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

Anetta Ptasinska, Celina Whalley, Andrew Bosworth, Charlotte Poxon, Claire Bryer, Nicholas Machin, Seden Grippon, Emma L. Wise, Bryony Armson, Emma L.A. Howson, Alice Goring, Gemma Snell, Jade Forster, Chris Mattocks, Sarah Frampton, Rebecca Anderson, David Cleary, Joe Parker, Konstantinos Boukas, Nichola GrahamDoriana Cellura, Emma Garratt, Rachel Skilton, Hana Sheldon, Alla Collins, Nusreen Ahmad, Simon Friar, Daniel Burns, Tim Williams, Keith M. Godfrey, Zandra Deans, Angela Douglas, Sue Hill, Michael Kidd, Deborah Porter, Stephen P. Kidd, Nicholas J. Cortes, Veronica Fowler, Tony Williams, Alex Richter, Andrew D. Beggs*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)
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Abstract

Objectives: Rapid, high throughput diagnostics are a valuable tool, allowing the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in populations so as 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 quantitative RT-PCR (RT-qPCR), particularly throughout the first months of the coronavirus disease 2019 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 3 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 to June 2020 were similarly tested from nasopharyngeal swabs. 

Results: In the asymptomatic cohort a total of 1200 participants supplied 23 427 samples (3966 swab, 19 461 saliva) over a 3-week period. The incidence of SARS-CoV-2 detection using LamPORE was 0.95%. Diagnostic sensitivity and specificity of LamPORE was >99.5% (decreasing to approximately 98% when clustered estimation was used) in both swab and saliva asymptomatic samples when compared with 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.

Original languageEnglish
Pages (from-to)1348.e1-1348.e7
Number of pages7
JournalClinical Microbiology and Infection
Volume27
Issue number9
Early online date24 Apr 2021
DOIs
Publication statusPublished - Sep 2021

Bibliographical note

Funding Information: ADB has received travel funding from the Oxford Nanopore Community Meeting 2019 from Oxford Nanopore. The other authors declare no competing interests. The research in this study was funded by an unrestricted grant from the United Kingdom Department of Health and Social Care via NHS Test and Trace; and NHS England and NHS Improvement. ADB is currently supported by a Cancer Research UK Advanced Clinician Scientist award (C31641/A23923) and his laboratory is supported by CRUK Centre Birmingham (C17422/A25154) and the Birmingham Experimental Cancer Medicine Centre (C11497/A25127). The Department of Health and Social Care gave input into the study design and coordination but had no influence on the analysis and conclusions of the paper. This report presents independent research and the views expressed in this publication are those of the authors and not necessarily those of the NHS, or the Department of Health and Social Care.

Open Access: This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Publisher Copyright: © 2021 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases.

Citation: Anetta Ptasinska, Celina Whalley, Andrew Bosworth, Charlotte Poxon, Claire Bryer, Nicholas Machin, Seden Grippon, Emma L. Wise, Bryony Armson, Emma L.A. Howson, Alice Goring, Gemma Snell, Jade Forster, Chris Mattocks, Sarah Frampton, Rebecca Anderson, David Cleary, Joe Parker, Konstantinos Boukas, Nichola Graham, Doriana Cellura, Emma Garratt, Rachel Skilton, Hana Sheldon, Alla Collins, Nusreen Ahmad, Simon Friar, Daniel Burns, Tim Williams, Keith M. Godfrey, Zandra Deans, Angela Douglas, Sue Hill, Michael Kidd, Deborah Porter, Stephen P. Kidd, Nicholas J. Cortes, Veronica Fowler, Tony Williams, Alex Richter, Andrew D. Beggs, 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,
Volume 27, Issue 9, 2021, Pages 1348.e1-1348.e7, ISSN 1198-743X.

DOI: https://doi.org/10.1016/j.cmi.2021.04.008.

Keywords

  • Detection
  • Loop-mediated isothermal amplification
  • Nanopore
  • Rapid testing
  • Severe acute respiratory syndrome coronavirus
  • SENSITIVITY

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