A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, in fulfillment of the requirements for the degree of Master of Science in Occupational Therapy. Johannesburg, January 2017 / Background and purpose Disability in people living with human immunodeficiency virus (HIV) has become a major health problem especially in HIV endemic countries like South Africa. In this study we determined the validity and reliability of the first specific disability assessment instrument for people living with HIV, the HIV Disability Questionnaire (HDQ). Methodology Adults living with HIV were recruited from hospital clinics and AIDS service organizations in South Africa. A demographic questionnaire and HDQ paired with two reference measures were administered. To assess construct validity, factor analysis, convergent and divergent validity and level of disability against known group variables were determined. Cronbach’s alpha was established to determine reliability of the HDQ. Results Of the 498 participants, the majority were females (68.27%) and were taking antiretroviral therapy (100%). Majority of the participants were black (95.18%) and have a median age of 41 years. Confirmatory factor analyses indicated goodness of fit similar to that previously shown for the HDQ, with the hypotheses for convergent and divergent validity and known group variables being accepted. Internal consistency was good with Cronbach’s alpha values above 0.7 for all domains on the HDQ. Conclusions The HDQ demonstrates a variable degree of construct validity and internal consistency when administered to adults living with HIV in South Africa. / MT2017

A research report submitted to the University of the Witwatersrand, Johannesburg in fulfillment of the requirements of the degree of Master of Medicine 2016/2017. / Background: The effect of HIV infection on the evolution of NCC constitutes a new area of interest. Purpose: To review the literature on the imaging appearances of NCC and HIV co-infection and compare it with our cases. Materialsand methods: Data from both published andlocal cases were analysed. HIV-infected cases were divided into “low” (<200 cells/mm3) and“high” (≥200 cells/mm3)CD4 groups. These groups were compared and the effect of treatmentwas evaluated. Results: Thirty-three cases were evaluated - 20of our, and 13 published, cases. The published cases had parenchymal brain cysts, whereas our cases had both parenchymal and subarachnoid cysts (p=0.0050). The published cases also had intra-axial cysts, whereas our cases had both intra- and extra-axial cysts (p=0.012). The published cases had predominantly cystic lesions, whereas our cases had both cystic and granulomatous lesions (p=0.019). There were no differences between cases with a CD4 count of <200 cells/mm3 and cases with a CD4 count of ≥200cells/mm3but, interestingly, 3% of the cases with a CD4 count of <500cells/mm3,compared with 50% of the cases with a CD4 count of ≥500cells/mm3,had racemose cysts. Conclusion:NCC is very prevalent in South Africa and may complicate the diagnosis and treatment of patients with concomitant HIV infection.Patients with a “low” CD4 count may present with atypical lesions, delaying the diagnosis of NCC. Early initiation of HAART may result in patients presenting with more classical symptoms and imaging appearances, thus improving outcomes. / MT2017

research report submitted to the School of Public Health, University of the Witwatersrand in partial fulfillment of the requirements for the degree of Master of Public Health. May 2015 / Introduction HIV and AIDS in South Africa has a considerable disease burden which places an enormous strain on the health care system. The increased workloads brought about by testing and counseling, prevention, treatment, care and support services with a concomitant decrease in the supply of health care workers impacts negatively on the quality of services. Health planners and managers need to implement approaches that enable maximum utilisation of available resources by integrating HIV and AIDS into the normal functioning of existing programmes to address increasing demands for HIV and AIDS services and to strengthen the health care system. Aim and Objectives The aim of the study was to describe the extent of integration of HIV and AIDS services at the different levels of care in the district health system. Method This is a descriptive cross sectional study that used structured pretested interview questionnaires, data review and a facility check list. A stratified random sample of five facilities that were accredited in the district from 2004 – 2007 was used. Fifty two interviews were conducted face to face with facility managers, doctors, nurses, dieticians, social workers, and lay counselors and seventeen self-administered questionnaires were completed by district programme managers. A total of 69 interviews were conducted. Results The study highlighted the fact that most of the facilities (96%) implemented the HIV and AIDS programme without a documented operational plan. Stakeholder participation on planning was limited at less than 30% across all levels of services within the district. Budgeting and resource allocation operated independently from the district and facility financial systems resulting in parallel systems. Technical support and programme reviews by the district and provincial managers were weak and irregular. Support of HIV and AIDS services was mainly given by facility management. The district`s monitoring and evaluation systems were not in place. The referral systems between the facilities and community structures were not well established. Lay counselors skills on PMTCT and nutrition was rated the lowest and compromised the implementation of an integrated approach. HIV and AIDS services were not implemented at well baby clinics. Conclusions The findings of this study suggests that the HIV and AIDS services have developed into separate vertical administrative and reporting systems operating differently from the mainstream services and not supporting the strengthening of the health care system and therefore not capable of achieving the intended goal of the programme.

M.Sc. (Med.), Faculty of Health Sciences, University of the Witwatersrand, 2009 / OBJECTIVE: To explore gender-related differentials of HIV prevalence in Limpopo Province, South Africa. METHODS: This is a cross-sectional study, data collected by the Rural AIDS and Development Action Research (RADAR) Program for the purpose of a controlled community trial in Limpopo Province. The study population consisted of 798 young men and 992 young women aged 14 to 25 years old. Subjects were tested for the presence of HIV antibodies and answered structured questionnaires. Logistic regression was used to examine risk factors related to gender differentials of HIV prevalence. RESULTS: The prevalence of HIV infection was 5.8% in men and 12.4% in women. Women often had older partners, while men had much younger partners or partners of a similar age. Men with primary education and reporting as students showed a reduced risk of HIV infection whereas unemployed women showed an increased risk of HIV infection. Sexual debut at the age of ≤ 16 was associated with increased risk of HIV infection among both sexes. A significantly higher HIV prevalence was found in women with more than four lifetime sexual partners, young women having an age difference of three to 9.9 years from their sexual partners, women having non-spousal sexual partners of 22 to 26 years of age, and women reporting no regular financial support. Frequency of sex of six to 20 times was a marker of increased risk of HIV among men. CONCLUSIONS: The risk of HIV infection was higher in young women than in men. The increased risk of HIV infection in women might be explained by social and behavioural factors that lead young women to select older partners, and is perhaps also a result of the biological susceptibility of women to HIV infection.

The principal aim of the study was to establish the HIV Seroprevalence in an acute Orthopaedic trauma setting in an urban teaching hospital. Secondary aims were (i), to establish if the seroprevalence compares with the national averages and findings from other similar studies, and (ii), to establish the effect of informed consent on the response rate to recruitment in HIV related studies. Methodology All illegible patients (able and qualified to give an informed consent for HIV testing) admitted to the Orthopaedic trauma unit at the Johannesburg hospital, were pre-counselled and tested for HIV after admission. Those that tested positive were then counselled again and referred accordingly to the HIV clinics for follow up. Results A total of 797 patients were admitted during the period. 159 (20%) did not meet the inclusion criteria, declined counselling or could not be counselled for various reasons. The main reason for non response was cited as a need to wait until after the acute event before they considered the test. A total of 648 patients were therefore eligible for recruitment. All patients were pre-counselled for the test and 246 (39%) consented and signed the informed consent form. Of those that were tested, 57 (23%) tested positive and were followed up accordingly. This result was then compared with previous non Orthopaedic studies on the HIV Seroprevalence. The rate of HIV infection in our acute orthopaedic trauma setting was found to be 23%. This is higher than the national averages but compares with other studies. Most acutely traumatized patients are not willing to be tested for HIV in the acute setting. This has a huge bearing on recruitment of suitable candidates for future studies in HIV in an acute trauma setting. Higher response rates to recruitment in HIV studies are directly proportional to the use of qualified counsellors in organized centres like the Voluntary Counselling and Testing centres.

Since the discovery of HIV-1, the production of an effective prophylactic or therapeutic vaccine remains elusive. An effective vaccine must be able to elicit a potent humoral and cellular immune response. Neutralizing antibodies target the envelope glycoproteins on the surface of HIV-1 virions thereby preventing viral entry. Unfortunately, to date only a handful of neutralizing antibodies have been identified that are capable of neutralizing different viral strains within diverse subtypes, and none have been isolated from HIV-1 subtype C infected patients. In this study, we screened four different HIV-1 subtype C infected patient cohorts for the presence of neutralizing antibodies against a panel of 5 subtype C and 1 subtype B pseudovirus/es in a pseudovirion based neutralizing antibody assay. The CT cohort comprised 9 slow progressor plasma samples, the FV cohort consisted of 11 antiretroviral drug naïve HIV-1 subtype C infected plasma samples. Plasma samples from 10 antiretroviral treatment experienced HIV-1 subtype C infected patients failing first line therapy made up the DR cohort and the JM cohort consisted of 10 serum samples from HIV-1 seropositive or seronegative individuals with an autoimmune disorder. A pseudovirion neutralizing antibody assay was successfully established, and all plasma and serum samples were heat inactivated and screened using this assay. Analysis of the percentage neutralization and IC50 data showed no correlation between the presence of neutralizing antibodies and delayed disease progression in the SP cohort. High levels of neutralizing antibodies were observed in the DR cohort, however future studies are required to confirm if the measured neutralization is due to residual antiretroviral drugs in the plasma or neutralizing antibodies. No samples within the FV cohort showed promising neutralizing antibody activity however the JM cohort harboured 3 serum samples (TN5, TN6 and TN8) that exhibited a greater than average breadth of neutralization and are worth investigating further in future studies. Patients TN5, TN6 and TN8 were all HIV-1 positive with an additional autoimmune disease. The availability of stored bone marrow samples for TN5, TN6 and TN8 will allow for the generation of antibody phage display libraries and isolation of monoclonal antibodies, with potentially broadly cross reactive activity.

Introduction: The spread and prevalence of the HIV epidemic has resulted in extensive social, cultural and economic consequences in sub-Saharan Africa. It is estimated that about 60% of adults living with HIV in sub-Saharan Africa are women. South Africa, with 5.2 million HIV infected people, is estimated to have the largest number of people living with HIV/AIDS in the world. HIV among older women is not well documented, despite high prevalence rates amongst women 45 years and older. Moreover, few HIV-related interventions are directed to the elderly in South Africa. HIV risk factors among older women have also not been well documented. It is important to determine the factors associated with older women, and how they affect their HIV infection rates. Understanding these factors may lead to better HIV prevention strategies. This study aimed to determine the HIV prevalence in older South African women and to determine the factors associated with HIV infection in older South African women living in Soweto, Johannesburg. Materials and Methods: We did an analytical cross-sectional study on a convenience sample of 500 women (45 years and older) recruited from various venues in Soweto, a large urban African setting in Johannesburg, South Africa, and who accepted to be tested for HIV. Private face-to-face interviews were conducted and included an assessment of socio-demographic characteristics and behavioural factors thought to be associated with HIV. Results: 449 women were included in the study and 52 (11.6%) women were found to be HIV positive. Increased odds of HIV infection was associated with condom use (OR=3.75, 95%CI: 1.71–8.19), transactional sex (OR=2.44, 95%CI: 1.04–5.69) and marital status. Compared to a married woman, a woman was more likely to be HIV positive if she was single, widowed or “cohabiting”. Decreased odds of HIV infection was associated with age (OR=0.90, 95%CI: 0.85–0.96) and education. With respect to a woman with less than 5 years of education, a woman was less likely to be HIV infected if she had more than 5 years of education. Conclusion: Further research needs to be done to determine the exact HIV prevalence amongst older women, as well as risk factors associated with HIV infection. It is also important that older women be encouraged to use condoms, as they are known to be an effective barrier to HIV infection. There is need for HIV-related interventions targeted to older women.

M.Sc.(Med.) (Molecular Medicine and Haematology), Faculty of Health Sciences, University of the Witwatersrand, 2011 / The Human Immunodeficiency Virus type 1 (HIV-1) integrase is an essential enzyme required for viral replication. Integrase forms part of an ensemble of proteins known as the preintegration complex and functions by a two-step process. Firstly, the cleaving of the 3’ ends of the viral cDNA genome, known as 3’-end processing. The second step is the insertion of these ends into host DNA by esterification, known as strand transfer. There is no human homologue to integrase which makes it an ideal drug target. However, the strand transfer inhibitor raltegravir is currently the only antiretroviral treatment available that inhibits integrase. The aims of this study were two-fold: firstly to characterise a cohort of South African patients so as to determine the viability of introducing raltegravir as a new treatment option, and secondly, to set up high-throughput integrase inhibitor screening assays (testing integrase enzymatic functionality). An HIV-1 subtype C specific RT-PCR and PCR assay was established for integrase genotyping using 51 integrase inhibitor-naïve patient plasma samples and 22 antiretroviral drug-naive primary viral isolates from South Africa. Seventy-one of the 73 samples were classified as HIV-1 subtype C and two samples were unique AC and CG recombinants in integrase. Amino acid sequence analysis revealed there were no primary mutations (Y143R/C/H, Q148H/R/K, and N155H/S) associated with reduced susceptibility to the integrase inhibitor raltegravir. However, one sample had the T97A mutation, three samples had the E157Q and V165I mutations, and the majority of samples contained the polymorphic mutation, V72I. The expected finding of no major integrase mutations conferring resistance to integrase inhibitors suggests that this new antiretroviral drug class will be effective in our region where HIV-1 subtype C predominates. However, the impact of E157Q and other naturally occurring polymorphisms warrants further phenotypic investigation. The integrase sequence of viral isolate, FV3, was closest to the consensus sequence, and thus chosen for preintegration complex isolation for use in strand transfer assays. Isolation of preintegration complexes following FV3 infections of several cell lines was unsuccessful as determined by western blot analysis. Subsequently, the focus was changed to isolation of HIV-1 subtype B recombinant integrase and its functional evaluation. Expression of native integrase (INwt) and soluble integrase (INsol) was induced in E. coli, and both proteins were purified by nickel chelating chromatography. The purified recombinant proteins were used to develop three assays to test for strand transfer activity, of which two were successfully established. Furthermore, only INsol showed strand transfer activity in the high-throughput microtitre plate assay and scintillation proximity assay (SPA)-bead strand transfer assay. Activity of INsol was shown to be inhibited by the control compound, chicoric acid with an IC50 of 101.5nM in the high-throughput microtitre plate assay, whereas INsol activity as well as a dose response to chicoric acid with an IC50 of 248.5nM was recorded in the SPA-bead strand transfer assay. Visualization of radiolabelled enzymatic products of strand transfer by polyacrylamide gel electrophoresis of urea sequencing gels was unsuccessful. Overall, the high-throughput microtitre plate and SPA-bead strand transfer assays have been successfully established in our laboratories, and are available to screen compound libraries for potential antiretroviral drug candidates targeting integrase strand transfer.

Like in other Sub-Sahara African countries, HIV has had significant devastating effects in Zimbabwe. Understanding the underlying and proximate determinants of infections in the population is important for knowing who needs intervention, where interventions are needed and for designing specific and relevant interventions. No studies appear to have assessed distributional patterns and risk factors of HIV prevalence simultaneously across the ten provinces in Zimbabwe using a combination of the proximatedeterminant framework approach and modern geostatistical techniques to identify spatial HIV hotspots. The overall aim of this study was to investigate the prevalence, spatial patterns and factors associated with HIV infection in Zimbabwe using the proximate-determinant framework approach and modern geostatistical techniques. Methods This study used the Zimbabwe demographic and health survey of 2010/2011 which included a representative sample of 9171 women and 7104 men- aged 15 to 49. Following the proximate determinants framework, multilevel models were fitted separately for men and women. Global and local spatial autocorrelations were assessed. Spatial regression models were also fitted to adjust for spatial random effects and non-random effects. Significant difference between hotspots and cold spots was examined at community level. Results The overall prevalence estimate was 15.4% (95%CI: 14.8% - 16.0%) [17.7% among women and 12.2% among men]. While prevalence was highest in women in the middle age categories 29.3%), a corresponding dose response relationship was observed among men. Highest prevalence was obtained in urban dwellers, widowed men (60%) and women (56%), and Matabeleland South. A dose response association was found between HIV prevalence and duration of cohabitation, total lifetime partners in both gender populations, and age of most recent partner in men. Evidence of global and local spatial autocorrelation was found. Spatial scan techniques identified three hotspots including Matabeleland South province. Prominent significant underlying risk factors of HIV infection in both gender populations were age group [men: AOR40-44: 5.19;(95%CI:1.92 – 14.02); AOR45-49 : 4.76 (95%CI: 1.70 – 13.30)] [women: AOR30-34: 2.17;(95%CI:1.32 – 3.54); AOR35-39: 1.91; (95%CI:1.14 – 3.19)] and widowed marital status[men:AOR: 7.37; (95%CI: 3.10 – 17.52)][women: AOR: 4.13; (95%CI: 2.49 – 6.85)], likewise Matabeleland South region in men [AOR: 2.32; (95%CI: 1.49-3.62)]. On the other hand, total lifetime partners [men: AOR5-9: 3.15; (95%CI: 2.08 – 4.77)][women: AOR5-9: 3.74; (95%CI:2.52 – 5.53)], and symptoms of sexually transmitted infections emerged as proximate predictors of the epidemic. No evidence of significant heterogeneity in geographical distribution of HIV prevalence was found after adjusting for significant underlying and proximate risk factors. However, persons living within hotspots are on the average 30% more likely to be within the richest wealth quintile (OR: 1.30; p: <0.001), more likely to have higher total lifetime partners and symptoms of sexually transmitted infections. Conclusions A combined application of traditional statistical procedures and modern geostatistical techniques to identify significant predictors of HIV infection and prevalence hotspots provide a more robust approach to investigate HIV spread in a generalized epidemic setting. The results showed excess risk of infections in certain demographic sub-groups, reinforcing the need for programmatic interventions to be directed at these locations and populations in order to maximize impact. The interventions should address the proximate determinants of infection in the population. Further analysis should examine the independent effect of condom use on HIV outcome in the context of marital status and sexual partnership. Proximate determinants of HIV infection should be explored at community level.

A research report submitted in partial fulfillment of the requirements for the degree of Master of Science in Epidemiology and Biostatistics University of the Witwatersrand, Faculty of Health Sciences, School of Public Health May, 2014 / Introduction HIV-associated TB is curable with standard TB therapy and yet it is the leading cause of illness and death in patients infected with HIV. Coinfection with HIV poses considerable challenges to early diagnosis of TB in HIV-infected people and diagnostic delay and the rapidly progressive TB associated with HIV results in rapid clinical deterioration and increased mortality. There is an urgent need for research to identify risk factors for TB in HIV-infected people in order to refine diagnostic algorithms for the early and accurate diagnosis of tuberculosis in HIV-positive patients. The aim of this study was to determine the prevalence of TB, and identify factors associated with prevalent TB in HIV-infected adults paying a subsidized, all-inclusive monthly fee for HIV care in a private setting in downtown Johannesburg – a unique sub-population. Material and Methods This study was a retrospective, cross-sectional, secondary analysis of data extracted from the routine electronic medical records of HIV-infected adults who attended ZuziMpilo from August 2009 to December 2011. The outcome of interest was prevalent TB at the time of enrollment into care and exposures included age, sex, ethnicity, CD4 count, WHO Clinical Stage, BMI, alcohol and tobacco use history, level of education, employment status, monthly income, monthly cell phone expenditure, medical insurance status, source of funding for HIV care and source of knowledge about ZuziMpilo Medical Centre. Multivariable logistic regression modeling was used to determine risk factors for prevalent TB at the time of enrollment. Results Approximately 8 out of every 100 HIV-infected adults enrolling at ZuziMpilo from August 2009 to December 2011 had prevalent TB disease (8.24%). Significant predictors for prevalent TB included BMI categorised as non-obese, CD4 count <350 cells/mm3 and duration on HAART of less than six months. With respect to BMI, individuals who were not obese had greater risk of prevalent TB, the risk increasing in a dose response fashion as the BMI decreased. Compared to obese patients, overweight patients were 2.8 times as likely (aOR = 2.83, CI 1.06 – 7.52, p = 0.037), normal weight patients were more than 3.7 times more likely (aOR = 3.72, CI 1.44 – 9.60, p = 0.007) and underweight patients were more than 6.4 times more likely to have prevalent TB (aOR = 6.42, CI 2.33 – 17.70, p = 0.000). A CD4 count of < 200 cells/mm3 predicted an 11.3 times increased risk of prevalent TB relative to CD4 count greater than 350 cells/mm3 (aOR = 11.27, CI 4.84 – 26.28, p = 0.000). Patients treated with HAART for longer than 6 months were significantly less likely to have prevalent TB than HAART-naïve patients (aOR = 0.47, CI 0.23 – 0.98, p = 0.043). Conclusion and Recommendations This study corroborates the growing body of evidence that underpins several key recommendations that have the potential to reduce mortality from TB in those people infected with HIV; vigilant and regular routine TB screening in HIV-infected patients at all CD4 counts and especially in those with profound immunosuppression and in the first three to four months following HAART initiation, the urgent development and distribution of more sensitive and point of care diagnostic tests for TB in HIV-infected patients at all levels of health care (most especially primary health care facilities) and the importance of initiation of HAART before CD4 counts drop below 350 cells/mm3. This study highlights that BMI is a useful proxy marker of TB risk among HIV-positive individuals. Height and weight are easily assessed anthropomorphic measures and should be conducted routinely in all patients at regular intervals. This study has described a unique population with the capacity to pay a subsidised monthly fee for their HIV care and thus the results may not be generalisable to the large population of HIV-infected adults in South Africa, who receive free-of-charge health care in public sector facilities. However, they may certainly be generalisable to other clinics that provide services for a fee and this information may be especially important if this model is replicated and scaled up in private and semi-private facilities around the country.