Navigating the Covid-19 Pandemic i) Insights from risk mitigation strategies in an Irish Third level Institution & ii) Developing a methodology for managing repeat COVID-19 positives to inform national policy

Introduction: The COVID-19 pandemic has challenged global public health systems, highlighting the need for robust institutional responses to manage outbreaks in high-density settings. Universities, as microcosms of broader society, faced unique challenges due to shared residential environments, diverse populations, and extensive interpersonal interactions. This PhD critically appraises the mitigation strategies employed on a university campus, University College Dublin, during different phases of the COVID-19 pandemic. Methods: Unlike traditional research projects, it was designed as a retrospective analysis from the outset, aiming to divide the response into distinct phases of the pandemic and critically appraise the response and identify the lessons to be learned for future. Three interconnected analyses were conducted, each corresponding to a specific phase of the pandemic. The first study focused on transmission patterns within UCD’s residential settings during the pre-vaccination phase (September 2020–September 2021), leveraging epidemiological analyses and Whole Genome Sequencing (WGS) to uncover key dynamics of virus spread. The second study examined the efficacy of antigen testing and vaccination status in outbreak management between October 2021 and May 2022, utilising integrated surveillance methodologies to assess their impact. The third study tackled the challenge of identifying repeat COVID-19 cases across Ireland by applying a novel algorithm that combined cycle threshold (Ct) values with genomic sequencing to distinguish between reinfections and prolonged viral sheddingData for these studies were derived from self-reports, contact tracing, and genomic analyses. Analyses of these data provided a comprehensive appraisal of the university’s response, offering actionable insights into the effectiveness of the implemented strategies and identifying critical areas for improvement in future pandemic planning. Results: Study 1 revealed significant heterogeneity in transmission dynamics across UCD’s residential environments, emphasising the importance of tailored public health interventions and the utility of WGS in uncovering hidden transmission pathways. Study 2 demonstrated the efficacy of integrated testing strategies and vaccination in reducing symptomatic disease and outbreak sizes. Study 3 provided critical insights into the classification of repeat positive cases, showcasing the operational value of Ct thresholds and genomic data in refining isolation protocols and enhancing surveillance systems. Conclusions: The findings underscore the importance of multidisciplinary approaches in pandemic response, integrating epidemiological, genomic, and behavioural insights. By addressing unique challenges in institutional settings, this research contributes to the development of scalable frameworks for outbreak management and informs future preparedness strategies. The integration of WGS with traditional epidemiological tools offers a transformative approach for managing high-risk environments during