SARS-CoV-2 testing in the community: testing positive samples with the TaqMan SARS-CoV-2 mutation panel to find variants in real time
Ashford, Fiona Best, Angus Dunn, Steven J Ahmed, Zahra Siddiqui, Henna Melville, Jordan Wilkinson, Samuel Mirza, Jeremy Cumley, Nicola Stockton, Joanne
Ashford, Fiona
Best, Angus
Dunn, Steven J
Ahmed, Zahra
Siddiqui, Henna
Melville, Jordan
Wilkinson, Samuel
Mirza, Jeremy
Cumley, Nicola
Stockton, Joanne
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.
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Date
2022-04-04
Type
Article
Subject
Oncology. Pathology., Genetics, Microbiology. Immunology
Collections
Citation
Ashford F, Best A, Dunn SJ, Ahmed Z, Siddiqui H, Melville J, Wilkinson S, Mirza J, Cumley N, Stockton J, Ferguson J, Wheatley L, Ratcliffe E, Casey A, Plant T; COVID-19 Genomics UK (COG-UK) Consortium; Quick J, Richter A, Loman N, McNally A. SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time. J Clin Microbiol. 2022 Apr 20;60(4):e0240821. doi: 10.1128/jcm.02408-21. Epub 2022 Apr 4
Journal / Source Title
Journal of Clinical Microbiology
DOI
10.1128/jcm.02408-21
PMID
35369709
Publisher
American Society for Microbiology
Publisher’s URL
https://journals.asm.org/journal/jcm