Human immunodeficiency virus-1 (HIV-1) and tuberculosis (TB) are significant global health issues today and the immunological correlates of protection to both diseases remain poorly defined. HIV-1 is the greatest risk factor for the development of TB and HIV-associated TB contributes significantly to the global TB burden, particularly in sub-Saharan Africa. The host T cell response to Mycobacterium tuberculosis (Mtb) is critical for control and is weakened in HIV-1 disease. However, the extent and precise mechanisms remain incompletely elucidated. Antiretroviral therapy (ART) for HIV-1 reduces TB risk in treated individuals significantly, although not to levels seen in HIV-uninfected individuals. This thesis studies HIV- and Mtb-specific T cell responses in 2 cohorts of individuals from a community with high HIV-1 and TB prevalence in Bloemfontein, South Africa. An analysis of HIV-specific CD8 T cell responses in Chapter 4, confirms the superior role of HIV-1 Gag-specific CD8 responses in controlling HIV-1 viraemia and demonstrates that the loss of such responses contributes to HIV-1 disease progression and likely susceptibility to opportunistic infection. I investigated the impact of HIV-1 infection on the Mtb-specific T cell response through a cross-sectional comparison of T cell responses in HIV-infected and HIV-uninfected individuals (Chapters 5 and 6). HIV-infected individuals had a significant depletion of both Th1 and Th17 CD4 responses to Mtb-specific antigens as well inhibition of Mtb-specific CD8 T cell responses, in comparison to those uninfected with HIV-1. PPD- and Rv2031c-specific responses were particularly reduced in HIV-infected individuals. Over a 12 month period of therapy, ART partially restored the Mtb-specific CD4 T cell response (Chapters 5 and 7). This effect was greater for Th1 than Th17 responses and had no detectable effect on the Mtb-specific CD8 response. However, despite some evident restoration, there remains a significant quantitative deficit in individuals on ART that is likely to contribute to persistent elevated TB risk. Overall, these data contribute to a better understanding of the mechanisms of susceptibility to TB during HIV-1 disease and ART, as well as of the correlates of protective immune responses to both pathogens.

Magister Public Health - MPH / Adolescents living with HIV (ALHIV) are notably underserved by national HIV programmes globally due to their unique needs. Of particular concern is limited access to and availability of adolescent-friendly ART services, which contributes to poor ART adherence and retention in care in many sub-Saharan African countries. Poor adherence in adolescents has been associated with medicine side effects, pill fatigue, non-disclosure of status to the child, inadequate information on HIV, caregiver-child communication, caregiver’s health beliefs and stigma, and lack of knowledge on the rationale of taking medicines. Several interventions have been developed to improve ART adherence and retention in care amongst ALHIV through peer groups and psychosocial support. The Teen Club intervention was introduced in 2010 at Intermediate Hospital Katutura Paediatric ART clinic in Windhoek to improve ART adherence and retention in care amongst ALHIV by providing psychosocial support in a group environment. However, to date no formal evaluation of the effectiveness of the Teen Club intervention in Namibia has been conducted. The aim of the study was to compare the effects of the Teen Club intervention against standard care on treatment outcomes for ART (i.e. adherence, retention in care and viral suppression) in adolescents at Intermediate Hospital Katutura Paediatric ART clinic in Namibia. Methods: A retrospective cohort analysis of HIV positive adolescents aged 10-19 years, who were accessing ART between 1 July 2015 and 30 June 2017 was conducted. Patient data was extracted from the electronic Patient Monitoring System (ePMS), individual Patient Care Booklets and the teen club attendance register. Adherence to ART was measured through pill counts; and retention by kept clinic visits. Viral load results were assessed to measure levels of viral suppression. Adolescents with viral loads ≥ 1000 copies/ml were classified as not virally suppressed whilst those with viral loads <1000 are virally suppressed (with those <40 fully suppressed). Results: The total sample was 385 participants; with 78 of them in the Teen Club (exposed) and 307 adolescents in standard care (unexposed).

Master of Public Health - MPH / Background: Globally, it is estimated that about 1.8 million adolescents (aged 10–19 years) were living with HIV in 2015. In Kenya an estimated 133,455 adolescents were living with HIV in 2015, of which 75% (105,679) were in need of antiretroviral therapy (ART). Among adolescents on ART in 2016, 63% reported viral suppression; which is far below the UNAIDS targets of 90%. Viral suppression (having less than 1000 copies of viral RNA/ml of blood) is a key indicator of HIV treatment success, and is associated with better quality of life and reductions in HIV incidence at a population level. Homabay County recorded the highest HIV prevalence (26%) and the highest number of adolescents living with HIV in Kenya (15,323) in 2015. By the end of June 2017 5,709 adolescents were initiated on ART in Homabay County. Despite the successes in initiating HIV positive adolescents on ART, little is known about the factors that are associated with viral suppression. The current study investigated the factors associated with viral suppression among adolescents initiated on ART before November 30, 2017 in Homabay County, Kenya. Methods: A descriptive cross-sectional study was conducted among 925 adolescents registered on ART for at least 6 months and with at least one documented viral load in the last 12 months, in six health facilities in Homabay County. Data was extracted from the electronic medical records and exported into an excel spreadsheet. Bivariate and multivariate logistic regression analyses were conducted to identify factors associated to viral suppression using Stata 12.0.

Magister Public Health - MPH / Background: TB is one of the most common opportunistic infections in the HIV infected population. In 2014, of the 9.6 million people estimated to have TB globally, 1.2 million were also infected with HIV. In the same year WHO reported 400 000 TB deaths in HIV infected people worldwide. TB Prevention strategies include ensuring HIV infected people take ART, TB infection control, treatment of TB cases and pharmacological prevention of primary TB infection or progression of latent TB into active TB. Isoniazid preventive therapy for a minimum of six months has been recommended to reduce the risk of TB in people living with HIV. Aim: The study’s aim was to determine the programmatic outcomes of isoniazid preventive therapy (IPT) and factors associated with treatment completion among people living with HIV aged 15 years and above at the AIDS Healthcare Foundation LaMvelase clinic in Manzini Swaziland, who were enrolled for IPT during the period March to December 2014. Methodology: This was a quantitative retrospective analytical cohort study that reviewed 3642 patient care records. IBM SPSS 20 was used for descriptive and statistical analysis of the data. Descriptive statistics were calculated and reported as frequencies and percentages. Bivariate statistics were carried out to test independent associations between socio-demographic and clinical characteristics, and IPT completion. Further multiple logistic regression analysis was done to determine the nature of association between the dependent and independent variables which had p < 0.1.

Magister Public Health - MPH / Background: The goal of ART therapy is sustained viral load suppression with good immunological and clinical response. This optimal response to therapy results in the prevention of emergent ART drug-resistant mutations, decrease morbidity, and AIDS-related mortality and sustained retention on ART. Kenya, like most countries in Sub-Saharan Africa, has scaled-up the use of ART and is currently implementing a “Test and Treat” strategy in which any client identified and confirmed with an HIV diagnosis is initiated ART. Few studies have been carried out to ascertain the response of HIV patients initiating treatment in resource-limited settings. Moreover, it has been demonstrated that a certain proportion of patients fail to adequately respond to therapy and therefore require therapy modification. Aim: To assess treatment outcomes and calculate retention of HIV infected adult patients’ (15 years and above) initiating ART at Kakamega County General Hospital. The primary study outcome was the treatment outcome of patients-initiated ART two to three years prior to the study; while, the role of WHO criteria for screening treatment failure was assessed as a secondary outcome. Methods: This was a retrospective cohort study in which patients initiating ART between June 2014 and March 2015 were followed up until they were censored or study closed in August 2017. 284 patients were enrolled in the study after accurately matching information in their clinic files and the electronic medical record. Data were collected from patient records using a chart abstraction tool and transferred to an Access database from where the cleaning and validation of entries were done. Data from Access was transferred to STATA 15.1 for analysis. Descriptive statistics and inferential statistics were then performed to answer the research questions.

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

The national programme of expanded access to antiretroviral therapy in the South African public health sector has resulted in hundreds of thousands of South Africans being subjected to prolonged therapy with the risk of adverse drug effects. Among the most common adverse effects are metabolic disorders one of which is mitochondrial toxicity. Mitochondrial toxicity may manifest as hyperlactatemia. The study was designed to determine the frequency with which hyperlactatemia occurs in HIV – infected adults on long-term antiretroviral therapy (ART). The objective was to determine the proportion of patients with blood lactate levels that exceed a predetermined cut-off level and to attempt to relate hyperlactatemia to a set of factors namely, gender, age, obesity, symptoms, type of ART regime and duration of ART use. The study was conducted at an ART clinic in the provincial state hospital of Bongani in the town of Welkom in Free State. The target population was male and female adult patients (18 years and above) on ART for a duration of 1 year or longer. Participants were selected by a random sampling of hospital case file numbers using random table numbers. The patients answered a set of 7 questions on symptoms, underwent weight and height measurements before having blood drawn for lactate assays Blood specimens for lactate assays were processed at the local National Health laboratory.

Introduction: South Africa has embarked on a massive roll out of ARVs to more than 1.4 million people living with HIV/AIDS. Provision of ARVs to people living with HIV/AIDS encounters many challenges associated with adherence. Properly taken ARVs have been shown to reduce viral loads to undetectable levels and increase the CD4 count. This in turn leads to a drop in opportunistic infections and better health outcomes but the requirements for adherence are high. Several patient-related factors have been reported to affect adherence rates. Nonadherence on the other hand has been reported to lead to the development of drug resistant strains of HIV. It recognised that the resistance to ARVs can quickly lead to build up of highly resistant strains in the blood due to one week of missed medication. Aims and objectives: This study set out to identify factors which affect adherence to HAART among adults on HAART in two health facilities in Gauteng province in 2006.The main objectives were to assess the patient adherence using viral load response and self-report data. Secondly, the study was to determine factors that facilitate adherence and finally barriers to adherence at the two sites. Materials and methods: A cross sectional study was done at the two ARV facilities in Gauteng from July to November 2006. Two physiological methods -CD4 counts and plasma viral load, and one subjective-3 day recall self- report methods were used to asses adherence. Exit interviews and record reviews were done to collect data. Virologic outcome was the preferred surrogate marker for adherence. Univariate and bivariate analyses were done to determine measures of association. Measures of association (Chi square) at a 95% significance level for factors affecting adherence were then determined and results obtained. Results: The mean age was 36.9 years (range 18-70 years) and 73.5% were women. Self-report data (n=343) indicated 98.4% in the higher adherence category (taken 100% of their doses). Viral load data (n=343) showed that 88.8% were in the adherence lower category (<400 RNA copies). Viral load outcome (“adherence”) was significantly associated with the length on treatment (p<0.05) and patients who had been on treatment for 12-24 months had lower viral load than those who had been treatment for a shorter time (<12 months) or longer (>24months). However, gender (p=1.000), age (p=0.223), level of education (p=0.697) and access to social grants (p=0.057) were not associated with “adherence”. Socio-economic status was significantly associated with viral load outcome (p<0.01) as well as cost (n=185; p<0.05). Individuals who incurred the highest costs (>R25) were the least likely to adhere followed by those facing average costs (R15-25) compared to the reference group (< R15). Conclusion: Adherence rates of 88.8% suggest that respondents from both facilities can optimally adhere to their medication when they have been on ARVs for longer than a year. These are minimum adherence rates. There were factors that still hinder adherence at both the individual patient level. There is still a need for more targeted interventions especially towards men who were noted to have a relatively low uptake of HAART within the two sites.

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.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, in fulfillment of the requirements for the degree of Master of Science Johannesburg, August 2012 / It is known that infectious agents elicit different responses in different individuals which strengthens the view that susceptibility and resistance to infectious diseases has a genetic component. These differences in susceptibility to disease can be observed in populations. APOBEC3G is a member of the cytidine deaminase gene family located on chromosome 22. It is crucial in non-permissive cells as it functions as part of the innate immunity system and is an inhibitor of the HIV-1 accessory protein vif. The goal of the study was to develop genotyping assays and estimate allele frequencies. Thus, genetic variation within APOBEC3G was identified and characterized in black South Africans. Indirect genotyping assays were designed to amplify regions within the upstream non-coding region, and in exon 4 of the coding region of the gene. Selected polymorphisms were then genotyped using allele-specific PCR, RFLP-PCR and Pyrosequencing™ assays. Reanalysis of sequence data from 2003 showed numerous SNPs were well represented. Comparison of sequence data at various SNPs showed that allele frequencies were similar to frequencies in other African populations. The only sequenced SNP that deviated from the frequencies in Ensembl was -590. Thus the sequencing was a useful tool for detection of variation. ASA proved to be the least reliable genotyping technique as the minor allele frequency of -571 (0.59) deviated from the published frequency of 0.894 in Africans. RFLP analysis proved more reliable for genotyping -571 and H186R. The minor allele frequency was estimated to be 0.84 and 0.32 for -571 and H186R respectively. The frequency of H186R is similar to published data from An et al (2004) and Reddy et al (2010). If SNPs are in LD they occur together on the same haplotype more often than by chance. Usually SNPs that are in LD are in close proximity. However our data suggests -571 and H186R SNPs which are 5kb apart are not in LD. A LD map of chromosome 22 shows highly variable pattern of LD (Dawson et al, 2002). Widespread regions of nearly complete LD up to 804 kb in length are intermingled with regions of little or uundetectable LD. Haplotype analysis showed the most frequent haplotype was GA. This was the most frequent haplotype when the sample types were subdivided according to spoken language. in comparison to studies from An et al, (2004) D’ of the two SNPs was estimated at 0.967. The linkage disequilibrium (LD) revealed a non-independence of allele segregation because the loci analyzed were strongly linked in the Apobec 3 G gene. The data are consistent with greater genetic diversity of African populations and can form the basis for further evaluation of the role of variation in this gene in response to HIV.