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About:
Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing
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Academic Article
research paper
schema:ScholarlyArticle
isDefinedBy
Covid-on-the-Web dataset
title
Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing
Creator
Kräusslich, Hans-Georg
Schnitzler, Paul
Chlanda, Petr
Freistaedter, Andrew
Anders, Simon
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source
MedRxiv
abstract
The SARS-CoV-2 (COVID-19) pandemic poses a significant public-health problem. In order to control the pandemic, rapid tests for detecting existing infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) hold outstanding promise towards greatly simplified and broadly applicable testing methods. RT-LAMP assays appear more robust than qPCR-based methods and only require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP protocol using clinical SARS-CoV-2 samples and also established a protocol that does not require prior RNA isolation (%22swab-to-RT-LAMP%22). Our study is based on several hundred clinical patient samples with a wide range of viral loads, thus allowing, for the first time, to accurately determine the sensitivity and specificity of the RT-LAMP assay for the detection of SARS-CoV-2 in patients. We found that RT-LAMP can reliably detect SARS-CoV-2 samples with a qPCR threshold cycle number (CT value) of up to 30 in the standard RT-qPCR assay. We used both, either purified RNA or direct pharyngeal swab specimens and showed that RT-LAMP assays have, despite a decreased sensitivity compared to RT-qPCR, excellent specificity. We also developed a multiplexed LAMP-sequencing protocol as a validation and backup procedure to double-check the results of visual RT-LAMP assays. LAMP-sequencing is fully scalable and can assess the results of thousands of LAMP reactions in parallel. We propose decentralised COVID-19 testing as a routine to allow facilities and institutions to return to near-to-full functionality.
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2020-05-09
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bibo:doi
10.1101/2020.05.05.20092288
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medrxiv
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fb77d8f63128f0c6522e2fe1f76c9cc76df7a73b
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https://doi.org/10.1101/2020.05.05.20092288
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Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing
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covid:fb77d8f63128f0c6522e2fe1f76c9cc76df7a73b#body_text
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named entity 'SARS-CoV-2'
named entity 'rapid tests'
named entity '95% confidence interval'
named entity 'medRxiv'
named entity 'gene'
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