De Oliveira , Tulio De Paiva Nazareth Andrade.Ramphal, Upasana.2026-07-212026-07-2120252025https://hdl.handle.net/10413/24544Doctoral Degree. University of KwaZulu-Natal, Durban.The Coronavirus Disease 2019 (COVID-19) pandemic necessitated a swift and coordinated global response, with genomic surveillance playing a crucial role in tracking the evolution and spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This study presents a comprehensive retrospective analysis of genomic surveillance data, drawing from multiple sources, including the Global Initiative on Sharing Avian Influenza Data (GISAID), Our World in Data (OWID), and national datasets. By leveraging genomic data, this research highlights the importance of surveillance in strengthening outbreak preparedness and public health responses. The thesis is structured into five key chapters. Chapter One presents a detailed literature review, contextualising the pandemic and highlighting the significance of genomic surveillance. Chapter Two, a published manuscript, retrospectively compares the performance of the Illumina MiSeq and Ion Torrent S5 sequencing platforms in detecting the Delta variant during its early emergence. It assesses their efficiency, accuracy, and suitability for genomic surveillance, while addressing challenges in comparing data generated by different sequencing technologies. Chapter Three conducts a retrospective trend analysis of 6,089 SARS-CoV-2 genomes from KwaZulu-Natal, South Africa. It examines genomic surveillance trends across urban and rural districts, focusing on lineage distribution and transmission dynamics. The study aims to identify surveillance gaps and propose strategies to enhance epidemic preparedness in localised settings. Chapter Four expands on this analysis by comparing South Africa’s genomic surveillance strategies with global initiatives, identifying strengths and areas for improvement. It evaluates data-sharing practices and pandemic response frameworks, highlighting successes and challenges relative to countries with similar or higher socioeconomic contexts and their impact on timely public health interventions. The final chapter synthesises the key findings, emphasising the need for sustained investment in genomic monitoring, technological advancements, and global collaboration to enhance preparedness for future public health threats. The study reveals that, while South Africa has made significant progress in genomic surveillance, disparities in sequencing coverage, particularly in rural areas and low-income countries, pose challenges to comprehensive outbreak monitoring. The comparative analysis of sequencing platforms offers critical insights into the reliability and efficiency of different methodologies, essential for optimising genomic surveillance systems. Additionally, the global comparison demonstrates the importance of international collaboration in genomic data sharing, providing strategic recommendations to strengthen surveillance efforts. In conclusion, this study demonstrates that genomic surveillance is indispensable for real-time pandemic response, variant tracking, and public health decision-making. By advocating for improvements in sequencing infrastructure, equitable data access, and enhanced global cooperation, this research contributes to building a more resilient and effective approach to managing future infectious disease outbreaks.enCC0 1.0 Universalhttp://creativecommons.org/publicdomain/zero/1.0/Cycle threshold.Kilometre squared.Polymerase chain reaction.Case fatality rate.Spike Gene.Thesis