Detection of the novel SARS-CoV-2 European lineage B.1.177 in Ontario, Canada

  1. Jennifer L. Guthrie
  2. Sarah Teatero
  3. Sandra Zittermann
  4. Yao Chen
  5. Ashleigh Sullivan
  6. Heather Rilkoff
  7. Esha Joshi
  8. Karthikeyan Sivaraman
  9. Richard de Borja
  10. Yogi Sundaravadanam
  11. Michael Laszloffy
  12. Lawrence Heisler
  13. Vanessa G. Allen
  14. Jared T. Simpson
  15. Nahuel Fittipaldi

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Abstract

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  1. Version published to 10.1016/j.jcvp.2021.100010
  2. ScreenIT

    SciScore for 10.1101/2020.11.30.20241265: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: ETHICS STATEMENT: PHO Ethics Review Board has determined that this project is exempt from research ethics committee review, as it describes analyses that were completed at PHO Laboratory as part of routine clinical respiratory testing during the COVID-19 pandemic in Ontario and are therefore considered public health practice.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Bioinformatic analysis used a modified version of the COVID-19 Genomics UK (COG-UK
    Bioinformatic
    suggested: (QFAB Bioinformatics, RRID:SCR_012513)
    Consensus FASTA sequences with ≤1% ambiguous bases were aligned with MAFFT (v7.471)[12], 5’ and 3’ ends (positions 1–54 and 29837–29903 in the reference, respectively) were masked.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Maximum-likelihood phylogenetic trees were constructed using IQ-TREE (v2.0.3) with –fconst used to specify the number of invariant sites [13].
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)

    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. Version published to 10.1101/2020.11.30.20241265 on medRxiv