HIV-1 integrase is an essential enzyme in the HIV replication cycle and is a validated target for antiretroviral drugs. Due to the inevitable emergence of drug resistance of HIV-1 strains to all currently approved FDA antiretroviral drugs, antivirals with new mechanisms of action are continuously investigated. As such, this study aimed to reposition existing drugs as HIV-1 integrase inhibitors by screening the NIH Clinical Collection compound library comprising 727 compounds. Recombinant integrase was expressed in bacterial cells, purified by nickel affinity chromatography, and used to set up a Scintillation Proximity Assay (SPA). The SPA was subsequently amended to an automated system to allow for rapid screening of compounds. The complete compound library was successfully screened using the newly established automated SPA. Overall, only two compounds were identified as HIV-1 IN inhibitors: cefixime trihydrate and a previously identified HIV integrase inhibitor, epigallocatechin gallate. These compounds exerted IC50 values < 10μM in the automated SPA. Cefixime trihydrate was not toxic to mammalian cells (CC50 > 200μM) while no appreciable antiretroviral activity was observed in in vitro phenotypic inhibition assays (23% inhibition of viral replication), thus concluding that this compound was non-selective. By contrast, epigallocatechin gallate was toxic to mammalian cells at the evaluated ranges (CC50 = 23 + 1μM) and therefore could not be validated as an integrase inhibitor in in vitro phenotypic inhibition assays. Overall, this study resulted in the establishment of an automated SPA, the successful screening of 727 compounds, and the availability of a platform to expedite the future screening of potential HIV-1 integrase inhibitors.

A research report submitted to the Faculty of Health Sciences (School of Public Health), University of the Witwatersrand, in partial fulfilment of the requirements for the degree of Master in Public Health in the field of Social and Behaviour Change Communication 4 June 2019, Johannesburg / Introduction HIV Testing Services (HTS) represents a critical entry point for reducing HIV risk through personalised counselling and testing (Colpin, 2006, Denison et al., 2008; Fonner, 2014). Despite the significant uptake of HTS since 2010, personal risk perception among South Africans remains low, with individuals continuing to engage in risky sexual behaviour (Statistics South Africa, 2017). This raises concerns about the quality and effectiveness of HTS in reducing HIV risk among HTS clients. In seeking to understand how best to strengthen HTS, lay counsellors who work at the forefront of HTS provision are primary targets for inquiry. This study sought to explore the experiences and perceptions of community-based HTS lay counsellors of providing HTS, the strategies they use to reduce HIV risk among diverse clients, and their perceptions of HTS training and supervision. Methods Qualitative semi-structured interviews were conducted with 12 community-based HTS counsellors at three government-accredited HTS sites in Gauteng and North West provinces. Ethical clearance was obtained in April 2015 and the interviews were conducted from July- October 2015. Interviews were audio-recorded, professionally transcribed, and coded using MaxQDA. Inductive and deductive thematic analysis was used to meet the study objectives. Results The HTS lay counsellors came from diverse personal and educational backgrounds. Their HTS training was not standardised, differing in scope, depth, and duration. Their sector influenced their scope of practice, remuneration and relationship with the Department of Health. HTS Counsellors tended to follow a client-centred approach to HIV counselling; balancing general HIV education with more tailored prevention counselling. Gender norms appeared to influence risk-reduction counselling, in which counsellors advised men to use condoms and women to be faithful to their partners. Counsellors resisted the notion of differential risk among HTS clients, and offered generic, simplified prevention messages tailored to clients‘ age and gender. Counsellors seldom explored known risk factors for HIV infection, such as alcohol and drug abuse, anal sex, and gender-based violence with clients. They prioritised post-test counselling for HIV-positive clients and tended to neglect post-test counselling for HIV-negative clients. . Counsellors recommended regular in-service training, enhanced supervision and debriefing, and formal recognition of the field through establishing standardised guidelines, career paths and a professional body. Discussion This study confirms previous research on the sub-optimal quality of risk-reduction counselling, which varies between sites and counsellors. Although HTS counsellors follow the nationally prescribed, client-centred approach, there is limited evidence that this approach effectively reduces HIV risk (Peltzer et al., 2013). In contrast, theory-based approaches, such as Motivational Behavioural Interviewing, which has effectively reduced unprotected sex, alcohol use before sex, number of sexual partners, and transactional sex among high risk groups globally and in South Africa (Petersen et al., 2014, Simbayi et al., 2004).were largely absent in HTS programmes covered in this study. The HTS lay counsellors in this study are among those who have contributed significantly to the rapid scale up of HTS in South Africa. However, they identified structural challenges detrimental to their work performance and motivation. HTS counsellors are not formally recognised or included within national human resources for health plans, and their job profiles and remuneration are not standardised. The inconsistent management and unfair treatment described by counsellors in this study has been reported across the country (Medecins Sans Frontieres, 2015). Conclusions The major recommendations that emerged from this study include the need for the government to create a supportive legal and policy framework to guide the integration of HTS counsellors into the formal health care system. This could happen by establishing a professional body for HTS counsellors and updating the minimum standards for HTS. Quality could be improved by training counsellors on use of individual and social theories of behaviour change (Petersen et al., 2014) and standardising HTS training curricula at national levels. Strengthening HTS vsupervision to ensure quality HTS counselling and testing nationally is also needed. Overall, this study confirmed that further research is needed to improve the quality of risk reduction interventions in HTS and develop a coherent framework for the integration of lay counsellors into the South African health and social service sectors. / E.K. 2019

A research report submitted in partial fulfilment of the requirements for the degree of Master of Science in Epidemiology in the field of Infectious Diseases School of Public Health, University of the Witwatersrand May 2014 / South Africa continues to grapple with the HIV/AIDS epidemic almost 30 years since the disease was first described. South Africa has 6.4 million people living with HIV thereby contributing 17% to the global burden of HIV/AIDs even though it makes up 0.7% of the world population translating to an HIV prevalence of 10.6% in the general population. . Multiple concurrent sexual partnerships (MCP) and inconsistent condom use are notably the major contributors to the spread or transmission of HIV in South Africa. The South African government has allocated massive financial resources to support HIV/AIDS interventions, however, the epidemic continues to amplify in South Africa and there is a growing need for targeted HIV prevention interventions which will address behaviour change. Objectives The objectives of the study were to determine the differences in sexual risk behaviour between self-identified HIV positive and HIV negative men and identify factors associated with sexual risk behaviour. Methodology This was secondary data analysis of a cross sectional design study called "Risk Perceptions of HIV Positive Men" and it was conducted in clinics from Soweto, Cape Town and the Cape Winelands from October 2010 to July 2011. The sample size was 451 and the study population comprised self-identified HIV positive and negative men between ages 18 - 60 years. Proportion of consistent condom use (CCU) and multiple concurrent partnerships (MCP) were calculated and difference between those self-identified HIV positive and negative were determined using Chi-square tests. Factors associated with MCP and CCU between the two groups was determined using univariable and multivariable logistic regression Results We analysed data for 451 men with a mean age of 39 years (std. dev. 11.30). Out of the 451 men 311 (69%) identified themselves as HIV positive and there was a statistical significant difference in baseline characteristics between HIV positive and HIV negative men (age, race, relationship status, employment status, education level, religion, area of residence, age at sexual debut, condom use at first sex, sexual orientation and circumcision status). HIV positive men were four times more likely to have used condoms consistently in the last six months compared to HIV negative men (AOR=3.72, CI: 1.95-7.11), however, HIV positive men were also four times more likely to have had Multiple Concurrent Partnerships in the last 12 months compared to HIV negative men (AOR=4.60, CI: 2.09- 10.12) . Other factors associated with sexual risk behaviour were; relationship status, age group, race, age at sexual debut, alcohol frequency, sexual orientation and perceptions about undetectable viral load reducing HIV transmission risk. Conclusion and recommendation There is a difference in sexual risk behaviour between men who identified themselves as HIV positive and those who identified themselves as HIV negative. Men who identified themselves as HIV negative were less likely to have used condoms consistently in the last six months. Though the HIV positive men are using condoms consistently they have multiple concurrent partners. There is need to strengthen post HIV test counselling coupled with targeted messages for both HIV positive and HIV negative men.

A research report submitted to the School of Public Health, University of the Witwatersrand (Johannesburg, South Africa) in partial fulfilment of the requirements for the degree of Master of Public Health for the year 2014 / Introduction: After 12 years of implementing the national Prevention of Mother-to-Child Transmission of HIV (PMTCT) programme in South Africa, interventions to prevent MTCT of HIV are now offered in more than 95% of public antenatal and maternity facilities country-wide free of charge (MRC, 2010), even though HIV/AIDS-related diseases are said to be a major cause of death in young children (UNICEF, 2011). The context within which women make decisions about PMTCT participation depends on, amongst other things, the level of their knowledge about HIV/AIDS (Leonard et al, 2001; Sematimba et al, 2004). The concept of behavior-based programming is central to a behavior change approach to reducing Mother-to-Child Transmission of HIV. This places behaviours at the centre of the program design process (Moore, 2003). Understanding the providers and users of the PMTCT interventions’ knowledge and experience on HIV and PMTCT is therefore important to ensure appropriate interventions to address beliefs, attitudes, myths and misunderstandings. Methodology: Semi-structured interviews were conducted with users of the PMTCT programme, while structured survey questionnaires were collected with the providers of the PMTCT programme in early 2012. Users of the PMTCT programme were asked questions regarding HIV knowledge, experience of HIV testing in pregnancy, PMTCT knowledge and experience of the PMTCT programme. We also asked questions on infant feeding choices and practices. Forty six interviews were carried out with participants at three ANC Clinics with PMTCT services in Soweto - Gauteng. Thirty were users of PMTCT programme and sixteen were providers of PMTCT service. Results: All participants understood that HIV was a virus that affected the immune system. Results show that there is generally a good understanding of HIV and how it is transmitted. In addition there was a good understanding on methods to prevent acquiring HIV. There was a general feeling that a lot of people were afraid of being tested. Interestingly, most participants believed that people who were pregnant or sick had no choice but to get tested. Most of the participants believed that education should be a tool used to motivate more people to get tested for HIV. Most users in this study disclosed their HIV status and PMTCT programme use. Overwhelmingly the decision to participate was based on the desire not to infect their infants. Women had been informed that mixed feeding increased the risk of transmission by breast feeding. There were a few participants who believed that HIV infected women should not breastfed. It was found that almost two-thirds of the women in this study were formula feeding their infants. Reason cited for formula feeding was that they did not want to infect their infants. As far as PMTCT knowledge was concerned, it was found that almost all health care providers knew that the most common route of HIV acquisition was through heterosexual sexual practices. All the HCWs knew that prolonged breastfeeding increased the risk of transmission. Reassuringly all HCWs knew not to use invasive delivery procedures and that risk of transmission was decreased with low maternal viral load. Only 50% of the HCWs indicated that the first choice of WHO- recommended mother-to-child regimen for antiretroviral prophylaxis in PMTCT was Zidovudine (ZDV) and Nevirapine (NVP) (WHO, 2012). The HCWs understood that infant formula did not provide superior nutritional support or antibody protection. They also knew that formula feeding carried increased risk of diahorrea or bacterial infections. There was confusion regarding the duration of exclusive breast feeding. Only half of the HCWs stated that post-natal infant-feeding counselling and follow-up are required whenever a mother decides to change her feeding practice. HCW participants felt that most patients fail to adhere to their medication requirements. This was cited to be mainly due to the fact that patients may not have disclosed their HIV status to the household members. Baby feeding choices are cited as the strongest barriers to the success of the PMTCT programmes. Mothers who have not disclosed their HIV status to their household members find it difficult to comply with the chosen feeding choices especially bottle feeding; they therefore opt for exclusive breastfeeding –which family members attempt to interrupt with mixed feeding practices for a number of reasons. Conclusion: Contrary to studies cited in the literature review, health systems failure was not a major problem in Soweto and therefore was not a factor that could impact on either the knowledge or the experience of users and providers. Even though disclosure rates were high amongst the users interviewed in this study, participants believed that the biggest barrier to people participating in the PMTCT programme was because of stigma, ignorance, and fear that they may be recognised while accessing services by people they may know. Although women had been provided with information on exclusively breastfeed, most users of the PMTCT programme interviewed were bottlefeeding – not due to stigma, but due to fear of transmission. In terms of barriers – adherence was noted as a major problem by providers. This linked to issues of feeding practices - if mothers bottle-feed they are stigmatised and opt for exclusive feeding, but are then forced by family to supplement with the bottle for various reasons. Mothers do not reveal their status, which jeopardises their success on the programme

there is a growing body of research on men who have sex with men (MSM) and risk factors for HIV in South Africa. However, in order to develop more appropriate and relevant interventions to reduce the transmission of HIV amongst MSM and MSMW, there was a need to deepen our understanding of sexual risk behaviour and protective practices. The aim of the study was to explore the sexual risk and protective behaviour of men who have sex with men and women in Soweto, South Africa.

A thesis completed by published work, Submitted to the School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, in fulfillment of the requirements for the degree of Doctor of Philosophy Johannesburg, South Africa 24 May 2017. / Introduction: Prevention of mother-to-child transmission (PMTCT) has potential to eliminate new HIV infections among infants. Yet, in many settings in sub-Saharan Africa, women are unable to adhere to PMTCT recommendations due to social constraints. One such factor may be intimate partner violence (IPV), or any actions taken by a relationship partner that cause physical, sexual, or psychological harm. Despite theoretical and empirical rationale for understanding the links between IPV and PMTCT adherence, few studies in the extant literature have explored this association. Methods: This thesis draws upon four distinct studies that interface using an overall mixed method study design. The first study is a systematic review of the literature around women’s experience of lifetime IPV and adherence to anti-retroviral treatment (ART). The second study is formative qualitative research with pregnant women, health workers, and other local stakeholders that explores how IPV may be related to PMTCT in the urban Johannesburg setting. The third study is a deeper qualitative examination of women living with both IPV and HIV, aiming to understand the mechanisms that link partner violence to PMTCT behaviors using a social constructionist lens. The final study is a quantitative cohort study nested within a randomized control trial testing an intervention for IPV in pregnancy. Using regression techniques and structural equation modeling, I aim to determine the association between IPV and ART adherence in pregnancy and postpartum and identify pathways that mediate the relationship between partner violence and PMTCT. Results: This doctoral research contributes several new findings to the extant literature around PMTCT. I find that IPV is related to ART adherence among HIV-positive women in extant literature, with meta-analysis showing significantly worse odds of ART uptake, self-reported adherence, and viral suppression among women reporting lifetime IPV. In one of first of studies among women in sub-Saharan Africa, I learn that impact of IPV on ART adherence in pregnancy and postpartum is marked. I identify several mechanisms through which IPV influences PMTCT adherence. Mental health emerges as a robust pathway linking IPV to worse adherence in both qualitative and quantitative papers. Partner non-disclosure due to IPV can impede adherence, or women can navigate this challenge through hiding their HIV status or medication. Women experiencing IPV may attend fewer antenatal clinic visits, leading to worsened adherence. An unexpected finding was that women in our qualitative and quantitative studies were resilient and used strategies to adhere despite IPV. Motherhood seems to be a central feature of women who are resilient to the effects of IPV on adherence. Conclusion: The findings of this research have implications for research, policy, and practice. Research should incorporate social factors, such as IPV, into future studies testing PMTCT adherence interventions. Clinical practice and HIV programs should recognize that partner-level dynamics such as IPV may drive persistent gaps in PMTCT coverage. HIV policy urgently needs to incorporate ethical and safety considerations for women who experience IPV around the time of pregnancy. Women living with recent or past IPV are highly resilient and often want to protect their own health and that of their children. Only by recognizing and addressing their experience within the context of HIV care can future PMTCT programs and studies ensure maternal and infant health. / MT2017

Research report submitted in partial fulfilment for MSc (Med) in Epidemiology and Biostatistics in the School of Public Health, 2013 / Concurrent sexual partnerships are a sexual network pattern that speeds the spread of HIV/AIDS and Sexual Transmitted Infections(1). Multiple and concurrent Sexual Partnerships (MCP) are part of behavioural drivers and are playing main role in the increase of HIV incidence(2). The main aim of the study is to identify the possible socio-demographic and behavioural factors that are associated with concurrent sexual partnership in 4 communities of South Africa(SA), so as to inform HIV prevention programmes in designing targeted interventions for addressing this problem in specific communities. The ultimate goal is to reduce the incidence of new HIV infections

A dissertation submitted to the Faculty of Health Sciences, University of Witwatersrand, Johannesburg in fulfillment of the requirements for the degree of Master of Science in Medicine, Johannesburg , 2013 / South Africa’s Prevention of Mother-to-Child Transmission (PMTCT) programme is critical for eliminating vertical HIV transmission and reducing infant mortality. Early treatment of HIV-infection to curb infant deaths requires earlier diagnostic testing than the currently recommended six-week test. This study describes the continuum of PMTCT care at a Johannesburg hospital to identify interventions for improvement and investigates birth HIV testing for infants. Data from a cohort study at the hospital evaluating diagnostic assays in HIV-exposed infants were collated with routine clinical data, validated and analysed. Among 838 mother-infant pairs, 38% of mothers attended antenatal clinics early enough to receive optimal antenatal prophylaxis. Only 72% of infants accessed six-week testing at the hospital; a further 10% underwent testing elsewhere. Of 38 HIV-infected infants, 29 were infected in-utero and could have been identified at birth (sensitivity of 76.3% for birth testing), compared to only 26 (68%) diagnosed by six-week testing at the hospital. Majority (88%) of these 26 infants accessed antiretroviral therapy, but treatment was only initiated at a median age of 16.0 weeks and 43% of HIV-infected infants who initiated treatment had defaulted or died before the end of the study. Mathematical modelling demonstrated that birth testing would be superior to a six-week test to maximise infants diagnosed and life years saved, with the ideal algorithm being a birth and ten-week test. The PMTCT programme can be enhanced by earlier antenatal care for women and earlier infant diagnosis. Birth testing would diagnose HIV-infection before infants die or default from the PMTCT programme, thereby enabling effective monitoring of MTCT, and would allow earlier treatment initiation to reduce early infant mortality.

Background Heroin dependence is associated with increased risk of the transmission of blood-borne viral (BBV) infections such as HIV, as a result of unsafe injecting practices. Opioid Substitution Treatment (OST) Programmes including Methadone Maintenance Treatment (MMT) programmes are a recommended way of addressing heroin dependence with the dual aims of reducing both heroin use and associated harms. However, OST programmes, particularly in prison settings, are often unavailable, in spite of large numbers of prisoners with heroin dependence and the high risk of HIV transmission in the prison setting. Little is currently known about the delivery of OST programmes within prison settings. A systematic literature review conducted within this study revealed that there are only a small number of studies from middle and lower-income countries and the perspectives of the range of stakeholders are often underrepresented. Aim and setting of this study This aim of this study was to understand the role of Methadone Maintenance Treatment (MMT) programmes within the context of HIV prevention programmes and to identify barriers and facilitators that influence the implementation, routine delivery and sustainability of methadone programmes in Indonesian prisons. Study design Three prison settings were selected as part of a qualitative case study. These comprised: a narcotics prison that provided methadone, a general prison that provided methadone, and a general prison, where there was no methadone programme. This allowed the exploration of multiple perspectives of prisoners and the diverse range of staff involved in the implementation of programmes. Interview and observational data were supplemented by data from medical case notes. Qualitative data underwent thematic analysis, with the help of framework analysis for data management. Principal findings This study found that there were many misconceptions about methadone programmes. HIV infection was not recognised as a problem and prison staff, healthcare staff and prisoners alike lacked understanding of the roles of methadone programmes. Prisoners participating in programmes were often stigmatised, while many prisoners believed methadone withdrawal was dangerous and could lead to death. These factors all contributed to low level participation, observed in both prisons with methadone programmes. Lack of confidentiality and associated stigmatisation as well as inappropriate assessment criteria also contributed to this, as did a lack of support systems. A reduction in international funding and a shift in national drug policy priorities away from the provision of methadone to drug-free Therapeutic Community (TC) programmes, together with a failure to embed methadone programmes within the daily prison routine currently pose challenges to effective implementation, delivery and programme sustainability. Conclusion Educating policy makers and practitioners could improve understanding of the roles of methadone programmes and increase support for programme delivery within prisons. It is therefore recommended that Indonesian government and prison policy focuses on ensuring effective delivery and sustainability of methadone programmes for people with heroin dependence in the prison setting.