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

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).

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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Contributors

Author: Daniel Burns

Author: Joel D Parker

Author: Joanne Slater-Jefferies

Author: Keith Godfrey

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