Reverse-transcriptase 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

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

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Abstract

Previous studies have described reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) method for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal and oropharyngeal swab and saliva samples. This study describes the validation of an improved sample preparation method for extraction-free RT-LAMP and defines the clinical performance of four different RT-LAMP assay formats for detection of SARS-CoV-2 within a multisite clinical evaluation. 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) of 70.35% (95% CI, 63.48%–76.60%) on swabs and 84.62% (95% CI, 79.50%–88.88%) on saliva was observed, with diagnostic specificity of 100% (95% CI, 98.98%–100.00%) on swabs and 100% (95% CI, 99.72%–100.00%) on saliva when compared with RT-qPCR; analyzing samples with RT-qPCR ORF1ab CT values of ≤25 and ≤33, DSe values of 100% (95% CI, 96.34%–100%) and 77.78% (95% CI, 70.99%–83.62%) for swabs were observed, 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 testing of saliva with direct RT-LAMP from asymptomatic individuals who may otherwise be missed using symptomatic testing alone.
Original languageEnglish
Pages (from-to)320-336
Number of pages17
JournalThe Journal of Molecular Diagnostics
Volume24
Issue number4
Early online date29 Mar 2022
DOIs
Publication statusPublished - 1 Apr 2022

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