Department of Advanced Nursing Science / MCur

Department of Advanced Nursing Science / PhD (Health Sciences)

MSc (Microbiology) / Department of Microbiology

MPH / Department of Public Health

Department of Public Health / MPH

MPH / Department of Public Health / Antiretroviral treatment (ART) roll-out presents new opportunities and challenges for nurse-initiated-andmanaged antiretroviral treatment (NIMART) trained nurses in the primary health care (PHC) facilities. Nurses have had central role in the management of the human immunodeficiency virus (HIV) since the disease was first reported. The purpose of this study was to explore and describe the challenges confronting professional nurses implementing the NIMART programme in PHC facilities under Thulamela B Municipality, Vhembe District. This study used a qualitative approach in which the interview was used as a data collection technique. The target population comprised professional nurses who were trained in NIMART and who were implementing the programme. Probability sampling, in particular its sub-type, the simple random sampling technique, was used to select fifteen PHC facilities within the sub-District. The non-probability purposive sampling technique was used to select the NIMART-trained professional nurses in Thulamela B sub-District. The sample size was determined by data saturation. Data were collected from the participants through semi-structured interviews, observations and field notes to assist in transcription. A digital recorder was used to log individual responses during the interview sessions. Data from the digital recordings were transcribed verbatim. Results were analysed and interpreted thematically. This study establsihed that nurses were facing several challenges such as shortages of infrastructure and medication, lack of support from management and non-NIMART-trained nurses and discrimination. The NIMART programme was poorly supported in terms of nurse training as nurses indicated that they faced problems in performing tasks such as obtaining blood from children. Doctors were also reported to not fully supporting the NIMART programme. NIMART-trained nurses were optimistic with the implementation of the programme dispite the challenges they faced. To overcome some of the challenges faced at workplaces, nurses devised mechanisms such as allocating different times for collecting tablets and review, and group education for those consulting. It was also established that nurses provided support to each other. Nurses were reported to be using their own transport to collect drugs from the local pharmacy store. Recommendations that emanated from the discussion of the findings and the conclusions of this study are likely to have implications and applications for supporting and advancing the NIMART programme.

MPH / Department of Public Health / Background: The provision of antiretroviral treatment for people living with HIV/AIDS has encountered many challenges associated with poor adherence in South African and other countries in Africa as a whole including globally. Taking ARVs Properly has shown to reduce viral load to a level where the virus becomes undetectable and these results in an increase of CD4 count cells. These decreases chances of oppotunistic infections but it requires a proper adherence and compliance to treatment which seems to be difficult to most patients on ART. Purpose: The study investigated factors contributing to clients defaulting antiretroviral treatment. Methodology: A qualitative explorative cross-sectional study design was conducted at Matoks in Capricon District, in the months of May, June and July 2017. A purposive sampling method was used to select 19 respondents whom where willing to voluntrily participate in the study from a population of People Living With HIV/AIDS (PLWHV). An indepth face to face interview was used to collect data, guided by a central question and probing. It was then analyzed by the use of eight steps of Tesch. Results: The findings revealed that women were more defaulters than men. Shortages of antiretroviral treatment and most clients were unable to collect ART on time due to lack of transport to the clinic and the long distance from their perspective homes to the clinic. Socio economic conditions and indegenious health beliefs were some of factors identified. Recommendations: extensive health education and promotion should be intensified to reach all community members of Matoks and PLWHA in terms of HIV/AIDS care and consistent taking of treatment that clients who live far away from the clinic will be able to collect the ARV treatment nearer to their place of residents. / NRF

MPH / Department of Public Health / Human Immune Deficiency Virus (HIV) and Acquired Immune Deficiency Syndrome (AIDS) place a significant burden on the caregivers for people living with HIV/AIDS (PLWHA). Caring for PLWHA is usually carried out by community members who are recruited from the same community as the PLWHA. These community members are trained to provide services as volunteer caregivers. The caregivers face various challenges in the process of giving care to PLWHA, often inadequately assisted by relatives, friends, neighbours, private individuals, grassroots traditional and political leaders. This results in caregivers being overwhelmed by their responsibilities, making their coping process even more difficult. The aim of this study was to explore the challenges experienced by community home-based caregivers (CHBCGs) caring for people living with HIV/AIDS at Tsianda Village, in Makhado Municipality, South Africa. This study adopted a qualitative explorative design. The population for this study were all CHBCGs caring for PLWHA. Non probability purposive sampling was used to select the community home-based caregivers working at Tsianda Community Home-based care organisation. In-depth interviews, using a semi-structured interview guide, was conducted by the researcher and a voice recorder were used to record data from participants. Data saturation was reached at the 11th participant. This is when the participants were no longer giving new information. The data collected from the study were analysed thematically. The following themes emerged from data analysis: Challenges for community home-based caregivers, perceived support for community home-based caregivers, coping strategies for community home-based caregivers. Measures to ensure trustworthiness and the code of ethics to protect the rights of the participants was applied and observed. The findings of the study revealed that community home-based caregivers experience various challenges which have a negative impact on their personal life, as well as their physical and psychological wellbeing. Community home-based care also uses different strategies to cope with these challenges. It was concluded that the community home-based caregivers are experiencing serious shortages of personal protective equipment, which makes them work with the fear of being infected with the diseases. It is recommended that the DOH should take it into consideration to provide the CHBCG’s organization with enough personal protective equipment for their safety and working without fear of being infected with deadly viruses. / NRF

PhD (Microbiology) / Department of Microbiology / Introduction Human Immunodeficiency Virus (HIV-1) continues to be a global public health concern, even though Antiretroviral drugs (ARV), especially Highly Active Antiretroviral Therapy (HAART) has significantly reduced morbidity and mortality due to AIDS globally in developed and developing countries. However, there is still a great need to explore every avenue for new therapeutic interventions due to the limitations and side effects of HAART. Potential major breakthroughs for future therapeutic development were the discoveries more than 10 years ago of the role of HIV-1 co-receptors and anti-viral activities of host restriction factors such as APOBEC3G protein, which is a member of the DNA cytosine deaminase family. Entry of HIV in to the host cell is through the attachment of the viral envelope glycoprotein to the CD4 receptor, and subsequent interaction, mainly with either CCR5 or CXCR4 co-receptors. Inhibitors, such as Maraviroc, which binds to CCR5 inhibiting entry of CCR5 utilizing viruses (R5 viruses), is currently reserved for salvage therapy in many countries including South Africa. In the course of HIV infection, CXCR4 utilizing viruses (X4 viruses) may emerge and outgrow R5 viruses, and potentially limit the effectiveness of Maraviroc. Several host cell APOBEC3 genes (A3D, A3F, A3G and A3H) have been shown to restrict HIV, and the HIV viral infectivity factor (Vif) protein serves to antagonize the action of APOBEC3 proteins, promoting viral replication. The CCR5 co-receptor and the HIV Env V3 loop have also been documented as playing roles in HIV-1 disease progression. The interplay between host and viral genes still needs widespread attention, given that disease outcomes of HIV depend on many factors, including host cell genetics. Since the discovery of these genes and their role in HIV replication, many studies have been conducted that show their association with viral polymorphism. The polymorphisms found in host cell genes can have significant effects on viral replication, transmission and fitness and can also contribute to the overall diversity in HIV-1 populations. It is hypothesized that there are significant polymorphisms in HIV-1 and cellular genes that may differ among different populations. Population-based studies have tried to establish a relationship between host factors such as APOBEC3 and CCR5 polymorphism and the rate of disease progression, but most studies have focused on Caucasian populations. In vi contrast, little information is available for the effects of variation in these genes in African populations such as South Africa, where the HIV epidemic has expanded at an alarming rate. Although several population studies have focused on African Americans, these do not give us a complete picture of the potential variation in Africans, though the studies can be a good guide on which to base additional studies. A more comprehensive analysis involving different African populations will likely provide a better understanding of the mechanisms underlying host-pathogen interactions, especially in view of the fact that African Americans are primarily infected with HIV subtype B, which is rarely seen in Africa. Methodology This study characterized the genetic variability of the APOBEC3 D, F, G and H genes as well as the HIV-1 vif, in an ethnically diverse HIV-1 infected South African cohort using Next Generation Sequencing (NGS). In addition, polymorphism in CCR5 was analyzed in conjunction with an analysis of the V3 loop sequences in HIV-1 from this cohort. Genomic DNA was extracted from peripheral blood mononuclear cells (PBMCs) of 192 HIV-1 infected drug-experienced individuals who presented for routine care at the HIV/AIDS Prevention Group Wellness Clinic (HAPG) in Bela-Bela, Donald Fraser Hope Clinic (DFHC) in Vhufhuli and in local clinics in the Vhembe district of Limpopo Province, South Africa. Next generation sequencing custom based (Tn5 tagmentation and amplicon based) protocols to prepare libraries for host and HIV-1 genes were developed and validated with commercially available library preparation kits. The Tn5 tagmentation methods were used for longer DNA fragments and the custom amplicon based methods were used mainly for the shorter DNA fragments. To determine the variability of the APOBEC3 and CCR5 host genes, gene-specific primers were designed to amplify complete 12.16 kb A3D, 13.31 kb A3F, 10.74 kb A3G, 6.8 kb A3H and 1.3 kb CCR5 genes targeting the regions containing the exons. Libraries for the resulting amplicons were prepared using Tn5 transposase tagmentation methods and sequenced on an NGS Illumina MiSeq platforms generating millions of reads with good read coverage for variant calling. Single nucleotide polymorphisms (SNPs) and indels were determined, verified in dbSNPs and compared to SNPs in other populations reported in the 1000 Genome Phase III and HapMap. A Chi-square goodness-of-fit was used to verify if whether observed genotype frequencies were in agreement with the Hardy-Weinberg Equilibrium. Haplotypes and Linkage disequilibrium were inferred to determine SNP association. vii The HIV-1 vif and env V3 loop genes were also sequenced to determine their degree of variability of these genes and to infer co-receptor usage in the South African population. Gene-specific primers were designed to amplify the 579 bp Vif region and 440 bp containing the 105 bp V3 loop. Sequencing libraries from the resulting amplicons were prepared using either the Tn5 transposase or custom-based library preparation methods and sequenced on either an Illumina MiSeq or a MiniSeq platform generating millions of reads with good read coverage for variant calling. Phylogenetic analysis was done to determine the relatedness of the sequences. Major and minor variants were determined for HIV-1 and env V3 loop quasispecies was analysed for co-receptor usage; in an effort to draw inferences for the subsequent utility of Maraviroc as salvage therapy in South Africa. Results and Discussion Next generation library preparation; Tn5 tagmentation based and custom amplicon based protocols to sequence host and HIV genes were successfully developed and used to sequence and characterize variability in host cell APOBEC3D, F, G H, CCR5 and the HIV-1 vif gene and the V3 loop region of the env gene. The HIV-1 env V3 loop sequences generated (and quasispecies analyzed) were used to infer co-receptor usage in treatment-experienced individuals; in an effort to draw inferences for the subsequent utility of Maraviroc as salvage therapy in South Africa. Quality V3 loop sequences were obtained from 72 patients, with 5 years (range: 0-16) median duration on treatment. Subtypes A1, B and C viruses were identified at frequencies of 4% (3/72), 4% (3/72) and 92% (66/72) respectively. Fifty four percent (39/72) of patients were predicted to exclusively harbor R5 viral quasispecies; and 21% (15/72) to exclusively harbor X4 viral quasispecies. Twenty five percent of patients (18/72) were predicted to harbor a dual/mixture of R5X4 quasispecies. Of these 18 patients, about 28% (5/18) were predicted to harbor the R5+X4, a mixture with a majority R5 and minority X4 viruses, while about 72% (13/18) were predicted to harbor the R5X4+ a mixture with a majority X4 and minority R5 viruses. The proportion of all patients who harboured X4 viruses either exclusively or dual/mixture was 46% (33/72). Thirty-five percent (23/66) of the patients who were of HIV-1 subtype C were predicted to harbor X4 viruses (χ2=3.58; p=0.058), and 57% of these (13/23) were predicted to harbor X4 viruses exclusively. CD4+ cell count less than 350 cell/μl was associated with the presence of X4 viruses (χ2=4.99; p=0.008). The effectiveness of Maraviroc as a component in salvage therapy may be compromised for a significant number of chronically infected patients harboring CXCR4 utilizing viii viruses in the study cohort. Although from the current study a subset of patients harboring CCR5 utilizing viruses may benefit from Maraviroc, characterizing and identifying if variation in CCR5 are located at Maraviroc binding sites was of importance to investigate. The following variants; P35P, S75S, Y89Y, A335V and Y339F and their varying frequencies were detected in the CCR5 gene. The A335V variant was detected at a higher frequency of 17.4% (29/167). The G265S variant is reported for the first time in this study at 0.6% (1/167) frequency. The SNPs detected were in strong LD (D’= 1, R2 = 0.0) with minor deviation from the Hardy-Weinberg Equilibrium. These variants were not located at the binding motif of Maraviroc. The variants A335V and Y339F were detected at a higher frequency in this study than previously reported in South Africa. Variability in APOBEC3 host cell genes was also characterized in our study cohort. The following APOBEC3 variants compared to the GRCh37 consensus sequence were detected: R97C, R248K and T316T in A3D; R48P, A78V, A108S, S118S, R143R, I87L, Q87L, V231I, E245E, S229S, Y307C and S327S in A3F; S60S, H186R, R256H, Q275E and G363R in A3G and N15Δ, G105R, K140E, K121D, E178D in A3H. Minor allele frequency variants (MAF<5%); L221L, T238I, C224Y and C320Y in A3D; I87L, P97L and S229S in A3F; R256H, A109A, F119F and L371L in A3G, which are frequent in the European population, were also detected. In addition, novel R6K, L221R and T238I variants in A3D and I117I in A3F were detected. Most of the SNPs were in strong LD with minor deviation from the Hardy-Weinberg Equilibrium. Four, six, four, and three haplotypes were identified for A3D, A3F, A3G, and A3H respectively. In general, polymorphism in A3D, 3F, 3G and 3H were higher in our South African cohort than previously reported among other African, European and Asian populations. The APOBEC3 antagonist HIV-1 vif gene was also sequenced to determine the level of diversity in a South African population and also correlated with APOBEC3 variation. Functional Vif without frameshift mutation was observed in all samples except in 4 samples. The functional domain and motifs, such as Zn binding motifs, proline-rich domain, human casein kinase, and the N and C-terminal CBF interaction site were highly conserved. APOBEC binding motifs and the nuclear localization signal were less conserved in the South African HIV-1 Vif. APOBEC3 H variation strongly correlates with Vif variation. All the Vif sequences were subtype C, except one sample, which was identified as an A1/C recombinant. The vif gene in a South African population was under purifying selection, with the dS= 0.2581 and dN= 0.0684 and the dN/dS value = 0.265. There is a high genetic diversity in the South African vif gene, which may ix influence the neutralization and restriction of APOBEC genes. Conclusions In conclusion, the protocols developed in this study can be applied to amplify and sequence any host and HIV-1 genes of interest allowing much deeper and more sensitive profiling of host gene and HIV-1 genetic diversity. Our findings show that a highly significant number of chronically HIV-1 subtype C infected patients in Maraviroc-free treatment harbor CXCR4 utilizing viruses. The data is useful in the consideration of whether to include entry antagonists such as Maraviroc in alternative forms of treatment for patients failing second line treatment regimen in the study setting. The determination of co-receptor usage prior to initiation of therapy consisting of Maraviroc is suggested. Variation in the CCR5 coding region were observed at higher frequencies compare to other studies conducted in South African populations at different locations. This data may suggest that different populations in South Africa have different SNP frequencies. All the polymorphisms identified in the study were not located at the Maraviroc binding motif, therefore the subset of patient infected by R5 viruses may benefit from this drug. We have shown that significant APOBEC3 variation exists among an ethnically diverse population of South Africa by providing extensive data for 4 different A3 genes that are known to restrict HIV infection, but have only been sparsely studied in African populations. This study provides a baseline for future studies that would functionally characterize SNPs identified in this population, in order to understand the role of novel and/or low frequency variants observed. Ex vivo and in vivo studies will increase our understanding of how these variants might have cumulatively impacted the epidemic in Northern South Africa. This study also shows that there is a high level of HIV-1 Vif diversity in the study area. This diversity may impact the expression and packaging of Vif proteins, and the infectivity of HIV. In addition, a significant correlation was observed between HIV-1 Vif variation and APOBEC3 H haplotypes. / NRF

PhD (Health Sciences) / Department of Advanced Nursing Science / The HIV/AIDS is a global epidemic which affects all people, regardless of their religion, race, age, ethnicity or geographic location. The church of Africa, which hosts the largest numbers of infected and affected people, is also challenged to be involved in the response against HIV/AIDS epidemic. Church leaders are experiencing difficulties in fulfilling their role in HIV/AIDS interventions of which they have not received training. The complexity of HIV/AIDS demands a training programme that does not simply deal with symptoms, but it must address the complexities behind and in front of the spread, and earnestly seek effective ways of controlling the spread, as well as various strategies of caring for the infected and those affected with HIV and AIDS. The purpose of this study was to develop an adapted HIV/AIDS training programme for church leaders in the Limpopo Province of South Africa. A convergent parallel mixed methods design was used; quantitative and qualitative data were collected during the same phase of the research process. The population comprised of church leaders from Christian churches in the Limpopo province. A non-probability purposive sampling was used for qualitative approach, while quota sampling was used for quantitative approach. Questionnaires were used to collect quantitative data, while in-depth interviews were used to collect qualitative data in this study. Data analysis was done separately and the two sets of results were merged into an overall interpretation of the study that informed the development of an adapted HIV/AIDS training programme. The findings of the study revealed that church leaders were not trained on how they can be involved in the response against HIV/AIDS epidemic in the Limpopo province. The current training programme did not clarify church leaders’ role towards the HIV/AIDS epidemic. The curriculum development process structure by Meyer and Van Niekerk (2008), and elements outlined by Dickoff, James and Wiedenbach (1968), were adapted to develop the training programme. A developed training programme was then validated by HIV/AIDS trainers and experts in programme development. Relevant recommendations were made to encourage churches to work effectively in addressing the HIV/AIDS epidemic in the Limpopo Province. / NRF