1. RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals
- Author
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Bryony Armson, Andrew D Beggs, Sarah Fouch, Seden Grippon, Nathan Moore, Whalley C, Morant N, Poxon C, Ferguson J, Kidd M, Kerrie Davies, Tom Lewis, Zandra Deans, Ptasinska A, Hannah Love, Bryer C, Walsh C, Zoe Vincent-Mistiaen, Burton J, Emma L. Wise, Alice Goring, Claire Cassar, Rebecca Houghton, Joe Parker, David Cross, Jason Sawyer, Joe James, Samantha Rivers, Amy Sowood, Nicholas Cortes, Howson Ela, Reid Sm, Andreou M, Sue Hill, Stephen P. Kidd, Ian H. Brown, Gemma Snell, Patrick H, Keith M. Godfrey, Veronica L. Fowler, Daniel Burns, Joanne L. Slater-Jefferies, Ashley C. Banyard, Claire Tillyer, Richter Ag, Skinner P, Angela Douglas, Williams A, Andrew Bosworth, Laxman S, Clark D, and Deborah Porter
- Subjects
medicine.medical_specialty ,2019-20 coronavirus outbreak ,Saliva ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Clinical performance ,Diagnostic Specificity ,Asymptomatic ,Gastroenterology ,stomatognathic system ,Internal medicine ,medicine ,Community setting ,medicine.symptom ,business ,Clinical evaluation - Abstract
Previous studies have described RT-LAMP methodology for the rapid detection of SARS-CoV-2 in nasopharyngeal (NP) and oropharyngeal (OP) 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 from asymptomatic and symptomatic individuals across healthcare 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% (79.50-88.88%) on saliva was observed, 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, DSe of 100% (96.34-100%) and 77.78% (70.99-83.62%) for swabs were observed, and 99.01% (94.61-99.97%) and 87.61% (82.69-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and DSp were 96.06% (92.88-98.12%) and 99.99% (99.95-100%) for swabs, and 80.65% (73.54-86.54%) and 99.99% (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 that may otherwise be missed using symptomatic testing alone.
- Published
- 2021