ENGLISH ABSTRACT: HIV/AIDS is the leading cause of death in Sub-Saharan Africa. According to 2001 estimates, there are 28.5 million people living with HIV in Africa, comprising more than 70% of the world’s HIV-infected population. HIV/AIDS remains one of the most important social and public health threats in Sub-Saharan Africa. UNAIDS 2006 estimates that 5.5 million people are living with HIV, and almost 1,000 AIDS deaths occur every day in South Africa. South Africa is currently one of the most severely affected countries in the world. Antiretroviral therapy (ART) is currently the only treatment available for HIV. It does not cure HIV infection, but reduces HIV related mortality and morbidity. / AFRIKAANS ABSTRACT: No abstract available

HIV/AIDS is a global pandemic that poses a great threat especially in Sub-Saharan Africa where the highest population of those infected with the virus is found. It has far reaching medical, socio-economic and scientific implications. The HIV-1 protease enzyme is a prime therapeutic target that has been exploited in an effort to reduce morbidity and mortality. However problems arise from drug toxicity and drug-resistant mutations of the protease which is a motivation for research for new, safer and effective therapies. Evidence exists to show that there are significant genomic differences in Subtype B and C that have a negative effect on the intrinsic binding of inhibitors. It is imperative to look at all perspectives from epidemiological, molecular to the pharmacological ones so as to achieve rational design of therapeutic agents. This study involved the use of in silico structural analysis of the effects of mutations in the active site. The data was provided by the National Institute of Communicable Diseases consisting of HIV-1 Subtype C protease sequences of 29 infants exhibiting drug-resistance to ritonavir and lopinavir. The major active site mutations causing drug resistance identified in this study were M46I, I54V and V82A using the Stanford HIV database tool. Homology modeling without extra restraints produced models with improved quality in comparison to those with restraints. MetaMQAPII results differed when models were visualized as dimers giving erroneous modeled regions in comparison to monomers. A broader study with a larger dataset of HIV-1 subtype C protease sequences is required to increase statistical confidence and in order to identify the pattern of drug resistant mutations. Homology modeling without extra restraints is preferred for calculating homology models for the HIV-1 subtype C. Further investigations needs to be done to ascertain the accuracy of validation results for dimers from MetaMQAPII as it is designed for evaluation of monomers.

The retention of persons on an HIV programme has been a global challenge. The success of any strategy to optimize adherence to anti-retroviral therapy (ART) depends on the intensive and effective adherence counselling and strategies. It is important to research whether persons receiving anti-retroviral therapy in public hospitals in Ghana are receiving the needed service that would optimize their adherence to the anti-retroviral therapy. Therefore, this study explored and described the experiences of healthcare professionals providing care, support and guidance to persons on ART at public hospitals in Ghana, as well as the best-practice guideline that could contribute to facilitating the ART adherence of patients. This study also explored and described the experiences of persons living with Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome (HIV/AIDS) on ART, regarding their adherence to the therapy. The study was organized into three phases. In Phase One: a qualitative, exploratory, descriptive and contextual design was employed. The research population included healthcare professionals, providing services at the HIV clinic at the public hospitals in Ghana, namely the Korle-Bu Teaching Hospital; the 37 Military Hospital and the Ridge Hospital. The healthcare professionals comprised of doctors, nurses, pharmacists and trained counsellors employed in any of the three public hospitals. Persons receiving ART at any of the three public hospitals were also part of the research population. Semi-structured interviews were conducted with healthcare professionals and persons receiving ART. Data were collected from healthcare professionals in relation to their experiences regarding the provision of ART services, their understanding of evidence-based practice and best-practice guidelines, as well as data on the experiences of persons receiving ART in relation to their adherence to the therapy. The data were analysed using Creswell’s six steps of data analysis; and the coding of the data was done according to Tesch’s eight steps of coding. Trustworthiness was ensured by using Lincoln and Guba’s framework which comprised credibility, transferability, dependability, confirmability and authenticity. Ethical principles such as beneficence and non-maleficence, respect for human dignity, justice, veracity, privacy and confidentiality were considered in the study. In phase two, the literature was searched by using an integrative literature review approach and critically appraising the methodological quality of the guidelines in order to identify the best available evidence related to adherence to ART. In Phase Three, a best-practice guideline for facilitating adherence to ART was developed for public hospitals in Ghana based on the findings of the empirical research of Phase One and the integrative literature review in Phase Two. The guideline was submitted to an expert panel for review; and it was modified, according to the recommendations of the panel.

The world has entered the third decade of the HIV and AIDS epidemic under different times in which the epidemic is treatable. The International Labour Organisation (ILO) (2005) declares HIV and AIDS a developmental crisis destroying developmental gains over generations. Since HIV and AIDS affect the most productive segment of the labour force, it is therefore not only a threat to development but also to the world of work without which development will be sacrificed (ILO, 2001). Collaborative response efforts that seek to mitigate the HIV pandemic by government, business and higher education institutions have been fraught with challenges. The main challenge that beset these efforts is that, in the absence of an HIV vaccine, voluntary counselling and testing remains the gateway to access treatment and care. Regrettably, participation in VCT has been confronted by challenges of low utilisation. This precedes the objectives of this study, which were to explore and describe factors that serve as barriers and facilitators of workplace VCT programmes with the objective to improve participation in these programmes. The current study was a product of a qualitative and exploratory-descriptive research design. A nonprobability convenience sampling method was used to sample participants for this study. The targeted population in this study were the non-academic employees of an academic institution in the Eastern Cape. Data was collected by means of focus group discussions and by using semi-structured interviews. The focus group samples comprised of an equal number of men and women with an overall participation of fifty-six participants. Data obtained was transcribed, thematically analysed and coded using Henning, Van Rensburg, and Smit's (2004) qualitative analysis and interpretation method. Findings of this research revealed that factors that facilitate and inhibit voluntary counselling and testing are psychosocial and cultural by nature. At psychosocial level, participants reported factors that facilitate voluntary counselling and testing to include psychological readiness to go for HIV testing, reassurances of confidentiality of HIV test results and normalising HIV testing (making the process more like that for screening and diagnostic testing). Cultural factors included cultural practices and beliefs such as "intonjane" and traditional circumcision - positive cultural nurturers that could facilitate VCT participation. Results of this study showed a lack of basic knowledge about VCT and fear of knowing one's status, fear of breach of confidentiality, fear of being stigmatised and a lack of trust towards health professional as the major psychosocial factors that serve as barriers to VCT participation. The cultural barriers to VCT pointed to hegemonic masculinity as a socially constructed gender identity that encourages gender inequalities and undermines efforts to improve HIV testing. The study suggested that strategies to increase VCT participation should consider leadership support of VCT programmes, incentivisation of VCT programmes, institutionalisation of HIV and AIDS education and the establishment of integrated wellness services for employees.

Submitted in fulfillment of the requirements for the Degree in Master of Health Sciences (Nursing), Durban University of Technology, Durban, South Africa, 2016. / Background South Africa, especially KwaZulu-Natal remains heavily burdened with HIV and AIDS. Timely HIV testing is the cornerstone to HIV prevention in terms of early diagnosis and access to treatment, care and support services. Factors that influence delayed HIV testing must be investigated and reported to inform plans that are directed at improving implementation of HIV testing services and access to care, treatment and support services for people living with HIV. Purpose of the study This study was aimed at identifying factors that lead to delayed HIV testing in a sample of people attending a Primary Health Care clinic in KwaZulu-Natal, South Africa. Methodology A descriptive qualitative design was used in this study. The population in this study was HIV positive patients who had recently tested for HIV and received their first CD4 count result of 350 mm3 or less. Purposive sampling, which is a type of non-probability sampling, was used to select the study participants from the population. Semi structured interviews using an interview schedule were used to collect data. Data was collected until data saturation was reached. Results The data was analysed by means of content analysis and raw data was coded and sorted into sub categories and categories. The underlying meaning of categories was formulated into one overarching theme: Testing for HIV is daunting and embedded with issues of stigma, denial and a fear of knowing one’s positive status. Conclusion To encourage early HIV testing before HIV positive people become noticeably ill requires efforts directed at change of attitude and improvement of support for HIV positive people in families, communities and health service institutions. Community forums to be actively involved in eliminating the stigma and discrimination associated with HIV positive people by creating awareness of these matters and encouraging community and family support for people with HIV. / M

A series of the Baylis-Hillman adducts have been obtained by reacting protected O-benzylated and unprotected substituted salicylaldehydes with methyl acrylate or tertbutyl acrylate, respectively, using DABCO as catalyst. Treatment of the Baylis-Hillman adducts with HCl in a mixture of acetic acid and acetic anhydride afforded the corresponding 3-(chloromethyl)coumarin derivatives with yields of up to 94%. Similar use of HI afforded the corresponding 3-(iodomethyl)coumarins but, depending on the reaction time, the reduced 3-methyl analogues could also be obtained. Arbuzov reactions of the 3-(halomethyl)coumarin derivatives have been undertaken to afford 4-phosphorylated and 1’-phosphorylated derivatives, regioselectivity being dependent on the halide-leaving group. The 3-(chloromethyl)coumarin derivatives have been subjected to nucleophilic (SN) attack by benzylamine to give the corresponding 3- [(benzylamino)methyl]coumarin derivatives in yields of up to 74%. Further treatment of the 3-[(benzylamino)methyl]coumarin derivatives with chloroacetyl chloride afforded the chloroacetamide derivatives, which exhibit hindered rotation about the amine C(O)-N bond. The acetamide derivatives have also been subjected to Arbuzov reaction conditions to afford the phosphorylated derivatives in yields of up to 86%. In a preliminary modelling study, hydrolysed analogues of the synthesized phosphorylated derivatives have been docked into the active site of the HIV-1 protease enzyme using the Cerius-2 Ligandfit software module to provide an insight into potential receptor-ligand hydrogen bonding interactions.

The socio-economic impact of HIV/AIDS on South Africa has resulted in lower gross domestic product, loss of skills in key sectors such as education, and increased health-care costs in providing access to treatment. Currently active pharmaceutical ingredients (API’s) such as stavudine (d4T) and azidothymidine (AZT) are imported from India and China, while formulation is conducted locally. A strategy was initiated between CSIR Biosciences and LIFElab under the auspices of Arvir Technologies to investigate the feasibility of local antiretroviral manufacture (d4T and AZT) or the manufacture of a key intermediate such as β- thymidine (dT). Several advantages associated with successful implementation of this strategy include ensuring a local supply of API’s, thus reducing reliance on procurement from foreign sources and reducing the effect of foreign exchange rate fluctuations on providing cost effective access to treatment. A local supply source would also reduce the imports and thus aid the balance of payments deficit, and in addition to this, provide stimulus in the local pharmaceutical manufacturing industry (which has been in decline for several decades), resulting in increased skills and employment opportunities. This thesis describes the development of a superior chemo-enzymatic process for the production of β-thymidine (72 percent yield, prior to isolation), a key intermediate in the preparation of anti-retrovirals. Alternative processes based purely on chemical or bioprocess transformations to prepare either 5-methyluridine (5-MU) or dT suffer from several disadvantages: lengthy transformations due to protection/deprotection strategies, low selectivties and product yields (30 percent in the chemical process) and isolation of the product from dilute process streams requiring the use of large uneconomical reactors (bioprocesss). This contributes significantly to the cost of d4T and AZT manufacture. Our novel chemoenzymatic process comprises of a biocatalytic reaction for the production of 5-MU, with subsequent chemical transformation into dT (3 steps) negating and circumventing the limitations of the chemical or bioprocess routes. During the course of this project development, the β-thymidine selling price declined from 175 $/kg (2005) to 100 $/kg (2008). However, the process described in this work is still competitive based on the current β- thymidine selling price of 100 $/kg. The process economics show that with further optimization and increasing the isolated dT yield from 70 percent to 90 percent, the variable cost decreases from 136 $/kg to 110 $/kg. The increase in isolated yield is highly probable, based on solubility data of β-thymidine. The decrease in β-thymidine selling price and technological improvement in dT manufacture should translate into lower API manufacture costs and more cost effective access to treatment. Our novel biocatalytic process producing 5-MU uses a coupled enzyme system employing PNP, Purine Nucleoside Phosphorylase and PyNP, Pyrimidine Nucleoside Phosphorylase. The overall transglycosylation reaction may be decoupled into the phosphorolysis reaction (PNP) and synthesis reaction (PyNP). During the phosphorolysis reaction, guanosine is converted into guanine and ribose-1-phosphate (R-1-P) in the presence of PNP enzyme. The reaction intermediate R-1-P is then coupled to thymine in the presence of PyNP enzyme during the synthesis reaction, producing 5-MU. The process was scaled up from lab-scale to bench-scale (10 - 20 L) and demonstrated to be robust and reproducible. This is evident from the average guanosine conversion (94.7 percent ± 2.03) and 5-MU yield (88.2 percent ± 6.21) and mole balance (104 percent ± 7.61) which were obtained at bench-scale (3 replicates, 10 L). The reaction was carried out at reactor productivities of between 7 – 11 g.L-1.h-1. The integration of the biocatalytic process and chemical processes was successfully carried out, showing that 5-MU produced using our novel biocatalytic process behaved similarly to commercially available 5- MU (ex. Dayang Chemicals, China). A PCT patent application (Ref. No. P44422PC01) on this chemo-enzymatic process has been filed and currently public private partnerships are being explored through Arvir Technologies to evaluate and validate this technology at one ton scale.

This study aimed to explore and describe the quality of life of adolescents living with early childhood HIV infection on Highly Active Antiretroviral Therapy (HAART) in Port Elizabeth. The advent of HAART has resulted in HIV being managed as a chronic illness, instead of the fatal disease that it once was. Children born with HIV can now live longer lives, progressing to adolescence and beyond. Chronic illness is known to impact one’s quality of life, so does adolescent development. A convenient sample of 31 adolescents was used in this study, with an exploratorydescriptive research design. The data was gathered using a cross cultural structured questionnaire developed by the World Health Organization, as well as through individual interviews. The data was then analysed by means of descriptive statistics and thematic content analysis. The results identified and presented the quality of life issues that are specific to this population. The results indicate that HIV as a chronic illness does impact the quality of life of adolescents. The adolescents living with early childhood HIV-infection on HAART in this study were very satisfied with their perceptions of their overall quality of life and general health perceptions. They were least satisfied in the Spirituality/Religion/Personal Beliefs and Social Relationships domains; and were most satisfied in the Level of Independence and the Psychological domains. There is a need for the development of (medical and psychosocial) services that can focus on adolescents as a special population with specific developmental needs in order to improve their treatment outcomes and quality of life.

To end the HIV epidemic, prevention of new HIV infections will be contingent on preventing at-risk individuals from acquiring HIV and supporting people living with HIV in achieving and sustaining viral suppression throughout their lifetime. The underlying motivation for this dissertation is the recent evidence that new HIV infections can be prevented when people living with HIV achieve and maintain viral suppression. In response, three studies were conducted. The goal of this dissertation was to advance our understanding of HIV viral suppression patterns over time among clinically engaged adults living with HIV and examine current limitations in viral suppression monitoring. First, a systematic review evaluated the existing literature for evidence of longitudinal assessments of viral suppression among people living with HIV. Among 896 publications identified during the database search, 50 publications met the study criteria and were included in the review. Among these studies, 78% were implemented in the United States, 72% assessed viral suppression using viral load results abstracted from clinical medical records, and 22% used surveillance data from HIV-laboratory based reporting. Five distinct longitudinal measurement methods were identified, including (a) estimates requiring more than one viral load within an observation period to be below a suppression threshold; (b) estimates comparing the first and last viral load during an observation period; (c) reporting multiple proportions of participants maintaining viral suppression across an observation period; (d) estimating viremia copy-years and estimating person-time above a suppression threshold, and; (e) other methodology to assess longitudinal viral suppression such as data weighting and group-based trajectory modeling. Half of the studies reported the proportion of individuals with all viral loads below a certain threshold (e.g., ≤200 copies/mL). Most studies (70.0%; 35/50) were published in the last five years (2015 – 2019) and describe viral load data collected between 2013 and 2018, highlighting recent efforts by researchers to describe viral suppression using longitudinal approaches. Next, data from a longitudinal electronic medical record-based prospective cohort study of people living with HIV seeking care in Washington, District of Columbia, were used to describe longitudinal changes in viral suppression and assess the relationship between prior virologic history and virologic failure events during follow-up. Among 3556 participants, 29% did not maintain viral suppression during a five-year period, and instances of viral suppression status fluctuations were observed. Participants with a history of fluctuating viral suppression were found to have a higher rate (RR=2.40; 95% CI: 2.03 – 2.84; P<0.01) of virologic failure events during follow-up, compared to participants with sustained viral suppression before the observation period. Lastly, a third study used the same data source to assess differences between viral suppression estimates derived from different measurement methods and evaluate the impact of data triangulation on longitudinal viral suppression measures. Among 3452 participants (median age 48; 73% cisgender males; 77% non-Hispanic black), 69% had all viral load results suppressed (<200 copies/mL) during a four-year observation period, 28% had both suppressed and unsuppressed viral loads, and 2% had all viral loads unsuppressed. Compared to cross-sectional viral suppression measurement methods, longitudinal measurement methods resulted in lower proportions of virally suppressed participants. Data triangulation added 2293 viral load data points and resulted in lower viral suppression estimates. These findings highlight the need to reconsider current viral suppression measurement methods to improve the accuracy of estimates reported in surveillance reports and epidemiologic studies. Overall, this dissertation addresses important questions related to viral suppression by describing the frequency of viral suppression status fluctuations that occur throughout an extended observation period, quantifying the occurrence of repeated virologic failure events, and comparing several measurement techniques to assess appropriate methods to describe viral suppression over time. Recently, the United States Department of Health and Human Services, together with the White House, set forth the “Ending the HIV Epidemic: A Plan for America” initiative, with a goal to end the HIV epidemic in the United States within the next ten years. To reach this goal, the initiative calls for a 75% reduction in new HIV infections by 2025 and a 90% reduction by 2030. Treating people living with HIV rapidly and effectively with ART is an important strategy to carry out these efforts. This dissertation demonstrates that assessing the ability of people living with HIV to maintain viral suppression over time is also critical.

Background: HIV transmission is greatly reduced when antiretroviral treatment (ART) suppresses an infected person’s HIV viral load. It is unclear, however, whether the contextual risk of incident HIV is optimally reduced by widespread individual-level suppression of HIV viral load alone or in combination with other HIV prevention services. HIV service coverage and community norms can influence risk in small area geographies; and contextual factors, like gender inequality and stigma, may foster environments conducive to HIV transmission. Yet, the relationship between places with high HIV levels and the clustering of area risk factors is unknown. The goal of this dissertation is to learn if and how a geographically focused combination implementation strategy could reduce population-level HIV risk. Analyses explored whether small area risk profiles explain area differences in HIV. The guiding hypothesis is that in high HIV prevalence settings, low HIV service uptake in a geographically defined area increases the prevalence of high HIV viremia, leading to greater HIV transmission and incident HIV. Methods: A systematic review was conducted to examine the association between population-level measures of HIV viral load and incident HIV infection in generalized and concentrated epidemics. Publications were English, peer-reviewed articles published from January 1, 1995 through February 15, 2019 that explicitly defined HIV viral load and assessed outcomes of HIV recency, incidence, seroconversion, or new diagnosis. Studies sampled general or key populations through population-based surveillance registries, household-based enumeration, cluster sampling, or respondent driven sampling. Descriptive statistics summarized review findings. The Swaziland HIV Incidence Measurement Survey (SHIMS) data were used for the remaining analyses. Using a two-stage cluster-based design, a nationally representative, household-based sample of adults, ages 18-49 years was enrolled from December 2010 to June 2011 in Eswatini. Consenting adults completed an interview and received home-based rapid HIV testing and counseling. All seropositive samples were tested for HIV viral load using the COBAS AmpliPrep/Taqman HIV-1 Test, v 2.0. Adults testing HIV-seronegative were enrolled in a prospective cohort for the direct observation of HIV seroconversion, completing an interview and home-based rapid HIV testing six months later. Multi-level latent class modeling was performed to identify statistically significant combinations of HIV risk factors and to classify the combinations into small area risk profiles. In the cross-sectional sample, linear regression with robust standard errors assessed the correlation between area profiles and places with high levels of uncontrolled HIV infection, or HIV core areas, measured by the area prevalence of detectable virus (≥20 copies/milliliter) among HIV-positive adults and among all adults, regardless of HIV status. In the prospective cohort, generalized linear regression of longitudinal data assessed the association between area profiles and places prone to new HIV infections (i.e., HIV susceptible areas), measured by area-level HIV seroconversions. Results: The systematic review found an evidence base primarily of lower quality studies and inconsistent HIV viral exposure measurement. Overall findings supported a relationship between increasing levels of suppressed HIV in HIV-infected populations and fewer new infections over time. Better quality studies consistently showed higher population viremia (i.e. HIV viral quantity among all persons, regardless of HIV status) associated with HIV incidence in high prevalence populations; population viral load (i.e., HIV viral quantity among only HIV-positive persons) did not show an association with incident HIV in high prevalence, general populations and was inconsistent in key populations. To determine whether area risk profiles can pinpoint HIV core areas, latent class modeling was used to categorize 18,172 adults into one of six HIV risk types. The risk typology, classified through unique combinations of HIV service uptake and sexual risk behaviors, conveyed an adult’s propensity for HIV transmission and/or acquisition risk. The model next identified the area-level composite prevalences of HIV risk types; estimated the three most frequent, unique composite combinations; and categorized them into area risk profiles characterizing HIV risk: low-moderate acquisition risk, moderate acquisition/transmission risk, and high acquisition/transmission risk. The high acquisition/transmission areas comprised the largest proportions of highest risk transmission and acquisition types. The prevalence of detectable viremia progressively increased from low-moderate acquisition, moderate acquisition/transmission, and high acquisition/transmission profiles [17.7%, 25.4%, and 35.1%, respectively]. When compared with low-moderate acquisition areas, the prevalence of detectable viremia was 7.4% [p<.001] higher in moderate acquisition/transmission areas and 17.1% [p<.001] higher in high acquisition/transmission areas. The prevalence of detectable viral load significantly decreased from low-moderate acquisition to moderate acquisition/transmission areas [76.6% versus 68.7%, p<.001], and was significantly higher in high acquisition/transmission areas by 7.3% [p<.001], when compared with low-moderate acquisition areas. To determine whether area risk profiles can predict HIV susceptible areas, a total of 18,172 adults were surveyed of which 4396 [24%] had detectable viremia. 11,880 [96%; n=12,357] HIV-seronegative adults enrolled in the prospective cohort and 11,155 [94%] of them completed an endline visit. Four area profiles were identified, defined by unique patterns in prevalence of HIV viremia and of sexual risk behaviors. The proportion of HIV susceptible areas progressively increased from Profiles A, B, C, and D [14.3%, 21.8%, 24.6%, and 30.8%, respectively]. HIV susceptible areas were more than twice as likely to occur in Profile D than Profile A environments [RR 2.13, 95% confidence interval (CI) (1.13, 4.00); p=0.02]. Profile D areas had prevalences of unknown partner HIV status and detectable viremia at 28% and 24%, respectively. In contrast, Profile A areas had prevalences of only 8% with unknown HIV status and 31% with detectable viremia. Conclusion: This dissertation shows that geographic risk profiles can explain differences in population-level HIV outcomes. Risk factors spatially cluster in predictable, meaningful combinations that can inform an area typology of HIV risk. The co-location of adults predisposed to greater HIV risk may heighten levels of uncontrolled HIV infection, thereby creating potential area sources of ongoing transmission; however, the concurrent levels of other risk factors may have more influence in reducing population-level incidence than previously considered. A composite indicator of contextual HIV risk may reveal places core to HIV transmission and susceptible to HIV acquisition. Such area profiles may help identify the combination of locally specific risk factors that readily promulgate HIV and better inform the design of place-based HIV intervention packages to enhance current strategies towards global HIV control.