A high-throughput strategy for COVID-19 testing based on next-generation sequencing

  1. Jian Huang
  2. Lan Zhao

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Abstract

COVID-19 testing as sufficient as needed is essential for healthcare workers, patients, and authorities to make informed decisions to confront and eventually defeat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, diagnosis of COVID-19 relies on quantitative reverse-transcription PCR, which is low-throughput, laborious, and often false-negative, making it overwhelmingly challenging to meet testing needs even in industrialized countries. Here we propose a new strategy, which employs a modified loop-mediated isothermal amplification (LAMP) assay, a simple procedure requiring no sophisticated instruments, to index and amplify viral genes from individual specimens, of which the products are readily available for construction of multiplexed libraries for next-generation sequencing. Our strategy would allow precise diagnosis of thousands of specimens in 1-2 days with significantly lower operating expenses. Furthermore, this strategy will make it possible for patients to collect, process, and mail their own samples to facilities for a quick, reliable diagnosis at a population scale.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.12.20129718: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    RandomizationThe primer sequences for LAMP reaction were designed using PrimerExplorer V5 (https://primerexplorer.jp) to target the same area in the N gene of SARS-CoV-2 targeted by the CDC-designed N2 RT-PCR assay, with the introduction of PstI or HindIII sites and randomized six bases (Supplemental Figure 1).
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    LAMP reactions: LAMP reactions were performed using the WarmStart LAMP Kit (DNA & RNA) (New England Biolabs, E1700S) according to the manufacturer’s instruction.
    LAMP
    suggested: (LAMP, RRID:SCR_001740)

    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.

  2. Version published to 10.1101/2020.06.12.20129718v1 on medRxiv