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

doi:10.1038/s41598-023-30754-1

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 journal › Article › peer-review

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
Journal	Scientific Reports
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41598-023-30754-1
Publication status	Published - 8 Mar 2023

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/s41598-023-30754-1Licence: CC BY

Cite this

Fraser, A. J., Greenland-Bews, C., Kelly, D., Williams, C. T., CONDOR Steering Group, LSTM Diagnostics Group, Body, R., Adams, E. R., Cubas Atienzar, A., Edwards, T., Allen, D. J., & Dark, P. (2023). A high-resolution melt curve toolkit to identify lineage-defining SARS-CoV-2 mutations. Scientific Reports, 13(1), Article 3887. https://doi.org/10.1038/s41598-023-30754-1

@article{cb2a3e5be4574982825a92489ca3016e,

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.",

keywords = "Humans, COVID-19, SARS-CoV-2/genetics, Mutation, Biological Assay, Genomics",

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

note = "Funding Information: This work was partially funded by UK Aid from the Department of Health and Social Care (https://www.gov.uk/government/collections/official-development-assistance-oda--2) via the UK Public Health Rapid Support Team Research Programme (Grant No. RST6_00_03, EPIDZK3828). The funder had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.This work was supported by the National Environment Research Council [grant number NE/V010441/1].We acknowledge the support of the National Institute for Health Research (NIHR) Clinical Research Network, which supports delivery of the FALCON study. The views expressed in this article are those of the authors and not necessarily those of the NIHR, or the Department of Health and Social Care. ERA acknowledges support from the Wellcome Trust and the NIHR HPRU EZI. The CONDOR study team comprises partners from Manchester University NHS Foundation Trust{\textquoteright}s Diagnostic and Technology Accelerator (DiTA), AHSN North East and North Cumbria (NENC), UK National Measurement Laboratory, University of Manchester, University of Nottingham, University of Oxford, Yorkshire and Humber AHSN, and NIHR MedTech and In Vitro Diagnostics Co-operatives (MICs) based in Oxford, Leeds, London and Newcastle. For CONDOR steering group, contact Prof Richard Body ([email protected]). For LSTM diagnostics group, contact Dr Helen Savage ([email protected]). Publisher Copyright: {\textcopyright} 2023, The Author(s).",

year = "2023",

month = mar,

day = "8",

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

language = "English",

volume = "13",

journal = "Scientific Reports",

issn = "2045-2322",

publisher = "Springer Nature",

number = "1",

}

TY - JOUR

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

AU - Fraser, Alice J.

AU - Greenland-Bews, Caitlin

AU - Kelly, Daniel

AU - Williams, Christopher T.

AU - CONDOR Steering Group

AU - LSTM Diagnostics Group

AU - Body, Rick

AU - Adams, Emily R.

AU - Cubas Atienzar, Ana

AU - Edwards, Thomas

AU - Allen, David J.

AU - Dark, Paul

N1 - Funding Information: This work was partially funded by UK Aid from the Department of Health and Social Care (https://www.gov.uk/government/collections/official-development-assistance-oda--2) via the UK Public Health Rapid Support Team Research Programme (Grant No. RST6_00_03, EPIDZK3828). The funder had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.This work was supported by the National Environment Research Council [grant number NE/V010441/1].We acknowledge the support of the National Institute for Health Research (NIHR) Clinical Research Network, which supports delivery of the FALCON study. The views expressed in this article are those of the authors and not necessarily those of the NIHR, or the Department of Health and Social Care. ERA acknowledges support from the Wellcome Trust and the NIHR HPRU EZI. The CONDOR study team comprises partners from Manchester University NHS Foundation Trust’s Diagnostic and Technology Accelerator (DiTA), AHSN North East and North Cumbria (NENC), UK National Measurement Laboratory, University of Manchester, University of Nottingham, University of Oxford, Yorkshire and Humber AHSN, and NIHR MedTech and In Vitro Diagnostics Co-operatives (MICs) based in Oxford, Leeds, London and Newcastle. For CONDOR steering group, contact Prof Richard Body ([email protected]). For LSTM diagnostics group, contact Dr Helen Savage ([email protected]). Publisher Copyright: © 2023, The Author(s).

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.

KW - Humans

KW - COVID-19

KW - SARS-CoV-2/genetics

KW - Mutation

KW - Biological Assay

KW - Genomics

UR - http://www.scopus.com/inward/record.url?scp=85150228906&partnerID=8YFLogxK

U2 - 10.1038/s41598-023-30754-1

DO - 10.1038/s41598-023-30754-1

M3 - Article

C2 - 36890186

AN - SCOPUS:85150228906

SN - 2045-2322

VL - 13

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

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this