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RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals

RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals
RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals
Objectives: To validate an improved sample preparation method for extraction free Direct RT-LAMP and define the clinical performance of four different RT-LAMP assay formats for detection of SARS-CoV-2 with a multisite clinical evaluation.

Method: We describe Direct RT-LAMP on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples collected from asymptomatic and symptomatic individuals across multiple healthcare and community settings.

Results: For Direct RT-LAMP, we found a diagnostic sensitivity (DSe) of 70.35% (95% CI 63.48-76.60%) on swabs and 84.62% (79.50-88.88%) on saliva, with diagnostic specificity (DSp) of 100% (98.98-100.00%) on swabs and 100% (99.72-100.00%) on saliva when compared to RT-qPCR. Analysing samples with RT-qPCR ORF1ab CT values of≤25 and ≤33 (high and medium-high viral copy number, respectively), we found DSe of 100% (96.34-100%) and 77.78% (70.99-83.62%) for swabs, and 99.01% (94.61-99.97%) and 87.32% (80.71-92.31%) for saliva. For RNA RT-LAMP DSe and DSp were 95.98% (92.74-98.06%) and 99.99% (99.95-100%) for swabs, and 80.65% (73.54-86.54%) and 99.99% (99.95-100%) for saliva, respectively.

Conclusions: The findings from these evaluations demonstrate that RT-LAMP testing of swabs and saliva is applicable to a variety of different use-cases, including frequent, interval-based testing of saliva from asymptomatic individuals via Direct RT-LAMP that may otherwise be missed using symptomatic testing alone.
Kidd, Stephen
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Douglas, Angela
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Hill, Sue
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Fowler, Veronica L.
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Kidd, Stephen, Burns, Daniel, Armson, Bryony, Beggs, Andrew D., Howson, Emma L. A., Williams, Anthony, Snell, Gemma, Wise, Emma L., Goring, Alice, Vincent-Mistiaen, Zoé, Grippon, Seden, Sawyer, Jason, Cassar, Claire, Cross, David, Lewis, Tom, Reid, Scott, Rivers, Samantha, James, Joe, Skinner, Paul, Banyard, Ashley, Davies, Kerrie, Ptasinska, Anetta, Whalley, Celina M., Poxon, Charlie, Bosworth, Andrew, Kidd, I. Michael, Richter, Alex G., Burton, Jane, Love, Hannah, Fouch, Sarah, Tillyer, Claire, Sowood, Amy, Patrick, Helen, Moore, Nathan, Andreou, Michael, Laxman, Shailen, Morant, Nick, Clark, Duncan, Walsh, Charlotte, Houghton, Rebecca, Parker, Joel D, Slater-Jefferies, Joanne, Brown, Ian, Deans, Zandra, Porter, Deborah, Cortes, Nicholas J., Godfrey, Keith, Douglas, Angela, Hill, Sue and Fowler, Veronica L. (2021) RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals. (doi:10.1101/2021.06.28.21259398).

Record type: Other

Abstract

Objectives: To validate an improved sample preparation method for extraction free Direct RT-LAMP and define the clinical performance of four different RT-LAMP assay formats for detection of SARS-CoV-2 with a multisite clinical evaluation.

Method: We describe Direct RT-LAMP on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples collected from asymptomatic and symptomatic individuals across multiple healthcare and community settings.

Results: For Direct RT-LAMP, we found a diagnostic sensitivity (DSe) of 70.35% (95% CI 63.48-76.60%) on swabs and 84.62% (79.50-88.88%) on saliva, with diagnostic specificity (DSp) of 100% (98.98-100.00%) on swabs and 100% (99.72-100.00%) on saliva when compared to RT-qPCR. Analysing samples with RT-qPCR ORF1ab CT values of≤25 and ≤33 (high and medium-high viral copy number, respectively), we found DSe of 100% (96.34-100%) and 77.78% (70.99-83.62%) for swabs, and 99.01% (94.61-99.97%) and 87.32% (80.71-92.31%) for saliva. For RNA RT-LAMP DSe and DSp were 95.98% (92.74-98.06%) and 99.99% (99.95-100%) for swabs, and 80.65% (73.54-86.54%) and 99.99% (99.95-100%) for saliva, respectively.

Conclusions: The findings from these evaluations demonstrate that RT-LAMP testing of swabs and saliva is applicable to a variety of different use-cases, including frequent, interval-based testing of saliva from asymptomatic individuals via Direct RT-LAMP that may otherwise be missed using symptomatic testing alone.

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More information

Published date: 6 July 2021

Identifiers

Local EPrints ID: 450566
URI: http://eprints.soton.ac.uk/id/eprint/450566
PURE UUID: 991256b1-bb21-49a3-aec2-9d21105ac69e
ORCID for Daniel Burns: ORCID iD orcid.org/0000-0001-6976-1068
ORCID for Joanne Slater-Jefferies: ORCID iD orcid.org/0000-0001-8325-1320
ORCID for Keith Godfrey: ORCID iD orcid.org/0000-0002-4643-0618

Catalogue record

Date deposited: 04 Aug 2021 16:31
Last modified: 05 Aug 2021 01:49

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Contributors

Author: Stephen Kidd
Author: Daniel Burns ORCID iD
Author: Bryony Armson
Author: Andrew D. Beggs
Author: Emma L. A. Howson
Author: Gemma Snell
Author: Emma L. Wise
Author: Alice Goring
Author: Zoé Vincent-Mistiaen
Author: Seden Grippon
Author: Jason Sawyer
Author: Claire Cassar
Author: David Cross
Author: Tom Lewis
Author: Scott Reid
Author: Samantha Rivers
Author: Joe James
Author: Paul Skinner
Author: Ashley Banyard
Author: Kerrie Davies
Author: Anetta Ptasinska
Author: Celina M. Whalley
Author: Charlie Poxon
Author: Andrew Bosworth
Author: I. Michael Kidd
Author: Alex G. 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: Shailen Laxman
Author: Nick Morant
Author: Duncan Clark
Author: Charlotte Walsh
Author: Rebecca Houghton
Author: Joel D Parker
Author: Ian Brown
Author: Zandra Deans
Author: Deborah Porter
Author: Nicholas J. Cortes
Author: Keith Godfrey ORCID iD
Author: Angela Douglas
Author: Sue Hill
Author: Veronica L. Fowler

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