A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection

Fowler, Veronica L.; Armson, Bryony; Gonzales, Jose L.; Wise, Emma L.; Howson, Emma L.A.; Vincent-Mistiaen, Zoe; Fouch, Sarah; Maltby, Connor J.; Grippon, Seden; Munro, Simon; Jones, Lisa; Holmes, Tom; Tillyer, Claire; Elwell, Joanne; Sowood, Amy; de Peyer, Oliver; Dixon, Sophie; Hatcher, Thomas; Patrick, Helen; Laxman, Shailen; Walsh, Charlotte; Andreou, Michael; Morant, Nick; Clark, Duncan; Moore, Nathan; Houghton, Rebecca; Cortes, Nicholas; Kidd, Stephen P.

The COVID-19 pandemic has illustrated the importance of simple, rapid and accurate diagnostic testing. This study describes the validation of a new rapid SARS-CoV-2 RT-LAMP assay for use on extracted RNA or directly from swab offering an alternative diagnostic pathway that does not rely on traditional reagents that are often in short supply during a pandemic. Analytical specificity (ASp) of this new RT-LAMP assay was 100% and analytical sensitivity (ASe) was between 1 × 10(1) and 1 × 10(2) copies per reaction when using a synthetic DNA target. The overall diagnostic sensitivity (DSe) and specificity (DSp) of RNA RT-LAMP was 97% and 99% respectively, relative to the standard of care rRT-PCR. When a C(T) cut-off of 33 was employed, above which increasingly evidence suggests there is a low risk of patients shedding infectious virus, the diagnostic sensitivity was 100%. The DSe and DSp of Direct RT-LAMP (that does not require RNA extraction) was 67% and 97%, respectively. When setting C(T) cut-offs of ≤33 and ≤25, the DSe increased to 75% and 100%, respectively, time from swab-to-result, C(T) < 25, was < 15 minutes. We propose that RNA RT-LAMP could replace rRT-PCR where there is a need for increased sample throughput and Direct RT-LAMP as a near-patient screening tool to rapidly identify highly contagious individuals within emergency departments and a care homes during times of increased disease prevalence ensuring negative results still get laboratory confirmation.