A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection. Issue 1 (January 2021)

• Record Type: Journal Article
• Authors: 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 J.; Kidd, Stephen P.
• Is Part Of: Journal of infection. Volume 82:Issue 1(2021)
• Page Start: 117
• Page End: 125
• Publication Date: 2021-01
• Subjects: SARS-CoV-2 -- COVID-19 -- RT-LAMP -- Rapid diagnostics -- Near patient testing -- Direct RNA detection; Infection -- Periodicals; Bacterial Infections -- Periodicals; Communicable Diseases -- Periodicals; Electronic journals; 616.905
• DOI: 10.1016/j.jinf.2020.10.039
• Languages: English
• ISSNs: 0163-4453

Abstract

Highlights: Novel rapid RT-LAMP assay with diagnostic sensitivity and specificity of 97% and 99%. Development of an RNA extraction free direct detection method for SARS-CoV-2. Use case modelling for rapid direct RT-LAMP in near-patient clinical practice. Developing diversity of testing modalities within a diagnostic laboratory during a pandemic. Summary: 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 CT 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 CT cut-offs of ≤33 and ≤25, the DSe increased to 75% and 100%, respectively, time from swab-to-result, CT < 25, was < 15 min. 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 care homes during times of increased disease prevalence ensuring negative results still get laboratory confirmation.