SARS-CoV-2 testing in the community: Testing positive samples with the TaqMan SARS-CoV-2 Mutation Panel to find variants in real-time (preprint)

Genome sequencing is a powerful tool for identifying SARS-CoV-2 variant lineages, however there can be limitations due to sequence drop-out when used to identify specific key mutations. Recently, Thermo Fisher Scientific have developed genotyping assays to help bridge the gap between testing capacity and sequencing capability to generate real-time genotyping results based on specific variants. Over a 6-week period during the months of April and May 2021, we set out to assess the Thermo Fisher TaqMan Mutation Panel Genotyping Assay, initially for three mutations of concern and then an additional two mutations of concern, against SARS-CoV-2 positive clinical samples and the corresponding COG-UK sequencing data. We demonstrate that genotyping is a powerful in-depth technique for identifying specific mutations, an excellent complement to genome sequencing and has real clinical health value potential allowing laboratories to report and action variants of concern much quicker.

Extrapolation of United Kingdom Pillar 2 Care home Covid-19 test data to ascertain effectiveness of lateral flow testing in low prevalence settings (preprint)

Lateral flow devices are quickly being implemented for use in large scale population surveillance programs for SARS-CoV-2 infection in the United Kingdom. These programs have been piloted in city wide screening in the city of Liverpool, and are now being rolled out to support care home visits and the return home of University students for the Christmas break. Very little data exists comparing the performance of the UK lateral flow tests with gold standard PCR diagnostics, especially against comparable test populations such as the national Pillar 2 testing program in the United Kingdom. Here we utilise thousands of pillar 2 test data from our University of Birmingham test lab, and by extrapolation against the validate limit-of-detection of the lateral flow assay, provide a potential sensitivity for the test in a comparable low prevalence population captured in the pillar 2 program. Our data suggests the lateral flow assay should successfully capture around 85% of all PCR positive tests performed in our pillar 2 laboratory, and that a fully designed comparative study of lateral flow versus PCR testing is merited in a real life testing environment