Unravelling pandemic drivers: Whole genome sequencing and routinely collected data is key in analyzing COVID-19 transmission and management

The COVID-19 pandemic has left an indelible mark on the world, reshaping societies, economies, and healthcare systems on a global scale. As the world grappled with the challenge, the virus continuously evolved, giving rise to formidable variants that altered the dynamics of COVID-19 transmission. This thesis investigated multiple COVID-19 outbreaks using whole genome sequencing (WGS) in various settings, including facilities for individuals with intellectual or developmental disorders, primary schools, and the catering industry. It also examined COVID-19 variants associated with breakthrough infections, highlighting the potential of whole genome sequencing in pandemic management. Additionally, this thesis utilized routinely collected data to research the effectiveness of non-pharmaceutical measures in primary schools, the positive predictive value of self-administered rapid antigen tests (self-tests), and the effect of carnival events on transmission, emphasizing the importance of a robust data infrastructure.