Modelling the effectiveness of quarantine and testing strategies during the COVID-19 pandemic

The COVID-19 pandemic prompted governments to enact stringent non-pharmaceutical interventions to control transmission and limit mortality. Core to this was the detection and isolation of individuals either infected with, or potentially exposed to, SARS-CoV-2. In this thesis, I describe the application of individual-based mathematical modelling to determine the effectiveness of such measures in their ability to control transmission, while evaluating their costs to individuals and wider society, as the pandemic progressed. Modelling of thermal screening at airports early in the pandemic revealed that approximately half of infected arrivals would go undetected, and go on to potentially spark outbreaks. I used mobile phone data to calculate the effectiveness of the cordon sanitaire around Hubei province in reducing spread to other provinces in China. As 14 days of quarantine became the norm, I estimated that this period could be reduced by half if arrivals were tested by PCR. When LFTs became available, I determined that daily testing could allow for the avoidance of quarantine entirely, provided repeatedly negative tests, despite their lower comparative sensitivity versus PCR. Finally, I assessed the hypothesis that lateral flow testing, through the detection of the most infectious individuals with the highest viral loads, could reduce the occurrence of superspreading, using a model incorporating real-world contact rates from the Comix contact survey. I identified uptake and adherence as key unknowns which may limit the effectiveness of such measures. Model structure and parameterisation were influenced by the evolving state of knowledge of the transmission dynamics of SARS-CoV-2 (e.g. viral load kinetics), the technology available (such as rapid lateral flow testing), and epidemic conditions (e.g. prevalence) over the course of the pandemic. Overall, my work demonstrates the value of information gained from testing to allow for targeted pandemic control measures, reducing the individual and societal costs of quarantine and isolation