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

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

doi:10.12688/wellcomeopenres.16517.1

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 in 25 minutes that is robust, reliable, repeatable, sensitive, 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]
An initial characterization of the technique was performed using 24 RNA samples purified from patient nasopharyngeal swabs, 12 of which were positive for SARS-CoV-2 as assessed by the CCC pipeline via RT-qPCR5

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. Controlling the spread of SARS-CoV-2 relies on the ability of healthcare systems to quickly identify infected individuals, which has mainly relied on RT-qPCR for viral RNA detection[4]. 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]. 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, the CCC was tasked with developing and validating alternative SARS-CoV-2 testing strategies

Methods

Results

Discussion

Conclusion