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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)

Abstract

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 × 101 and 1 × 102 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.

Original languageEnglish
Pages (from-to)117-125
Number of pages9
JournalJournal of Infection
Volume82
Issue number1
DOIs
Publication statusPublished - Jan 2021
Externally publishedYes

Bibliographical note

Funding Information:
We would like to thank the clinical teams and Helen Denman the Microbiology laboratory manager at Hampshire Hospitals NHS Foundation Trust. No ethical approval was required for this service evaluation study. Initial reagents were supplied free of charge by Optigene Ltd. (Horsham, UK), the remainder of the service evaluation was self-funded by Hampshire Hospitals NHS Foundation Trust. Optigene Ltd. representatives played no part in study design or data analysis.

Publisher Copyright:
© 2020

Keywords

  • COVID-19
  • Direct RNA detection
  • Near patient testing
  • Rapid diagnostics
  • RT-LAMP
  • SARS-CoV-2

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