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, Ferguson, Jack, Wheatley, Lucy, Ratcliffe, Elizabeth, Casey, Anna, Plant, Tim, The COVID-19 Genomics UK (COG-UK) Consortium, Quick, Joshua, Richter, Alex, Loman, Nicholas, McNally, Alan and Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504 2022. Sars-cov-2 testing in the community: testing positive samples with the taqman sars-cov-2 mutation panel to find variants in real time. Journal of Clinical Microbiology 60 (4) , e02408-21. 10.1128/jcm.02408-21

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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.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Biosciences
Additional Information:	Thomas R. Connor is a member of the COVID-19 Genomics UK Consortium 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.
Publisher:	American Society for Microbiology
ISSN:	0095-1137
Date of First Compliant Deposit:	7 October 2022
Date of Acceptance:	14 February 2022
Last Modified:	21 May 2023 06:31
URI:	https://orca.cardiff.ac.uk/id/eprint/153159

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