Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing

  1. Chongwei Bi
  2. Gerardo Ramos-Mandujano
  3. Yeteng Tian
  4. Sharif Hala
  5. Jinna Xu
  6. Sara Mfarrej
  7. Concepcion Rodriguez Esteban
  8. Estrella Nuñez Delicado
  9. Fadwa S. Alofi
  10. Asim Khogeer
  11. Anwar M. Hashem
  12. Naif A.M. Almontashiri
  13. Arnab Pain
  14. Juan Carlos Izpisua Belmonte
  15. Mo Li

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Abstract

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  1. Version published to 10.1016/j.medj.2021.03.015
  2. Version published to 10.1101/2020.06.12.20129247v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.12.20129247: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The use of clinical samples in this study is approved by the institutional review board (IRB# H-02-K-076-0320-279) of MOH and KAUST Institutional Biosafety and Bioethics Committee (IBEC).
    IACUC: The use of clinical samples in this study is approved by the institutional review board (IRB# H-02-K-076-0320-279) of MOH and KAUST Institutional Biosafety and Bioethics Committee (IBEC).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    p. Variant calling was performed using samtools (v1.9) and bcftools (v1.9)32.
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)

    Results from OddPub: Thank you for sharing your code and data.

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.

  4. Version published to 10.1101/2020.06.12.20129247v1 on medRxiv