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.

>Magister Scientiae - MSc / Adverse effects are a significant factor that determine how long patients will tolerate a given antiretroviral drug regimen. They also influence treatment options, and play an important role in the much needed adherence to treatment by patients on Highly Active Antiretroviral Therapy (HAART). This study is aimed at understanding adverse effects experienced by patients on the first line antiretroviral therapy at Keetmanshoop Hospital in Namibia. Methods : A retrospective quantitative method was used to review records of patients on first line antiretroviral treatment who started treatment between November 1st 2007 and December 1st, 2008 and followed up until they reached 36 – 48 months on treatment. Records of 94 patients were found eligible to be included in the study. Data was analysed using Stata 12 data analysis software. Results : The most reported adverse effect was musculoskeletal disorders (25%) whereas headache (16%) was the least reported. Low haemoglobin (78%) was the most common recorded hematologic adverse effect whereas low red cell distribution width and low mean platelet volume were the least recorded adverse effects (0%). A Male patient was more likely to experience a low haemoglobin levels compared to a female patient (adjusted OR: 3.29, 95% CI: 1.3 – 8.3). A male patient was found to be 64% times less likely to experience a higher mean cell haemoglobin compared to a female patient (adjusted OR. 0.31, 95% CI: 0.11 – 0.87). A patient on nevirapine was more likely to experience an elevated creatinine level compared to a patient on efavirenz (adjusted OR; 36.0, 95%CI: 2.02 – 62.5). At baseline, a patient who had prior exposure to ART had an 81 times (adjusted OR: 81.4, 95%CI: 5.3 – 119, p-value=0.00) increased odds of experiencing a high mean cell volume (MCV) compared to a patient with no ART exposure. A patient with a higher CD4 count was also less likely to experience a low hemoglobin compared to a patient with low CD4 count (adjusted OR; 0.31, 95% CI: 0.12 – 0.77). The author recommends further studies with higher sample size to confirm whether higher creatinine levels are more prevalent in patients on nevirapine compared to patients on efavirenz; this will have clinical implications especially in patients with impaired renal system. Antiretroviral treatment increases chances of developing macrocytosis anaemia; clinical implication of this condition may need to be investigated.

MSc, Paediatrics and Child Health, Faculty of Health Sciences,University of the Witwatersrand / Background To investigate whether in-utero exposure to highly active antiretroviral treatment (HAART) is associated with low birth weight and/or preterm birth in a population of South African women with advanced HIV infection. Methods A retrospective observational study was performed on women with CD4 cell counts ≤250 cells/mm3 attending antenatal antiretroviral clinics at two clinics in Johannesburg between October 2004 and March 2007. Low birth weight (<2.5kg) and preterm birth rates (<37 weeks) were compared in those exposed versus unexposed to HAART during pregnancy. Effects of different HAART regimen and duration (<28 weeks or ≥ 28 weeks) were assessed. Results Among HAART-unexposed infants 27% (60/224) were low birth weight (LBW) compared to 23% (90/388) of early HAART-exposed and 19% (76/407) of late HAART-exposed infants (P=0.05). In the early HAART group, older maternal age was associated with LBW and higher CD4 cell count protective against LBW (AOR 1.06, 95% CI 1.00- 1.12 and AOR 0.58, 95% CI 0.46-0.73, P<0.001, respectively). HAART-exposed infants had an increased risk of preterm birth vii (<37 weeks) (15% [138/946] versus 5% [7/147], p=0.001), with early (<28 weeks) nevirapine and efavirenz having the strongest associations with preterm birth (AOR 5.4, 95%CI 2.1-13.7, P<0.001 and AOR 5.6, 95%CI 2.1-15.2, P=0.001, respectively). Conclusion Among infants born to women with CD4 cell counts <250 cells/mm3, HAART exposure was associated with preterm birth, but not with low birth weight. More advanced immunosuppression was a significant risk factor for both LBW and preterm birth, highlighting the importance of earlier HAART initiation in pregnant women, both to optimize maternal health and to improve infant outcomes

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.

MPH, Faculty of Health Sciences, University of the Witwatersrand / Background: The increase use of highly active antiretroviral therapy (HAART) among patients with HIV infection and AIDS has led to increasing reports of metabolic abnormalities such as diabetes mellitus, hypertension, dyslipidaemia and obesity. Therefore, it is important to explore the burden of these diseases among HIV infected patients. Objectives: To determine the burden of metabolic diseases (hypertension, diabetes, obesity and dyslipidaemia) in patients attending HIV clinic at the Charlotte Maxeke Johannesburg Academic Hospital (JHBH). Methodology: It was a cross-sectional study. The study population included patients attending JHBH HIV clinic and on HAART for more than one year. A sample size of 304 patients, including 237 females and 67 males partook in this study. Anthropometric measurements were taken from patients and blood samples of these patients were sent to laboratory for lipograms, HbA1c, random glucose, CD4 lymphocytes counts as well as HIV viral load testing. The data was analysed with standard statistical software Epi-info version 6.0. Both descriptive and analytical statistics was used. Results: The prevalence of metabolic syndrome according to the IDF was 20.4 %; obesity (BMI 30 kg/m2) was 16.8% and patients that were overweight (BMI > 25 kg/m2 and BMI < 29.9 kg/m2) was 28.6%; hypercholesterolemia (TC 5.0 mmol/l) = 35.5%; HDL< 1.29 mmol\L in females was 58% and HDL <1.04 mmol/l in males was 36%; elevated triglycerides 1.7 mmol/l was 30% and only 16% was classified as being hypertensive (BP 140/90 mmHg and / or on Hypertensive medication). The majority of the patients (86.2%) had a CD4 lymphocyte count 200 X 106 cells/l and 84% of patients had less than detectable limits for viral loads (VL< 40 copies / μl), which has been reported as optimum levels for metabolic diseases in HAART recipients. Conclusion: These results clearly indicate that there is a growing burden of metabolic diseases among HIV patients on HAART attending the Johannesburg hospital HIV clinic. The current study also indicates that the metabolic disturbances are more frequent in women than in men, except for hypertension.

The manifestation of HIV-1 infection is different in children and adults. Most of the children who acquire HIV perinatally progress to disease within the first two years of life, while adults can remain asymptomatic for up to ten years. However, a small minority group of children can control the virus for years in the absence of antiretroviral therapy. We characterized CD8+ T cell responses critical for the containment of HIV infection in a cohort of infants HIV infected from birth using IFN- γ ELISPOT, multicolour flow cytometry and viral sequencing of the Gag protein. We investigated whether the age at the time of infection, specificity and functionality of the generated responses, genetic make up and the maternal immune responses to HIV, influenced disease progression in the child. We found that the majority of in-utero infected infants mounted CD8+ T cell responses from the first days of life. In contrast to chronically infected children or adults, the specificity of the initial response in acutely infected infants was directed towards Env and Rev proteins and CD4+ T cell responses were minimal during the first 6 months of life. Slow progression to disease was associated with possession of one of the protective HLA-B alleles by either the mother or the child (P=0.007) and targeting of Gag epitopes presented by the protective HLA-B alleles. Mothers who expressed protective alleles but whose children did not possess these alleles, transmitted less fit viruses that benefited their children. Furthermore, slow progressor children had more polyfunctional CD8+ T cell responses in early infection when compared to rapid progressors (P=0.05). The ability of infants to induce CD8+ T cell responses early in life is encouraging for vaccine interventions. The differences in the specificity of the initial responses between adults and children, insufficient priming of these responses as a result of minimal CD4+ T cell help during infancy and possession of non-protective HLA alleles shared between mother and child, may explain the rapid disease progression generally noted in most infants. However, slow progression to disease in the minority group of children may be attributed to functional capacity of the CD8+ T cells generated by the child, mediation by protective HLA alleles, acquisition of low fitness viruses from the mother or de novo attenuation of the virus by the child’s own immune responses. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2011.

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.

Thesis (Ph.D.)--Kent State University, 2007. / Title from PDF t.p. (viewed Mar. 11, 2009). Advisor: Miguel Quiñones-Mateu. Keywords: HIV/AIDS, drug discovery, small molecule library screening, characterization of new antiretroviral drugs, highly active antiretroviral therapy. Includes bibliographical references (p. 180-200).