Rapid and simultaneous identification of three mutations by the Novaplex™ SARS-CoV-2 variants I assay kit

  1. Wakaki Kami
  2. Takeshi Kinjo
  3. Wakako Arakaki
  4. Hiroya Oki
  5. Daisuke Motooka
  6. Shota Nakamura
  7. Jiro Fujita

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Abstract

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  1. Version published to 10.1016/j.jcv.2021.104877
  2. ScreenIT

    SciScore for 10.1101/2021.04.27.21255987: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: This study was approved by the Institutional Review Board of the University of the Ryukyus (approval number: 1621).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    RNA was extracted from the nasal swabs stored in a deep freezer using MagLEAD 12gC (Precision System Science, Chiba, Japan).
    MagLEAD
    suggested: None

    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: We detected the following sentences addressing limitations in the study:
    Although genome sequencing is considered the gold standard for identifying SARS-CoV-2 variants, it has several limitations in terms of swiftness and convenience. In Japan, as of April 23, 2021, randomly selected COVID-19-positive samples were tested for the N501Y mutation at local public health institutes and affiliated hospitals, and the positive samples along with a few negative ones were sent to a central public health institute (National Institute of Infectious Diseases, Tokyo, Japan) for whole-genome sequencing [9]. Although dependent upon several factors, such as the local situation of the COVID-19 epidemic and geographical conditions, it usually takes a week to receive the final report of genome sequencing. This limitation can be overcome by the Novaplex™ SARS-CoV-2 Variants I Assay kit that can substantially shorten the turnaround time. Since many variants are emerging, there is a possibility that monoplex-based testing can miss detecting some of the characteristic mutations in the variants. We detected two samples with the E484K mutation and without the N501Y mutation in this study. This variant has been named R.1 and categorized as a VOI in Japan as of April 7, 2021; however, this variant could bypass the screening stage in our country. Therefore, we need a multiplex-based test that can examine several mutations simultaneously. In conclusion, the Novaplex™ SARS-CoV-2 Variants I Assay is a simple, rapid, and easy to perform method, and can identify three important mu...

    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.

    Results from scite Reference Check: We found no unreliable references.

    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. Version published to 10.1101/2021.04.27.21255987 on medRxiv