TY - JOUR
T1 - 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
AU - Kidd, Stephen P.
AU - Burns, Daniel
AU - Armson, Bryony
AU - Beggs, Andrew D.
AU - Howson, Emma L.A.
AU - Williams, Anthony
AU - Snell, Gemma
AU - Wise, Emma L.
AU - Goring, Alice
AU - Vincent-Mistiaen, Zoe
AU - Grippon, Seden
AU - Sawyer, Jason
AU - Cassar, Claire
AU - Cross, David
AU - Lewis, Thomas
AU - Reid, Scott M.
AU - Rivers, Samantha
AU - James, Joe
AU - Skinner, Paul
AU - Banyard, Ashley
AU - Davies, Kerrie
AU - Ptasinska, Anetta
AU - Whalley, Celina
AU - Ferguson, Jack
AU - Bryer, Claire
AU - Poxon, Charlie
AU - Bosworth, Andrew
AU - Kidd, Michael
AU - Richter, Alex
AU - Burton, Jane
AU - Love, Hannah
AU - Fouch, Sarah
AU - Tillyer, Claire
AU - Sowood, Amy
AU - Patrick, Helen
AU - Moore, Nathan
AU - Andreou, Michael
AU - Morant, Nick
AU - Houghton, Rebecca
AU - Parker, Joe
AU - Slater-Jefferies, Joanne
AU - Brown, Ian
AU - Gretton, Cosima
AU - Deans, Zandra
AU - Porter, Deborah
AU - Cortes, Nicholas J.
AU - Douglas, Angela
AU - Hill, Sue L.
AU - Godfrey, Keith M.
AU - Fowler, Veronica L.
PY - 2022/4/1
Y1 - 2022/4/1
N2 - 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.
AB - 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.
UR - https://www.sciencedirect.com/science/article/pii/S1525157822000150?via%3Dihub
U2 - 10.1016/j.jmoldx.2021.12.007
DO - 10.1016/j.jmoldx.2021.12.007
M3 - Article
SN - 1525-1578
VL - 24
SP - 320
EP - 336
JO - The Journal of Molecular Diagnostics
JF - The Journal of Molecular Diagnostics
IS - 4
ER -