Background In 2010, 2.2 million adolescents were living with HIV (Human Immunodeficiency Virus) worldwide. This study aimed to describe the socio-demographic and clinical characteristics of the adolescents (10-19 years old) initiating anti-retroviral treatment (ART) and to investigate characteristics that are associated with virological failure in adolescents on ART. Methods This was an analysis of adolescents initiating ART from June 2004-2010 at the Hlabisa Treatment and Care Programme in KwaZulu-Natal, South Africa. Data was collected from two datasets at Africa Centre for Health and Population Studies. Time to outcomes of death and lost to follow up (LTFU) were quantified using Kaplan-Meier estimates. The outcome was virologic response (< 70copies/ml) after at least 6 months on ART and the associations with an unsuppressed viral load were investigated using multivariable logistic regression. Results 543 adolescents, median age 15 years (IQR 12-18), initiated ART; 67.8% (368) were females. Age at treatment initiation showed a bimodal distribution, with a peak at 11 years and another at 17-19 years; 61 females aged 16-19 years initiated ART whilst pregnant. At baseline, median CD4 count was 152 cells/μl (IQR 72-251), 392 (72.2%) had prior TB and 129 (23.8%) a weight-for-age z-score ≤ -2 (i.e. were under-nourished). Numbers of adolescents starting ART increased from 53 in the years 2004-2006 to 196 in 2010. Overall mortality was 36.5 per 1000 person years (95% CI 27.2 - 48.8); LTFU 98.8 per1000 person years (95% CI 82.8-118). Adjusting for age and gender, LTFU was significantly higher in females initiating in late adolescence (15-19 years) (p<0.001) and 24 (39.3%) of those initiating ART whilst pregnant were LTFU. The first viral load after initiation was taken at a median time of 11.25 months (IQR 7.78-16.20). Of the 364 adolescents with a viral load result after at least 6 months of ART, 119 (32.7%) had an unsuppressed viral load (95% CI 27.9- 37.5). Adolescents who initiated in the year 2010 were found to have less odds of an unsuppressed viral load compared to those who initiated between 2004 and 2006 [adjusted Odds Ratio (aOR) 0.29 (95% CI 0.11-0.79)]. Those who had the first viral load test done after > 30 months of ART had higher odds of an unsuppressed viral load compared to those tested after 6-12 months of ART [ aOR 6.88 (95% CI 1.29-36.66)]. Conclusion Despite the yearly increase in adolescents initiating ART, good virological responses can be obtained through increased ART support to both individuals and health care providers. Timely viral load monitoring identifies those in need of increased adherence support on ART and may result in good virological responses. Recommendations Adolescents on ART are a vulnerable group that requires special attention to improve clinical and virological outcomes. Adolescent friendly ART clinics may be useful in providing this service and mitigate the high attrition rates of those on treatment for HIV. Public health awareness campaigns on HIV and its treatment may have a positive impact on virological response to ART and therefore campaigns targeting adolescents must be intensified. Early virological testing after 6 months on ART to monitor treatment responses helps to identify those with sub-optimal response to ART and reduce the progression to virological failure and drug resistance to anti-retroviral drugs.

Submitted in partial fulfilment of the requirements for the degree of Master of Public Health, in the field of Maternal and Child Health, to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, September 2014 / Introduction: Nevirapine (NVP) is used in combination antiretroviral treatment especially for pregnant HIV infected women. NVP has been shown to be inferior and more toxic than other similar drugs, but continues to be used in developing countries due to cost. Aim: This study aimed to determine the prevalence of NVP toxicity and associated factors among 478 pregnant women from three public health facilities in inner city Johannesburg. Materials and methods: We employed a cross-sectional retrospective record review study design to analyse the records of 478 pregnant women in the above mentioned public health facilities. Variables including demographic (age, weight, gestational age) and clinical (CD4 cell count, WHO HIV clinical stage, prior ART experience) characteristics were extracted and the association between these characteristics and the development of toxicity post NVP exposure was explored. Results: The study found that approximately nine out of ten women (89.5%) were ART naïve at the time of NVP initiation. When compared with ART naïve women, ART experienced women had a slightly higher mean CD4 cell count, however, for both groups of women, mean CD4 cell count was less than 250 cells/mm3. Overall, 85.1% of women had a CD4 cell count less than 250 cells/mm3. More than half (55.3%) of the women were in the third trimester of pregnancy and the majority (82%) classified as WHO HIV clinical stage one. At least one adverse event was reported in 63 (13.2%) women. Mild skin rash was the most prevalent adverse event, occurring in 9.6% of women. Hepatotoxicity occurred in 5.3% of women and severe skin rash occurred in 1.5% of women. Almost 85% of adverse events occurred in women with CD4 cell counts <250 cells/mm3. WHO HIV clinical stage II and IV were significantly associated with the overall development of toxicity (ρ <0.01). Conclusions: Whilst the overall prevalence of mild and severe skin rash in this sample was less than that demonstrated in earlier studies, a higher overall prevalence of hepatotoxicity was found. When compared with ART naïve women, ART experienced women were found to have a higher prevalence of mild skin rash. Hepatotoxicity and severe skin rash only occurred in ART naïve women. In this sample, CD4 cell count ≥250 cells/mm3 was not associated with the development of NVP adverse events. Recommendations: Our findings support the continued use of NVP as part of combination ART regimens in women of African descent. In contrast with previously published data, our study showed a significant association between WHO HIV clinical stage and NVP toxicity, our study also included relatively few women with higher CD4 cell counts. Further research including predominantly healthy HIV infected pregnant African women as well as women with higher CD4 cell counts is required in order to fully explore the association between these variables and the development of NVP post-exposure toxicity.

Despite the improved survival of human immunodeficiency virus (HIV) infected individuals with the introduction of highly active anti-retroviral therapy (HAART) in the South African public sector in 2004, new challenges have been brought to the fore. These include drug-related toxicities, particular those of stavudine, which remains in common use within developing countries. A prospective analysis of 9040 HIV-1-infected adults initiated on HAART from 2004 to 2007 at the Themba Lethu Clinic, Helen Joseph Hospital in Johannesburg, confirmed the ability to roll out a successful HAART programme in a resource limited environment with a high retention rate of 70%. Nearly 30% of patients switched to non-stavudine based regimens due to side effects - predominantly peripheral neuropathy, symptomatic hyperlactataemia and lipoatrophy. In an attempt to look for safer options, a prospective randomized controlled trial comparing standard and low dose stavudine with tenofovir was undertaken in 2009. Sixty patients were randomized 1:1:1 to either standard (30-40 mg), low (20-30 mg) dose stavudine or tenofovir (300 mg) each combined with lamivudine and efavirenz. Adipocyte mitochondrial DNA (mtDNA) levels, gene expression, anthropometry, markers of inflammation, lipid and glucose metabolism were assessed at various time intervals. Results demonstrate early mitochondrial depletion among black South African patients receiving low and standard doses of stavudine, with preservation of gene expression levels, except for NRF1 and MTCYB, when compared to patients on tenofovir. Mitochondrial toxicities occurred in both the stavudine arms. Immunological and virological outcomes were similar for all three arms. Both drugs caused lipid changes, but tenofovir had a more favourable effect on anthropometry and adipokines. Both stavudine regimens increased fasting insulin and C-peptide levels, with the higher stavudine dose also causing increased fasting glucose and HOMA levels. This study demonstrates an early association between mitochondrial depletion and stavudine therapy in the black South African population and shows that tenofovir has a minimal effect on mitochondrial numbers. Only two of eight adipocyte genes were significantly affected by stavudine therapy when compared with tenofovir, but this was only seen with the standard dose. This study highlights the occurrence of significant metabolic abnormalities with both drugs. Therefore, awareness of the potential increased cardiovascular risk should be of concern with tenofovir and stavudine, although toxicity is lower in the low dose compared to the standard dose stavudine regimen with no attenuation of anti-retroviral effectivity.

Research Report submitted in fulfillment of the requirements for the degree of Master in Public Health (MPH) at the University of the Witwatersrand. April 2015 / Introduction: Antiretroviral therapy (ART) is a lifesaving clinical intervention for people living with HIV (PLHIV). An important barrier to accessing therapy is the shortage of the health workforce particularly doctors. In order to mitigate the shortage, a nurse driven ART delivery approach known as Nurse Initiated and Managed Antiretroviral Therapy (NIMART) has been implemented in the public sector in South Africa and in other countries. NIMART enables professional nurses to initiate HIV positive persons on ART and manage their care at primary health care clinics. This study sought to explore and describe perceptions of operational managers, facility managers and professional nurses on the facilitators and barriers to the implementation of NIMART in the City of Joburg (CoJ) clinics. Methodology: This was an exploratory descriptive qualitative study which used in-depth interviews with a variety of respondents in order to gain insights into their perceptions of the implementation of NIMART in the CoJ clinics. In total, 26 respondents, comprising of operational managers, facility managers and professional nurses participated in the study. Thematic content analysis was used to analyse data drawing from the Donabedian structure-process-outcome framework. Results: The respondents identified the adequacy of NIMART training and mentoring; the availability and use of NIMART guidelines and the integration of NIMART into Primary Health Care (PHC) services as structural facilitative factors for NIMART implementation. The shortage of the health workforce, shortage of antiretrovirals (ARVs), poor referral feedback, food insecurity and the mobility of patients were identified as key structural and process barriers to the implementation of NIMART. Respondents perceived the improvement in quality of life of NIMART patients and the clinics’ ability to retain patients in care as indicative of the success of iii NIMART implementation. Finally, respondent’s suggestions for improving NIMART implementation in CoJ clinics focussed on improving shortage of the health workforce, improving the availability of ARV drugs and providing opportunities for continuing education for professional nurses. Discussion, conclusion and recommendations: In order to mitigate the barriers identified in this study, recommendations were that the City of Joburg should utilize lower level health care cadres such as nursing assistants and lay counsellors to reduce the professional nurses’ workload and thus improve access to treatment. In addition, the City of Joburg should revise the antiretroviral drug allocations to clinics and revise delivery schedules to ensure that clinics do not run out of ARV drugs. The referral feedback process should be strengthened through the referring clinic and the referral hospital jointly developing referral protocols that should be used by both institutions. Finally, the City of Joburg should consider conducting consultative discussions with professional nurses prior to introduction of new programmes and provide opportunities for regular updates for operational managers, facility managers and professional nurses. Future research could look at the role of PHC qualification in the implementation of NIMART.

Thesis (MPH) -- University of Limpopo, 2012. / No Summary

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, in partial fulfillment for the degree Masters of Medicine in Paediatrics (MMed) Johannesburg 2012 / Introduction: Highly active antiretroviral treatment (HAART) programs in heavily HIV-TB burdened countries may reduce the risk of TB in children directly by improving the immune system of HIV-infected children; and indirectly by reducing the force of transmission from the adult population. The incidence of childhood TB is a sentinel measure of the control of infectious adult TB cases in the community. Objective: We evaluated the impact that scaling-up of the HAART program in Soweto had on the incidence of hospitalization for culture-confirmed TB in children. Methods: The study was undertaken in Soweto, where the prevalence of HIV was 4-5% in children between 2005 and 2009. The estimated HAART coverage increased from 43% in 2005 to 84% by 2009 in children with HIV/AIDS. Hospitalized cases of culture-confirmed TB in children 3 months to 14 years of age were identified through laboratory and clinical electronic databases. Results: Overall, the incidence (per 100 000) of hospitalization for culture-confirmed TB declined by 58% (95%CI 49.3-65.2) from 2005 (71.4) compared to 2008-9 (30.0); p<0.0001. This included a 67% (95%CI 58.5-74.8) reduction in incidence among HIV-infected children from 2005 (1 601) compared to 2008-9 (517; p<0.0001). v In addition, a 33% reduction was observed in HIV-uninfected children (incidence 19.3 vs 12.9; p=0.016). Fifty-six percent of TB episodes, across all study periods, occurred in HIV-infected children who were mainly (76%) severely immunocompromised. Conclusions: Up-scaling of the HAART program in South Africa has been associated with decline in the incidence of culture-confirmed TB, more so in HIV-infected than HIV-uninfected children. Severely immunocompromised HIV-infected children, however, need to be identified and targeted with HAART and other strategies to further reduce the burden of TB in this group.

Thesis (M.Sc. in Epidemiology)--University of the Witwatersrand, Faculty of Health Sciences, 2014. / Introduction: The prevalence of the Human Immunodeficiency Virus (HIV) in South Africa was 17.8% among 15 to 49 year olds in 2010. Antiretroviral therapy (ART) has thus played a crucial role in mitigating the impact of the HIV epidemic. Themba Lethu Clinic is one of the largest single clinics providing ART in South Africa. One of the challenges of ART provision is ensuring adherence to taking the medication. To date there has been no clear consensus on the ideal way to measure adherence in resource limited settings (RLS). Viral load is perhaps the best and most reliable indicator of poor adherence but is expensive and not easily accessible or available in many RLS. Surrogate markers such as mean cell volume (MCV), CD4 cell count, self-reported adherence and missed visits have been shown to be useful to measure adherence but their reliability remains unclear. The aim of the study was to identify other markers that can be used to measure adherence using viral load as the gold standard. Materials and methods: The study was a retrospective analysis of HIV-positive ART-naïve adults (≥ 18 years) initiating standard first-line ART at the Themba Lethu Clinic in Johannesburg, South Africa between April 2004 and January 2012. The association between the last self-reported adherence, change in MCV calculated from baseline to 6 months, change in CD4 count calculated from baseline to 6 months (≥ or < the expected increase of 50 cells/mm3 at 6 months) and missed visits (defined as a scheduled appointment that had been missed by ≥ 7 days but not by more than 3 months) and poor adherence (defined as a viral load ≥ 400copies/ml after 6 months on ART) was tested using Poisson regression models with robust error variance to estimate incidence rate ratio (IRR) and 95% confidence interval (CI). The IRR was used to approximate the relative risk (RR) of poor adherence. Interacting variables were stratified by each other, to create a new variable. The diagnostic accuracy of each identified marker of adherence was also tested using sensitivity, specificity, positive predictive values and negative predictive values. Results: 7160 patients were eligible for the study and of these 63.2% were female. The median age was 36.7 years. The median CD4 count was 101 cells/mm3 at baseline and 18.9% of the patients had poor adherence at 6 months. Variables associated with poor adherence at 6 months were change in CD4 count stratified by change in MCV at 6 months (change in CD4 count ≥ expected and change in MCV ≥ 14.5fL; adjusted relative risk (aRR) 1, change in CD4 count ≥ expected and change in MCV < 14.5fL; aRR 3.11 95% CI 2.41 – 4.02, change in CD4 < expected and change in MCV ≥ 14.5fL; aRR 1.23 95% CI 0.76 – 2.00 and change in CD4 count < expected and change in MCV < 14.5fL; aRR 6.98 95% CI 5.35 – 9.09), CD4 count at baseline (> 200 cells/mm3; aRR 1, 101 – 200 cells/mm3; aRR 1.05 95% CI 0.80 – 1.38, 51 – 100 cells/mm3; aRR 1.08 95% CI 0.80 – 1.47 and ≤ 50cells/mm3; aRR 1.34 95% CI 1.02 – 1.76) , WHO stage at baseline (stage I; aRR 1, stage II; aRR 1.16 95% CI 0.90 – 1.48, stage III; aRR 1.27 95% CI 1.04 – 1.55 and stage IV; aRR 1.44 95% CI 1.12 – 1.84) and MCV at baseline (< 80fL; aRR 1, 80 – 100fL; aRR 1.33 95% CI 1.01 – 1.75 and > 100fL aRR 0.98 95% CI 0.62 – 1.55). Sensitivity and specificity of the change in CD4 stratified by change in MCV at 6 months to predict poor adherence were 86.5% and 37.3% respectively for all eligible patients. For patients on AZT-based regimens the variables associated with poor adherence at 6 months were change in CD4 count at 6 months (≥ expected; aRR 1 and < expected; aRR 7.66 95% CI 0.98 – 59.91) and pregnancy during the first 6 months on ART (Never pregnant; aRR 1 and pregnant during follow up; aRR 9.11 95% CI 2.17 – 38.25). Sensitivity and specificity of the change in CD4 count at 6 months to predict poor adherence were 64.7% and 75.2% respectively for all eligible patients on AZT-based regimens. Sensitivity and specificity of pregnancy during the first 6 months on ART to predict poor adherence were 20% and 97.6% respectively for all eligible patients on AZT-based regimens. Discussion: Change in CD4 count stratified by change in MCV at 6 months was an expected marker of adherence as CD4 count is expected to rise in adherent patients on ART and since most patients (62.9%) were on d4T or AZT-based regimens. Pregnancy during the first 6 months on ART appeared as a marker of adherence for patients on AZT-based regimens before multiple imputation possibly due to missing data hence results for this variable should be interpreted with caution. Contrary to previous studies, self-reported adherence was not associated with poor adherence at 6 months before multiple imputation. This could have been due to the fact that that > 50% of patients had missing data for this variable. The variable is also vulnerable to recall and reporting bias so even after multiple imputation, the area under the receiver operating characteristic (ROC) curve remained < 0.55. The number of missed medical visits and regimen change were also markers of adherence in a few of the models after multiple imputation and require further investigation. In conclusion, the markers of adherence to ART are change in CD4 count stratified by change in MCV at 6 months and pregnancy during the first 6 months on ART for patients on AZT-based regimens. These could help health workers identify poor adherence in the absence of viral load testing and target patients for adherence interventions to prevent virological failure.

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, in partial fulfilment of the requirements for the degree of Master of Medicine in Family Medicine. / Introduction South Africa has more people living with HIV than any other country in the world.1 Women infected with HIV have a high risk in the development of cervical dysplasia and cancer of the cervix more so than women who are not infected.2,3 Methods A cross-sectional descriptive study was carried out by reviewing cervical smears of HIV positive women in a district hospital. Three hundred and ninety cervical Pap smears were classified according to the Bethesda system. Adherence was measured by the patient’s report and viral load. Data was collected through the use of self administered questionaire and data capture sheet. Results The prevalence of abnormal Pap smears was 57 per cent and LSIL was the commonest abnormality seen (142/390, 36%). Eighty-four per cent (328/390) had stage 1 WHO-HIV classification. WHO stage 3 participants seemed to be three times more likely to have abnormal Pap smears than those with WHO stage 1 (OD 3.3, STD. error 1.70, p=0.018, 95% CI 1.23-9.04). Abnormal pap smears were seen more in participants with CD4 cell count ≤ 350 cells/μL as compared to participants with CD4 cell count ≥ 500 cells/μL { 122/172, (71.00 %) vs 48/117, (41.03%), p-0.000, 95% CI : 0.09-0.37}. Similarly, participants who did not use HAART had more abnormal results as compared to those who used HAART {42/60(70.00%) vs 180/330 (55.00%), p-0.028, 95% CI 0.28-0.93}.Adherence to HAART did not show any link with abnormal smears. Conclusion The more immune-suppressed a woman is, the higher the risk of developing cervical cancer precursors. The high risk group in this study was found to be the participants with the CD4 cell count of ≤ 350 cells/μL and the viral load ≥1000 copies/mm3. The self-reported adherence level did not show any impact.

This research investigated the ethical and legal issues that impact on the urgent implementation of Nurse Initiated and Managed Anti-Retroviral Treatment (NIMART) in South Africa, which is part of the task-shifting strategy recommended by the World Health Organization (WHO) to deal with the human resource shortage that has negatively impacted access to Anti-Retroviral Treatment (ART) in developing countries (WHO;2006). The objectives were to review and analyse the existing legal framework and provisions for NIMART in South Africa; and to identify ethical issues and implications of NIMART within the current legal framework. It analysed the legal issues that impact on the implementation of NIMART within the public health service in South Africa, as well as the ethical basis and implications of NIMART on the practice of nurses in the scale-up of Anti-Retroviral Treatment in Primary Health Care (PHC). A comparative analysis was done with case studies of task-shifting in other developing countries and evidence-based recommendations for an enabling and long-term sustainable ethico-legal approach to task-shifting were established. The research concluded that despite the existing legal framework for NIMART in South Africa being firmly founded in the Constitution and further enabled by health policy, challenges exist in implementation of certain critical aspects of the enabling legislation relating to nurse training and accreditation required for full authorization to practice NIMART and that these technical challenges if not attended to could threaten the long-term sustainability of NIMART.

Reverse transcription of human immunodeficiency virus type-1 (HIV-1) is primed by cellular tRNALys3, which is selectively packaged into viral particles where it is bound at its 3' terminus to a complementary sequence of viral RNA termed the primer binding site (PBS). In addition to the PBS, other regions within the viral genome also interact with tRNALys3. Initiation of HIV-1 reverse transcription requires specific recognition of the viral genome, tRNA primer, and reverse transcriptase (RT). In this work, we study the important role played by the initiation complex in the initiation of HIV-1 reverse transcription. An "A-rich loop" located upstream of the PBS has been shown to interact with the anticodon loop of tRNALys3 and deletion of this A-rich loop caused diminished viral replication fitness. We have now studied the mechanisms involved in the altered replication capacities of the deletion-containing viruses in the context of both wild type HIV-1 and viruses also containing the M184V substitution in RT. We found that the M184V mutation in RT compromises the ability of deletion-containing viruses to restore wild-type replication. Further biochemical study indicates that both the M184V mutation in RT and deletion of sequences upstream of PBS caused diminished viral replication fitness by compromising the efficiency of reverse transcription initiation. / Since the initiation of DNA synthesis was shown to be a highly specific process, it represents a potential target for the development of novel antiviral agents. We developed strategies for inhibition of the HIV-1 replication via interference with the tRNALys3/viral RNA complex. To target primer tRNALys3, we employed oligodeoxyribonucleotides (ODNs) that are complementary to different parts of the tRNA primer. To target viral RNA, we devised a tRNALys3-like molecule, termed tRNA Lys*, that contained sequence alterations that direct initiation from a region distant from the natural PBS, designated PBS*. PBS* is involved in the formation of the natural tRNA/PBS complex and binding of tRNALys* was shown to interfere specifically with the initiation of reverse transcription. Inhibition of the synthesis of (-) strand strong-stop DNA was achieved successfully with both strategies by interfering with the formation of the initiation complex.