SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay.

Michael D Buck ,Ok‐Ryul Song ,Paul Grant ,Simon Caidan ,George Kassiotis ,Ming Jiang ,Davin P Miller ,Steve Hindmarsh ,Ana Cardoso ,Nicola O’reilly ,Johnathan Canton ,Robert Goldstone ,Jessica Olsen ,Mary Wu ,Michael Howell ,Sam Barrell ,Wei-Ting Lu ,Luke Nightingale ,Anett Rideg ,Amin Oomatia ,Kiran Gulati ,Michael Hubank ,Margaret Crawford ,Enzo Z Poirier ,Charles Swanton ,Jérôme Nicod ,James I Macrae ,Rachael Instrell ,Rupert Beale ,Sonia Gandhi ,Amy Strange ,Samra Turajlic ,Eleni Nastouli ,Bruno Frederico ,Iana Martini ,Richard Byrne ,Laura Cubitt ,David Moore ,Caetano Reis E Sousa

doi:10.12688/wellcomeopenres.16517.2

Abstract

The ongoing pandemic of SARS-CoV-2 calls for rapid and cost-effective methods to accurately identify infected individuals. The vast majority of patient samples is assessed for viral RNA presence by RT-qPCR. Our biomedical research institute, in collaboration between partner hospitals and an accredited clinical diagnostic laboratory, established a diagnostic testing pipeline that has reported on more than 252,000 RT-qPCR results since its commencement at the beginning of April 2020. However, due to ongoing demand and competition for critical resources, alternative testing strategies were sought. In this work, we present a clinically-validated procedure for high-throughput SARS-CoV-2 detection by RT-LAMP that is robust, reliable, repeatable, specific, and inexpensive.

Highlights

The current pandemic caused by novel coronavirus SARS-CoV-2, first detected in late 2019 in the province of Wuhan, China, has rapidly spread worldwide, infecting more than 68 million individuals as of 11 December 20201–3
In an effort to increase the diagnostic capacity for SARS-CoV-2 infection in the UK, the Francis Crick Institute, a biomedical research institute based in London, rapidly repurposed its staff and facilities in late March 2020 to serve as a clinical diagnostic testing facility through a partnership between a major local healthcare provider (University College London Hospitals National Health Services Trust) and an accredited clinical diagnostic laboratory (Health Services Laboratories, HSL), termed the CRICK COVID-19 Consortium (CCC)[5]
In order to avoid dependence on any singular testing methodology, to continue increasing testing capacity, and to provide a potential means to deliver diagnostics at the point-of-care, Our results demonstrate that within the CCC pipeline, RT-Loop-mediated isothermal amplification (LAMP) can readily replace RT-qPCR as a means for detecting SARS-CoV-2 transcripts within RNA extracted from nose-throat swabs and endotracheal secretions/bronchoalveolar lavage fluid

Summary

Introduction

The current pandemic caused by novel coronavirus SARS-CoV-2, first detected in late 2019 in the province of Wuhan, China, has rapidly spread worldwide, infecting more than 68 million individuals as of 11 December 20201–3. The pipeline utilises a series of in-house buffers to first inactivate patient samples received from care homes and hospitals, and to extract RNA before using a CE marked commercial kit to detect SARS-CoV-2 by RT-qPCR. In order to avoid dependence on any singular testing methodology, to continue increasing testing capacity, and to provide a potential means to deliver diagnostics at the point-of-care, Our results demonstrate that within the CCC pipeline, RT-LAMP can readily replace RT-qPCR as a means for detecting SARS-CoV-2 transcripts within RNA extracted from nose-throat swabs and endotracheal secretions/bronchoalveolar lavage fluid. The procedure developed here is ready to be deployed for diagnostic testing of SARS-CoV-2

Methods

Results

Discussion

Conclusion