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

Lead Research Organisation: University of Edinburgh
Department Name: Ctr for Genomic & Experimental Medincine

Abstract

The TestEd programme at the University of Edinburgh will develop and evaluate an affordable whole system approach for early detection of COVID-19 that will provide a blueprint for large-scale regular testing to protect workplaces and communities from COVID-19 and, potentially, future pandemics. Specifically we will:

- Implement our system that has now been established in two Institutes of the University of Edinburgh for streamlined, effective and accessible participant and sample registration, COVID-19 based on novel sample pooling strategies, automated, timely feedback of results, across the entire University of Edinburgh population, for twice weekly testing and rapid isolation of asymptomatic carriers

- Conduct online surveys of all participants, and qualitative interviews on those who test positive for the virus, to understand attitudes and behaviour in the face of the pandemic, and the views of staff and students regarding regular testing and the potential need for self-isolation

- Carry out health economic modelling of the pipeline, including our strategy to test for the virus in pooled samples that our preliminary analyses (see Additional Information Form) have shown have the potential for tests costing 40p per sample, at least ten-fold lower than other testing strategies

- Evaluate efficacy and efficiency of the two pooling strategies - PCR-based hypercube pooling and sequence-based SwabSeq - by side-by-side comparison of their performance against individual PCR tests on a minimum of 10,000 samples and then, by using the pooling strategy with better performance, to test half a million samples collected from University staff and students within the 12 month period of the award

- Engage with our collaborators within and outside the University to optimise the logistics of our laboratory processes, thereby minimising the time of each laboratory step and hands-on lab staff time, maximising use of robotic automation, thereby minimising overall turnaround time. Our current turnaround time is 100% return of results within 24 hours of the end of the 8-hour sample collection period. We shall monitor this through the course of the study period, providing reports to our participant community and to the MRC, aiming to remain as close as possible to 100% return of results within 24 hours throughout scale up and to full testing capacity

- Engage with our participant community, the University leadership team, our collaborators within the NHS, our collaborators providing equipment and reagents and Edinburgh Innovations (our technology transfer organisation) to develop opportunities for future funding and deployment of our pipeline and knowhow within and outside the University at the conclusion of the funding period. This includes the opportunity to work with Government and non-governmental organisations to influence policy and to deploy our system, knowledge and experience to other workplaces and communities

- Engage with policymakers and healthcare providers to ensure that our results and experience with large-scale testing can be fed into national and possibly international policy and practice for pandemic responses.

Technical Summary

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.

Publications

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Description We have established a method for mass testing of asymptomatic individuals for carriage of COVID-19. Our work has tested of 100,000 samples using pooled saliva as the test reagent. We have demonstrated cost efficacy and shown how these methods can lead to new findings on viral prevalence in the community.
Exploitation Route We are engaging with policy makers and industry experts to investigate how our outcomes can be taken forward.
Sectors Healthcare,Government, Democracy and Justice,Manufacturing, including Industrial Biotechology

URL https://www.medrxiv.org/content/10.1101/2022.02.21.22270847v1
 
Description Regional Champion for Scotland, The Academy of Medical Science
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact National meeting in planning.
URL https://acmedsci.ac.uk/more/news/new-regional-champions-appointed-for-2022?utm_medium=email
 
Description Scottish Genomics Leadership Group
Geographic Reach National 
Policy Influence Type Participation in a national consultation
Impact Research and practice implications for whole-genome sequencing, liquid biopsy and COVID-19 testing.
 
Description The Academy of Medical Sciences, Annual Fellows' Meeting and Jean Shanks Lecture 2021, delegate 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Engagement with covid testing community.
Year(s) Of Engagement Activity 2021