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

Kidd, S. P.; Burns, D.; Armson, B.; Beggs, A. D.; Howson, E. L. A.; Williams, A. P.; Snell, G.; Wise, E. L.; Goring, A.; Vincent-Mistiaen, Z.; Grippon, S.; Sawyer, J.; Cassar, C.; Cross, D.; Lewis, T.; Reid, S. M.; Rivers, S.; James, J.; Skinner, P.; Davies, K.; Ptasinska, A.; Whalley, C.; Poxen, C.; Bosworth, A.; Kidd, M.; Machin, N.; Richter, A.; Burton, J.; Love, H.; Fouch, S.; Patrick, H.; Moore, N.; Andreou, M.; Laxman, S.; Morant, N.; Clark, D.; Walsh, C.; Houghton, R.; Parker, J.; Slater-Jefferies, J.; Brown, I.; Deans, Z.; Porter, D.; Cortes, N. J.; Godfrey, K. M.; Douglas, A.; Hill, S

Previous studies have described RT-LAMP methodology for the rapid detection of SARS-CoV-2 in nasopharyngeal/oropharyngeal swab and saliva samples. Here we describe the validation of an improved simple sample preparation method for Direct SARS-CoV-2 RT-LAMP, removing the need for RNA extraction, using 559 swabs and 86,760 saliva samples from asymptomatic and symptomatic individuals across multiple healthcare settings. Using this improved method we report 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) 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 loads, 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. We also describe RNA RT-LAMP (on extracted RNA) performed on 12,619 swabs and 12,521 saliva samples to provide updated performance data with DSe and DSp of 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. We also report on daily samples collected from one individual from symptom onset where both Direct and RNA RT-LAMP detected SARS-CoV-2 in saliva collected on all six days where symptoms were recorded, with RNA RT-LAMP detecting SARS-CoV-2 for an additional further day. The findings from these studies demonstrate that RT-LAMP testing of swabs and saliva is potentially applicable to a variety of use-cases, including frequent, interval-based testing of saliva from asymptomatic individuals via Direct RT-LAMP that may be missed using symptomatic testing alone.