@article{e7eb302150044c9cba7ad6016bc3523b,
title = "SARS-CoV-2 testing in the community: Testing positive samples with the TaqMan SARS-CoV-2 mutation panel to find variants in real time",
abstract = "Genome sequencing is a powerful tool for identifying SARS-CoV-2 variant lineages; however, there can be limitations due to sequence dropout when used to identify specific key mutations. Recently, ThermoFisher Scientific has 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 ThermoFisher TaqMan mutation panel genotyping assay, initially for three mutations of concern and then for an additional two mutations of concern, against SARS-CoV-2- positive clinical samples and the corresponding COVID-19 Genomics UK Consortium (COG-UK) sequencing data. We demonstrate that genotyping is a powerful in-depth technique for identifying specific mutations, is an excellent complement to genome sequencing, and has real clinical health value potential, allowing laboratories to report and take action on variants of concern much more quickly.",
keywords = "genome sequencing, genotyping, PCR, real time, SARS-CoV-2, SNPs, variants of concern",
author = "Fiona Ashford and Angus Best and Dunn, {Steven J.} and Zahra Ahmed and Henna Siddiqui and Jordan Melville and Samuel Wilkinson and Jeremy Mirza and Nicola Cumley and Joanne Stockton and Jack Ferguson and Lucy Wheatley and Elizabeth Ratcliffe and Anna Casey and Tim Plant and Joshua Quick and Alex Richter and Nicholas Loman and Alan McNally and Dinesh Aggarwal and Beth Blane and Ellena Brooks and Carabelli, {Alessandro M.} and Churcher, {Carol M.} and Katerina Galai and Girgis, {Sophia T.} and Gupta, {Ravi K.} and Hadjirin, {Nazreen F.} and Danielle Leek and Catherine Ludden and McManus, {Georgina M.} and Sophie Palmer and Peacock, {Sharon J.} and Smith, {Kim S.} and Elias Allara and David Bibby and Chloe Bishop and Andrew Bosworth and Daniel Bradshaw and Vicki Chalker and Meera Chand and Gavin Dabrera and Mather, {Alison E.} and Justin O'Grady and Steven Rudder and Carl Jones and Samir Dervisevic and Meader, {Emma J.} and Rachael Stanley and Davidson, {Rose K.} and {The COVID-19 Genomics UK (COG-UK) Consortium}",
note = "All Rights Reserved. This article is made available via the PMC Open Access Subset for unrestricted noncommercial re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. Funding Information: The UoB Turnkey COVID-19 diagnostic lab was created wholly from funds directly attributed by DHSC. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research &hx0026; Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute.",
year = "2022",
month = apr,
day = "20",
doi = "10.1128/jcm.02408-21",
language = "English",
volume = "60",
journal = "Journal of Clinical Microbiology",
issn = "0095-1137",
publisher = "American Society for Microbiology",
number = "4",
}