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

Alice Fraser; Caitlin Greenland-Bews; Daniel Kelly; Chris Williams; Daisy Bengey; Kate Buist; Karina Clerkin; Lorna Finch; Susie Gould; Nadia Kontogianni; Helen Savage; Caitlin Thompson; Jahanara Wardale; Rachel Watkins; Dom Wooding; A. Joy Allen; Richard Body; Julian Braybrook; Peter Buckle; Eloïse Clark; Paul Dark; Kerrie Davis; Adam Gordon; Gail Hayward; Anna Halstead; Charlotte Harden; Colette Inkson; Naoko Jones; William Jones; Dan Lasserson; Joseph Lee; Clare Lendrem; Andrew Lewington; Mary Logan; Massimo Micocci; Brian Nicholson; Rafael Perera-Salazar; Graham Prestwich; Ashley Price; Charles Reynard; Beverley Riley; A. J. Simpson; Valerie Tate; Philip Turner; Mark Wilcox; Melody Zhifang; Emily Adams; Ana Cubas Atienzar; Thomas Edwards; David J. Allen

doi:10.1038/s41598-023-30754-1

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

Alice Fraser, Caitlin Greenland-Bews, Daniel Kelly, Chris Williams, Daisy Bengey, Kate Buist, Karina Clerkin, Lorna Finch, Susie Gould, Nadia Kontogianni, Helen Savage, Caitlin Thompson, Jahanara Wardale, Rachel Watkins, Dom Wooding, A. Joy Allen, Richard Body, Julian Braybrook, Peter Buckle, Eloïse ClarkPaul Dark, Kerrie Davis, Adam Gordon, Gail Hayward, Anna Halstead, Charlotte Harden, Colette Inkson, Naoko Jones, William Jones, Dan Lasserson, Joseph Lee, Clare Lendrem, Andrew Lewington, Mary Logan, Massimo Micocci, Brian Nicholson, Rafael Perera-Salazar, Graham Prestwich, Ashley Price, Charles Reynard, Beverley Riley, A. J. Simpson, Valerie Tate, Philip Turner, Mark Wilcox, Melody Zhifang, Emily Adams, Ana Cubas Atienzar, Thomas Edwards, David J. Allen

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

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 language	English
Article number	3887
Pages (from-to)	e3887
Journal	Scientific Reports
Volume	13
Issue number	1
Early online date	8 Mar 2023
DOIs	https://doi.org/10.1038/s41598-023-30754-1
Publication status	Published - 8 Mar 2023

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41598 2023 Article 30754Final published version, 1.63 MBLicence: CC BY

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Fraser, A., Greenland-Bews, C., Kelly, D., Williams, C., Bengey, D., Buist, K., Clerkin, K., Finch, L., Gould, S., Kontogianni, N., Savage, H., Thompson, C., Wardale, J., Watkins, R., Wooding, D., Allen, A. J., Body, R., Braybrook, J., Buckle, P., ... Allen, D. J. (2023). A high-resolution melt curve toolkit to identify lineage-defining SARS-CoV-2 mutations. Scientific Reports, 13(1), e3887. Article 3887. https://doi.org/10.1038/s41598-023-30754-1

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title = "A high-resolution melt curve toolkit to identify lineage-defining SARS-CoV-2 mutations",

abstract = "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.",

author = "Alice Fraser and Caitlin Greenland-Bews and Daniel Kelly and Chris Williams and Daisy Bengey and Kate Buist and Karina Clerkin and Lorna Finch and Susie Gould and Nadia Kontogianni and Helen Savage and Caitlin Thompson and Jahanara Wardale and Rachel Watkins and Dom Wooding and Allen, \{A. Joy\} and Richard Body and Julian Braybrook and Peter Buckle and Elo{\"i}se Clark and Paul Dark and Kerrie Davis and Adam Gordon and Gail Hayward and Anna Halstead and Charlotte Harden and Colette Inkson and Naoko Jones and William Jones and Dan Lasserson and Joseph Lee and Clare Lendrem and Andrew Lewington and Mary Logan and Massimo Micocci and Brian Nicholson and Rafael Perera-Salazar and Graham Prestwich and Ashley Price and Charles Reynard and Beverley Riley and Simpson, \{A. J.\} and Valerie Tate and Philip Turner and Mark Wilcox and Melody Zhifang and Emily Adams and \{Cubas Atienzar\}, Ana and Thomas Edwards and Allen, \{David J.\}",

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doi = "10.1038/s41598-023-30754-1",

language = "English",

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journal = "Scientific Reports",

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Fraser, A , Greenland-Bews, C, Kelly, D, Williams, C, Bengey, D, Buist, K, Clerkin, K, Finch, L, Gould, S , Kontogianni, N, Savage, H, Thompson, C, Wardale, J, Watkins, R, Wooding, D, Allen, AJ, Body, R, Braybrook, J, Buckle, P, Clark, E, Dark, P, Davis, K, Gordon, A, Hayward, G, Halstead, A, Harden, C, Inkson, C, Jones, N, Jones, W, Lasserson, D, Lee, J, Lendrem, C, Lewington, A, Logan, M, Micocci, M, Nicholson, B, Perera-Salazar, R, Prestwich, G, Price, A, Reynard, C, Riley, B, Simpson, AJ, Tate, V, Turner, P, Wilcox, M, Zhifang, M, Adams, E, Cubas Atienzar, A , Edwards, T & Allen, DJ 2023, 'A high-resolution melt curve toolkit to identify lineage-defining SARS-CoV-2 mutations', Scientific Reports, vol. 13, no. 1, 3887, pp. e3887. https://doi.org/10.1038/s41598-023-30754-1

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T1 - A high-resolution melt curve toolkit to identify lineage-defining SARS-CoV-2 mutations

AU - Fraser, Alice

AU - Greenland-Bews, Caitlin

AU - Kelly, Daniel

AU - Williams, Chris

AU - Bengey, Daisy

AU - Buist, Kate

AU - Clerkin, Karina

AU - Finch, Lorna

AU - Gould, Susie

AU - Kontogianni, Nadia

AU - Savage, Helen

AU - Thompson, Caitlin

AU - Wardale, Jahanara

AU - Watkins, Rachel

AU - Wooding, Dom

AU - Allen, A. Joy

AU - Body, Richard

AU - Braybrook, Julian

AU - Buckle, Peter

AU - Clark, Eloïse

AU - Dark, Paul

AU - Davis, Kerrie

AU - Gordon, Adam

AU - Hayward, Gail

AU - Halstead, Anna

AU - Harden, Charlotte

AU - Inkson, Colette

AU - Jones, Naoko

AU - Jones, William

AU - Lasserson, Dan

AU - Lee, Joseph

AU - Lendrem, Clare

AU - Lewington, Andrew

AU - Logan, Mary

AU - Micocci, Massimo

AU - Nicholson, Brian

AU - Perera-Salazar, Rafael

AU - Prestwich, Graham

AU - Price, Ashley

AU - Reynard, Charles

AU - Riley, Beverley

AU - Simpson, A. J.

AU - Tate, Valerie

AU - Turner, Philip

AU - Wilcox, Mark

AU - Zhifang, Melody

AU - Adams, Emily

AU - Cubas Atienzar, Ana

AU - Edwards, Thomas

AU - Allen, David J.

PY - 2023/3/8

Y1 - 2023/3/8

N2 - 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.

AB - 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.

U2 - 10.1038/s41598-023-30754-1

DO - 10.1038/s41598-023-30754-1

M3 - Article

SN - 2045-2322

VL - 13

SP - e3887

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 3887

ER -

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

Abstract

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