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

Ptasińska, 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 E.; Anderson, Rebecca; Cleary, David W.; Parker, Joe; Boukas, Konstantinos; Graham, Nichola; Cellura, Doriana; Garratt, Emma; Skilton, Rachel J.; Sheldon, Hana; Collins, Alla; Ahmad, Nusreen; Friar, Simon; Burns, Daniel; Williams, Tim; Godfrey, Keith M.; Deans, Zandra C.; Douglas, Angela; Hill, Sue; Kidd, Michael; Porter, Deborah; Kidd, Stephen P.; Cortes, Nicholas; Fowler, Veronica L.; Williams, Tony; Richter, Alex; Beggs, Andrew D

doi:10.1016/j.cmi.2021.04.008

Cited by 39 publications

(26 citation statements)

References 18 publications

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“…Various other RT-LAMP tests using extraction/purification steps were developed to detect SARS-CoV-2 30 – 33 . Their sensitivities on NPS samples were equivalent to that of RT-qPCR 30 – 32 . Nagura-Ikeda et al 34 compared six different NAATs (including one RT-LAMP) and an antigen test using self-collected saliva from hospitalized patients.…”

Section: Discussionmentioning

confidence: 97%

Performances of rapid and connected salivary RT-LAMP diagnostic test for SARS-CoV-2 infection in ambulatory screening

Schneider

Molina

Picot

et al. 2022

Sci Rep

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In the context of social events reopening and economic relaunch, sanitary surveillance of SARS-CoV-2 infection is still required. Here, we evaluated the diagnostic performances of a rapid, extraction-free and connected reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay on saliva. Nasopharyngeal (NP) swabs and saliva from 443 outpatients were collected simultaneously and tested by reverse-transcription quantitative PCR (RT-qPCR) as reference standard test. Seventy-one individuals (16.0%) were positive by NP and/or salivary RT-qPCR. Sensitivity and specificity of salivary RT-LAMP were 85.9% (95%CI 77.8–94.0%) and 99.5% (98.7–100%), respectively. Performances were similar for symptomatic and asymptomatic participants. Moreover, SARS-CoV-2 genetic variants were analyzed and no dominant mutation in RT-LAMP primer region was observed during the period of the study. We demonstrated that this RT-LAMP test on self-collected saliva is reliable for SARS-CoV-2 detection. This simple connected test with optional automatic results transfer to health authorities is unique and opens the way to secure professional and social events in actual context of economics restart.

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Section: Discussionmentioning

confidence: 97%

Performances of rapid and connected salivary RT-LAMP diagnostic test for SARS-CoV-2 infection in ambulatory screening

Schneider

Molina

Picot

et al. 2022

Sci Rep

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“…These approaches have been adapted to Illumina platforms as well and have found wide application in viral epidemiology. Furthermore, ONT linked a LAMP reaction for viral amplification to a sequencing readout using their long read technology in an assay termed LamPORE™ ( 68 , 69 ). While NGS has the potential for extremely high throughput, some implementations require 12–24 h to return a result because of the complexities of library preparation and runtime on the instrument.…”

Section: Discussionmentioning

confidence: 99%

COVID-19 Seroprevalence and Active Infection in an Asymptomatic Population

et al. 2021

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In response to the COVID-19 pandemic, immediate and scalable testing solutions are needed to direct return to full capacity planning in the general public and across the Department of Defense (DoD). To fully understand the extent to which a population has been affected by COVID-19, active monitoring approaches require an estimation of overall seroprevalence in addition to accurate, affordable, and rapid tests to detect current SARS-CoV-2 infection. In this study, researchers in the Air Force Research Laboratory's 711th Human Performance Wing, Airman Systems Directorate evaluated the performance of various testing methods for the detection of SARS-CoV-2 antibodies and viral RNA in asymptomatic adults working at Wright-Patterson Air Force Base and the surrounding area during the period of 23 July 2020–23 Oct 2020. Altogether, there was a seroprevalance of 3.09% and an active infection rate of 0.5% (determined via the testing of saliva samples) amongst individuals tested, both of which were comparable to local and national averages at the time. This work also presents technical and non-technical assessments of various testing strategies as compared to the gold standard approaches (e.g., lateral flow assays vs. ELISA and RT-LAMP vs. RT-PCR) in order to explore orthogonal supply chains and fieldability. Exploration and validation of multiple testing strategies will allow the DoD and other workforces to make informed responses to COVID-19 and future pandemics.

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“…´enne in vitro diagnostic (CE-IVD)-marked RT-qPCR assay. In the symptomatic cohort (incidence, 13.4%), the sensitivity and specificity were 100% (Ptasinska et al 2020).…”

Section: Lampore Oxford Nanopore Technologies Sequencingmentioning

confidence: 93%

“…LamPORE from Oxford Nanopore Technologies combines LAMP with extremely portable and rapid nanopore sequencing (McIntyre et al 2016, McIntyre et al 2019 and, thus, has some parallels with the corresponding RT-qPCR-NGS method SARSeq (saliva analysis by RNA sequencing; Yelagandula et al 2020). This technique involves a simple library preparation that adds unique molecular identifier (UMI) barcodes to each sample and sequencing using a standard Oxford Nanopore Technologies flow cell, allowing for many samples to be multiplexed and analyzed simultaneously (Ptasinska et al 2020). For example, using 12 different LAMP barcodes combined with 96 rapid nanopore barcodes results in 1152 multiplexed samples.…”

Section: Lampore Oxford Nanopore Technologies Sequencingmentioning

confidence: 99%

“…Using the GridIon equipped with 5 flow cells allowed for scalability and high throughput with laboratory information management system (LIMS)-compatible quality control reports. This high-throughput approach has been successfully employed in a large-scale European study involving more than 20 000 samples (Ptasinska et al 2020). In a 3-week clinical validation study with 1200 participants (3966 swab and 19 461 saliva samples) LamPORE showed a sensitivity of greater than 99.5% using both swab and saliva samples from asymptomatic participants, compared with a reference Conformite ´Europe…”

Section: Lampore Oxford Nanopore Technologies Sequencingmentioning

confidence: 99%

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Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

Moore

Cahill²,

Aidelberg

et al. 2021

J Biomol Tech

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As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.

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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

Cited by 39 publications

References 18 publications

Performances of rapid and connected salivary RT-LAMP diagnostic test for SARS-CoV-2 infection in ambulatory screening

Performances of rapid and connected salivary RT-LAMP diagnostic test for SARS-CoV-2 infection in ambulatory screening

COVID-19 Seroprevalence and Active Infection in an Asymptomatic Population

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

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