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Socio-ecological factors affecting compliance with COVID-19 preventative measures, amongst staff and students at a selected university in Limpopo Province, South Africa
No full textMaster of Public HealthDepartment of Public HealthCorona virus was declared a pandemic worldwide in 2019. In South Africa, COVID-19 became noticeable from the fifth of March 2020 when the first case was reported and confirmed. To protect staff and students, educational institutions, like universities, were forced to close, and were only to re-open with COVID-19 precautionary measures in place. The purpose of this study was to investigate socio-ecological factors that contributed to non-compliance to COVID-19 preventative measures amongst staff and students at a selected university campus, as a baseline to inform interventions for future pandemics. The study adopted a quantitative, cross-sectional, descriptive, online survey design, with respondents selected through convenience sampling. The collected data was analysed through SPSS version 29.0. The researcher ensured that research ethics - informed consent, obtaining permission, as well as ensuring confidentiality, beneficence and privacy - were adhered to. The study findings indicated that most of the respondents (86.9%) where aware of COVID-19, however, the university’s student representatives council (SRC) members (55,5%) were not compliant with Covid-19 preventative measures. The results also indicated that a significant number of respondents (72.3%) were not aware of the COVID-19 regulations of wearing face masks on the campus. Furthermore, a total of 389 respondents attested that they did know about the penalties for not wearing a mask in public. The researcher recommends that the Department of Public Health should collaborate with campus health and organise health education awareness campaigns which would emphasise the importance of wearing masks and encouraging staff and students, especially public figures such as SRC members, to adhere to the standard precautions against pandemics like, COVID-19
The pharmacogenetics and pharmacokinetics of ADME polymorphisms in-drug-sensitive and drug-resistant tuberculosis patients from rural healthcare facilities in the Vhembe District of Limpopo (South Africa)
No full textPHD in Life Sciences: MicrobiologyDepartment of Biochemistry and MicrobiologyBACKGROUND
Tuberculosis (TB) is the second leading cause of death after the recent Coronavirus (COVID-19) pandemic. The rate of TB mortality remains high due to the emergence and spread of drug-resistant TB (DR-TB), which includes multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. Although TB is curable, the most common side effect associated with the use of anti-TB drugs globally is hepatotoxicity. This observation has been associated with the host genetic variation in the genes involved in drug absorption, distribution, metabolism, and excretion (ADME). The African population has been reported to have a high genetic diversity, yet their genomic information on the genetic contribution to TB and treatment is understudied.
AIM OF THE STUDY
This study sought to investigate the pharmacogenetic analysis of ADME polymorphisms in TB patients from rural healthcare facilities in the Vhembe District, Limpopo province of South Africa.
METHODOLOGY
Thirty-five TB outpatients were recruited from various healthcare facilities in Vhembe District. In this study, data and samples were collected from August 2022 to December 2023. Interviews were conducted to collect socio-demographic information and other factors related to TB, and samples (Sputum, urine, and blood) of the participants. DNA isolated from sputum was used to confirm (Anyplex MTB/NTM) and determine the extent of the MDR/XDR-TB using Allplex™ MTB/MDR/XDRe kit from Seegene, and the Zymo kit was used for blood DNA extraction. The whole genome sequencing was achieved by Next-generation sequencing (NGS) technique to analyse the SNPs involved in drug ADME to understand the risk associated with treatment failures and
predisposition to anti-TB induced toxicity on only seven genomic DNA (gDNA) samples, and untargeted metabolomics were used to evaluate the metabolites in the urine of the TB/MDR-TB patients.
RESULTS
Among the 35 participants, 54,3% (19/35) were females. The ages of the participants ranged from 23 to 72 years. The estimated prevalence of DR-MTB was 11.4% (4/35). Unemployment constituted 65% (23/35) of the participants’ status. Fifty-one percent (18/35) of the patients were co-infected with HIV. In total, the co-infections included MTB+NTM (40%, 14/35), MDR-MTB+NTM (5,7%, 2/35), XDR-MTB+NTM (2,9%, 1/35) and XDR-MTB+HIV (2.9%, 1/35). ANOVA analysis across groups identified 42 significantly altered metabolites (p < 0.05), where 2149 were annotated from a spectrum of 4191. The metabolomics resulted in 5 pathways, including i) One carbon pool by folate, ii) Folate biosynthesis, iii) Sphingolipid metabolism, iv) Tryptophan metabolism, and v) Fatty acid biosynthesis. Pharmacogenomics revealed a high prevalence of variants in UGT1A9 (94), ABCB1 (88), SLCO1B1 (69) and CYP24A1 (49) genes affecting drug metabolism and transport. NAT2 genotyping predicted diverse acetylator phenotypes with slow and intermediate acetylators predominating, suggesting variable isoniazid metabolism and potential differences in treatment efficacy and toxicity risk.
CONCLUSION
The study's findings underscore the urgent need for targeted strategies in addressing MTB and DR-TB. The high prevalence of co-infection, particularly NTM+DR-MTB, and HIV+DR-MTB should be a primary focus in MTB control in the Vhembe district. The significant proportion of unemployment among TB patients and late healthcare consultation were identified as key risk factors. Strategies should prioritise education on TB co-infection diagnosis/ treatment and address unemployment, as these are crucial areas where interventions can significantly impact the health of the individuals and the overall public health in this region. Integration of metabolomic and genetic analyses highlights complex host-pathogen interactions in DS-TB and DR-TB, underscoring metabolic pathway disruptions and genetic polymorphisms that influence
drug response. Therefore, this initiative is crucial for assessing the likelihood of drug resistance, toxicity, and treatment failure. Therefore, these findings emphasize the need for personalised medicine approaches to optimize anti-TB therapy in genetically diverse populations, thus preventing individuals predisposed to ADR attributable to anti-TB drugs. Further validation and functional studies are warranted to translate these insights into clinical practice
Hydrogeochemical evaluation and groundwater quality assessment for drinking and irrigation purposes in Bushbuckridge, South Africa.
No full textMESMEGDepartment of Earth SciencesThis study was conducted in Bushbuckridge, situated within the Sand River Catchment (SRC), Mpumalanga Province, South Africa, with the aim of evaluating the hydrochemistry and assessing the quality of groundwater for drinking and irrigation purposes. Groundwater samples (n= 40) were collected from different boreholes in different locations around the study area. Groundwater hydrochemical parameters including pH, total dissolved solids (TDS), electrical conductivity (EC), total hardness, major cations (Ca2+, Na+, K+ and Mg2+) and major anions (F-, Cl-, NO3- HCO3-and SO42) concentrations were assessed for the study area. Suitability for drinking was assessed based on comparison with selected standards and guidelines, such as the South African National Standard (SANS), Department of Water and Sanitation (DWS), World Health Organization (WHO) and by computation of Water Quality Index (WQI). Groundwater suitability for irrigation was assessed using eight irrigation indices: TDS, EC, Sodium Adsorption Rate (SAR), Sodium Percent (%Na), Kelly's Index (KI), Residual Sodium Carbonate (RSC), Permeability Index (PI) and Magnesium Hazard (MH). Groundwater type and facies characteristics was determined with the Piper diagram while geochemical controls were ascertained using Gibbs diagram. The results indicate cation and anion concentrations in the order; Na+ > Ca2+> Mg2+ > K+, and HCO3- > Cl- > SO42- > F- > NO3- respectively, while EC (14 – 551mS/m), TDS (99 – 4411 mg/l), Cl (1.1 – 1290.6 mg/l), Na (16 – 758 mg/l), Mg (0.54 – 181 mg/l) and TH (15 – 1085) were variables with upper ranges significantly above SANS and WHO guidelines. According to the DWS guidelines the suitability of groundwater for drinking was classified as class – 0 (ideal; 10%), class – 1 (good; 24%), class – 2 (marginal; 40%), class – 3 (poor; 20%) and class – 4 (unsuitable; slightly over 7%). The WQI indicated that 40% of the analysed groundwater samples were of excellent quality, 56% good and 4% were found to be poor to unsuitable for drinking. Results for groundwater irrigation suitability potential for the analysed samples (n=40) revealed four clusters; (a) most or all the samples are suitable based on TDS (65%), EC (75%) and SAR (100%), (b) just over half are suitable based on PI (59%) and %Na (55% permissible), (c) most of the samples are unsuitable based on RSC (77%), and (d) equal
distribution between suitable and unsuitable based on MH and KI (50%). According to the dominant cations and anions, the main water types were Na-HCO3, Ca-HCO3 and Mg-Ca-HCO3 mixed type. Rock weathering was the dominant geochemical process, associated with evaporation. Water-rock interactions through silicate weathering and ion exchange reactions between Ca2+, Mg2+ and Na+ were determining factors influencing the hydrochemical evolution of groundwater in the study area. The findings of the study suggest that the groundwater quality in the Bushbuckridge area is under threat. There is need for prompt mitigation actions that seek to intensify water quality monitoring, more in-depth studies to characterize the source and fate of potential pollutants in the area.Nurturing Emerging Scholars Programme (NESP) and University of Fort Har
Mapping roadkill in the Kruger National Park
No full textMENVSCDepartment of Geography and Environmental SciencesRoads not only create barriers for animals by preventing the free movement of individuals between populations but also cause mortality through collisions with vehicles (i.e. roadkill). In South Africa, most of our understanding of roadkill events stems from research on national and regional roads, but the impacts of roads in protected areas have been understudied. Though there have been ad hoc roadkill reports in protected areas by members of the public on social media, there have been little systematic roadkill surveys undertaken in South African protected areas and, road signage aside, no effective mitigation measures have been applied except traffic officers who are unable to monitor all roads simultaneously.
This study formed part of a five-year project to undertake an assessment of roadkill in protected areas and assess mitigation measures to reduce it. This two-year project has recorded temporal and spatial roadkill in one section of the Kruger National Park, on both paved and unpaved roads.
During this study a total of 189 roadkill were recorded in a period of 90 days covering 90 kilometres per day, and average roadkill rate was 0.4586 roadkill.km-1day-1. Roadkill incidents were randomly distributed along the roads. Reptiles and birds had most roadkill, and paved roads had a higher number of roadkill than unpaved roads on a per kilometre basis. Most roadkill happened during the hot-wet season. More awareness of roadkill risks is needed to ensure protection of biodiversity in the protected areas.Green Matter, TRAC N4 and National Research Foundation (NRF
Strategies to improve the effectiveness and efficiency of village health workers in service delivery in a seleceted district of Zimbabwe
No full textPhD (in Public Health)Department of Public HealthBackground
The advent of the Alma-Ata Conference has sparked a renewed global interest in community health programs to strengthen primary healthcare systems. The goal is to address inequities, respond to community health needs, and realise universal health coverage. Village Health Workers are vital for health systems to achieve universal health coverage by bringing primary healthcare services closer to the communities. They complement healthcare systems in low- and middle-income countries (LMICs), including Zimbabwe, that are affected by shortages of nurses. Their social connectedness fosters positive behaviour change and helps build trust in the healthcare system. Despite their importance, in Zimbabwe, these continue to face numerous challenges that impact their effectiveness and efficiency in service delivery, such as limited training and skills, poor remuneration, support and supervision, inadequate resource provision, and a lack of clear-cut implementation strategies, as evidenced by the 2017 Village Health Worker Strengthening Program, which was never operationalised. This necessitated the development and validation of strategies to enhance the effectiveness and efficiency of VHWs in service delivery.
Aim
The study aimed to develop and validate strategies to improve the effectiveness and efficiency of Village Health Workers in service delivery, leveraging the empirical findings and reviewing relevant literature.
Setting
Beitbridge district, Matabeleland South Province, Zimbabwe.
Methods
A review of the literature, using Rodgers’ Evolutionary Concept Analyses, identified the antecedents, attributes, and consequences of effective and efficient community health systems. An exploratory sequential mixed methods design was used to explore the roles of Village Health Workers in primary health care. . In-depth interviews in the first stage collected qualitative data from 45 purposely selected healthcare workers and Village Health Workers using interviews,and then they were thematically analysed with MAXQDA Software. The variables generated were validated by a cross-sectional survey, which collected quantitative data from 134 Village Health Workers and was analysed using SPSS. The strengths, weaknesses, opportunities, and threats enabled the identification of internal and external factors of the village health worker program. The program logic models were used to develop strategies, which were validated by a panel of experts using the Delphi technique and key stakeholders.
Results
Fifty-two articles and two reports were reviewed and analysed. Antecedents included an enabling work environment, community participation, motivation, incentives, community health integration into national health systems, and the use of information and communication technology. Attributes were ongoing training and skills development, mutual respect and trust, enhanced contact between Village Health Workers and communities, and supportive supervision. The consequences were equitable access and improved quality of primary healthcare services. The exploratory sequential mixed methods study revealed that health education, child growth monitoring, and referrals are the primary roles of Village Health Workers, who frequently face challenges with logistical supplies, allowances, knowledge, and skills. Eight strategies, developed and validated, included community engagement, ongoing training, role clarification, supportive supervision, optimal resourcing, mobile health technology, incentives, and the integration of VHWs into the mainstream healthcare system.
Conclusion
This paper clarifies the roles and strategies of Village Health Workers, providing valuable insights for program managers and stakeholders seeking to improve primary healthcare service delivery.
Contribution
Findings from the reviewed literature informed the development of a conceptual framework. Context-specific Village Health Worker service delivery strategies were developed through the novel application of strategic planning frameworks, models, and validation by a consensus of experts and key stakeholders
Isolation, identification, and characterization of antibiotic-producing microorganisms from soil
No full textPhD (Microbiology)Department of Biochemistry and MicrobiologyThe emergence and spread of antibiotic resistance in pathogenic bacteria have posed a serious concern in global healthcare. Highlighting a need for novel antimicrobial agents with diverse mechanisms of action to combat current pathogenic threats. Soil-borne bacteria are constantly exposed to various environmental stresses, which leads to the production of antimicrobial compounds as a strategy for their survival. In this context, soil-borne bacteria are key producers of antimicrobials with valuable applications in medicine, agriculture, and animal husbandry. The main aim of this study was to isolate, identify, and characterize microorganisms with the potential to produce antimicrobial compounds from soil.
Preliminary screening was conducted using agar well diffusion, revealing that the bacterial isolates exhibited significant antimicrobial activity against the four pathogenic bacterial strains tested (Chapter 3). Furthermore, the use of 16S rRNA sequencing aided the identification of the active bacterial isolates at the molecular level, where isolates 1 and 2 were identified as strains of Bacillus pumilus, whilst isolate 3 was found to be Bacillus subtilis (Chapter 3). This study further explored the chemical composition of the bacterial extract using ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry and classical molecular networking. Computational metabolomic analysis revealed that metabolites from these soilborne Bacillus species are predominantly composed of peptides, dipeptides, benzenoids, organic acids, and derivatives. Interestingly, the methanolic crude extract of the Bacillus subtilis isolate was mainly characterized by the abundance of dipeptides and lipopeptides, such as surfactins, suggesting that the combination of cyclopeptides and lipopeptides together could be the attribute of the enhanced antimicrobial activity observed in agar well diffusion (Chapter 4).
The current study further explored the applications of Whole Genome Sequencing (WGS) to enhance understanding of the overall distribution of genomic elements that contribute toward the adaptability and biosynthesis of antimicrobial compounds (Chapter 5). The results of the WGS showed that Bacillus species presented several genes for adaptability, such as genes that encode for motility, quorum sensing, stress response, desiccation tolerance, heavy metal tolerance, synthesis of siderophores, and most genes involved in antibiotic biosynthesis, such as NRPS, beta lactone, RiPP, and terpene gene clusters. Furthermore, the use of WGS aided a more precise taxonomic classification of the identities of the strains, highlighting the importance of WGS in the identification of bacterial isolates.
Lastly, inspired by the diverse chemical composition and bioactivity of Bacillus subtilis, this study further explored the potential to enhance metabolite detection and expand the data coverage in the data-dependent acquisition (DDA) mode of the UHPLC-qTOF-MS technique (Chapter 6). Interestingly, using Central composite design (CCD), this study has demonstrated that even though both collision energy and intensity threshold independently enhance metabolite coverage, it is noteworthy that when both parameters are combined, the comprehensiveness in maximizing metabolome coverage is even greater. Therefore, revealing that to enhance exploration and maximize the potential of untargeted metabolomics, this study recommends future studies transitioning from single-point optimization to group-based optimization. Overall, contributes to the growing field of natural product discovery and provides insights into the biosynthetic pathways and insight into the chemical diversity of microbial secondary metabolites. Furthermore, these findings highlight the diverse potential of microbial-derived compounds as potential sources of new bioactive molecules.National Research Foundation (NRF
Exploring the role of traditional leaders in conflict resolution amongst Vatsonga at Bungeni Area: Limpopo Province
No full textM. A. in African StudiesDepartment of Indigenous Knowledge Systems and Heritage StudiesThis study explored the role of African traditional leaders in conflict resolution amongst Vatsonga at Bungeni area in Vhembe district of the Limpopo Province. The researcher argues that the advent of formal courts in the South African dispensation has resulted in the role of African traditional leaders being overshadowed.The objective of the study was to examine the institution of traditional leadership as a sector of conflict resolution; to outline the nature, scope and processes of different conflict resolution mechanisms used by Vatsonga traditional leaders; to assess the implications associated with adopting the Vatsonga traditional conflict resolution mechanisms; to appraise legislation and policies that govern traditional leadership and African conflict resolution mechanisms; and to explore possible palliatives to ensure that African conflict resolution mechanisms can be strengthened and/or can operate at an equal footing with the formal courts.
The study adopted the Sankofa and Conflict Transformation Theory.The study used qualitative method involving semi-structured interviews and focus group discussions to collect data. The population of the study was sampled using non-probability sampling. Purposive sampling was used to sample participants. Data was analyzed using thematic analysis to give the probable results that would help to bridge the gap identified in the process.
The study reveals that traditional leaders in South Africa are unaware of legislations and policies governing conflict resolution, and most are unaware of their content due to English language barriers. While traditional leaders are custodians of customary law, they are not experts in western laws. Traditional leadership is a crucial sector for conflict resolution in sub-villages, particularly in the Bungeni area, to resolve conflicts through mediation, reconciliation and arbitration. The chieftaincy, led by Chief Bungeni, is hierarchical and based on hereditary lineage which is similar to other African countries
The Role of Parents in Developing Mathematical Skills of Their Children in Grade 1
No full textMEDDepartment of Educational StudiesParental involvement in children's education from an early age substantially impacts their academic success, which continues into later years. However, many parents face difficulties supporting their children’s mathematics learning due to limited mathematical knowledge, low confidence, and a lack of resources. This study explored the role of parents in developing the mathematical skills of their Grade 1 children. The study aimed to identify parents' challenges in helping their children with mathematics, examine how parental involvement influenced children's mathematical performance, and explore strategies parents used to support their children. This study was based on Bronfenbrenner’s Ecological Systems Theory (1979), which explains that child development occurs within multiple interconnected systems that influence growth. A qualitative research design focused on parents of Grade 1 children in Mvudi Circuit, Vhembe East District. The sample consisted of sixteen parents selected through purposive sampling. Data were collected using semi-structured interviews and analysed using a thematic approach. The study found that parents who actively participated in their children's mathematics learning by offering guidance, using household materials, and creating a positive learning environment contributed significantly to their children’s mathematical progress. It also found that many parents lacked confidence in their mathematical abilities, making it difficult for them to help their children effectively. The unavailability of suitable learning materials worsened this issue. Based on these findings, the study recommends that schools provide workshops and training to help parents develop basic mathematical skills and learn effective strategies for supporting their children. It also suggests that policymakers and educators create and distribute accessible learning resources for parents at home. This study focused only on Grade 1 parents in Mvudi Circuit, Vhembe East District, so its findings may not apply to other areas or grade levels. To ensure trustworthiness, the study used triangulation, member checking, and a clear record of the research process. Ethical considerations included obtaining informed consent, maintaining confidentiality, and protecting participants’ identities. The study highlights the vital role of parents in early mathematical development and emphasizes the need for targeted support to help them overcome challenges in assisting their children
UV-assisted isomerization studies of active compounds in bush tea (Athrixia phylicoides) leaf extracts and investigations of their potential to inhibit acid corrosion of mild steel and zinc
No full textMNPDPCCorrosion of metals can be controlled by using corrosion inhibitors. Plant metabolites undergo geometrical isomerization under the influence of UV light radiation. The use of corrosion inhibitors is one of the useful methods to reduce or decrease corrosion on metals. While synthetic inhibitors are useful in preventing the corrosion of metals, they can sometimes be harmful and costly. There is an alternative solution in the form of green inhibitors, which can offer the same level of protection at an affordable price. Inhibitors of corrosion are applied to the environment and the metal they protect against deterioration. Considering this information, it is necessary to examine different metals exposed to an acidic environment in the presence and absence of inhibitors. The impact of UV light radiation on bush tea (A. phylicoides) plant extract was investigated for zinc, and mild steel corrosion exposed to 1.5 M hydrochloric and sulphuric acids at 303-333K. This study employs liquid chromatography-mass spectrometry (LC-MS) to investigate the geometric isomerization of compounds within plant extracts, aiming to identify and quantify different isomers and understand the conditions influencing their stability and transformation. Gravimetric analysis (GA), Electrochemical Impedance Spectroscopy (EIS), and Potentiodynamic Polarization (PDP) were used to study corrosion inhibition, Fourier Transform Infrared Spectroscopy (FTIR) was used to analyze functional groups in the presence and absence of corrosion inhibitors. Contact angle or wettability studies (CA / WS) have been conducted to assess the hydrophobicity or hydrophilicity of the surface. Scanning Electron Microscopy (SEM) and computational studies were employed to gain a deeper understanding of the surface morphology and interactions between the A. phylicoides plant extracts and the metal surface. LC-MS chromatograph shows that the extract undergoes geometric isomerization. The GA, EIS, and PDP tests showed that the extracts were able to reduce the amount of corrosion that occurred on the metal surface. FTIR tests confirmed that the extracts were able to form a protective layer on the metal surfaces, which inhibited the corrosion process. The SEM and computational studies provided additional evidence that the extracts were able to reduce the corrosion rate by forming a protective layer on the metal surfaces. The results of the study showed that the extracts had a strong adhesive capacity and were able to form a stable protective layer on the metal surfaces. This layer was able to resist the corrosive action of the environment and prevent further corrosion. The study also showed that the extracts had good stability and were able to remain intact on the metal surface for a long time
Studies on severe acute respiratory syndrome coronavirus type -2 in Northern South Africa
No full textPhD (Microbiology)Department of Biochemistry and MicrobiologyBackground: The last three decades have been characterized by the re-emergence of the Coronaviridae family into the human population, causing severe respiratory disease with increased morbidity rates. A dearth of information exists on human coronavirus (HCoV) molecular epidemiology, and circulation in different populations in Africa. As the COVID-19 pandemic progressed across the globe, wastewater-based epidemiology (WBE) was proposed as an alternative tool for assessing and monitoring the occurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the community level. Additionally, through wastewater-based genomic surveillance of SARS-CoV-2, the evolutionary patterns and distribution of viral types at the population level can be comprehensively characterized. This study systematically reviewed literature published prior to the SARS-CoV-2 outbreak to investigate the prevalence and molecular epidemiology of HCoVs circulating in Africa. Secondly, this study established a wastewater-based surveillance (WBS) system to track the trends of SARS-CoV-2, investigate SARS-CoV-2 variants of concern (VOC) circulating in the population, and determine the prevalence of people infected in the Vhembe and Mopani districts. Thirdly, through WBS, to describe the molecular epidemiology of SARS-CoV-2 and document the respiratory viruses occurring in the Vhembe and Mopani districts.
Methodology: A systematic literature review was conducted according to the PRISMA guidelines, to understand the prevalence and molecular epidemiology of HCoVs in Africa. For the second and third objectives, wastewater influents from seven wastewater treatment plants (WWTPs) and one waste sedimentation pond (WSP) were collected weekly from January 2021 to June 2022. Out of a total of 487 samples collected, about 75% (365/487) were positive for SARS-CoV-2 RNA by qRT-PCR. Of these, 80 met the criteria for allele-specific genotyping (ASG). Positive SARS-CoV-2 RNA detected throughout the surveillance period were compared to 7-day moving average (7D-MA) of clinical cases reported per sub-district. Next, SARS-CoV-2 RNA detected during the surveillance period was normalized using the flow rate and population size. The Spearman’s correlation coefficient was used to determine the relationship between non-normalized, and normalized SARS-CoV-2 RNA data when compared to the reported clinical cases. Finally, positive SARS-CoV-2 RNA copies with a standard deviation of less than one (SD <1) were used to predict the prevalence of people infected in the study sites using the Monte Carlo simulation model. This predicted prevalence
was also compared to the 7D-MA clinical cases reported per sub-district, and the correlation between them was determined. Subsequently, samples positive for SARS-CoV-2 were subjected to whole genome sequences (WGS) using the ATOPlex next-generation sequencing method and analyzed for lineage and clade assignment using the Pangolin and Nextclade tool. Relatedness of identified sequences was determined by phylogenetic analysis. VOC was analyzed for prevalence and geographical distribution. Concordance for VOC between ASG and WGS analyses was determined.
Results: Findings from the systematic literature review showed that thirteen out of 54 (24%) African countries had published data on HCoV prevalence and/or genomic epidemiology, from hospitals, clinics, homes, community gatherings, farms, and individuals at airports. The first published data on HCoV was from South Africa in 2008. There was heterogeneity in the type of tests used in determining HCoV prevalence. Two studies reported that risk factors for HCoV include exposure to infected animals or humans. The second objective, establishing a wastewater-based surveillance system was achieved. Briefly, SARS-CoV-2 viral load was detected in wastewater one week prior to increased infection cases reported at the district level during the third and fourth waves, thus serving as an early warning system. Of interest, towards the end of the surveillance period, increased SARS-CoV-2 viral load detected in wastewater were not reflected in the reported clinical cases. Comparing the reported number of cases per district to the predicted prevalence revealed more cases in the Vhembe District than in the Mopani District. Third, SARS-CoV-2 molecular epidemiology and the distribution of respiratory virus were described. A total of 60 SARS-CoV-2 full genomes were analyzed. Delta and Omicron variants were detected as early as January and February 2021, respectively, while the Beta variant was detected in July 2021. Delta variant was significantly predominant at a prevalence of 45%, followed by Omicron (32%), and Beta (5%). Eighteen percent (11/60) of the sequences were assigned a lineage by Pangolin tool, but not a specific WHO variant name. Upon phylogenetic analysis, some of these sequences were seen clustering with the Alpha (2/11) and Delta (2/11) variants, while the remaining sequences clustered with each other. Mutations in the receptor-binding domain (RBD) of the Spike protein (S-protein) were investigated, with some peculiarities observed such as mutation E484K absent in all Beta variant study sequences. Three previously undescribed mutations (A631S, V327I, D427Y) were detected in Delta variant sequences. Concordance in variant
assignments between allele-specific genotyping and WGS was seen in 51.2% of the study sequences. Respiratory virus surveillance revealed year-round circulation of human Adenoviruses (HAdVs), while HCoVs, influenza viruses and human parainfluenza viruses (HPIVs) were mostly detected in winter. Influenza A and B viruses (IAV and IBV) detected in the study site in 2021 were remarkably different from those reported in circulation nationwide by the NICD. Specifically, IAV (H5N1)/Guandong, a highly pathogenic influenza virus, was detected, although at a low frequency.
Discussion and Conclusion: The systematic review revealed that despite the outbreaks of SARS in Southeast Asia in 2002 and MERS in 2012 in the Middle East, the quantum of virologic investigations on HCoV on the African continent was scanty. Pandemic preparedness requires cognizance of disease outbreaks in other continents, establishment of test and surveillance protocols, and infrastructure for eventualities. Regarding the establishment of a wastewater-based surveillance system for SARS-CoV-2 monitoring, this study demonstrates effective surveillance over an extended period in rural settings. This is important because most reports about the application of WBE for monitoring SARS-CoV-2 and circulating variants are predominantly from more urbanized regions in South Africa and other parts of the world. Thus, it reveals applicability of monitoring pathogens in rural areas, despite challenges encountered such as poor or non-existent sewerage systems. Such challenges are common in the African continent, highlighting the need for more of such investigations to strengthen pandemic preparedness measures. The presence of Delta and Omicron VOCs observed prior to other reports in South Africa highlights the importance of population-based approaches in genomic surveillance over approaches that rely on individual samples. Again, it also emphasizes the need for pandemic preparedness efforts to be extended to all geographic regions. Wastewater is known to potentially capture more viral diversity, including SARS-CoV-2 genetic diversity, and could reveal new viruses and VOCs in circulation before they emerge in the wider human population. Thus, continuous surveillance is necessary for documentation of cryptic lineages, which may contribute towards improving vaccine.Solidarity Fund, the South African Medical Research Council (SAMARC) and the Research and Publication Committee of the University of Vend