A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science. Johannesburg, 2014. / Determining e ective treatment strategies for life-threatening illnesses such as HIV is a signi cant problem in clinical research. Currently, HIV treatment involves using combinations of anti-HIV drugs to inhibit the formation of drug-resistant strains. From a clinician's perspective, this usually requires careful selection of drugs on the basis of an individual's immune responses at a particular time. As the number of drugs available for treatment increases, this task becomes di cult. In a clinical trial setting, the task is even more challenging since experience using new drugs is limited. For these reasons, this research examines whether machine learning techniques, and more speci cally batch reinforcement learning, can be used for the purposes of determining the appropriate treatment for an HIV-infected patient at a particular time. To do so, we consider using tted Q-iteration with extremely randomized trees, neural tted Q-iteration and least squares policy iteration. The use of batch reinforcement learning means that samples of patient data are captured prior to learning to avoid imposing risks on a patient. Because samples are re-used, these methods are data-e cient and particularly suited to situations where large amounts of data are unavailable. We apply each of these learning methods to both numerically generated and real data sets. Results from this research highlight the advantages and disadvantages associated with each learning technique. Real data testing has revealed that these batch reinforcement learning techniques have the ability to suggest treatments that are reasonably consistent with those prescribed by clinicians. The inclusion of additional state variables describing more about an individual's health could further improve this learning process. Ultimately, the use of such reinforcement learning methods could be coupled with a clinician's knowledge for enhanced treatment design.

A thesis submitted to the Faculty of Science University of the Witwatersrand Johannesburg in fulfillment for the requirements of the degree of Master of Science. 14 May 2015. / Peptidomimetic compounds have been shown to exhibit both anti-HIV and anti-malarial activity. A multicomponent reaction was used to create a library of peptidomimetic compounds with an α-hydroxy-β-amino acid unit. The Passerini reaction between an aldehyde, carboxylic acid and isocyanide was used to prepare compounds containing both ester and amide functionalities. These compounds were then subjected to a deprotection-acyl migration strategy giving rise to the target compounds. This approach, known as the Passerini Amine Deprotection Acyl Migration (PADAM) sequence was successfully used to create a library of novel peptidomimetic compounds. From this library, 22 compounds were tested for activity against HIV and malaria. The Passerini reaction gives rise to a product containing a new stereogenic centre, and as the starting aldehyde used (N-Boc-phenylalaninal) has a stereogenic centre, the products were isolated as a mixture of diastereomers. Our research was also focused on finding ways of influencing the stereoselectivity of the reaction and the separation of the resulting diastereomers. The diastereomeric ratio of the Passerini products was found to be approximately 2:1 for all the reactions performed. This ratio could be modified slightly when using certain carboxylic acids and isocyanides that were either very bulky or had a stereogenic centre. Attempts to enzymatically resolve the diastereomeric products were not successful after trials using a library of 25 lipase enzymes. However, use of preparative HPLC enabled the successful separation of most of the diastereomeric mixtures, affording compounds with high purity. X-ray crystallography enabled us to identify the major diastereomers as having the R,S configuration, whilst the minor diastereomers had the S,S configuration at the two stereogenic centres. A possible explanation for the observed stereoselectivity is based on the Felkin-Anh chelation control model. It suggests that mono-protected amino aldehydes follow a chelation controlled mechanism in nucleophilic addition reactions. Chelation occurs, albeit in the form of hydrogen bonding, between the NH and carbonyl oxygen. The library of compounds was tested for activity against both HIV-1 and malaria. Only three compounds showed moderate activity against the malaria parasite, inhibiting parasitic growth by 37-42% at 5 μM respectively. Significantly, all of the active compounds contained an adamantyl moiety. Unfortunately no anti-HIV activity was seen for any of the compounds tested in the HIV-assay.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Master of Science in Genetics. Johannesburg, South Africa 2017 / Background: Stavudine (d4T) use is associated with the development of sensory neuropathy (SN), several mechanisms may underlie d4T-induced toxicity, including: (1) Inter-patient genetic variability in the genes modulating the deoxynucleotide triphosphate (dNTP) pool sizes. (2) Variation in intracellular ARV drug concentrations due to genetic variation in drug transporters. In our study we examined the genetic variation in four stavudine transporter genes and seven genes regulating the deoxythymidine triphosphate (dTTP) synthesis and their associations with d4T-induced SN or CD4+ T cell count or mtDNA copy number. Methods: We examined a cohort of HIV-positive South African (SA) adults exposed to d4T, including 143 cases with SN and 120 controls without SN. 26 single nucleotide polymorphisms (SNPs) from the literature were chosen, prioritised on being tagSNPs with minor allele frequency >5% in Kenyan Luhya (a proxy population for the SA Black population); SNP functional effects and suitability for multiplex analysis on the genotyping platform. Genotyping was performed using Sequenom mass spectrometry. A qPCR assay was used to measure the mtDNA copy number. Association of sensory neuropathy, CD4+ T cell count and mtDNA copy number with genetic variants was evaluated using PLINK. Results: All 26 SNPs were in Hardy-Weinberg equilibrium (HWE) in both the cases and controls. SNP rs8187758 of the SLC28A1 transporter gene and a 3-SNP haplotype ABCG2 were significantly associated with CD4+ T cell count after correction for multiple testing (p = 0.043 and p=0.042 respectively), but were not significant in multivariate testing. No SNP remained significantly associated with SN or mtDNA copy number, after correction for multiple testing. Conclusion: Variation in genes encoding molecular transporters of d4T may influence CD4+ T cell counts after ART. This study presents a positive step towards achieving personalized medicine in SA. / MT 2018

This dissertation uses three types of routinely collected data from HIV care and treatment facilities in sub-Saharan Africa to investigate the association between the availability of adherence support and active outreach services on patient non-retention, loss to follow-up, and measured death after ART initiation. Following a literature review summarizing the state of knowledge concerning the influence of programmatic services on patient retention in care and survival, these relationships are first examined in an aggregate analysis of over 232,000 patients at 349 HIV care and treatment facilities initiating ART between January 2004 and December 2008. Key findings are that several adherence support and outreach services are associated with reduced rates of non-retention, loss to follow-up, and death. Specifically, facilities offering three or more adherence support services, written educational materials promoting ART adherence, one-on-one or group adherence counseling sessions, reminder tools, and food rations to promote ART adherence were associated with reduced non-retention and loss to follow-up, while facilities offering on-site support groups for HIV+ patients, peer educators, provision of reminder tools, and food rations to promote ART adherence were associated with reduced death rates. In sub-analyses investigating six- and 12-month retention after ART initiation, facilities offering three or more separate adherence support services, routine review of medication pickup and/or dedicated ART pharmacists, and active patient outreach to trace patients missing visits had lower non-retention. Taken together, this analysis provides evidence that program-level services found efficacious in experimental settings are also effective in operational settings. Next, a sub-analysis is conducted among facilities also providing electronic patient-level data to investigate similarities and differences in the association between adherence support and outreach services and patient non-retention, loss to follow-up, and measured death using aggregate vs. patient-level estimates of these outcomes, and to assess whether adjustment for patient-level differences between facilities change these measures of association. In multivariate analyses, clinics offering active patient outreach had lower rates of non-retention in both the ART cohort analysis and the patient-level analysis, and clinics offering food rations to promote ART adherence were associated with a lower risk of ascertained death in both the facility-level and patient-level analyses, but this association was diminished after adjustment for patient-level covariates. In contrast, various adherence counseling or support services were associated with lower non-retention in the ART cohort analyses but not in the patient-level data analyses. When compared with the results in the first paper, fewer associations were observed, suggesting either that the countries with patient-level databases are not representative of the entire range of HIV care and treatment facilities assessed in the first paper, and/or the specific facilities with electronic databases are more similar to each other than they are to facilities without electronic databases. Finally, the dissertation concludes with an investigation into the relationship between loss to follow-up and measured death. For this analysis, estimates of the death probability among patients lost to follow-up are created under varying assumptions (either assuming that the death probability among those lost to follow-up is equivalent to the death probability within various strata of covariates, or assuming that the probability of death is greater among patients lost to follow-up). Key findings from this analysis are that ratio comparisons of death rates between facilities offering different services are robust to changes in the death probability if patients lost to follow-up are assumed to have a similar probability of death, conditioned on covariates, as those not lost to follow-up, but that associations between facility services and death rates are masked under the scenario where the facility service is associated with loss to follow-up and the death probability is assumed to be higher, conditioned on covariates, then the death probability among patients not lost to follow-up.

published_or_final_version / Public Health / Master / Master of Public Health

Background: Since the beginning of 21st century, several Asian countries started implementing their national free antiretroviral therapy (ART) programs to tackle one of the most striking public health issues in Asia – HIV/AIDS. Despite the efforts being made, the treatment coverage remains as low as 44% in 2010. Previous studies have identified financial constraint is a major barrier in accessing ART and an important reason of poor ART adherence in Asia. The purpose of this literature review is to explore the extent of financial burden experienced by people living with HIV (PLHIV) where free ART policy is implemented, and to provide valuable information for policy-making in reducing financial barriers and improve uptake of ART. Methods: Literature search was performed by entering keywords in PubMed and Medline. Articles were screened and selected for in-depth review according to the inclusion and exclusion criteria. A process on data synthesis was performed on the final eligible papers. Results: Five studies from four Asian countries describing the out-of-pocket health expenditure incurred by PLHIV during the delivery of ART were included in this review. Findings: Out of all direct medical costs, the cost of drug was most important in contributing to the total costs for patients without health insurance, while the cost of transportation was more important for patients covered by health insurance. Direct medical costs increased with advancing stage of disease. Rural patients would have spent up to 1,173% of their monthly income per capita, or more than 100% of their total household expenditure even when ART was provided free-of-charge. Patients have also highlighted free ARV drugs were sometimes not available in the health facility and they had to turn to the private market. Hence, the extent of financial burden in this review might be underestimated. Conclusion: Based on the data available, we concluded that increased accessibility of free ART should be accompanied with sustained ARV drugs supply and increased financial support for PLHIV. / published_or_final_version / Community Medicine / Master / Master of Public Health

Over the 30 years since it was first identified, the HIV/AIDS epidemic has had historically unprecedented severity and impact. There are approximately 33.4 million people living with HIV-1/AIDS which urges to seek novel approaches for HIV-1 diagnosis and HIV-1 therapy. Men who have sex with men (MSM) are severely affected by HIV-1 and constitute a large proportion of HIV-infected individuals. In Hong Kong, the transmission route of homosexual and bisexual contacts accounted for nearly 50% of incidence in 2012. To investigate HIV-1 prevalence among MSM in Hong Kong, the combination of fast antibody test (FAT) and real-time dried-blood-spot-based quantitative polymerase chain reaction (DBS-qPCR) was employed for 474 participants chosen randomly from community testing sites of MSM within a one-year period which showed a 4.01% (19/474) rate of HIV-1 prevalence among MSM in Hong Kong with three cases at the acute phase among the newly infected participants. The new survey demonstrated that the risk factors of MSM are mostly correlated with the receptive role during anal sex and syphilis infection. In this study, two traditional Chinese herbal medicines (TCHM), Sanguisorba officinalis (SO) and Spatholobus suberectus (SS), inhibited the infection of model cell lines expressing HIV-1 targets by HIV-1 pseudoviruses, while the anti-HIV-1 properties of SO were demonstrated for the first time. Both SO and SS were able to block not only infection by pseudoviral HIV-1 CCR5-tropic and CXCR4-tropic strains, but also RT and PI drug-resistant strains. Mechanistic studies revealed that SO and SS interact with the viral envelope to prevent the infection of target cells by HIV-1. Two compounds derived from SO and SS, named Gallic acid (GA) and Jiazhi (JZ), retained anti-HIV-1 properties and blocked HIV-1 infection by acting on the viral envelope. Small molecules derived from TCHM were also investigated for their capacity to activate HIV-1 from latency. A small molecule derived from SS, Daidzein (DDZ), demonstrated the potentials to trigger HIV-1 reactivation in latently infected cell lines. DDZ enhanced gene expression from HIV-1 LTR in which the Sp1 binding site plays an important role. The Akt pathway is also involved in the initiation of DDZ-induced activation. Phosflow analysis revealed that DDZ activated the Akt pathway in various subpopulations of T cells, including memory CD4+ T cells which are considered to be a major reservoir for HIV-1. The structure-activity relationships (SARs) study demonstrated the 4'-hydroxyisoflavone as bio-functional core structure. Addition of a hydroxyl group on C-5 position significantly decreases its biological function of HIV-1 latency activation. In summary, this study investigates HIV prevalence and incidence using an assay for early HIV-1 diagnosis and performs an analysis of risk factors of behavior which contributes to the effective control of HIV transmission in Hong Kong and its neighbors in Asia. It also demonstrates a drug research sourced from traditional Chinese herbal medicines that which sheds lights on drug discovery from traditional herbal medicines and facilitates mechanistic drug design for HIV-1 eradication. / published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy

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Background: HIV-1 envelope (Env) diversity is arguably the most significant challenge for the development of an efficacious vaccine. An ideal vaccine would elicit the production of broadly neutralizing antibodies (nAb), capable of retaining potent activity against a diverse panel of viral isolates. The evolutionary forces that shape the diversity of envelope and ensuing nAb responses are incompletely understood in HIV-1 subtype C infection, the dominant subtype globally. Therefore there is an urgent need to define the patterns of envelope diversity, determine the correlates of immune protection and to discover subtype C immunogens in order to develop a globally relevant vaccine. Methods: We applied the single genome sequencing strategy to study plasma derived viruses from four slow progressors and four progressors over a median of 21 months between study entry and study exit. The participants‘ samples were from the Sinikithemba cohort of antiretroviral therapy-naïve chronically infected individuals and were termed slow progressors or progressors based on CD4 T-cell counts and viral loads over two years. We analyzed env sequence diversity, divergence patterns and envelope characteristics across the entire HIV-1 subtype C gp160. We studied the evolution of autologous nAb (AnAb) and heterologous nAb responses in order to test the hypothesis that slow disease progression is associated with more potent autologous or heterologous nAb responses. Furthermore, genotypic env characteristics were correlated to potency of neutralization in order to understand possible differences in nAb responses with divergent rates of disease progression and to describe genotypic differences associated with differential nAb potencies. In addition, the binding affinities of HIV-specific immunoglobulins (IgGs) and the affinities of the IgGs to various Fcγ receptors (both activating- FcγRI, FcγRIIa, FcγRIIIa; inhibitory- FcγRIIb) were assessed. These binding affinities were used as a surrogate for the recruitment of effector functions of cells of the innate immune system e.g. macrophages or natural killer cells to initiate antibody-dependent cell-mediated cytotoxicity (ADCC) or antibody dependent cell-mediated viral inhibition (ADCVI) and these were correlated to markers of disease progression namely CD4 T-cell counts and viral loads. Results: Intra-patient diversity was higher in slow progressors for regions C2 (p=0.0006), V3 (p=0.01) and C3 (p=0.005) compared to progressors. Consistent with this finding, slow progressors also had significantly increased amino acid length in V1-V4 with fewer potential N-linked glycosylation sites (PNGs) compared to progressors (p=0.009 and p=0.02 respectively). Similarly, in progressors, the gp41 region was significantly longer and had significantly fewer PNGs compared to slow progressors (p=0.02 for both parameters). Positive selection was prominent in regions V1, C3, V4, C4 and gp41 in slow progressors, whereas in progressors, it was prominent in gp41. Signature consensus sequence differences between the groups occurred mainly in gp41. Neutralizing antibodies (nAb) evolved over time in progressors, as evidenced by significantly higher nAb IC50 titers to baseline (study entry) viruses when tested against study exit time-point plasma compared to contemporaneous responses (p=0.003). In contrast, slow progressors‘ nAb titers did not differ significantly between study entry and study exit time points. nAb IC50 titers significantly correlated with amino acid lengths for C3-V5 (p=0.03) and V1-V5 (p=0.04) for slow progressors and V1-V2 for progressors (p=0.04). Slow progressors and progressors displayed preferential heterologous activity against the subtype C panel. There were no significant differences in breadth of responses between the groups for either subtype A or C. Neutralization breadth and titers to subtype B reference strains however, was significantly higher in progressors compared to slow progressors (both p<0.03) with increasing nAb breadth from study entry to study exit in progressors. Progressors had cross-reactive neutralizing antibodies that targeted V2 and V3. Binding affinities of non-neutralizing antibodies to HIV-specific gp120, gp41 and p24 and to activating and inhibitory Fcγ receptors (FcγRs) were similar in both groups. However, in slow progressors, CD4 T-cell counts correlated inversely with antibody binding affinity for the activating FcγRIIa (p=0.005). Conclusions: These data suggest that separate regions of Env are under differential selective forces, and the heterogeneity of env diversity and evolution differ with HIV-1 disease course. Single genome sequence analysis of circulating viruses in slow progressors and progressors indicate that diversity, length polymorphisms, sites under positive selection pressure, and PNGs consistently map to specific regions in Env. Cross-reactive neutralizing antibodies targeting epitopes in V2 and V3 indicate that nAb breadth may be dictated by a limited number of target Env epitopes. Certain key N-linked glycosylation sites were shown to be crucial for antibody neutralization. The potencies of autologous nAbs were directly affected by the amino acid lengths in certain regions of Env gp160 and by the numbers of PNGs. Target vaccine immunogens may have to be given over long periods of time and may have to include multiple subtype immunogens to elicit the production of potent, broad cross neutralizing antibodies with high binding affinity. Overall, the data suggest that neither nAbs nor non-neutralizing antibodies could be directly associated with disease attenuation in this cohort of chronically infected individuals. However, continuous evolution of nAbs was a potential marker of HIV-1 disease progression. Further studies on larger cohorts to identify people with potent nAbs and to identify specific targets of these antibodies are needed. Furthermore studies of non-neutralizing antibodies in HIV-1 infection using functional assays will be required in order to determine their role in HIV-1 pathogenesis. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2011.

In South Africa 1 000 people die of AIDS everyday and 100 000 more people require ARVs every year. There is therefore an urgent need to provide access to ARVs andother essential medicines. The South African Constitution requires the government totake reasonable measures to ensure access to health care. The government has cited financial constraints as the major ohstacle to fulfilling this constitutional imperative. In an effort to stretch their budgetary resource other medium-income countries have used measures such as compulsory licences, voluntary licences and parallel importation. These measures, provided for in the TRIPS Agreement and the Doha Declaration, are available under South African legislation but have not been properly implemented due to a lack of political will. The proper use of compulsory licences by the South African government is vital because all twelve of the ARVs on the World Health Organisation's Essential Medicines List are protected in South Africa by our patent laws. However, in order to issue compulsory licences more easily and quickly the South African Legislature will need to pass legislation which clarifies the ambiguities contained in TRIPS and the Doha Declaration. Other methods to lower the price of medicines include the segmentation of the South African market in order to facilitate differential pricing. The State must balance its use of such measures with programmes to incentivise research and development into neglected diseases and HIV/AIDS. Such programmes will also assist the State's capacity to conduct its own research and development into new medicines, whilst bolstering its domestic pharmaceutical manufacturing capacity. The ultimate solution to South Africa's access to medicine problem is to create a pharmaceutical manufacturing industry capable of producing the most complex medicines, so as to lessen its dependence on drug manufacturers reducing their prices. The way to create a sophisticated pharmaceutical manufacturing capacity is to use the flexibilities in TRIPS and to uphold South Africa's high patent standards. The Constitutional Court's involvement is essential in order to force the State to implement its own policies so as to provide access to affordable medicines. / Thesis (LL.M.)-University of KwaZulu-Natal, Durban, 2008.