SARS-CoV-2 testing in the community: testing positive samples with the TaqMan SARS-CoV-2 mutation panel to find variants in real time

COVID-19 Genomics UK (COG-UK) Consortium

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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.

Original languageEnglish
Article numbere0240821
JournalJournal of Clinical Microbiology
Issue number4
Publication statusPublished - 4 Apr 2022

Bibliographical note

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.

Publisher Copyright:
© 2022 American Society for Microbiology.


  • COVID-19/diagnosis
  • COVID-19 Testing
  • Humans
  • Mutation
  • SARS-CoV-2/genetics
  • SARS-CoV-2
  • variants of concern
  • genotyping
  • SNPs
  • genome sequencing
  • PCR
  • real time
  • Variants Of Concern
  • Genome sequencing
  • COVID-19
  • Sars-cov-2
  • Genotyping

ASJC Scopus subject areas

  • Microbiology (medical)


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