese blootstelling an ongeskraagde PI-behandeling. Dit het tot uitgebreide weerstandigheid tot PIs en tru-transkritptase inhibitors (RTI) in sommige kinders gelei. Gevolgtrekkings: ‘n Gekombineerde regimen van ‘n kort kursus AZT met NVP tydens kraam vir VKMO, mag bykomend tot die vermindering die risiko van pasgebore infeksie, ook die kans vir weerstandigheid teen NVP in die moeders verlaag in vergelyking met ‘n regimen van NVP-alleen. Die voorkoms van oorgedraagde ARVMW is tans laag in vergelyking met geïndustrialiseerde lande, waarskynlik aangesien daar nog betreklik min tyd verloop het sedert k-ART wyd beskikbaar gemaak is. Volwassenes wat eerstelyn kombinasie terapie faal sal waarskynlik goed reageer op tweede-linie terapie, sonder terapie faling weens middelweerstandigheid. Daarenteen kan sommige kinders met protease inhibitor en tru-transkriptase weerstandigheid nie voldoende behandel word met die huidig-beskikbare middels in die uitrol program nie. Dit beklemtoon die dringende noodsaaklikheid van ‘n rasionele en wetenskaplike benadering tot k-ART in kinders, met ‘n lang terapie geskiedenis, wat toegang tot bykomende medikasie behels om `n derde-linie regimen saam te stel.

Les mutations de résistance génotypiques constituent un problème majeur pour l’optimisation du traitement antirétroviral chez les patients infectés par le VIH-1 naïfs au traitement ou prétraités. Cependant, l’analyse de l’impact des mutations sur la réponse au traitement est compliquée par i) le nombre élevé de mutations, ii) la colinéarité possible entre ces mutations, iii) le faible nombre de patients inclus dans les études et iv) la définition du critère de jugement. Les objectifs de cette thèse sont 1) de donner une vue d’ensemble et de discuter, en collaboration avec le réseau européen NEAT (European AIDS treatment network), les critères de jugement utilisés dans les essais cliniques récents et ceux utilisés lors de l’analyse des mutations de résistance, 2) d’évaluer l’impact des mutations génotypiques sur la réponse au traitement chez les patients naïfs dans le cadre d’une grande collaboration Européenne (EuroCoord-CHAIN) et 3) de comparer des méthodes adaptées pour les données à haute-dimension dans le but de construire un score génotypique pour la prédiction de la réponse virologique chez les patients prétraités. Les critères de jugement composites sont les plus utilisés dans les essais cliniques récents mais un critère purement virologique devrait être utilisé pour l’analyse de l’impact des mutations génotypiques. Les mutations de résistance transmises impactent sur la réponse à la première ligne de traitement si le traitement antirétroviral n’est pas adapté au génotype du virus du patient. L’analyse en composantes principales et l’analyse partial least square avaient une bonne capacité à prédire la réponse virologique mais n'étaient guère meilleures que le score génotypique. Nous allons continuer à travailler sur la comparaison de ces méthodes utilisant des critères de jugement différents dans le cadre de notre collaboration avec le Forum for collaborative HIV research. / Genotypic resistance mutations are a major concern for antiretroviral treatment optimisation in HIV-1 infected treatment naïve and treatment experienced patients. However, the analysis of the impact of genotypic mutations on treatment outcome is hampered by methodological issues such as the i) high number of possible mutations, ii) the potential collinearity between mutations, iii) the low number of patients included in those studies and iv) the definition of a virological endpoint. The objective of this thesis are 1) to give an overview and to discuss endpoints used in recent clinical trials in collaboration with European AIDS treatment network (NEAT) and those used in the context of drug resistance analysis, 2) to investigate the impact of genotypic resistance mutations on treatment outcome in treatment naïve patients in a huge European collaboration EuroCoord-CHAIN and 3) to compare methods adapted for high-dimensional data in order to construct a genotypic score to predict treatment outcome in treatment experienced patients. We saw that most of the endpoints used in recent clinical trials are composite endpoints but pure virological outcomes should be used for the evaluation of drug resistance mutations. Transmitted drug resistance mutations impact on virological outcome of initial antiretroviral therapy if the treatment of the patient is not adapted to the viral genotype the patient is harbouring. Principal component analysis and partial least square showed a good performance but had only a slightly better predictive capacity for a virologal outcome compared to the genotypic score. We continue working on the comparison of these and other methods using different endpoints in the context of a collaboration with the Forum for collaborative HIV research.