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

  1. Anetta Ptasinska
  2. Celina Whalley
  3. Andrew Bosworth
  4. Charlotte Poxon
  5. Claire Bryer
  6. Nicholas Machin
  7. Seden Grippon
  8. Emma L. Wise
  9. Bryony Armson
  10. Emma L.A. Howson
  11. Alice Goring
  12. Gemma Snell
  13. Jade Forster
  14. Chris Mattocks
  15. Sarah Frampton
  16. Rebecca Anderson
  17. David Cleary
  18. Joe Parker
  19. Konstantinos Boukas
  20. Nichola Graham
  21. Doriana Cellura
  22. Emma Garratt
  23. Rachel Skilton
  24. Hana Sheldon
  25. Alla Collins
  26. Nusreen Ahmad
  27. Simon Friar
  28. Daniel Burns
  29. Tim Williams
  30. Keith M. Godfrey
  31. Zandra Deans
  32. Angela Douglas
  33. Sue Hill
  34. Michael Kidd
  35. Deborah Porter
  36. Stephen P. Kidd
  37. Nicholas J. Cortes
  38. Veronica Fowler
  39. Tony Williams
  40. Alex Richter
  41. Andrew D. Beggs

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Abstract

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  1. Version published to 10.1016/j.cmi.2021.04.008
  2. ScreenIT

    SciScore for 10.1101/2020.12.15.20247031: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: The retrospective study was undertaken by collating surplus sample from patients having diagnostic samples sent to the Public Health England West Midlands laboratory for respiratory panel testing for influenza like illness (ILI) from January 2020 – June 2020 (National Research Ethics Service Committee West Midlands - South Birmingham 2002/201 Amendment Number 4).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Test methods: Clinical material used for analytical performance: To assess the limit of detection, a tenfold? dilution series (from 20,000 copies/ml to 0.2 copies/ml) of droplet digital polymerase chain reaction (ddPCR) quantified SARS-CoV-2 was constructed from the lysate of the Public Health England SARS-CoV-2 reference strain grown on Vero E6 cells and diluted in nuclease free water.
    Vero E6
    suggested: RRID:CVCL_XD71)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. ScreenIT

    SciScore for 10.1101/2020.12.15.20247031: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementThe retrospective study was undertaken by collating surplus sample from patients having diagnostic samples sent to the Public Health England West Midlands laboratory for respiratory panel testing for influenza like illness (ILI) from January 2020 – June 2020 (National Research Ethics Service Committee West Midlands - South Birmingham 2002/201 Amendment Number 4).Randomizationnot detected.BlindingResults interpretation: The readers of RT-qPCR and LamPORE tests were blinded to any clinical information relating to study participants.Power Analysisnot detected.Sex as a biological variablenot detected.Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Clinical material used for analytical performance: To assess the limit of detection, a tenfold? dilution series (from 20,000 copies/ml to 0.2 copies/ml) of droplet digital polymerase chain reaction (ddPCR) quantified SARS-CoV-2 was constructed from the lysate of the Public Health England SARS-CoV-2 reference strain grown on Vero E6 cells and diluted in nuclease free water.
    Vero E6
    suggested: RRID:CVCL_XD71)
    For every batch of RNA extraction performed (95 samples/batch) an RNA extraction control was utilised consisting of heat inactivated SARS-CoV-2 virus grown on Vero-E6 cells (PHE SARS-CoV-2 England reference strain) normalised to 20,000 copies/ml via droplet digital PCR targeted against the E (Envelope) gene of SARS-CoV-2.
    Vero-E6
    suggested: None
    Software and Algorithms
    SentencesResources
    Reference test (RT-QPCR): Single step reverse transcription quantitative polymerase chain reaction (RT-QPCR) against the ORF1ab and N1 gene targets of SARS-CoV-2 was carried out using the CerTest ViaSure SARS-CoV-2 real time PCR kit (CerTest Biotech SL, Zaragoza, Spain) according to manufacturer’s instructions for use (IFU) on ThermoFisher QuantStudio 5 or BioMolecular Systems MIC instruments, using 5uL of extracted RNA per reaction.
    ThermoFisher QuantStudio
    suggested: (Primer Express Software, RRID:SCR_017376)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.12.15.20247031v1 on medRxiv