Products & Services
Applications

Applications

Nanopore sequencing offers advantages in all areas of research. Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins.

Learn about applications
View all Applications
Resources
News Explore
Contact
Back

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

Publication

Date: 23rd April 2021 | Source: Clinical Microbiology and Infection

Authors: 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, 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.

Introduction 
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% 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.

Read the full text

Recommended for you

Open a chat to talk to our sales team