Author:
Fraser Alice J.,Greenland-Bews Caitlin,Kelly Daniel,Williams Christopher T.,Bengey Daisy,Buist Kate,Clerkin Karina,Finch Lorna S,Gould Susan,Kontogianni Konstantina,Savage Helen R,Thompson Caitlin R,Wardale Jahanara,Watkins Rachel L,Wooding Dominic,Allen A. Joy,Body Richard,Braybrook Julian,Buckle Peter,Clark Eloïse,Dark Paul,Davis Kerrie,Gordon Adam,Hayward Gail,Halstead Anna,Harden Charlotte,Inkson Colette,Jones Naoko,Jones William,Lasserson Dan,Lee Joseph,Lendrem Clare,Lewington Andrew,Logan Mary,Micocci Massimo,Nicholson Brian,Perera-Salazar Rafael,Prestwich Graham,Price Ashley,Reynard Charles,Riley Beverley,Simpson A. J.,Tate Valerie,Turner Philip,Wilcox Mark,Zhifang Melody,Body Richard,Adams Emily R.,Atienzar Ana Cubas,Edwards Thomas,Allen David J., ,
Abstract
AbstractThe 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.
Funder
Natural Environment Research Council
Department of Health and Social Care
National Institute for Health Research
Publisher
Springer Science and Business Media LLC