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Welcome to the University of Venda Institutional Repository, an open digital archive of the research output of the University of Venda. Univen IR contains theses and dissertations, research papers as well as conference papers. For further information and assistance please contact Mr Keith Malabi at +27 15 9628564 or +27 15 962 8314 during office hours

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Genetic divesity of Human Herpesvirus Type 8 in Northern South Africa

(2024-09-06) Raphalalani, Mulalo; Bessong, Pascal Obong; Mavhandu-Ramarumo, Lufuno Grace

Background: Human herpesvirus type 8 (HHV-8), is an oncogenic virus responsible for causing all forms of Kaposi`s sarcoma (KS). HHV-8 prevalence varies globally, however, it is more prevalent in African countries, with South Africa having over 50% of HHV-8 infections. HHV-8 encodes a highly diverse open reading frame (ORF) K1 gene, which has led to the identification of seven major genotypes (A-F and Z) that are heterogeneously distributed across the world. The viral genetic landscape of any geographical area is of paramount importance in vaccine development and diagnostics. However, data on HHV-8 genotypes is scarce in northern South Africa. Therefore, this study will provide genetic diversity of HHV-8 in northern South Africa, and this may aid in the selection of genes for vaccine development. Objective: The main objective of the study was to describe the genetic diversity of human herpesvirus type 8 in northern South Africa. Methodology: Deoxyribonucleic acid (DNA) was extracted from 115 archived mouthwash samples collected from five healthcare facilities in northern South Africa. The partial open reading frame (ORF) K1 gene (~840bp) was amplified in a two round conventional PCR using JumpStart REDTaq master mix. The band of interest was extracted by phenol-freeze protocol and enriched using conventional PCR. Enriched amplicons were purified and sequenced in an Illumina MiniSeq platform. K1 genotypes were inferred using an online BioAfrica HHV-8 subtyping tool and confirmed by computing a phylogenetic tree. Intra-genetic diversity among HHV-8 genotypes was described by aligning study sequences with their respective prototype strains. Synonymous and nonsynonymous mutation rates were computed by the online SNAP tool. Results: K1 gene was successfully amplified in 61.7% (71/115) samples, along with unspecified DNA bands. The band of interest was successfully recovered in 67 amplicons (94.4%). Sixty-five gel extracted products (65/67; 97%) were successfully enriched and purified using magnetic beads. Of the 65 purified samples, 63 were sequenced using Illumina MiniSeq platform. Thirty-seven sequences had an acceptable nucleotide base call. The prevalence of HHV-8 in the study sequences was 94% (35/37) and majority of the sequences (24/35;68%) had sequence reads that span partial or complete K1 gene. Two major genotypes were detected (A and B); genotype B (19/24;79%) had a higher prevalence than genotype A (5/24; 21%). All sequences which grouped with genotype A were further classified as subtype A5. Interestingly, all sequences that were classified as genotype B did not cluster to any of the B subtypes. A higher genetic drift was observed among the study sequences reaching up to 33.7% at the amino acid level. Genotypes A and B exhibited 16.67% and 7.41% intra-genetic diversity at the amino acid level, respectively. Several amino acid polymorphisms were observed at the ITAM region of genotype A sequences (OUHC 013 and ODF 029), while the ITAM region of the B sequence was conserved. Conclusion: In this study, a predominance of HHV-8 genotype B was observed in northern South Africa. Additionally, there was a high degree of evolutionary divergence among the studied sequences. A higher frequency of nonsynonymous mutations was detected at the ITAM region of A5 sequences and these mutations may potentially affect the functionality of ITAM.

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Attributes of Ideal Grassroots Community Leaders for Sustainable Rural Development: The Case of Ward Committees in Vhembe District Municipality of South Africa

(2024-09-06) Nemathithi, Awelani Jeannette; Francis, J.; Kone, L. R.; Lavhelani, N. P.

Most municipalities in South Africa have been struggling to put in place functioning Ward Committees across the country. It is crucial to have an effective Ward Committee that can facilitate processes that lead to the improved well-being of the residents of the local community. The study explored the attributes of ideal grassroots community leaders for sustainable development, focusing on the case of ward committees in Ha-Mashau area. The specific objectives were to determine the community-preferred qualities of persons eligible to serve in ward committees and to determine whether age and gender of community members influence their perceptions. An exploratory sequential mixed method design was adopted for this study. Purposive sampling and stratified random sampling were applied to draw a sample of 57 and 120 participants from the residents of Ha-Mashau community for Phase 1 and Phase 2 respectively. Focus group discussions (FGDs) and a Likert-type scale questionnaire were used to collect data. Thematic content analysis, Descriptive statistics, Man Whitney & Kruskal Wallis tests from (SPSS) were run for analysis. The findings revealed several crucial attributes of ideal grassroots community leaders, including strong communication skills, a genuine commitment to community development, a strong personality, fair educational background, and accessibility to the community. Age influenced community members' perceptions of the need (1) to consider women for ward committee membership, (2) for aspiring leaders to be empathic, and (3) for leaders to show love and respect for the people. Furthermore, adult community members prefer ward committee members who are “dedicated to community development work” than their youthful counterparts. These findings contribute to the existing literature on grassroots leadership and offer practical insights for policymakers, development practitioners and community members aiming to foster sustainable development in similar contexts. It is recommended that policymakers and practitioners consider the importance of the identified attributes and their contribution to sustainable development when implementing programs aiming to enhance leadership capacity. Keywords

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Environmental Impacts of Tin Mine Waste: A Case Study of the Zaaiplaats Tin Mine, Limpopo Province, South Africa

(2024-09-06) Nemadodzi, Matodzi Bridget; Mundalamo, H. R.; Ogola, J. S.

This research focused on the potential impacts of the Zaaiplaats tin mine waste on the environment and on human health. It investigated the heavy metals and their distribution pattern at the Zaaiplaats tin mine. Heavy metals were investigated in the tailings, water and plants found at the mine. A radiation survey was also conducted to check for the possibility of potential radionuclides induced by the mine. Fieldwork involved collection of tailings within the old river channel, Heap A, B and C. A total of 65 samples were collected, 15 of them, across the river profile, while 6, 24 and 20 were collected from Heap A, B and C respectively. Samples were prepared and analysed at the Mining and Environmental Geology laboratory at the University of Venda using X-ray Fluorescence Spectrometry. The maximum values were 2842.4 ppm, 885.1 ppm, and 740.7 ppm for lead from Heap B followed by copper, and zinc from the river channel respectively. The distribution pattern of some metals like lead, zinc and copper were increasing with depth. The highest Pi (Environmental quality index of the pollutant) was registered by Pb followed by Cu and As and the values are 47.11, 29.95 and 26.89 respectively. Cu, Zn, As, Pb, Th and U had shown a higher degree of pollution which is presented by Pi values of 3 and above in all the different sampling locations of the tailings. The total water samples collected were depending on the availability. Therefore, only 3 water samples were obtained by use of 250 ml bottles. Water samples were prepared and analysed using Atomic Absorption Spectrometry. There are no values for metals such as Cr, Ni and Co in water samples collected at Zaaiplaats tin mine. However, the maximum values of Pb and Cu metals were 0.67 ppm and 0.59 ppm respectively which is higher as compared to the South African water quality guidelines and it is thus polluted. A plant commonly known as horsetail (Equisetum ramosissimum) was collected during dry and wet season for comparison purposes. A total of 9 plant samples were collected, prepared and analysed using Atomic Absorption Spectrometry. Bioaccumulation factor of these plant samples were higher during the dry season and lower during the wet season. The trend in the BAF for heavy metals during dry season are in the ranking order of Cr > Cu > Pb > Co. The trend in the BAF for heavy metals during wet season are in the ranking order of Co > Cu > Pb > Cr. Cr was transferred effectively in dry season while cobalt was transferred effectively in wet season. Cr and Cu metals were absorbed and accumulated during dry season as opposed to wet season wherein Co was absorbed and accumulated in wet season than in dry season. BAF and TF values were lower in both dry and wet season. The horsetail plant is a hyper-accumulator of these metals and can be used for their clean up as a remediation strategy paired with other remediation measures. Radiation dose rate and dose surveying was also conducted by means of a portable radiation survey meter DP802i-RAYTECH Radiation Detector. Radiation dose is increasing from a higher elevation which is the first surveying point along the river channel to low elevation. Radiation dose rate is inconsistent and does not have a general trend. The radiation dose rate mean, minimum, maximum values in microsievent per year (mSv/y) were 4.03 mSv/y, 0.96 mSv/y, and 11.65 mSv/y respectively. The maximum value of radiation dose rate was slightly higher compared to UNSCEAR background radiation of 2.4 mSv/y to 10 mSv/y. However, Zaaiplaats tin mine tailings are of no immediate concern since there are some areas that have had a radiation dose rate of 10 times higher than that of UNSCEAR and no deleterious health effects were associated with this elevated radiation exposure.

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Effect of location and drying methods on nutrient composition, apparent digestibility, growth performance and carcass characteristics of South African Mutton Merino Lambs fed different levels of dried marula fruit peels

(2024-09-06) Murovhi, Ronewa; Murovhi, R.; Mikasi, M. S.

The purpose of this study was to determine the effect of location and drying methods on nutrient composition of dried marula fruit peels and apparent digestibility, and growth performance as well as carcass characteristics of South African mutton merino lambs fed different levels of dried marula fruit peels. Marula (Sclerocarya birrea) is a medium sized tree belonging to the Brachystegia genus. Several experiments were conducted to evaluate the chemical composition of dried marula fruit peels where the DM, OM, CP, CF, ADF, NDF, and GE were determined. All the data in this experiment were subjected to analysis of variance for a 2x2 factorial in a completely randomised design using a GLM procedure of Minitab 19(Minitab, 2019). Tukey’s studentised multiple range test determined statistically significant differences among the means. The dry matter of fresh marula fruit peels has shown a significant difference (P<0.01). The dry matter of fresh marula fruit peels from Tzaneen using freeze and oven-drying methods was higher than those from Phalaborwa. The dry matter, crude protein, ash, ether extract, acid detergent lignin, and gross energy contents of dried marula fruit peels for both locations and drying methods were not significantly different (P>0.05). The crude fibre, Acid detergent fibre, and nitrogen detergent fibre results for both location and drying methods were significantly different (P<0.01). The crude fibre and nitrogen detergent fibre from Tzaneen were found to be higher than those from Phalaborwa when a freeze-drying method was used. However, when using an oven-drying method, the crude fiber, nitrogen detergent fiber, and acid detergent lignin contents were higher in Phalaborwa. Apparent digestibility of DM, CP, and OM of the diet was determined in a completely randomised design and the means were compared using a Tuckey method at a 95% confidence level. The experiment was conducted in the last ten days of growth trial. A total of 9 male South African mutton merino sheep of approximately 35kg of weight were used in this experiment. The results revealed that the inclusion levels of dried marula fruit peels in the animal diet did not affect (P>0.05) the CP intake. However, a significant difference (P<0.01) was observed in the OM intake by the lambs. The inclusion levels of dried marula fruit peels in the diet did not affect (P>0.05) the faecal excretion of nutrients by lambs. A non-significance difference (P>0.05) was observed in the digestibility of nutrients. The determination of growth performance and carcass characteristics of the lambs fed different levels of dried marula fruit peels was conducted, where the ADFI, ADG, FCR and hot carcass weight, cold carcass weight, dressing percentage were measured respectively. A completely randomised design was used in this experiment with seven animals per treatment. Before the trial, the lambs were vaccinated against brucellosis, pulpy kidney and treated for internal parasites. The inclusion levels of dried marula fruit peels had no significant impact (P>0.05) on the growth performance and carcass characteristics. This research has revealed that dried marula fruit peels can be used as a potential energy source for lambs without negatively affecting the growth and carcass characteristics of lambs at up to 10% inclusion level.

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Comparison of Some Statistical and Machine Learning Models for Continuous Survival Analysis

(2024-09-06) Ndou, Sedzani Emanuel; Mulaudzi, T. B.; Bere, A.

While statistical models have been traditionally utilized, there is a growing interest in exploring the potential of machine learning techniques. Existing literature shows varying results on their performance which is based on the dateset employed. This study will conduct a comparative evaluation of the predictive accuracy of both statistical and machine learning models for continuous survival analysis utilizing two distinct datasets: time to first alcohol intake and North Carolina recidivism data. LassoCV was used to select variables for both datasets by encouraging limited coefficient estimates. Kaplan-Meier survival curves were utilized to compare the survival distributions among groups of variables incorporated in the model, alongside the logrank test. The proposed methods include the Cox Proportional Hazards, Lasso-regularized Cox, Survival Trees, Random Survival Forest, and Neural Networks. Model performance was evaluated using Integrated Brier score (IBS), Area Under the Curve and Concordance index. Our findings shows consistent dominance of Neural Network (NN) and Random Survival Forest (RSF) models across multiple metrics for both datasets. Specifically, Neural Network demonstrates remarkable performance, closely followed by RSF, CoxPH and CoxLasso models with slightly lower performance, and Survival Tree (ST) consistently lags behind. This study can contribute to advancing knowledge and provides practical guidance for improving survival in recidivism and alcohol intake