Development and evaluation of a rapid CRISPR-based diagnostic for COVID-19

  1. Tieying Hou
  2. Weiqi Zeng
  3. Minling Yang
  4. Wenjing Chen
  5. Lili Ren
  6. Jingwen Ai
  7. Ji Wu
  8. Yalong Liao
  9. Xuejing Gou
  10. Yongjun Li
  11. Xiaorui Wang
  12. Hang Su
  13. Bing Gu
  14. Jianwei Wang
  15. Teng Xu

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1371/journal.ppat.1008705
  2. ScreenIT

    SciScore for 10.1101/2020.02.22.20025460: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIACUC: This study was approved by the ethical review committee of Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College.
    Consent: Written informed consent was waived given the context of emerging infectious diseases. mNGS Assay for 2019-nCoV: The RNA concentrations were measured by a Qubit Fluorometer (Thermo Fisher Scientific, Carlsbad, CA,
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Alignment of multiple sequences was performed with the ClustalW program (MEGA software, version 7.0.14).
    ClustalW
    suggested: (ClustalW, RRID:SCR_017277)
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Data analyses were performed using SPSS 22.0 software.
    SPSS
    suggested: (SPSS, RRID:SCR_002865)

    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. PREreview

    This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/3832925.

    Tatiana Hillman

    PLOS

    5/10/20

    Development and Evaluation of A CRISPR-based Diagnostic 2 For 2019-novel Coronavirus

     

    (Hou et al., 2020)

    PLOS Discussion:

     

    The CRISPR-nCoV assay is convenient and greatly needed in the laboratory and in the

    clinical setting. Because the CRISPR-nCoV assay does not require thermal cyclers, the time of the testing is decreased, and this assay can operate in a setting with minimal resources.

    Presently, there is a demand for more testing of the 2019-nCoV virus. In some states and

    counties testing is limited. Also, the current tests take a long time to produce results. The

    fastidious and rapid diagnosis of 2019-nCoV may help many quarantine earlier before the

    symptoms become too intense. The CRISPR-nCoV is exceptional because less instruments as thermal cyclers are required, which could help transfer the CRISPR-nCoV into the clinical setting. However, mNGS, a metagenomic test, is still needed to track any signs of genetic drift in the 2019-nCoV viral genome.

     

    CRISPR detection of 2019-nCoV is an extremely promising assay with much potential

    because it can provide tests with high sensitivity and specificity. The inclusion of CRISPR

    technology increases and produces test results for 2019-nCoV with higher specificity because

    Cas13a can directly target and cleave RNA, using crRNA as guide RNAs. The 2019-nCoV is a

    single strand RNA virus, so the synthesized guide RNAs can bind to and guide the Cas13a

    nuclease to that specific RNA sequence for cleavage.The CRISPR-nCoV assay detected RNA sequences of 2019-nCoV, fluorescent signals were produced, and then collected. The

    sensitivity of CRISPR detection for 2019-nCoV was extremely sensitive during serial dilutions at many different nucleic acid concentrations.

     

    The results of the sensitivity tests determined that 7.5 copies of 2019-nCoV were

    detected in all 10 replicates, 2.5 copies were found in 6 out of 10 replicates, and 1.25 copies were in 2 out of 10 replicates (Hou et al., 2020). Specificity tests for CRISPR-nCoV were tested against DNA from human cells, microbes, human coronaviruses, and other respiratory viruses where nonetriggered false positive results. From ROC analysis 100% sensitivity and specificity results of the curves were produced from the positive 2019-nCoV test results. The ROC results are important for use of CRISPR-nCoV in the clinical setting where highly sensitive and specific tests are required. No false positives were detected from all 62 cases. Transferring the CRISPR-nCoV tests to the clinical setting has much promise and potential.

     

    References

    Hou T, Zeng W, Yang M, Chen W, Ren L, Ai J, Wu J, Liao Y, Gou X, Li Y, Wang X. Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus. medRxiv. 2020 Jan 1.

     

  4. Version published to 10.1101/2020.02.22.20025460v2 on medRxiv
  5. Version published to 10.1101/2020.02.22.20025460v1 on medRxiv