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 Laxman; Charlotte Walsh; Michael Andreou; Nick Morant; Duncan Clark; Nathan Moore; Rebecca Houghton; Nicholas Cortes; Stephen P. Kidd

doi:10.1016/j.jinf.2020.10.039

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 Cortes, Stephen P. Kidd

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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 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.

Original language	English
Journal	Journal of Infection
Early online date	30 Nov 2020
DOIs	https://doi.org/10.1016/j.jinf.2020.10.039
Publication status	Early online - 30 Nov 2020

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10.1016/j.jinf.2020.10.039

A highly effective reverse-transcription Post-printAccepted author manuscript (Post-print), 446 KBLicence: CC BY-NC-ND

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Fowler, V. L., Armson, B., Gonzales, J. L., Wise, E. L., Howson, E. L. A., Vincent-Mistiaen, Z., Fouch, S., Maltby, C. J., Grippon, S., Munro, S., Jones, L., Holmes, T., Tillyer, C., Elwell, J., Sowood, A., De Peyer, O., Dixon, S., Hatcher, T., Patrick, H., ... Kidd, S. P. (2020). A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection. Journal of Infection. Advance online publication. https://doi.org/10.1016/j.jinf.2020.10.039

@article{f110e42a076e4a099cc25d9a3e21026c,

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

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 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.",

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

year = "2020",

month = nov,

day = "30",

doi = "10.1016/j.jinf.2020.10.039",

language = "English",

journal = "Journal of Infection",

issn = "0163-4453",

publisher = "Elsevier",

}

Fowler, VL, Armson, B, Gonzales, JL, Wise, EL, Howson, ELA, Vincent-Mistiaen, Z, Fouch, S, Maltby, CJ, Grippon, S, Munro, S, Jones, L, Holmes, T, Tillyer, C, Elwell, J, Sowood, A, De Peyer, O, Dixon, S, Hatcher, T, Patrick, H, Laxman, S, Walsh, C, Andreou, M, Morant, N, Clark, D, Moore, N, Houghton, R, Cortes, N & Kidd, SP 2020, 'A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection', Journal of Infection. https://doi.org/10.1016/j.jinf.2020.10.039

TY - JOUR

T1 - A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection

AU - Fowler, Veronica L.

AU - Armson, Bryony

AU - Gonzales, Jose L.

AU - Wise, Emma L.

AU - Howson, Emma L.A.

AU - Vincent-Mistiaen, Zoe

AU - Fouch, Sarah

AU - Maltby, Connor J.

AU - Grippon, Seden

AU - Munro, Simon

AU - Jones, Lisa

AU - Holmes, Tom

AU - Tillyer, Claire

AU - Elwell, Joanne

AU - Sowood, Amy

AU - De Peyer, Oliver

AU - Dixon, Sophie

AU - Hatcher, Thomas

AU - Patrick, Helen

AU - Laxman, Shailen

AU - Walsh, Charlotte

AU - Andreou, Michael

AU - Morant, Nick

AU - Clark, Duncan

AU - Moore, Nathan

AU - Houghton, Rebecca

AU - Cortes, Nicholas

AU - Kidd, Stephen P.

PY - 2020/11/30

Y1 - 2020/11/30

N2 - 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 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.

AB - 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 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.

UR - https://linkinghub.elsevier.com/retrieve/pii/S0163445320307313

U2 - 10.1016/j.jinf.2020.10.039

DO - 10.1016/j.jinf.2020.10.039

M3 - Article

SN - 0163-4453

JO - Journal of Infection

JF - Journal of Infection

ER -

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

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