In silico characterization of missense mutations in infectious diseases: case studies of tuberculosis and COVID-19
- Authors: Barozi, Victor
- Date: 2023-10-13
- Subjects: Microbial mutation , COVID-19 (Disease) , Drug resistance in microorganisms , Antitubercular agents , Tuberculosis , Molecular dynamics , Single nucleotide polymorphisms
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431626 , vital:72791 , DOI 10.21504/10962/431626
- Description: One of the greatest challenges facing modern medicine and the global public health today is antimicrobial drug resistance (AMR). This “silent pandemic,” as coined by the world health organization (WHO), is steadily increasing with an estimated 4.95 million mortalities attributed to AMR in 2019, 1.27 million of which were directly linked to AMR. Some of the contributors to AMR include self-prescription, drug overuse, sub-optimal drug prescriptions by health workers, and inaccessibility to drugs, especially in remote areas, which leads to poor adherence. The situation is aggravated by the upsurge of new zoonotic infections like the coronavirus disease 2019, which present unique challenges and take the bulk of resources hence stunting the fight against AMR. Quite alarming still is our current antimicrobial arsenal, which hasn’t had any novel antimicrobial drug discovery/addition, of a new class, since the 1980s. This puts a burden on the existing broad-spectrum antimicrobial drugs which are already struggling against multi-drug resistant strains like multi-drug resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB). Besides the search for new antimicrobial agents, the other avenue for addressing AMR is studying drug resistance mechanisms, especially single nucleotide polymorphisms (SNPs), that change drug target characteristics. With the advancement of computational power and data storage resources, computational approaches can be applied in mutational studies to provide insight into the drug resistance mechanisms with an aim to inform future drug design and development. Therefore, in the first part of this thesis, we employ integrative in silico approaches, including 3D structure modeling, molecular dynamic (MD) simulations, comparative essential dynamics (ED), and protein network analysis approaches i.e., dynamic residue network (DRN) analysis to decipher drug resistance mechanisms in tuberculosis (TB). This involved an investigation of the drug resistance mutations in the catalase-peroxidase (KatG) and pyrazinamidase (MtPncA) enzymes which are responsible for activation of TB first-line drugs; Isoniazid (INH) and Pyrazinamide (PZA), respectively. In the case of KatG, eleven high confidence (HC) KatG mutations associated with a high prevalence of phenotypic INH resistance were identified and their 3D structures modeled before subjecting them to MD simulations. Global analysis showed an unstable KatG structure and active site environment in the mutants compared to the wildtype. Active site dynamics in the mutants compromised cofactor (heme) interactions resulting in less bonds/interactions compared to the wildtype. Given the importance of the heme, reduced interactions affect enzyme function. Trajectory analysis also showed asymmetric protomer behavior both in the wildtype and mutant systems. DRN analysis identified the KatG dimerization domain and C-terminal domain as functionally important and influential in the enzyme function as per betweenness centrality and eigenvector centrality distribution. In the case of the MtPncA enzyme, our main focus was on understanding the MtPncA binding ability of Nicotinamide (an analogue of PZA) in comparison to PZA, especially in the presence of 82 resistance conferring MtPncA mutations. Like in KatG, the mutant structures were modeled and subjected to MD simulations and analysis. Interestingly, more MtPncA mutants favored NAM interactions compared to PZA i.e., 34 MtPncA mutants steadily coordinated NAM compared to 21 in the case of PZA. Trajectory and ligand interaction analysis showed how increased active site lid loop dynamics affect the NAM binding, especially in the systems with the active site mutations i.e., H51Y, W68R, C72R, L82R, K96N, L159N, and L159R. This led to fewer protein-ligand interactions and eventually ligand ejection. Network analysis further identified the protein core, metal binding site (MBS), and substrate binding site as the most important regions of the enzyme. Furthermore, the degree of centrality analysis showed how specific MtPncA mutations i.e., C14H, F17D, and T412P, interrupt intra-protein communication from the MtPncA core to the MBS, affecting enzyme activity. The analysis of KatG and MtPncA enzyme mutations not only identified the effects of mutations on enzyme behaviour and communication, but also established a framework of computational approaches that can be used for mutational studies in any protein. Besides AMR, the continued encroachment of wildlife habitats due to population growth has exposed humans to wildlife pathogens leading to zoonotic diseases, a recent example being coronavirus disease 2019 (COVID-19). In the second part of the thesis, the established computational approaches in Part 1, were employed to investigate the changes in inter-protein interactions and communication patterns between the severe acute respiratory coronavirus 2 (SARS-CoV-2) with the human host receptor protein (ACE2: angiotensin-converting enzyme 2) consequent to mutations in the SARS-CoV-2 receptor binding domain (RBD). Here, the focus was on RBD mutations of the Omicron sub-lineages. We identified four Omicron-sub lineages with RBD mutations i.e., BA.1, BA.2, BA.3 and BA.4. Each sub-lineage mutations were modeled into RBD structure in complex with the hACE2. MD analysis of the RBD-hACE2 complex highlighted how the RBD mutations change the conformational flexibility of both the RBD and hACE2 compared to the wildtype (WT). Furthermore, DRN analysis identified novel allosteric paths composed of residues with high betweenness and eigenvector centralities linking the RBD to the hACE2 in both the wildtype and mutant systems. Interestingly, these paths were modified with the progression of Omicron sub-lineages, highlighting how the virus evolution affects protein interaction. Lastly, the effect of mutations on S RBD and hACE2 interaction was investigated from the hACE2 perspective by focusing on mutations in the hACE2 protein. Here, naturally occurring hACE2 polymorphisms in African populations i.e., S19P, K26R, M82I, K341R, N546D, and D597Q, were identified and their effects on RBD-hACE2 interactions investigated in presence of the Omicron BA.4/5 RBD mutations. The hACE2 polymorphisms subtly affected the complex dynamics; however, RBD-hACE2 interaction analysis showed that hACE2 mutations effect the complex formation and interaction. Here, the K26R mutation favored RBD-hACE2 interactions, whereas S19P resulted in fewer inter-protein interactions than the reference system. The M82I mutation resulted in a higher RBD-hACE2 binding energy compared to the wildtype meaning that the mutation might not favor RBD binding to the hACE2. On the other hand, K341R had the most RBD-hACE2 interactions suggesting that it probably favors RBD binding to the hACE2. N546D and D597Q had diminutive differences to the reference system. Interestingly, the network of high betweenness centrality residues linking the two proteins, as seen in the previous paragraph, were maintained/modified in presence of hACE2 mutations. HACE2 mutations also changed the enzyme network patterns resulting in a concentration of high eigenvector centrality residues around the zinc-binding and active site region, ultimately influencing the enzyme functionality. Altogether, the thesis highlights fundamental structural and network changes consequent to mutations both in TB and COVID-19 proteins of interest using in silico approaches. These approaches not only provide a new context on impact of mutations in TB and COVID target proteins, but also presents a framework that be implemented in other protein mutation studies. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2023
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- Date Issued: 2023-10-13
Exploring the involvement of the SARS-CoV-2 Replicase in the synthesis of polyamines and heat shock proteins
- Authors: Mthembu,Yamkela
- Date: 2023-07
- Subjects: Post COVID-19 condition (Disease) , COVID-19 (Disease) , Polyamines in the body
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/${Handle} , vital:74275
- Description: A disease named COVID-19 almost destroyed the human population. It is caused by the SARS CoV 2 virus which emerged in 2019 and rapidly spread worldwide forcing all countries to shut down. This virus uses non-structural proteins to complete its invasion and development inside the host. The non-structural protein 2 NSP2 defined as the RNA binding protein involved in coronavirus genome replication and decreases the human immune response is key for this virus’s development and invasion. It is believed that the NSP2 associate themselves with polyamines and heat shock proteins inside the host cell, to proceed with the viral development and this study aimed to investigate how SARS CoV 2 virus key non-structural proteins NSP2 utilizes polyamines and heat shock proteins using the molecular docking approach and molecular dynamics MD. In this present study a docking approach was used. The dockings were done on ClusPro, and analysis was done on Discovery Studio, chimera, and PyMOL. One of the enzymes that are involved in the regulation of polyamine biosynthesis, adenosylmethionine decarboxylase AdoMetDC was used in investigating the polyamine binding to the viral NSP2, and major heat shock proteins HSPs HSP40, HSP70, and HSP90 were used in the investigation of the binding of HSPs to viral non-structural proteins NSP2. The results obtained show that 32 interactions were formed when docking heat shock protein 40 HSP40 with the SARS CoV 2 NSP2, but the area that has the highest interactions was from amino acid Ala554 to His557. Asp553 plays a very crucial role in this interaction forming six interactions. Heat shock protein 70 produced about 28 interactions when docked with the SARS CoV 2 NSP2. But the section with the most bonds was from position 550 to 560 of the ligand. Human heat shock protein 90 HSP90 formed 19 interactions when docked with the SARS CoV 2 viral NSP2. MD revealed Arg458, Asn508, Met297, Arg301 and Tr417 active residues. And pharmacophore modeling indicated zinc inhibitors as crucial for inhibiting this virus. Enough interactions were produced with ideal bonds lengths, and it can be said that the functioning of the SARS CoV2 viral non-structural proteins functioning majorly depends on the presence of the heat shock proteins at hand for proper formation and depends on polyamines for complete development and correct functioning. , Thesis (MSc) -- Faculty of Science and Agriculture, 2023
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- Date Issued: 2023-07
The factors influencing professional commitment and job performance of pharmacists in the Nelson Mandela Bay within the Covid-19 environment
- Authors: Sayster, Gary
- Date: 2022-12
- Subjects: Professional ethics , Pharmacists (Nelson Mandela Bay) , COVID-19 (Disease)
- Language: English
- Type: Master's theses , Thesis
- Identifier: http://hdl.handle.net/10948/60232 , vital:63986
- Description: Job performance and professional commitment are potent drivers of organisational efficiency and overall organisational prosperity, respectively. The severe lack in research regarding these constructs in relation to the pharmaceutical industry or to pharmacists specifically, provided the prime opportunity for the present research to fill this gap. The aim of the present research was therefore to determine the factors influencing professional commitment and job performance in pharmacists in Nelson Mandela Bay, given the Covid-119 environment. A quantitative research approach was adopted for the present study and involved the distribution of a likert—scale questionnaire measuring the dependent variables – professional commitment and job performance and the independent variables – work stress, job commitment, self-esteem and emotional intelligence. A total of 142 surveys were analysed, signalling a response rate of 94.6 67 %. The key findings of the statical analysis show that work stress is negatively related to affective professional commitment and job performance. Job commitment was positively related to job performance and affective professional commitment and self-esteem have a directly positive effect on affective professional commitment. Social skills and self-motivation (as components of emotional intelligence) had a positive relationship with job performance and professional commitment, respectively. Based on these findings, several managerial implications and recommendations were offered. , Thesis (MBA) -- Faculty of Business and Economic Sciences, 2022
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- Date Issued: 2022-12
The Impact of COVID-19 on Maritime Operations at the Port of Mossel Bay
- Authors: Mthembu, Sandile
- Date: 2022-12
- Subjects: COVID-19 (Disease) , Maritime Operations, Port of Mossel Bay
- Language: English
- Type: Master's theses , Thesis
- Identifier: http://hdl.handle.net/10948/59768 , vital:62422
- Description: The goal of this study is to evaluate the impact of COVID-19 on maritime operations at the Port of Mossel Bay, South Africa (SA) before and during the COVID-19 pandemic. The Port of Mossel Bay is the smallest commercial port in SA. The Transnet National Ports Authority (TNPA), which is owned by the South African government and reports directly to the Department of Public Enterprises, manages and operates the Port of Mossel Bay. The oil and gas industry, as well as a small fishing fleet, are served by the port at Mossel Bay. Although fishing industry is crucial to the local population in the Southern Cape, the Port of Mossel Bay also manages a number of other commercial activities, which greatly contributes to the South African economy and Growth Domestic Product (GDP). The study focused on four companies, which conduct maritime operations at the Port of Mossel Bay, namely, Mossel Bay Transnet Port Authority, PetroSA, SeaVuna and Viking Fishing Operations. Various literature studies were utilised to gather background information for each company, as well as data for comparison, evaluation and interpretation of maritime operations before, during and after the COVID-19 pandemic. Using an interpretivist approach as a research philosophy, a qualitative research methodology was employed. For the qualitative data collection, participants were contacted, after which the data was analysed, leading to the identification of themes. COVID-19 has had a financial and operational influence on maritime operations at the Port of Mossel Bay, according to the empirical findings. Companies created are continuing to implement, steps to ameliorate the impact of the COVID-19 pandemic to ensure that operations are carried out effectively and efficiently. The intention of this study is to contribute to the body of knowledge to improve the effectiveness and efficiency of marine operations in South African waters and beyond before, during and after the COVID-19 pandemic. Additional benefits of this research are to provide a framework of analysis for restoring maritime operations but also to serve as a preventative framework for prolonged or recurring pandemic phenomena in the future. , Thesis (MPhil) -- Faculty of Business and Economic Science, School of Applied Accounting, 2022
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- Date Issued: 2022-12
Design, synthesis, manufacture, characterization and evaluation of lipid nanocapsules in chitosan-iota-carrageenan based hydrogel scaffold as a potential anti-Covid-19 drug delivery system
- Authors: Mukubwa, Grady Kathondo
- Date: 2022-10-14
- Subjects: Nanocapsules Design , Hydrogel , COVID-19 (Disease) , Characterization , Drug delivery systems
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/364955 , vital:65665
- Description: Covid-19 is a deadly viral disease that has been rampant around the world since 2019. Although the successful introduction of the vaccine has reduced the spread of covid-19, new cases and deaths are still being recorded. To date, no specific curative antiviral treatment has been approved for covid-19. However, many existing antiviral drugs have been and are still being studied against covid-19 and some of them, such as Remdesivir, have shown promise and could be repurposed to treat this infection. Unfortunately, antiviral drugs are prone to resistance as most of them have poor biopharmaceutical properties, including low solubility, permeability and bioavailability, which could hinder any clinical success. Recent advances in nanotechnology-based delivery systems have made it possible to improve the biopharmaceutical properties of many drugs, especially those of poorly water-soluble drugs, by formulating them as lipid nanoparticles (LNP). Thus, in order to contribute to the fight against covid-19, this work aimed to develop Lipid Nanocapsules (LNC), based on some natural raw materials, which could improve the biopharmaceutical properties of antiviral drugs. In addition, since covid-19 infection is mainly respiratory, this work also aimed to fabricate a targeted delivery system based on a hydrogel capable of entrapping LNC and ensuring their efficient deposition and release in the lungs. The LNC consisted of a mixture of medium-chain triglycerides oil (MCT oil), crude soy lecithin, tween 80, NaCl and water, while the hydrogel consisted of a chitosan-grafted-iota carrageenan-grafted-poly (acrylamide-co-acrylic acid) system (CS-iCar-p (AAm-Co-AA)). Efavirenz (EFV), a drug with very low water solubility that has recently been demonstrated to have the potential to influence sars-cov-2 life cycle through different targets (3CLP, RdRp, Hellicase, 3’to5’exonuclease, 2’-O-ribose methyltransferase and EndoRNAse), was chosen as the model drug to evaluate the developed delivery system. The combination of LNP and hydrogel results in a delivery system known as the LNP-hydrogel composite, an emerging area of research in the field of drug delivery. To date, no research has reported the design and fabrication of an LNC-CS-iCar-p (AAm-Co-AA) hydrogel composite that could effectively deliver an antiviral drug to the lungs in addition to its advantages in terms of biological activities. Prior to the design of experiment, EFV solubility was assessed in water, labrafac lipophile 1349 and MCT oil. After that, the Design Expert Software version 13 was used to design the different experiments performed in this work. The I-optimal mixture design of experiments was performed for both LNC preparation and CS-iCar-p (AAm-Co-AA) hydrogel synthesis to study the impact of raw materials on the characteristics of these delivery systems. LNC were prepared using the phase inversion method while the free radical precipitation graft copolymerization method was used to synthesize hydrogel. In order to build polynomial models that could predict the amount of drug both LNC and CS-iCar-p (AAm-Co-AA) hydrogel can entrap, a D-optimal (custom) randomized design was performed. Moreover, various characterization techniques were used to investigate the physicochemical properties of the developed delivery systems. Thereafter, drug release studies were performed using a 1% sodium lauryl sulfate solution adjusted to either pH 4 or 7. Solubility studies revealed that EFV was more soluble in labrafac lipophile 1349 and in MCT oil than in water; therefore, given its affordability, MCT oil was used for the LNC formulation. The design of experiment carried out allowed the construction of polynomial models that could predict, on the one hand, the droplet size, the polydispersity index and the Zeta potential of LNC, which were respectively around 50nm, below 0.2 and below -33. On the other hand, the model could predict the swelling capacity of the synthesized hydrogel, which was optimised to about 30,000% (300 g of water to 1 g of hydrogel). This turned out to be influenced by the proportion of polymers, the ratio of monomers as well as the concentration of the cross-linking agent. In addition, the characterization techniques further supported the improvement of EFV solubility by highlighting its conversion into its amorphous state after encapsulation in LNC. They also confirmed successful synthesis of CS-iCar-p (AAm-co-AA) hydrogel. LNC were able to encapsulate about 87% of EFV while the synthesized CS-iCar-p (AAm-co-AA) hydrogel entrapped around 53% of EFV encapsulated in LNC. While LNC were able to release 42% and 27% of EFV after 74 hours in a 1% sodium lauryl sulfate solution (SLS) at pH 7 and pH 4 respectively, the LNC-CS-iCar-p (AAm-co-AA) hydrogel composite released about 50% and 40% of the drug after 9 days in the same release medium. Interestingly, the chemical integrity of the drug was preserved throughout the manufacturing process up to after its release, suggesting that the developed LNC-CS-iCar-p (AAm-co-AA) hydrogel composite could be used as a novel potential anticovid-19 drugs delivery system. , Thesis (MSc) -- Faculty of Science, Chemistry, 2022
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- Date Issued: 2022-10-14
In silico substrate binding profiling for SARS-COV-2 main protease (mpro) using hexapeptide substrates
- Authors: Zabo, Sophakama
- Date: 2022-10-14
- Subjects: COVID-19 (Disease) , Peptides , Chymotrypsin like , Chymotrypsin , Proteases , Proteolytic enzymes
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365566 , vital:65760
- Description: COVID-19, as a disease resulting from SARS-CoV-2 infection, and a pandemic has had a devastating effect on the world. There are limited effective measures that control the spread and treatment of COVID-19 illness. The homodimeric cysteine main protease (Mpro) is crucial to the life cycle of the virus, as it cleaves the large polyproteins 1a and 1ab into matured, functional non-structural proteins. The Mpro exhibits high degrees of conservation in sequence, structure and specificity across coronavirus species, making it an ideal drug target. The Mpro substrate-binding profiles remain, despite the resolution of its recognition sequence and cleavage points (Leu-Gln↓(Ser/Ala/Gly)). In this study, a series of hexapeptide sequences containing the appropriate recognition sequence and cleavage points were generated and screened against the Mpro to study these binding profiles, and to further be the basis for efficiency-driven drug design. A multi-conformer hexapeptide substrate library comprising optimised 81000 models of 810 unique sequences was generated using RDKit within the context of python. Terminal capping with ACE and NMe was effected using SMILES and SMARTS matching. Multiple hexapeptides were complexed with chain B of crystallographic Mpro (PDS ID: 6XHM), following the validation of chain B for this purpose using AutoDock Vina at high levels of exhaustiveness (480). The resulting Vina scores ranged between -8.7 and -7.0 kcal.mol-1, and the reproducibility of best poses was validated through redocking. Ligand efficiency indices were calculated to identify substrate residues with high binding efficiency at their respective positions, revealing Val (P3), Ala (P1′); and Gly and Ala (P2′ and P3′) as leading efficient binders. Binding efficiencies were lowered by molecular weight. Substrate recognition was assessed by mapping of binding subsites, and Mpro specificity was evaluated through the resolution of intermolecular interaction at the binding interface. Molecular dynamics simulations for 20 ns were performed to assess the stability and behaviour of 132 Mpro systems complexed with KLQ*** substrates. Principal component analysis (PCA), was performed to assess II protein motions and conformational changes during the simulations. A strategy was formulated to classify and evaluate relations in the Mpro PCA motions, revealing four main clades of similarity. Similarity within a clade (Group 2) and dissimilarity between clades were confirmed. Trajectory visualisation revealed complex stability, substrate unbinding and dimer dissociation for various Mpro systems. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
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- Date Issued: 2022-10-14
Profiling Rhodes University students’ substance use during the Covid-19 pandemic lockdown: comparing the AUDIT and CCAPS-62 substance abuse sub-scale
- Authors: Goosen, Jeslyn Chrismaré
- Date: 2022-10-14
- Subjects: College students Substance use South Africa Makhanda , College students Alcohol use South Africa Makhanda , College students Mental health South Africa Makhanda , College students Attitudes , College students Economic conditions , COVID-19 (Disease) , Rhodes University
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/405974 , vital:70224
- Description: Students are vulnerable to academic distress and mental health concerns. Many struggle to effectively cope with the many demands placed on them from various factions; included but not limited to institutional demands, financial concerns, and parental expectations. With the most recent outbreak of the SARS-Co V-2 (better known as the COVID-19 pandemic) many students have struggled to effectively cope with the changes relating to the nationwide lockdown. Universities had to change the way in which they provide students with the necessary academic material, and many had to return to their familial homes. This had a deleterious effect on the way students performed their daily activities and coping. A rise in impaired mental health was noted. Many students used alcohol as a means of coping during this tumultuous and unprecedented time. Undergraduate students at Rhodes University were asked to complete a survey questionnaire via SurveyMonkey, an online survey service. Data was collected over a ten-day period during July 2020. The AUDIT and the CCAPS-62 Substance Use subscale were used to measure their alcohol intake during lockdown and results was compared. Results indicated a significant positive correlation between the CCAPS-62 substance use subscale and the AUDIT (r = 0.80, n = 930, p < 0.01). Outcomes identified that men tend to drink more than females, and white students tend to drink more than black students. Findings suggests that the CCAPS-62 a multidimensional instrument measuring general distress among students could positively contribute to the reliability and validity of the measure used in a multicultural and multilingual society such as South Africa. , Thesis (MA) -- Faculty of Humanities, Psychology, 2022
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- Date Issued: 2022-10-14
Analysis of early-phase contact tracing during the coronavirus disease 2019 outbreak in Mangaung Metro, Free State
- Authors: Monyobo, Priscilla Kesaletseng
- Date: 2022-09
- Subjects: COVID-19 (Disease) , Contact tracing (Epidemiology) , Public health
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/23533 , vital:58105
- Description: Background and Aim Contact tracing is a critical public health measure for controlling and preventing the spread of infectious diseases. Although the principles underlying this strategy are not novel, understanding the changes in infectiousness of COVID-19 is indeed novel. As are the capacity and operating procedures required to support disease investigation in Mangang Metro during the SARS-CoV-2 (COVID-19) pandemic. On 16 March 2020, the first coronavirus disease case in the area, which led to a larger outbreak, occurred in Mangaung Metro, Free State province, South Africa. To date, Mangaung Metro remains the epicentre of the COVID-19 pandemic and the primary driver of the caseload in the Free State province. The aim of this study was to analyse contact tracing data in Mangaung Metro during the early phase of the COVID-19 outbreak (16 March 2020 – 30 June 2020) in order to measure the viral transmissibility of COVID-19 in the early stages of the outbreak, specifically in the context of Mangaung Metro. Methods A descriptive systematic analysis of index COVID-19 cases and their contacts in Mangaung Metro was conducted. The review period ran from 16 March to 30 June 2020, during which there was a total of 1 001 cases in Mangaung Metro. Data was captured on an Excel spreadsheet using the contact line list variables from the established National Institute of Communicable Disease contact line list framework. The inferential statistics were based on a time series analysis to compare the impact of contact tracing stratified by symptomatology and the root cause of the cases to the overall cases in Mangaung Metro. The study determined whether isolation, quarantine, and contact tracing were able to control outbreaks in the early phase using characteristics of disease transmission and parameters particularised to the COVID- 19 pathogen. Results As of 30 June 2020, the Free State province had a total of 2 072 COVID-19 cases. Mangaung Metro contributed 1 001 cases (48percent) of the total number of cases in the study period. Between March and June 2020, 3 553 contacts were traced in Mangaung Metro. This number translates to at least three investigated and traced contacts per index or laboratory confirmed positive case. From the traced contacts, 1 080 samples were collected and sent for laboratory testing. In April 2020, the greatest number of samples were collected. This high rate in sample collection is posited to be the result of the high rate of contacts traced, as well as the initial clinical guidelines followed for contact tracing. Most positive contacts were discovered in March 2020. One of the possible reasons for the high detection of COVID-19 confirmed positive contacts during the early stages of the outbreak was the focus and importance of contact tracing while the caseload remained relatively low. However, as the outbreak progressed in the Mangaung Metro context, the number and relative percentage of positive cases detected through contact tracing decreased. In total, the positive contacts recorded in March 2020 amounted to 92 (51.3percent), 18 in April (10.5percent), 41 in May (22.9percent), and 28 in June (15.6percent). The March 2020 tracking rate was the highest at 73.2percent, with an average contact tracing rate of 15.5percentby the end of June 2020. Of all the contacts traced, 7.9percent involved healthcare workers in the Free State. Conclusion The study’s findings show that contact tracing was an effective control measure during the early stages of the COVID-19 outbreak in Mangung Metro district. Furthermore, the impact was greatest when the caseload was low and the burden on the healthcare system less severe. Mangaung Metro demonstrated the capability of tracing more contacts in the early-early phase of the outbreak; however, as the outbreak progressed to the latent early phase, the caseload increased and fewer contacts were traced. The consequence of contact tracing not being as effective during the latent early phase relates to the increase in both exposed and untraceable contacts, which in turn fueled the increase of new cases. This further impacted the at-risk and vulnerable population, especially the elderly, who were at an increased risk if not traced in a timely manner, possibly resulting in mortality. , Thesis (MPH) -- Faculty of Health Sciences, 2022
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- Date Issued: 2022-09
The impact of COVID-19 on depression, anxiety, and post-traumatic stress levels in doctors and nurses at a South African health facility
- Authors: Finger-Motsepe, Kelebogile
- Date: 2021-12
- Subjects: COVID-19 (Disease) , Mental health
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/27920 , vital:70880
- Description: Introduction: The emergence of the coronavirus disease of 2019 (Covid-19) has wrought profound and enduring transformations in global health, economic dynamics, and social interactions. However, the comprehensive quantification of the psychological repercussions of the Covid-19 pandemic remains elusive and is poised to compound the preexisting burden of mental health disorders within the general populace. Elevated transmission rates, rapid disease progression within vulnerable demographics, and the absence of definitive curative or preventive measures have collectively contributed to a heightened worldwide state of stress and anxiety. Extensive research has demonstrated that the apprehension and stress associated with Covid-19 are markedly pronounced among healthcare professionals, commonly referred to as front-line workers, in comparison to the general population. The Covid-19-related psychological distress is anticipated to act as a catalyst, exacerbating mental health conditions within high-risk groups. Aims and Objectives: This study endeavours to ascertain the prevalence and severity of depression, anxiety, and post-traumatic stress disorder (PTSD) among medical doctors and nurses employed at a regional hospital in South Africa. Methodology: A cross-sectional investigation was conducted to evaluate the presence of anxiety, depression, and stress symptoms among medical doctors and nurses working at a Regional Hospital situated in the Free State Province of South Africa. A purposive sample of 200 participants, comprising all willing doctors and nurses employed at the study site, was enrolled in the study. Findings: The participants exhibited an average age of 42 years and an average tenure of approximately 72 months at the hospital. The majority of participants were of African descent, with a male-to-female ratio of 1:2.3. Female healthcare workers reported significantly higher instances of PTSD than their male counterparts. In the aggregate, 71.4percent of doctors reported symptoms indicative of depression, 73.2percent reported anxiety-related symptoms, and 19.6percent reported PTSD-related symptoms. Among nurses, 72percent displayed clinically significant symptoms of depression, 81percent exhibited anxiety-related symptoms, and 27.7percent manifested symptoms suggestive of PTSD. A moderately robust positive correlation was discerned between PTSD and Anxiety (p = .000; r = .466) as well as PTSD and Depression (p = .000; r = .315). Additionally, a strong positive correlation was identified between Anxiety and Depression (p = .000; r = .631). A statistically significant disparity (p = .030) in anxiety levels was observed among workers in different risk-prone areas. Nurses reported substantially higher levels of anxiety (p = .039; M = 10.63, sd = 4.03) compared to doctors (M = 9.01, sd = 3.80) and administrators (M = 10.50, sd = 4.32). Moreover, both nurses (M = 27.06, sd = 13.61) and administrators (M = 33.33, sd = 14.44) exhibited significantly higher instances of PTSD (p = .003) than doctors (M = 19.96, sd = 15.03). Conclusions: The healthcare workers under scrutiny reported elevated levels of anxiety and depression attributable to the Covid-19 pandemic, although the prevalence of posttraumatic stress symptoms was comparatively lower within the hospital setting. Furthermore, this study illuminates that depressive, anxiety, and post-traumatic stress symptoms were more prevalent among nurses than doctors. Additionally, healthcare professionals operating in high-risk Covid-19 environments, such as the Covid-19 ward, demonstrated heightened levels of anxiety when juxtaposed with their counterparts stationed in low-risk Covid-19 areas within the healthcare facility. , Thesis (MPH) -- Faculty of Health Sciences, 2022
- Full Text:
- Date Issued: 2021-12
Curriculum adjustment and adaptive leadership in two service-learning courses at Rhodes University as a consequence of the COVID-19 pandemic
- Authors: Khuhlane, Heide Nozuko
- Date: 2021-10-29
- Subjects: COVID-19 (Disease) , Curriculum planning South Africa Makhanda , Rhodes University , Service learning South Africa Makhanda , Educational leadership South Africa Makhanda , Educational change South Africa Makhanda , Adaptive leadership
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/191192 , vital:45069
- Description: The COVID-19 global pandemic altered many aspects of learning. Learning through service, a component of community engagement in higher education linking academic learning and the community was no exception. Informed by Experiential Learning Theory, this study investigated the curriculum adjustment of two service-learning courses at Rhodes University and the leadership development of those who lead the courses as a consequence of COVID-19. The study’s initial goal was to highlight the position of service-learning as a component of academic learning. With the onset of the COVID-19 pandemic the goal was extended to understanding the impact of the pandemic not only on service-learning, but on leadership as well. Furthermore, the study sought to determine the responsiveness of service-learning policies at Rhodes University at a time of crisis. The study was designed as an interpretivist case study with four participants and one secondary participant. The study employed document analysis, individual interviews and a focus group interview to collect data. Data analysis took the form of content analysis and coding, through the lens of Experiential Learning Theory and an alternative service-based model. The study findings revealed that as a result of the COVID-19 global pandemic both service-learning courses had to be adapted to ensure successful completion. The adaptations included attention to scaffolded learning, assessment and course outcomes; in one course the service engagement aspect with the community was lost entirely to ensure the saftey of students through adherence to COVID-19 safety regulations. The study also found that the participants developed adaptive leadership competencies and skills, technological and collaboration skills as well as a heightened regard for pastoral care and social justice. However, it was evident that the pandemic revealed gaps in the conceptual understanding of service-learning in the context of the two courses, a need for responsive policy, and practical strategies to implement those policies in smaller units in the institution. The study thus recommends an alternative service-based model approach to service-learning, increased policy responsiveness to issues posed by the ‘new normal’ to support adaptive leadership development, re-defining of the university-community partnership and the identification of opportunities for innovation and collaboration intra-departmentally through service-learning. , Thesis (MEd) -- Faculty of Education, Education, 2021
- Full Text:
- Date Issued: 2021-10-29
Exploring knowledge, attitudes and psychosocial experiences of health care workers regarding covid-19 in Bufalo City municipality
- Authors: Notununu, Zintle
- Date: 2020-03
- Subjects: COVID-19 (Disease) , Medical personnel
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/27028 , vital:66231
- Description: The purpose of this study was to explore and describe the knowledge, attitude and psychosocial experiences of health care workers regarding Covid-19 in Buffalo City Municipality. Covid-19 is a disease that attacks the respiratory system and functions. It is a highly infectious disease with a lengthy 5-6 sometimes even 14-day incubation period. It is very serious condition and has killed a lot of people including the Health Care Workers A qualitative descriptive explorative contextual design was employed in this research study. The design was relevant for this study to explore and describe the knowledge, attitude, and psychosocial experiences of health workers regarding Covid-19 in Buffalo City Municipality. The non-probability sampling method was used and a convenient sampling technique was used to select the participants. Professional nurses who met the criteria and who were on duty on the day of data collection were included in the study. The researcher interviewed 15 professional nurses and stopped as the data was saturated. A semi-structured Interview guide was used as an instrument to collect data containing open-ended questions. The researcher maintained ethical principles throughout the study. Concepts of trustworthiness of the study were applied throughout the research. Tech’s eight steps approach was used to guide the data analysis process. The findings of this study indicate that health care workers have a high level of knowledge about Covid-19. They know what Covid-19 is, how it started, its signs and symptoms, how to protect themselves from it and its complications. Negative attitudes, fears were noticed from the HCWs and thus the need for psychological support was identified. Feelings of neglect and lack of motivation were also identified. Psychological support for health care workers must be provided to prevent staff burnout. Personal Protective Equipment used in the hospital premises must be left and washed in the hospital laundry to prevent the spread of infection to the families of the HCWs. It was indicated that there are health care workers who experienced chronic illnesses after being diagnosed with Covid-19. These chronic illnesses include diabetes and high blood pressure. It was brought to light that myths circulating on the social media about Covid-19 vaccines are delaying the end of Covid-19 epidemic by putting the health care workers at risk of being infected with it as they will be expected to treat patients diagnosed with Covid-19; therefore, government should develop a policy that will limit people from spreading things that they are not true and cannot prove. In conclusion, community awareness and forced vaccination are recommended to end the Covid-19 virus. Monitory incentives should be provided to motivate health care workers. Their overtime that they have worked during Covid-19 must be paid. The Department of Health and hospital managers must make sure that working conditions are improved. This includes the availability of machines to test for Covid-19. More research needs to be done to find out why some people who were diagnosed with Covid-19 end up having chronic illnesses that they never had previously. , Thesis (MPH) -- Faculty of Health Science, 2020
- Full Text:
- Date Issued: 2020-03
Exploring knowledge, attitudes and psychosocial experiences of health care workers regarding covid-19 in Bufalo City Municipality
- Authors: Notununu, Zintle
- Date: 2020-03
- Subjects: Medical personnel and patient , Health services administration , COVID-19 (Disease)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/23545 , vital:58122
- Description: The purpose of this study was to explore and describe the knowledge, attitude and psychosocial experiences of health care workers regarding Covid-19 in Buffalo City Municipality. Covid-19 is a disease that attacks the respiratory system and functions. It is a highly infectious disease with a lengthy 5-6 sometimes even 14-day incubation period. It is very serious condition and has killed a lot of people including the Health Care Workers A qualitative descriptive explorative contextual design was employed in this research study. The design was relevant for this study to explore and describe the knowledge, attitude, and psychosocial experiences of health workers regarding Covid-19 in Buffalo City Municipality. The non-probability sampling method was used and a convenient sampling technique was used to select the participants. Professional nurses who met the criteria and who were on duty on the day of data collection were included in the study. The researcher interviewed 15 professional nurses and stopped as the data was saturated. A semi-structured Interview guide was used as an instrument to collect data containing open-ended questions. The researcher maintained ethical principles throughout the study. Concepts of trustworthiness of the study were applied throughout the research. Tech’s eight steps approach was used to guide the data analysis process. The findings of this study indicate that health care workers have a high level of knowledge about Covid-19. They know what Covid-19 is, how it started, its signs and symptoms, how to protect themselves from it and its complications. Negative attitudes, fears were noticed from the HCWs and thus the need for psychological support was identified. Feelings of neglect and lack of motivation were also identified. Psychological support for health care workers must be provided to prevent staff burnout. Personal Protective Equipment used in the hospital premises must be left and washed in the hospital laundry to prevent the spread of infection to the families of the HCWs. It was indicated that there are health care workers who experienced chronic illnesses after being diagnosed with Covid-19. These chronic illnesses include diabetes and high blood pressure. It was brought to light that myths circulating on the social media about Covid-19 vaccines are delaying the end of Covid-19 epidemic by putting the health care workers at risk of being infected with it as they will be expected to treat patients diagnosed with Covid-19; therefore, government should develop a policy that will limit people from spreading things that they are not true and cannot prove. In conclusion, community awareness and forced vaccination are recommended to end the Covid-19 virus. Monitory incentives should be provided to motivate health care workers. Their overtime that they have worked during Covid-19 must be paid. The Department of Health and hospital managers must make sure that working conditions are improved. This includes the availability of machines to test for Covid-19. More research needs to be done to find out why some people who were diagnosed with Covid-19 end up having chronic illnesses that they never had previously. , Thesis (MPH) -- Faculty of Health Sciences, 2020
- Full Text:
- Date Issued: 2020-03