Department of Microbiology

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Browsing Department of Microbiology by browse.metadata.advisor "Archer, Edward"

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    Delineating the transmission and evolution of SARS-CoV-2 through genomic analysis as a platform for wastewater-based epidemiology
    (Stellenbosch : Stellenbosch University, 2024-03) Mangwana, Noluxabiso; Wolfaardt, Gideon M. ; Johnson, Rabia; Archer, Edward; Muller, Christo; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
    ENGLISH ABSTRACT: This dissertation explored the application of wastewater-based epidemiology (WBE) as a valuable tool for public health decision-making. The research examined multiple aspects of WBE to determine its suitability and adaptability for use in low- and middle-income countries (LMICs), including method standardisation for SARS-CoV-2 surveillance, employing WBE for tracking spatiotemporal trends of SARS-CoV-2, and investigating different normalisation techniques. The study further utilised WBE as an early warning system in closed communities such as university residences, monitoring pharmaceutical usage as a predictive indicator for disease outbreaks in communities, and extending the use of the established methodology to address other viral threats such as rotavirus. Therefore, this dissertation established that composite samples yielded the most reliable results, providing higher viral loads and facilitating efficient spatiotemporal assessments. Additionally, the Qiagen RNeasy PowerSoil Total RNA Kit was recognised as a consistent and time-efficient method for extracting RNA. Subsequently, WBE was employed to monitor the spatiotemporal trends of SARS-CoV-2 in wastewater from specific communities, utilising physicochemical parameters for population normalisation. The wastewater data provided valuable insights into the prevalence of SARS-CoV-2 in these communities, with the peak viral load correlating with an increase in reported positive COVID-19 cases. In light of these results, WBE can be used as a complementary surveillance tool to evaluate the efficacy of targeted interventions within high-risk communities. The research also demonstrated the significance of wastewater surveillance in student residences for the early detection of SARS-CoV-2 on campus, leading to informed decision-making by university management, which helped to mitigate the impact of potential superspreader events. Furthermore, WBE was used to detect acetaminophen concentrations in wastewater and to establish correlations with COVID- 19 cases and the prevalence of SARS-CoV-2 in communities through wastewater analysis. An increase in acetaminophen levels in wastewater was observed ahead of reported rises in clinical cases, particularly during the delta variant-driven wave, indicating that pharmaceuticals can be used as an early warning predictor of disease outbreaks. This underscores the use of WBE in monitoring pharmaceutical usage and offering insights into overall population health for informed public health decision-making. Lastly, WBE was implemented to monitor rotavirus prevalence, revealing that rotavirus persisted throughout the year, with higher viral loads in 2022, particularly in densely populated areas. The research demonstrated the effectiveness of WBE as an invaluable community-wide surveillance tool and an early warning system for detecting pathogens such as rotavirus, supporting targeted interventions in high-risk communities. In summary, this dissertation showcases the adaptability and effectiveness of WBE in monitoring a range of pathogens, providing invaluable data for informing public health decisions to effectively manage disease outbreaks.