<p>In 2018, the World Health Organization (WHO) reported approximately 37 million people are living with the Human Immunodeficiency Virus (HIV). Suppressing replication of the virus down to undetectable levels was achieved by combination antiretroviral therapy (cART) which effectively reduced the mortality and morbidity rates of HIV positive individuals. Despite the improvements towards combatting HIV/AIDS, no successful treatment exists to eradicate the virus from an infected individual. Treatment regimens are lifelong and prompt less than desirable side effects including but not limited to; drug-drug interactions, toxicity, systemic organ complications, central nervous system HIV triggered disorders and most importantly, drug resistance. Current therapies are becoming ineffective against highly resistant HIV strains making the ability to treat long-term viral suppression a growing issue. Therefore, potent and more effective HIV inhibitors provide the best chance for long-term successful cART. </p> <p>HIV-1 protease (PR) enzyme plays a critical role in the life cycle and replication of HIV. Significant advancements were achieved through structure-based design and X-ray crystallographic analysis of protease-bound to HIV-1 and brought about several FDA protease inhibitors (PI). Highly mutated HIV-1 variants create a challenge for current and future treatment regimens. This thesis work focuses on the design, synthesis, and evaluation of two new classes of potent HIV-1 PIs that exhibit a novel bicyclic oxazolidinone feature as the P2 ligand and a novel bis squaramide scaffold as the P2/P3 ligand. Several inhibitors displayed good to excellent activity toward HIV-1 protease and significant antiviral activity in MT-4 cells. Inhibitors 1.65g and 1.65h were further evaluated against a panel of highly resistant multidrug-resistant HIV-1 variants and displayed antiviral activity similar to Darunavir. X-ray crystal structures of inhibitor 1.65a and inhibitor 1.65i were co-crystallized with wild type HIV-1 protease and solved at a 1.22 Å and 1.30 Å resolution and maintained strong hydrogen bond with the backbone of the PR enzyme. </p>

O estudo objetivou identificar a colonização nasal por Staphylococcus aureus em PVHA hospitalizadas e relacionar com adesão a TARV. Trata-se de um estudo transversal, realizado em duas unidades de cuidados especializados às doenças infecciosas de um hospital universitário, do interior do Estado de São Paulo. A coleta de dados ocorreu no período entre 01 de agosto de 2011 e 31 de janeiro de 2015, procedida do levantamento dos dados sociodemográficos, clínicos e imunológicos; os quais foram obtidos através do prontuário e entrevista individual; da coleta de duas amostras de swab nasal; e da identificação da retirada dos medicamentos antirretrovirais, através do SICLOM. Todos os aspectos éticos foram contemplados. Os swabs foram coletados, encaminhadas e processadas pelo Laboratório de Microbiologia e Sorologia onde foram utilizados cartões AST-P585 para avaliar a sensibilidade dos Staphylococcus aureus aos antibióticos. A organização dos dados foi feita no Microsoft® Office Excel® 2010 for Windows 8 e transportada para o software IBM® SPSS®, versão 23.0 for Windows para a análise descritiva e analítica. Utilizouse o procedimento PROC LOGISTIC do software SAS 9.4®, para a análise exploratória pela variável resposta. Adotou-se o nível de significância de todos os testes de 5%. Dos 236 participantes elegíveis, a maioria era do sexo masculino (59,3%), na faixa etária entre 40 e 49 anos (48,3%), de etnia branca (66,1%), procedente de Ribeirão Preto-SP (59,7%), com ensino primário incompleto (40,2%), com ocupação profissional (52,5%), heterossexual (81,8%) e não teve parceria sexual nos últimos 6 meses (57,6%). Houve a predominância do tempo de diagnóstico pelo HIV em > 5 e <= 10 anos (44,4%), a contaminação se deu pela via sexual (66,1%), a admissão foi via o ambulatório da intituição (45,5%), a carga viral foi detectável (56,4%), a contagem de linfócitos T+ CD4 foi menor que 350 células/mm3 (61,8%), a antibioticoterapia estava prescrita (65,3%), assim como a terapia antirretroviral (51,7%) e haviam recebido procedimentos invasivos (67,4%). Quanto a colonização nasal por Staphylococcus aureus, 36,0% foram identificados como colonizados, no primeiro dia de internação hospitalar. Dos 137 participantes que permaneceram internados no sétimo dia, em 37 (27,0%) houve a identificação da colonização nasal por Staphyloccocus aureus. Quanto a classificação da adesão aos medicamentos antirretrovirais, houve o predomínio dos participantes na categoria de adesão indesejável (67,8%). Concluiu-se que a prevalência da colonização nasal por Staphylococcus aureus foi de 38,13%. A classificação quanto a categoria da adesão aos antirretrovirais interfere na presença/ausência da colonização nasal por Staphylococcus aureus, assim as PVHA hospitalizadas e categorizadas em adesão indesejável possuem 2,597 vezes o risco de obter presença de colonização nasal por Staphylococcus aureus, em relação àquelas classificadas na categoria de adesão desejável / The research aimed to identify nasal colonization by Staphylococcus aureus in hospitalized PLWHA and to correlate with ART adherence. It was a cross-sectional study carried out in two specialized care units for infectious diseases at a university hospital in the interior of the State of São Paulo. The data collection took place between August 1, 2011 and January 31, 2015, proceeding from the survey of sociodemographic, clinical and immunological data, which were obtained through the medical record and individual interview; the collection of two samples of nasal swab and the identification of the withdrawal of antiretroviral drugs through SICLOM. All ethical aspects have been contemplated. The swabs were collected, sent and processed by the Laboratory of Microbiology and Serology, AST-P585 cards were used to evaluate the sensitivity of Staphylococcus aureus to antibiotics. Data organization was done in Microsoft® Office Excel® 2010 for Windows 8 and shipped to IBM® SPSS® software, version 23.0 for Windows for descriptive and analytical analysis. The PROC LOGISTIC procedure of the SAS 9.4® software was used for the exploratory analysis by the response variable. The level of significance was 5%. Results: From the 236 eligible participants, the majority were male (59.3%), aged 4049 (48.3%), white (66.1%), from Ribeirão Preto-SP (59.7%), with incomplete primary education (40.2%), with occupational (52.5%), heterosexual (81.8%) and had no sexual partner in the last 6 months (57.6% ). There was a predominance of HIV diagnosis time in > 5 and <= 10 years (44.4%), contamination occurred through the sexual route (66.1%), admission was from the outpatient clinic (45.5%), the viral load was detectable (56.4%), the T + CD4 count was lower than 350 cells / mL (61.8%), antibiotic therapy was prescribed (65.3%), and antiretroviral therapy (51.7%) and had received invasive procedures (67.4%). Regarding nasal colonization by Staphylococcus aureus, 36.0% were identified as colonized, on the first day of hospital admission. From the 137 participants who remained hospitalized on the seventh day, 37 (27.0%) were identified the nasal colonization by Staphylococcus aureus. Regarding the classification of adherence to antiretroviral drugs, the participants were predominant in the category of undesirable adherence (67.8%). Concludes that the prevalence of nasal colonization by Staphylococcus aureus was 38.13%. The classification as to the category of antiretroviral adherence interferes with the presence/absence of nasal colonization by Staphylococcus aureus, so the hospitalized PLWHA and categorized as undesirable adherence have 2,597 times the risk of nasal colonization by Staphylococcus aureus in relation to those classified in desirable membership category

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree in Master of Science in the School of Molecular and Cell Biology August 2017 / Antiretroviral therapy (ART) drugs such as stavudine (d4T) are known to have off-target side-effects, including the inhibition of DNA polymerase gamma which replicates mitochondrial DNA (mtDNA). ART-induced depletion of mtDNA copy number may cause mitochondrial toxicities such as sensory neuropathy (SN). Genetic variation in DNA polymerase gamma or in other nuclear genes influencing mtDNA replication and mtDNA copy number may therefore contribute to susceptibility to d4T-induced SN. DNA samples from 263 HIV-positive South African adults exposed to d4T were classified as cases with SN (n = 143) and controls without SN (n = 120). A total of 28 single nucleotide polymorphism (SNPs) were chosen in nuclear genes from the mtDNA replication pathway and from a GWAS paper examining SNP association with ART-induced SN (Leger et al. 2014). Genotyping was performed using Sequenom Mass Spectrometry. MtDNA copy number was determined using a qPCR assay. Associations between SN and genetic variants, between genetic variants and mtDNA copy number, and between mtDNA copy number and SN were evaluated in univariate and multivariate models using Plink v1.07 and GraphPad v7. Age and height were significantly different in the cases with SN vs controls without SN. In univariate analyses, three SNPs and two haplotypes were significantly associated with SN, three SNPs were associated with pain intensity and three haplotypes were significantly associated with mtDNA copy number. However, there were no significant associations with SN, pain intensity or mtDNA copy number after correction for multiple SNP testing. No significant difference in mtDNA copy number in cases vs. controls was observed. In conclusion variation in nuclear-encoded mitochondrial genes examined in the current study do not play a role in ART-related mitochondrial complications such as changes in mtDNA copy number, or occurrence of SN. / MT2018

Purpose: The main objective of the current study was to investigate and monitor the auditory status in a group of adult patients with AIDS receiving antiretroviral therapy (ART) and other therapies in a hospital outpatient clinic in Gauteng, South Africa. Specific objectives included estimating the prevalence of hearing loss and the presence of other otologic effects over and above hearing impairment (tinnitus, aural fullness, disequilibrium, and so forth); assessing the type, degree and configuration of the hearing loss; exploring the type of hearing symptom onset; documenting case history data such as signs and symptoms of each participant and identifying any associations between obtained signs and symptoms and hearing loss; documenting the names of all medications used and their possible impact on hearing function (specifically ototoxicity monitoring of ART); and comparing the results of the experimental group to those of a control group.

Executive Function is conceptualized in this study as the ability to form (the planning functionality obtained through initiation and working memory), maintain (response selection and the ability to self-regulate and inhibit) and switch (cognitive flexibility, mental tracking, organization and sequencing) mental processes in order to effect a positive outcome. The present research is a quasi-experimental study embedded in the Positivist tradition that sets out to empirically evaluate the Executive Function profile of seropositive adolescents (n = 29) emerging from a low socio-economic background and currently on a managed ART programme when compared to a healthy contrast group (based on age, socio-demographic and educational system). As a quantitative study, Executive Function was operationalized through the use of multiple tests of Executive Function such as the Delis-Kaplan Executive Function Colour Word Interference Test (D-KEFS CWIT), the Wisconsin Card Sorting Test (WCST) and the Trail Making Test Part B (TMT-B). As the study formed part of a larger study that included additional neurocognitive tests, including the WISC-R, selected subtests from the WISC-R were used to validate specific arguments relating to the study. The results showed that HIV positive adolescents were inclined to have poorer Executive Function performance especially under situations of higher cognitive load when compared to the unaffected group. The implications of these results are discussed in this research.

PhD (Molecular Medicine and Haematology), Faculty of Health Sciences, University of the Witwatersrand / Background: The availability of highly active antiretroviral (ARV) treatment in the South African government sector has reduced the morbidity and mortality associated with HIV-1 infection. However, ARV drug resistance and toxicity are major obstacles to achieving and maintaining virus suppression, but there is no provision for ARV drug resistance testing in the public sector. To date, most studies of ARV drug resistance in HIV-1 reverse transcriptase (RT) and protease (PR), are based on sequence data from HIV-1 subtype B, whereas subtype C is the predominant circulating subtype in South Africa. Moreover, host genetic polymorphisms associated with ARV drug toxicity have not been investigated in South African populations. This study evaluated viral and host genetic factors associated with ARV treatment outcome in 812 ARV drug-naive South African AIDS participants enrolled on the CIPRA-SA study from Johannesburg and Cape Town. Methodology: An affordable in-house genotyping protocol (subtype C specific) was established and validated to monitor the emergence of ARV drug resistance. This assay was used to genotype all CIPRA-SA participants failing the first- and second-line ARV drug regimens. Allellic discrimination assays to identify the G1344A, A6986G, G516T and C3435T SNPs in CYP3A4, 3A5, 2B6 and MDR-1, respectively, associated with ARV metabolism and absorption were performed. Results: The in-house ARV drug resistance assay successfully genotyped 95% of patient samples, including non-C subtypes from 8 African sites. Treatment failure was experienced in 371 participants, mainly due to toxicity (n=134) or virological failure (n=83). Overall, CIPRA-SA participants with a lower CD4+ T-cell count at study onset were more likely to experience viral failure. Genotyping using the in-house assay revealed that 6 participants had ARV drug resistance mutations at study entry. Treatment failure of 58 participants was a result of ARV drug resistance mutations, whereas 19 had no known ARV drug resistance mutations. The most frequent mutations were M184V (67%) and K103N (50%). K65R was present (3%) and one participant harboured TAMs. Longitudinal genotypic analysis showed that NNRTI mutations accumulated at a rate of one per three months left on failing therapy. No PR mutations were detected amongst participants experiencing second-line failure. The four SNPs analysed occured in similar frequencies between a background and the CIPRA-SA cohort. Furthermore, no statistically significant association could be found between these four SNPs and viral failure and/or toxicity. Conclusion: Overall, HIV-1 subtype C-infected individuals receiving ARV therapy develop many of the known subtype B drug resistance mutations. However, the ARV drug resistance patterns in the closely monitored CIPRA-SA cohort were less complex compared to published data from the region, confirming that more frequent viral load monitoring, genotyping, and a virological failure cut-off value of 1000 RNA copies/ml ensure a better prognosis, and preserve future ARV treatment options.

ABSTRACT Successful communication with patients in a multicultural, multilinguistic environment is a challenge to health professionals, particularly in the context of HIV/Aids and antiretroviral (ARV) treatment. Although the introduction of ARVs has brought hope, high levels of adherence are required to ensure treatment success and numerous barriers to adherence exist. Pharmacists play an important role in encouraging adherence to ARV treatment regimens by providing education and counselling. However, previous research indicates that interactions are often dominated by the pharmacist. Also, verification of patients’ understanding of information is infrequent and that patients are often passive recipients of instructions. This study aims to identify and describe interactive processes in pharmacy interactions while considering the impact of the disease and macro context on communication. Twenty-six cross-cultural, cross-linguistic pharmacist-patient interactions from a South African HIV/Aids pharmacy are described. Data collection included video recordings, interviews with participants and ethnographic observations in the pharmacy. A hybrid analytical approach incorporated aspects of Conversation Analysis (CA) and Discourse Analysis (DA). The results of this study are particularly encouraging. They demonstrate that despite the presence of cultural, linguistic and other contextual barriers, pharmacist-patient interactions can be efficient. The use of facilitative verbal and non-verbal communication strategies ensures that dosage instructions are successfully communicated by the pharmacist to the patient. In line with prior research, collaboration is promoted when pharmacists create rapport and focus on the lifeworld of the patient. The study shows that intuition and sensitivity to atmosphere in interactions is essential for achieving concordance. The disease context of HIV/Aids has a profound influence on the pharmacistpatient interaction and this study demonstrates the significant impact of the macro ii context on micro aspects of communication. The evidence suggests that the nature of humanity and the daily interface between culture and language in South Africa enables pharmacists and patients to transcend some of the barriers to communication and collaboration that have been identified in previous studies. The findings imply that the diversity of South Africa provides both hope and a resource which can inform policy and future practice.

In 2009 an estimated 33 million people were living with the Human Immunodeficiency Virus (HIV). Of this global population, 35% live in South Africa. Furthermore, sub-Saharan Africa is home to 80% of the world’s population of HIV-1 positive children and adolescents. The most prominent form of transmission of HIV in children in South Africa is from mother to child. Until 2004, South Africans had limited access to ARV treatment at and after birth due to the government legislation. As a consequence, treatment of HIV in children may only have been initiated after clinical presentation of immune deficiency. Therefore, currently, HIV-1 positive adolescents born during the period of restricted ARV-access may have experienced physical and developmental symptoms associated with the virus including neurological deficits, prior to initiating treatment. This study investigated the current psychomotor functioning, such as psychomotor speed, manual dexterity, graphomotor and visual-motor coordination of a group of low socio-economic HIV-1 positive adolescents in Johannesburg, South Africa, who are now on a managed antiretroviral programme and how this compared to a HIV negative contrast group. A Mann-Whitney U Test indicated a significant difference in mean non-dominant hand performance in the Grooved Pegboard Test between the two groups (U = 738, p < .05), with the HIV positive group performing slower than the HIV negative group. An independent samples t-test indicated a significant difference between groups in the Block Design subtest of the WISC-R [t(88) = -2.93, p < .01] where the HIV positive group performed significantly worse than the HIV negative group. Additionally, a Mann-Whitney U Test revealed a significant difference in number of errors made in the WISC-R Mazes subtest between groups (U = 736.50, p < .05), where the HIV negative group made more errors. Another Mann-Whitney U Test revealed a significant difference between groups in the ROCFT Copy score (U = 534.50, p < .01) where the HIV positive group achieved a significantly lower score than the HIV negative group. Lastly, a Mann-Whitney U Test demonstrated significant differences between the groups in the Trail Making Test A time (U = 445.00, p < .01), Trail Making Test B time (U = 509.00, p < .01), the number of errors made on the Trail Making Test B (U = 729.00, p < .05) and the difference between Trail Making Test B – A time (U = 769.50, p < .05) with the HIV positive group performing slower and making more errors in Part B than the contrast group. The findings of the current study imply that HIV-1 vertically-infected adolescents in Johannesburg, South Africa, on a delayed HAART programme appear to have persisting difficulties in complex psychomotor skills where an integration of functions is required. Furthermore, these results indicate an overall poor psychomotor performance in comparison to international normative data, supporting previous findings. Developmental, remedial and therapeutic recommendations were made.

South Africa has the most prominent percentage of individuals living with the Human Immunodeficiency Virus (HIV) in the world, with the most prominent form of transmission of HIV in South Africa being vertical mother-to-child transmission. From 1997 until 2004, South Africa had limited access to ARV treatment at and after birth due to the government legislation. As a consequence, treatment of HIV may only have been initiated after clinical presentation of immune deficiency. A paucity of information therefore exists regarding this population in addition to the specific age demographic of adolescents. Adolescents may be negatively influenced by the cortical thinning associated with HIV, and this study therefore aims to investigate the verbal fluency and vocabulary (in English) of 30 bi- or multilingual seropositive adolescents that are currently on a managed anti-retroviral programme in comparison to an HIV-negative contrast group of 70 bi- or multilingual adolescents in South Africa (matched for age, education, and socioeconomic status). The study found that there were no significant results between the HIV-positive and HIV-negative groups on the measures of vocabulary, semantic naming, or phonemic naming in ‘F’ as determined by their performance on the neuropsychological assessments. Significant results were noted between the HIV-positive and HIV-negative groups on the phonemic naming categories of ‘A’ and ‘S’ however, and negative correlations between performance in these categories and current viral load, and viral load at Highly Active Antiretroviral Therapy (HAART) initiation were also noted. This research formed part of a broader study examining the overall neurocognitive effects of HIV-1 infection in adolescents in South Africa.

A research report submitted to the Faculty of Health Sciences, the University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Master of Science in Medicine in Child Health Neurodevelopment Johannesburg, 2013 / Human Immunodeficiency Virus (HIV) infection in infancy may influence the developing brain and lead to adverse neurodevelopmental consequences. We aim to describe the neurodevelopmental characteristics of a cohort of young children infected with HIV prior to antiretroviral therapy (ART) initiation and after achieving viral suppression. A retrospective analysis of data collected as part of a randomised equivalence trial between April 2005 and May 2009, at a hospital in Johannesburg, South Africa. 195 HIV-infected children under 2 years of age were assessed. A simple, inexpensive screening questionnaire (Ages and Stages Questionnaire - ASQ) was used to identify neurodevelopmental delays. The ASQ was administered prior to ART initiation, and again after viral suppression on a protease inhibitor-based regimen had been achieved. Median age pre-ART was 8.8 months (range 2.2 - 24.9), 53.9% were male. Mean time to viral suppression was 9.4 months (range 5.9 - 14.5) and the ASQ was administered to 108 caregivers at this time. Compared to pre-ART, at viral suppression, there was significant reduction in the proportion of children failing the gross motor (31.5% vs. 13%, p<0.01), fine motor (21.3% vs. 10.2%, p=0.02), problem solving (26.9% vs. 9.3%, p<0.001) and personal social (17.6% vs. 7.4%, p=0.02) domains. The proportion of children failing the communication domain was similar at each time point (14.8% vs. 12%, p=0.61). At time of viral suppression 10.2% failed at least one of the five domains. Achieving viral suppression on ART resulted in significant improvements in the neurodevelopmental function of young HIV-infected children, however, neurodevelopmental problems still persisted in a large proportion. Appropriate screening for neurodevelopmental delay and timely referral could help improve outcomes.