Comparison of 12 molecular detection assays for SARS-CoV-2

  1. Yasufumi Matsumura
  2. Tsunehiro Shimizu
  3. Taro Noguchi
  4. Satoshi Nakano
  5. Masaki Yamamoto
  6. Miki Nagao

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Abstract

Molecular testing for SARS-CoV-2 is the mainstay for accurate diagnosis of the infection, but the diagnostic performances of available assays have not been defined. We compared 12 molecular diagnostic assays, including 8 commercial kits using 155 respiratory samples (65 nasopharyngeal swabs, 45 oropharyngeal swabs, and 45 sputum) collected at 2 Japanese hospitals. Sixty-eight samples were positive for more than one assay and one genetic locus and were defined as true positive samples. All the assays showed a specificity of 100% (95% confidence interval, 95.8 to 100). The N2 assay kit of the US Centers for Disease Control and Prevention (CDC) and the N2 assay of the Japanese National Institute of Infectious Disease (NIID) were the most sensitive assays with 100% sensitivity (95% confidence interval, 94.7 to 100), followed by the CDC N1 kit, E assay by Corman, and NIID N2 assay multiplex with internal control reactions. These assays are reliable as first-line molecular assays in laboratories when combined with appropriate internal control reactions.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.24.170332: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethical statement: The Ethics Committee of Kyoto University Graduate School and the Faculty of Medicine approved this study (R2379).
    RandomizationIn this study, we included all 68 SARS-CoV-2-positive samples and 87 randomly selected negative samples from 107 patients.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All statistical analyses were performed using SAS® Studio 3.8 (SAS Institute Inc.
    SAS Institute
    suggested: (Statistical Analysis System, RRID:SCR_008567)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    The study limitations included a relatively small sample size of each specimen type and lack of clinical information, measurements by multiple investigators, and genomic variation analysis. In conclusion, we validated the NIID N2 assay with EAV control reaction and found that the CDC EUA kit (N1/N2/RNaseP), NIID N2 with/without EAV, and Corman E assays were the most sensitive assays. They are feasible as references and clinical diagnostic tests until commercial kits with internal control reactions or fully automated systems that have high diagnostic performances are available in clinical laboratories. Continuous efforts to improve COVID-19 diagnostics are important to control this pandemic.

    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.
    • No funding statement was detected.
    • 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 10.1101/2020.06.24.170332v1 on bioRxiv