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Reverse-transcription loop-mediated isothermal amplification has high accuracy for detecting severe acute respiratory syndrome coronavirus 2 in saliva and nasopharyngeal/oropharyngeal swabs from asymptomatic and symptomatic individuals

Reverse-transcription loop-mediated isothermal amplification has high accuracy for detecting severe acute respiratory syndrome coronavirus 2 in saliva and nasopharyngeal/oropharyngeal swabs from asymptomatic and symptomatic individuals
Reverse-transcription loop-mediated isothermal amplification has high accuracy for detecting severe acute respiratory syndrome coronavirus 2 in saliva and nasopharyngeal/oropharyngeal swabs from asymptomatic and symptomatic individuals
Previous studies have described reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal/oropharyngeal swab and saliva samples. This multisite clinical evaluation describes the validation of an improved sample preparation method for extraction-free RT-LAMP and reports clinical performance of four RT-LAMP assay formats for SARS-CoV-2 detection. Direct RT-LAMP was performed on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples from asymptomatic and symptomatic individuals across health care and community settings. For direct RT-LAMP, overall diagnostic sensitivity (DSe) was 70.35% (95% CI, 63.48%-76.60%) on swabs and 84.62% (95% CI, 79.50%-88.88%) on saliva, with diagnostic specificity of 100% (95% CI, 98.98%-100.00%) on swabs and 100% (95% CI, 99.72%-100.00%) on saliva, compared with quantitative RT-PCR (RT-qPCR); analyzing samples with RT-qPCR ORF1ab C T values of ≤25 and ≤33, DSe values were 100% (95% CI, 96.34%-100%) and 77.78% (95% CI, 70.99%-83.62%) for swabs, and 99.01% (95% CI, 94.61%-99.97%) and 87.61% (95% CI, 82.69%-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and diagnostic specificity were 96.06% (95% CI, 92.88%-98.12%) and 99.99% (95% CI, 99.95%-100%) for swabs, and 80.65% (95% CI, 73.54%-86.54%) and 99.99% (95% CI, 99.95%-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use cases, including frequent, interval-based direct RT-LAMP of saliva from asymptomatic individuals who may otherwise be missed using symptomatic testing alone.
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Kidd, Stephen P., Burns, Daniel, Armson, Bryony, Beggs, Andrew D., Howson, Emma L.A., Williams, Anthony, Snell, Gemma, Wise, Emma L., Goring, Alice, Vincent-Mistiaen, Zoe, Grippon, Seden, Sawyer, Jason, Cassar, Claire, Cross, David, Lewis, Thomas, Reid, Scott M, Rivers, Samantha, James, Joe, Skinner, Paul, Banyard, Ashley, Davies, Kerrie, Ptasinska, Anetta, Whalley, Celina, Ferguson, Jack, Bryer, Claire, Poxon, Charlie, Bosworth, Andrew, Kidd, Michael, Richter, Alex, Burton, Jane, Love, Hannah, Fouch, Sarah, Tillyer, Claire, Sowood, Amy, Patrick, Helen, Moore, Nathan, Andreou, Michael, Morant, Nick, Houghton, Rebecca, Parker, Joe, Slater-Jefferies, Joanne, Brown, Ian, Gretton, Cosima, Deans, Zandra, Porter, Deborah, Cortes, Nicholas J., Douglas, Angela, Hill, Sue L., Godfrey, Keith M. and Fowler, Veronica L. (2022) Reverse-transcription loop-mediated isothermal amplification has high accuracy for detecting severe acute respiratory syndrome coronavirus 2 in saliva and nasopharyngeal/oropharyngeal swabs from asymptomatic and symptomatic individuals. Journal of Molecular Diagnostics, 24 (4), 320-336. (doi:10.1016/j.jmoldx.2021.12.007).

Record type: Article

Abstract

Previous studies have described reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal/oropharyngeal swab and saliva samples. This multisite clinical evaluation describes the validation of an improved sample preparation method for extraction-free RT-LAMP and reports clinical performance of four RT-LAMP assay formats for SARS-CoV-2 detection. Direct RT-LAMP was performed on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples from asymptomatic and symptomatic individuals across health care and community settings. For direct RT-LAMP, overall diagnostic sensitivity (DSe) was 70.35% (95% CI, 63.48%-76.60%) on swabs and 84.62% (95% CI, 79.50%-88.88%) on saliva, with diagnostic specificity of 100% (95% CI, 98.98%-100.00%) on swabs and 100% (95% CI, 99.72%-100.00%) on saliva, compared with quantitative RT-PCR (RT-qPCR); analyzing samples with RT-qPCR ORF1ab C T values of ≤25 and ≤33, DSe values were 100% (95% CI, 96.34%-100%) and 77.78% (95% CI, 70.99%-83.62%) for swabs, and 99.01% (95% CI, 94.61%-99.97%) and 87.61% (95% CI, 82.69%-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and diagnostic specificity were 96.06% (95% CI, 92.88%-98.12%) and 99.99% (95% CI, 99.95%-100%) for swabs, and 80.65% (95% CI, 73.54%-86.54%) and 99.99% (95% CI, 99.95%-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use cases, including frequent, interval-based direct RT-LAMP of saliva from asymptomatic individuals who may otherwise be missed using symptomatic testing alone.

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Accepted/In Press date: 28 December 2021
e-pub ahead of print date: 2 February 2022
Published date: April 2022
Additional Information: Funding Information: OptiGene Ltd. supplied reagents free of charge for this study. Supported in part by a UK Department of Health and Social Care award to the University of Southampton grant reference number 2020/032 (feasibility study for city-wide testing using saliva 315 based LAMP testing). The views expressed are those of the authors and not necessarily those of the Department of Health and Social Care. K.M.G. is supported by the UK Medical Research Council MC_UU_12011/4, the National Institute for Health Research (NIHR) Senior Investigator NF-SI-0515-318 10042 and NIHR Southampton Biomedical Research Center IS-BRC-1215-20004, and the British Heart Foundation RG/15/17/3174. For part of this project, E.L.A.H. was on secondment at GeneSys Biotech Ltd, which was part supported by The Pirbright Institute Flexible Talent Mobility Account under Biotechnology and Biological Sciences Research Council grant BB/S507945/1. A.D.B. is currently supported by a Cancer Research UK Advanced Clinician Scientist award C31641/A23923, and his laboratory is supported by CRUK Center Birmingham C17422/A25154 and the Birmingham Experimental Cancer Medicine Center C11497/A25127. V.L.F., S.P.K., B.A., and Z.D. were on secondment to the Department of Health and Social Care for a period during this study. Animal and Plant Health Agency laboratory activities and expertise were supported by both the Safe and Certain project APHACSKL0085 and Defra project APHANSOM0416.Disclosures: M.A. is an employee of OptiSense Limited, and N.M. is an employee of GeneSys Biotech Limited; neither had any role in study design or data analysis. K.M.G. is part of an academic consortium that has received research funding from Abbott Nutrition, Nestec, BenevolentAI Bio Ltd, and Danone. Funding Information: OptiGene Ltd. supplied reagents free of charge for this study. Supported in part by a UK Department of Health and Social Care award to the University of Southampton grant reference number 2020/032 (feasibility study for city-wide testing using saliva 315 based LAMP testing). The views expressed are those of the authors and not necessarily those of the Department of Health and Social Care. K.M.G. is supported by the UK Medical Research Council MC_UU_12011/4 , the National Institute for Health Research (NIHR) Senior Investigator NF-SI-0515-318 10042 and NIHR Southampton Biomedical Research Center IS-BRC-1215-20004 , and the British Heart Foundation RG/15/17/3174 . For part of this project, E.L.A.H. was on secondment at GeneSys Biotech Ltd, which was part supported by The Pirbright Institute Flexible Talent Mobility Account under Biotechnology and Biological Sciences Research Council grant BB/S507945/1. A.D.B. is currently supported by a Cancer Research UK Advanced Clinician Scientist award C31641/A23923 , and his laboratory is supported by CRUK Center Birmingham C17422/A25154 and the Birmingham Experimental Cancer Medicine Center C11497/A25127 . V.L.F., S.P.K., B.A., and Z.D. were on secondment to the Department of Health and Social Care for a period during this study. Animal and Plant Health Agency laboratory activities and expertise were supported by both the Safe and Certain project APHACSKL0085 and Defra project APHANSOM0416 . .
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Identifiers

Local EPrints ID: 455878
URI: http://eprints.soton.ac.uk/id/eprint/455878
DOI: doi:10.1016/j.jmoldx.2021.12.007
ISSN: 1525-1578
PURE UUID: d47bfde0-04b2-41bf-8304-53062e63c387
ORCID for Daniel Burns: ORCID iD orcid.org/0000-0001-6976-1068
ORCID for Joe Parker: ORCID iD orcid.org/0000-0003-3777-2269
ORCID for Joanne Slater-Jefferies: ORCID iD orcid.org/0000-0001-8325-1320
ORCID for Keith M. Godfrey: ORCID iD orcid.org/0000-0002-4643-0618

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Date deposited: 07 Apr 2022 16:41
Last modified: 17 Mar 2024 03:54

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Contributors

Author: Stephen P. Kidd
Author: Daniel Burns ORCID iD
Author: Bryony Armson
Author: Andrew D. Beggs
Author: Emma L.A. Howson
Author: Anthony Williams
Author: Gemma Snell
Author: Emma L. Wise
Author: Alice Goring
Author: Zoe Vincent-Mistiaen
Author: Seden Grippon
Author: Jason Sawyer
Author: Claire Cassar
Author: David Cross
Author: Thomas Lewis
Author: Scott M Reid
Author: Samantha Rivers
Author: Joe James
Author: Paul Skinner
Author: Ashley Banyard
Author: Kerrie Davies
Author: Anetta Ptasinska
Author: Celina Whalley
Author: Jack Ferguson
Author: Claire Bryer
Author: Charlie Poxon
Author: Andrew Bosworth
Author: Michael Kidd
Author: Alex Richter
Author: Jane Burton
Author: Hannah Love
Author: Sarah Fouch
Author: Claire Tillyer
Author: Amy Sowood
Author: Helen Patrick
Author: Nathan Moore
Author: Michael Andreou
Author: Nick Morant
Author: Rebecca Houghton
Author: Joe Parker ORCID iD
Author: Joanne Slater-Jefferies ORCID iD
Author: Ian Brown
Author: Cosima Gretton
Author: Zandra Deans
Author: Deborah Porter
Author: Nicholas J. Cortes
Author: Angela Douglas
Author: Sue L. Hill
Author: Keith M. Godfrey ORCID iD
Author: Veronica L. Fowler

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