A high-resolution melt curve toolkit to identify lineage-defining SARS-CoV-2 mutations

Alice J. Fraser, Caitlin Greenland-Bews, Daniel Kelly, Christopher T. Williams, CONDOR Steering Group, LSTM Diagnostics Group, Rick Body, Emily R. Adams, Ana Cubas Atienzar, Thomas Edwards, David J. Allen, Paul Dark

Research output: Contribution to journalArticlepeer-review


The emergence of severe acute respiratory syndrome 2 (SARS-CoV-2) variants of concern (VOCs), with mutations linked to increased transmissibility, vaccine escape and virulence, has necessitated the widespread genomic surveillance of SARS-CoV-2. This has placed a strain on global sequencing capacity, especially in areas lacking the resources for large scale sequencing activities. Here we have developed three separate multiplex high-resolution melting assays to enable the identification of Alpha, Beta, Delta and Omicron VOCs. The assays were evaluated against whole genome sequencing on upper-respiratory swab samples collected during the Alpha, Delta and Omicron [BA.1] waves of the UK pandemic. The sensitivities of the eight individual primer sets were all 100%, and specificity ranged from 94.6 to 100%. The multiplex HRM assays have potential as a tool for high throughput surveillance of SARS-CoV-2 VOCs, particularly in areas with limited genomics facilities.

Original languageEnglish
Article number3887
JournalScientific Reports
Issue number1
Publication statusPublished - 8 Mar 2023


  • Humans
  • COVID-19
  • SARS-CoV-2/genetics
  • Mutation
  • Biological Assay
  • Genomics


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