Mutations in the nonstructural proteins of SARS-CoV-2 may contribute to adverse clinical outcome in patients with COVID-19

  1. Takaya Ichikawa
  2. Shiho Torii
  3. Hikoyu Suzuki
  4. Akio Takada
  5. Satoshi Suzuki
  6. Masahide Nakajima
  7. Akihito Tampo
  8. Yasutaka Kakinoki

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Abstract

No abstract available

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  1. Version published to 10.1016/j.ijid.2022.05.010
  2. ScreenIT

    SciScore for 10.1101/2021.10.19.21265062: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Opt-out consent was obtained instead of written informed consent.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Our raw sequence data were converted to FASTQ format by in-house Python script with BioPython module [14], followed by trimming first 50 bps and the region after 900 bps by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
    Python
    suggested: (IPython, RRID:SCR_001658)
    BioPython
    suggested: (Biopython, RRID:SCR_007173)
    http://hannonlab.cshl.edu/fastx_toolkit/
    suggested: (FASTX-Toolkit, RRID:SCR_005534)
    The constructed phylogenetic tree was drawn and edited by MEGA X [17].
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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:
    There are some limitations to this retrospective study. First, the recommended therapy for COVID-19 have been changing dynamically. Because the best treatment strategies are selected based on the evidence at that time, it is difficult to compare clinical outcomes between different periods of time in real-life practice. Second, this is a single institution study; not all cases in cluster K have been assessed. The mortality and severity rate would be different when including cases admitted to other hospitals. Third, we examined only two samples from each group in this study. Due to the limited human and financial resources, we were unbale to perform the viral genome analysis of much more samples. In conclusion, the present study demonstrated that some viral factors, four non-synonymous mutations on nsp3, 6 and 15 but not on S protein, could be responsible for adverse clinical outcomes in COVID-19 patients. Though scientists and physicians all over the world have focused on the S protein mutations, in order to comprehensively understand the epidemiology of COVID-19, we should have an insight into other type of mutations such as those on NSPs.

    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 10.1101/2021.10.19.21265062 on medRxiv