TestEd: Developing and evaluating an affordable whole-system approach for early detection of viral infections in workplaces and communities

Individuals with COVID-19 symptoms are eligible for diagnostic testing in the UK. However, due to cost and logistical constraints, pre and asymptomatic individuals are rarely tested or are screened with low-efficacy lateral flow devices, potentially allowing viral transmission. Although vaccination programmes provide grounds for optimism, there is no guarantee they will eliminate the virus if immunity is short lived, the virus mutates or there is low uptake. An efficient testing system is still needed for suppressing this and future pandemics. We have developed and validated two high-sensitivity, high-throughput approaches for detecting asymptomatic SARS-CoV-2 infection in saliva: (i) PCR-based hypercube pooling and (ii) sequence-based SwabSeq. We will directly compare the two approaches and test the hypothesis that they can be used at scale to detect asymptomatic SARS-CoV-2 infection early, reliably and affordably in up to half a million saliva samples from asymptomatic students and staff at Edinburgh University. We will survey participants to ensure our system is accessible and appropriate, and interview those who test positive to understand attitudes and behaviour regarding self-isolation. We will model the health economics of hypercube pooling and SwabSeq to compare their cost-efficiency and overall value with current testing methods. With an automated, user friendly system of participant registration, sample tracking, robotic processing and rapid result reporting, we aim to reduce the costs of regular screening to below 40p per test. This will enable testing of the whole University community twice a week, thereby minimising transmission from asymptomatic carriers. Our link to NHS Lothian Virology and its COVID service will allow positive cases to be re-tested and immediately entered into NHS public health systems. The study will provide a blueprint for large scale, regular testing to protect workplaces and communities from COVID-19 and future pandemics.