Diagnostic accuracy of loop mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations.

Ptasinska, Anetta, Whalley, Celina, Bosworth, Andrew, Poxon, Charlotte, Bryer, Claire, Machin, Nicholas, Grippon, Seden, Wise, Emma L, Armson, Bryony, Howson, Emma L A, Goring, Alice, Snell, Gemma, Forster, Jade, Mattocks, Chris, Frampton, Sarah, Anderson, Rebecca, Cleary, David, Parker, Joe, Boukas, Konstantinos, Graham, Nichola, Cellura, Doriana, Garratt, Emma, Skilton, Rachel, Sheldon, Hana, Collins, Alla, Ahmad, Nusreen, Friar, Simon, Burns, Daniel, Williams, Tim, Godfrey, Keith M, Deans, Zandra, Douglas, Angela, Hill, Sue, Kidd, Michael, Porter, Deborah, Kidd, Stephen P, Cortes, Nicholas J, Fowler, Veronica, Williams, Tony, Richter, Alex G and Beggs, Andrew D (2021) Diagnostic accuracy of loop mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. ISSN 1469-0691.

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Official URL: http://www.clinicalmicrobiologyandinfection.com/

Abstract

OBJECTIVES

Rapid, high throughput diagnostics are a valuable tool, allowing the detection of SARS-CoV-2 in populations, in order to identify and isolate people with asymptomatic and symptomatic infections. Reagent shortages and restricted access to high throughput testing solutions have limited the effectiveness of conventional assays such as reverse transcriptase quantitative PCR (RT-qPCR), particularly throughout the first months of the COVID-19 pandemic. We investigated the use of LamPORE, where loop mediated isothermal amplification (LAMP) is coupled to nanopore sequencing technology, for the detection of SARS-CoV-2 in symptomatic and asymptomatic populations.

METHODS

In an asymptomatic prospective cohort, for three weeks in September 2020 health care workers across four sites (Birmingham, Southampton, Basingstoke and Manchester) self-swabbed with nasopharyngeal swabs weekly and supplied a saliva specimen daily. These samples were tested for SARS-CoV-2 RNA using the Oxford Nanopore LamPORE system and a reference RT-qPCR assay on extracted sample RNA. A second retrospective cohort of 848 patients with influenza like illness from March 2020 - June 2020, were similarly tested from nasopharyngeal swabs.

RESULTS

In the asymptomatic cohort a total of 1200 participants supplied 23,427 samples (3,966 swab, 19,461 saliva) over a three-week period. The incidence of SARS-CoV-2 detection using LamPORE was 0.95%. Diagnostic sensitivity and specificity of LamPORE was >99.5% (reducing to ∼ 98% when clustered estimation was used) in both swab and saliva asymptomatic samples when compared to the reference RT-qPCR test. In the retrospective symptomatic cohort, the incidence was 13.4% and the sensitivity and specificity were 100%.

CONCLUSIONS

LamPORE is a highly accurate methodology for the detection of SARS-CoV-2 in both symptomatic and asymptomatic population settings and can be used as an alternative to RT-qPCR.

Item Type: Article
Subjects: QW Microbiology. Immunology
QZ Pathology. Oncology
W Public health. Health statistics. Occupational health. Health education
WC Communicabable diseases
Divisions: Planned IP Care > Respiratory Medicine
Related URLs:
Depositing User: Jamie Edgar
Date Deposited: 05 May 2021 15:26
Last Modified: 05 May 2021 15:26
URI: http://www.repository.uhblibrary.co.uk/id/eprint/4279

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