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

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 tradition...

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Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Published by Elsevier Ltd on behalf of The British Infection Association. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7703389/
https://www.ncbi.nlm.nih.gov/pubmed/33271166
http://dx.doi.org/10.1016/j.jinf.2020.10.039
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author 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.
author_facet 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.
author_sort Fowler, Veronica L.
collection PubMed
description 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 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.
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spelling pubmed-77033892020-12-01 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 J. Kidd, Stephen P. J Infect Article 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 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. Published by Elsevier Ltd on behalf of The British Infection Association. 2021-01 2020-11-30 /pmc/articles/PMC7703389/ /pubmed/33271166 http://dx.doi.org/10.1016/j.jinf.2020.10.039 Text en Crown Copyright © 2020 Published by Elsevier Ltd on behalf of The British Infection Association. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
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.
A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection
title A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection
title_full A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection
title_fullStr A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection
title_full_unstemmed A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection
title_short A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection
title_sort highly effective reverse-transcription loop-mediated isothermal amplification (rt-lamp) assay for the rapid detection of sars-cov-2 infection
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7703389/
https://www.ncbi.nlm.nih.gov/pubmed/33271166
http://dx.doi.org/10.1016/j.jinf.2020.10.039
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