COVID-19 testing: disparity between national and institution-based case detection

Reports of COVID-19 prevalence through national statistics, community surveys and targeted testing at places of work or study have guided national and institutional responses to the pandemic. The University of Edinburgh established a mass testing programme, TestEd, for detection of COVID-19 in asymptomatic staff and students who are studying or working on campus. The study has tested more than 100,000 samples with more than 170 confirmed positive results. Since the introduction of a change in policy in England and the UK devolved nations in early January 2022, to limit eligibility for PCR testing in the community to those with symptoms, we have noticed a divergence between the reports in Scottish and UK-wide prevalence, and the magnitude and frequency of positive results in the University datasets. While the national UK-wide and Scottish case figures show declining or stable prevalence, University case reports have risen more than five-fold since early December 2021 and continue to rise. These observations could be important in the face of future variants of concern and emphasise the need for continued access to high sensitivity PCR testing and other forms of surveillance.

A strategy for finding people infected with SARS-CoV-2: optimizing pooled testing at low prevalence

Suppressing SARS-CoV-2 will likely require the rapid identification and isolation of infected individuals, on an ongoing basis. RT-PCR (reverse transcription polymerase chain reaction) tests are accurate but costly, making regular testing of every individual expensive. The costs are a challenge for all countries and particularly for developing countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups. We propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, uniquely identifies infected individuals in a small number of tests. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof of concept experiments in which a positive subsample was detected even when diluted a hundred-fold with negative subsamples. Using these methods, the costs of mass testing could be reduced by a large factor. If infected individuals are quickly and effectively quarantined, the prevalence will fall and so will the cost of regular, mass testing. Such a strategy provides a possible pathway to the longterm elimination of SARS-CoV-2. Field trials of our approach are now under way in Rwanda.