1. Academic Wits Research Publications (Faculties submissions)
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Item Draft genome sequence of the fungal pathogen Penicillium expansum (PPRI25879) isolated in South Africa(Elsevier, 2025-02) Chan, Wai Yin; Rauwane, Molemi; Figlan, Sandiswa; Ntushelo, KhayalethuObjectives: Penicillium expansum, a necrotrophic plant pathogen with a wide range of fruit hosts, is an important causal agent of blue mold rot. The fruit business suffers significant financial losses because of blue mold rot that occurs during fruit storage, transportation, and sale. The objective of this work was to generate a high-quality draft genome assembly of P. expansum, which will contribute to enhancing the management of blue mold, especially in stone and pome fruits, including grapes, by improving our understanding of the epidemiology of the pathogen and its interactions with the host. Data description: Here, we describe the genome sequence of Penicillium expansum isolate PPRI25879, one of the most virulent strains isolated from grapes in South Africa. Sequencing reads from P. expansum produced approximately 3.5 Gb. The assembly generated a draft genome of size 32.1 Mb, consisting of 1648 contigs, with an N50 of 508 KB. Examination of the genome completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) showed the draft genome carries 97.9% of the 746 genes in the Eurotiomycetes_odb10 database. The draft genome sequence will allow improved genomic comparisons among the most important pathogens belonging to the Penicillium genus, with the aim of improving our knowledge of their plant-pathogen interactions, population biology, and control.Item Resistance mutations that distinguish HIV-1 envelopes with discordant VRC01 phenotypes from multi-lineage infections in the HVTN703/HPTN081 trial: implications for cross-resistance(Elsevier, 2025-02) Cohen, Paula; Lambson, Bronwen E.; Mkhize, Nonhlanhla N.; Morris, Lynn; Moore, Penny L.; Moodley, Chivonne; Yssel, Anna E. J.; Moyo-Gwete, Thandeka; York, Talita; Gwashu-Nyangiwe, Asanda; Ndabambi, Nonkululeko; Thebus, Ruwayhida; Williamson, CarolynThe Antibody Mediated Prevention (AMP) trials showed that passively infused VRC01, a broadly neutralizing antibody (bNAb) targeting the CD4 binding site (CD4bs) on the HIV-1 envelope protein (Env), protected against neutralization-sensitive viruses. We identified six individuals from the VRC01 treatment arm with multi-lineage breakthrough HIV-1 infections from HVTN703, where one variant was sensitive to VRC01 (IC50 < 25 ug/mL) but another was resistant. By comparing Env sequences of resistant and sensitive clones from each participant, we identified sites predicted to affect VRC01 neutralization and assessed the effect of their reversion in the VRC01-resistant clone on neutralization sensitivity. In four pairs, a single mutation restored partial or full sensitiv ity to VRC01, whereas in the fifth participant, transfer of the entire β23-V5 loop was required. No VRC01 resistance mutations could be identified in the sixth participant, with the discordant clones differing by >100 amino acids. Mutations responsible for the differential neutralization phenotypes occurred at distinct sites across Env, including residues in loop D, the CD4-binding loop, and between the β23 and V5 loops. Analysis of deep sequencing env data showed that VRC01 resistance was likely the property of the acquired virus, rather than occurring through post-acquisition evolution. Although VRC01-resistant parental clones generally retained sensitivity to other CD4-binding site bNAbs, they were less potently neutralized than the VRC01-sensitive clones. In conclu sion, VRC01 resistance mutations occurred through multiple mutational pathways, but sensitivity to second-generation CD4bs bNAbs was retained even in VRC01-resistant transmitted viruses, confirming the potential of these bNAbs for HIV-1 prevention studies.Item Genetic therapies for movement disorders ‑ current status(Springer, 2025-02) Waddington, S. N.; Sartorelli, J.; Ng, J.; Rahim, A. A.; Kurian, M. A.Movement disorders are a group of heterogeneous neurological conditions associated with alterations of tone, posture and voluntary movement. They may either occur in isolation or as part of a multisystemic condition. More recently, the advent of next generation sequencing technologies has facilitated better understanding of the underlying causative genes and molecular pathways, thereby identifying targets for genetic therapy. In this review, we summarize the advances in genetic therapy approaches for both hyperkinetic and hypokinetic movement disorders, including Parkinson’s Disease, Huntington’s Disease and rarer monogenic conditions of childhood onset. While there have been significant advances in the field, multiple challenges remain, related to safety, toxicity, efficacy and brain biodistribution, which will need to be addressed by the next generation of genetic therapies.Item Deep-crustal layered mafic complexes in the Mesoproterozoic oceanic-arc of the Tugela Terrane, South Africa(Elsevier, 2025-03) Wilson, Allan H.Layered mafic intrusions are important in understanding the generation of continental crust in oceanic arcs. The Mesoproterozoic (c. 1200 Ma) Tugela Terrane in southeast South Africa is made up of a series of thrust slices of varied rock-types purported to have been derived in oceanic arcs prior to accretion onto the southern margin of the Archean Kaapvaal Craton. They are not ophiolites. Mafic intrusions in two adjacent thrust slices are known as the Tugela Rand and Mambula Complexes. Both intrusions are intensely layered on scales of centimetres to several tens of metres but clear cyclic units are not apparent and crystal fractionation is limited indicating these were open systems with magma chamber through-flow. Tugela Rand is made up of dominantly olivine-bearing rocks ranging from dunite and pyroxenite to gabbro. In contrast, Mambula is dominantly gabbroic with only rare olivine-bearing rocks and is more evolved with layers of titaniferous-magnetite. Primary magmatic structures in both complexes include graded bedding, slumping and erosion features. Relatively high pressure of formation is indicated by the aluminous nature of the pyroxenes and corona textures by reaction between plagioclase and olivine. Chromitites in Tugela Rand range from massive to podiform with the rare orbicular variety indicating complex controls on chromite accretion. They include the high-Al compositional variety. There are no other similar chromitite occurrences in South Africa. The complexes, together with their enclosing rock-types, draw striking parallels with the lower arc crust observed in the late Cretaceous Kohistan arc complex in NE Pakistan. The Tugela Rand Complex shares many similarities with the Chilas Complex in that terrane, while the Mambula Complex is considered to be a more evolved derivative of the same magma. This study shows that generation of juvenile continental crust formation in mature island arc systems may have been firmly established by the Mesoproterozoic.Item Spatio-temporal trends in daily precipitation extremes over the Enkangala escarpment of South Africa: 1961–2021(Springer, 2025-02) Abubakar, Hadisu Bello; Scholes, Mary C.; Engelbrecht, Francois A.The Intergovernmental Panel on Climate Change in its Sixth Assessment Report reported that increases in extreme weather events can already be detected in every region in the world. For eastern southern Africa the report provides evidence of an increasing trend in extreme precipitation events, but more research is needed to understand how this change is manifesting over regions as diverse as South Africa’s eastern escarpment and northern Mozambique. This study evaluates the trends in extreme precipitation over the Enkangala Escarpment, part of South Africa’s eastern escarpment, over the period 1961 to 2021. Daily precipitation data covering 22 stations with fewer than 10% missing values over 61 years were obtained from the South African Weather Service. A total of twelve extreme events precipitation indices were computed using the ClimPACT2 package, and a time series trend analysis was performed using the Trend Free Whitening Mann Kendal test and a field significance test. The results indicate significant increasing trends in nine out of the twelve extreme events indices that were investigated. The three indices which have shown significant decreasing trends include Consecutive Wet days (CWD) at (0.03 day/year total annual rainfall (PRCPTOT) (0.61 mm/decade) and the annual count of days when precipitation≥10 mm (R10mm) of 0.32 days/decade. Indices such Rx1 days, Rx3 days and Rx5 days exhibited increasing trends of 0.2 days/decade each. Other indices with an increasing trend are CDD (3.6 day/decade), R20mm (0.2 days/decade) and R30mm (0.2 days/decade). The R95p (11.2 mm/decade) and R99p (6.0 mm/decade) indices, and Simple Daily Intensity Index(0.4 mm/decade) also exhibit positive trends over the study period. Overall the analysis is indicative of a change in the nature of rainfall over the Enkangala escarpment of South Africa, with annual rainfall totals, the number of consecutive wet days and the frequency of events with smaller thresholds such as 10 mm/day decreasing, but with extreme events of larger thresholds occurring more frequently. That is, when it rains, it tends to rain more intensely than in the past. The use of a field significance test was useful to formalise when relatively small but spatially homogeneous trends detected at separate weather stations yield statistical significance. The findings of the paper are relevant to decision and policy in multiple of socio-economic sectors active in South Africa’s eastern escarpment.Item A Technique to Solve a Parabolic Equation by Point Symmetries that Incorporate Initial Data(Springer, 2025-03) Jamal, Sameerah; Maphanga, RivoningoIn this paper, we show how transformation techniques coupled with a convolution integral can be used to solve a generalised option-pricing model, including the Black–Scholes model. Such equations are parabolic and the special convolutions are extremely involved as they arise from an initial value problem. New symmetries are derived to obtain solutions through an application of the invariant surface condition. The main outcome is that the point symmetries are effective in producing exact solutions that satisfy a given initial condition, such as those represented by a call-option.Item Prevalence and factors associated with caesarean section among Tanzanian women of reproductive age: evidence from the 2022 Tanzania demographic and health survey data(BioMed Central, 2025-02) Olorunfemi, Gbenga; Nahayo, Bonfils; Ndayishimye, Samuel; Nsanzabera, CharlesBackground: Caesarean Section (CS) is one of the commonest surgical procedures worldwide. It is an important medical intervention for reducing the risk of poor perinatal outcomes. However, there was increased trends in CS in sub-Saharan Africa as maternal and neonatal mortality and morbidity remains high. This study aims to determine the prevalence and factors associated with CS rates in Tanzania. Methodology: This was a secondary data analysis of 4,768 women of reproductive age (15–49) in Tanzania. The data utilized was from the Tanzania Demographic Health and Survey (TDHS) 2022. The factors associated with CS were identified using multivariable binary logistic regression. Results: Out of 4,768 women of reproductive age in Tanzania, 497 (10.4%) had CS. Attaining primary (Adjusted Odds Ratio (aOR): 1.79,95% CI 1.23–2.60), secondary (aOR:2.07,95% CI 1.36–3.14) and higher education (aOR: 2.35, 95% CI 1.08–5.12); having a husband/partner with higher education; being in richest household wealth quintile (aOR:1.98,95% CI (1.31-3.00), having a job (aOR:1.29, 95% CI: 1.05–1.58 and having attended more than 4 antenatal care (ANC) visits (aOR: 1.36, 95% CI: 1.11–1.67) were associated with a higher odds of undergoing CS compared to their respective counterparts. However, living in rural areas (aOR: 0.74, 95% CI:0.58–0.94), being multiparous women with 2–4 births (aOR: 0.67, 95% CI: 0.53–0.84) and 5 or more births (aOR: 0.44, 95% CI: 0.32–0.60) were associated with lower odds of CS. Conclusion: The overall prevalence of CS among women of reproductive age in Tanzania was 10.4%. The highest educational level, husband/partner’s educational attainment, household wealth quintile, type of residence, employment status, increased ANC number, and high parity were associated with CS. The CS prevalence is at the lower limit of the recommendation of the World Health Organisation of 10–15%. Further researches are necessary to highlight other barriers, facilitators and outcome of CSs in Tanzania to advise policy stakeholders.Item Group-based trajectory modeling to describe the geographical distribution of tuberculosis notifcations(Springer Nature, 2025-02) Martinson, Neil A.; Lebina, Limakatso; Dagnew, Alemnew F.; Hanrahan, Colleen F.; Dowdy, David W.; Nonyane, Bareng A. S.Background Tuberculosis (TB) is a major public health problem, and understanding the geographic distribution of the disease is critical in planning and evaluating intervention strategies. This manuscript illustrates the application of Group-Based Trajectory Modeling (GBTM), a statistical method that analyzes the evolution of an outcome over time to identify groups with similar trajectories. Specifically, we apply GBTM to identify the evolution of the number of TB notifications over time across various geographic locations, aiming to identify groups of locations with similar trajectories. Locations sharing the same trajectory may be considered geographic TB clusters, indicating areas with similar TB notifications. We used data abstracted from clinic records in Limpopo province, South Africa, treating the clinics as a proxy for the spatial location of their respective catchment areas. Methods Data for this analysis were obtained as part of a cluster-randomized trial involving 56 clinics to evaluate two active TB patient-funding strategies in South Africa. We utilized GBTM to identify groups of clinics with similar trajectories of the number of TB patients. Results We identified three trajectory groups: Groups 1, comprising 57.8% of clinics; Group 2, 33.9%; and Group 3, 8.3%. These groups accounted for 30.8%, 44.4%, and 24.8% of total TB-diagnosed patients, respectively. The estimated mean number of TB-diagnosed patients was highest in trajectory group 3 followed by trajectory group 2 across the 12 months, with no overlap in the corresponding 95% confidence intervals. The estimated mean number of TB-diagnosed patients over time was fairly constant for trajectory groups 1 and 2 with exponentiated slopes of 0.979 (95% CI: 0.950, 1.004) and 1.004 (95% CI: 0.977, 1.044), respectively. In contrast, there was a statistically significant 3.8% decrease in the number of TB patients per month for trajectory group 3 with an exponentiated slope of 0.962 (95% CI: 0.901, 0.985) per month. Conclusions GBTM is a powerful tool for identifying geographic clusters of varying levels of TB notification when longitudinal data on the number of TB diagnoses are available. This analysis can inform the planning and evaluation of intervention strategies.Item The synergetic effect of drought and land use changes on Ethiopian Rift Valley Northwestern Escarpment livelihood systems(Springer, 2025-02) Gidey, Eskinder; Mhangara, Paidamwoyo; Nasir, Jemal; Zeleke, Tesfaye; Assefa, Engdawork; Kahsay, Shishay; Birhane, EmiruClimate change has significantly impacted smallholder farmers in developing countries, where most livelihoods rely on rain-fed agricultural systems. The Northwestern Escarpment of the Ethiopian Rift Valley (NEERV) is among Ethiopia’s most drought-vulnerable areas and is highly affected by land use and land cover change (LULCC). This study aimed to analyze the synergistic impacts of drought and LULCC in the three major livelihood zones (LZs) of NEERV between 1983 and 2019. The study used socioeconomic, climatic, and earth observation datasets. Utilizing a mix of socioeconomic, climatic, and earth observation datasets, this paper investigated the combined effects of these factors on three major livelihood zones: Alagie-Ofla (ALOFLZ), Tsirare catchment (TCLZ), and Raya Valley (RVLZ). The analysis revealed significant rainfall variability, with annual fluctuations between 31 and 50% and seasonal variations ranging from 39 to 99%. This variability has contributed to frequent drought occurrences, with intervals of approximately 2.13 years in ALOFLZ, 2.2 years in TCLZ, and 2.13 years in RVLZ. There has been a notable increase in cultivated and built-up areas across all zones. The study found that drought and LULCC have severely impacted agricultural productivity and local ecosystems, with the most pronounced effects observed in RVLZ, TCLZ, and ALOFLZ. The findings highlight a critical need for integrated approaches to manage and monitor the synergistic impacts of drought and LULCC. The study underscores the importance of enhancing drought and LULCC monitoring systems to improve resilience and adaptability in vulnerable regions. The research contributes to a deeper understanding of how these intertwined factors exacerbate environmental and socioeconomic challenges, offering valuable insights into policy and management strategies for mitigating their effects. Recommendations include enhancing the current drought and LULCC monitoring systems to improve predictions and mitigation efforts, thus bolstering resilience and adaptability among affected communities.Item Improving poor outcomes of children with Biliary Atresia in South Africa by early referral to centralized units(Wolters Kluwer., 2021) van der Schyff, Francisca; Terblanche, Alberta J.; Botha, Jean F.Objectives: Biliary atresia (BA) is a progressive fibrosing cholangiopathy of infancy, the most common cause of cholestatic jaundice in infants and the top indication for liver transplantation in children. Kasai portoenterostomy (KPE) when successful may delay the requirement for liver transplantation, which in the majority offers the only cure. Good outcomes demand early surgical intervention, appropriate management of liver cirrhosis, and in most cases, liver transplantation. These parameters were audited of children with BA treated at the Steve Biko Academic Hospital (SBAH) in Pretoria, South Africa. Methods: All children with BA who were managed at SBAH between June 2007 and July 2018 were included. Parameters measured centered on patient demographics, timing of referral and surgical intervention, immediate and long-term outcomes of surgery, and follow-up management. Results: Of 104 children treated, 94 (90%) were KPE naive. Only 23/86 (26%) of children were referred before 60 days of life and 42/86 (49%) after 120 days. Median time to surgical assessment and surgery was 4 (IQR 1–70) and 5 (IQR 1–27) days post presentation, respectively. The median age at KPE was 91 days (IQR 28–165), with only 4/41 (12%) of KPEs performed before 60 days of life. Of those with recorded outcomes, 12/33 (36%) achieved resolution of jaundice. Only a third of the cohort were referred for transplantation. Conclusion: Children with BA have poor outcomes in the public health sector in South Africa. Late referrals, delayed diagnostics, advanced age at KPE with low drainage rates, poor follow–up, and low transplant rates account for low survival. Early referral to units offering expert intervention at all stages of care, including transplantation, would offer the best outcomes.