Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

  1. Marco Gerdol
  2. Klevia Dishnica
  3. Alejandro Giorgetti

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1016/j.virusres.2022.198674
  2. Version published to 10.1101/2021.04.17.440288v4 on bioRxiv
  3. Version published to 10.1101/2021.04.17.440288v3 on bioRxiv
  4. Version published to 10.1101/2021.04.17.440288v2 on bioRxiv
  5. ScreenIT

    SciScore for 10.1101/2021.04.17.440288: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Briefly, nucleotide sequences were aligned with MAFFT [39] and the resulting multiple sequence alignment was used as an input for a maximum likelihood phylogenetic inference analysis, carried out with IQ-TREE [40] under a generalized time reversible (GTR) model of molecular evolution.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Phylogenetic trees were rooted based on the oldest genotype available, which in this case was Wuhan-Hu-1, and graphically rendered using FigTree v.1.1.4.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    The number of non-synonymous mutations, insertions and deletions affecting the spike protein of at least 50% of the genomes belonging to the A.2.5 and B.1.214.2 lineages sampled from February 1st 2021 was calculated with MEGA X [41], compared with the reference genotype Wuhan-Hu-1.
    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: 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.
    • 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.

  6. Version published to 10.1101/2021.04.17.440288v1 on bioRxiv