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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.

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.
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.
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.
1198-743X
Ptasinska, Anetta
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Machin, Nicholas
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Grippon, Seden
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Howson, Emma L. A.
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Goring, Alice
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Forster, Jade
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Mattocks, Christopher
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Boukas, Konstantinos
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Graham, Nichola
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Cellura, Doriana
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Garratt, Emma
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Sheldon, Hana
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Collins, Alla
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Ahmad-Saeed, Nusreen
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Friar, Simon
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Burns, Daniel
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Williams, Tim
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Godfrey, Keith
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Cortes, Nicholas J
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Williams, Tony
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Richter, Alex G.
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Beggs, Andrew D.
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Whalley, Celina M.
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Bosworth, Andrew
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Poxon, Charlotte
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Machin, Nicholas
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Grippon, Seden
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Wise, Emma L
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Armson, Bryony
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Howson, Emma L. A.
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Goring, Alice
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Snell, Gemma
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Forster, Jade
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Mattocks, Christopher
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Collins, Alla
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Friar, Simon
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Burns, Daniel
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Williams, Tim
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Godfrey, Keith
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Kidd, Michael
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Porter, Deborah
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Kidd, Stephen P.
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Cortes, Nicholas J
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Fowler, Veronica L.
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Williams, Tony
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Richter, Alex G.
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Beggs, Andrew D.
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Ptasinska, Anetta, Whalley, Celina M., 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, Christopher, Frampton, Sarah May, Anderson, Rebecca, Cleary, David, Parker, Joe, Boukas, Konstantinos, Graham, Nichola, Cellura, Doriana, Garratt, Emma, Skilton, Rachel, Sheldon, Hana, Collins, Alla, Ahmad-Saeed, Nusreen, Friar, Simon, Burns, Daniel, Williams, Tim, Godfrey, Keith, Deans, Zandra, Douglas, Angela, Hill, Sue, Kidd, Michael, Porter, Deborah, Kidd, Stephen P., Cortes, Nicholas J, Fowler, Veronica L., 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. (In Press)

Record type: Article

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.

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Accepted/In Press date: 13 April 2021

Identifiers

Local EPrints ID: 448861
URI: http://eprints.soton.ac.uk/id/eprint/448861
ISSN: 1198-743X
PURE UUID: b8f4e59d-6e52-4e79-bb9c-bcc9216871ae
ORCID for David Cleary: ORCID iD orcid.org/0000-0003-4533-0700
ORCID for Emma Garratt: ORCID iD orcid.org/0000-0001-5268-4203
ORCID for Daniel Burns: ORCID iD orcid.org/0000-0001-6976-1068
ORCID for Keith Godfrey: ORCID iD orcid.org/0000-0002-4643-0618

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Date deposited: 07 May 2021 16:30
Last modified: 02 Jul 2021 01:54

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Contributors

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

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