Independent acquisition of short insertions at the RIR1 site in the spike N‐terminal domain of the SARS‐CoV‐2 BA.2 lineage

  1. Samuele Greco
  2. Marco Gerdol

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 10.1111/tbed.14672
  2. ScreenIT

    SciScore for 10.1101/2022.04.11.487924: (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

    Experimental Models: Organisms/Strains
    SentencesResources
    Separate fasta files were created for viral genomes belonging to the following lineages: alpha; beta; gamma; delta; BA.1; BA.1.1; BA.2 (excluding genomes with RIR1 insertions; BA.2+ins(L) and BA.2+ins(LIII) (see Table 1 and Figure 1); sequences not belonging to any VOC from the year 2020 Particular attention was placed in an additional filtering step, which involved the fasta file including the BA.2 sequences bearing RIR1 insertions, aimed at discarding the sequences that may possibly derive from low quality assemblies.
    alpha; beta; gamma; delta; BA.1; BA.1.1; BA.2
    suggested: None
    Software and Algorithms
    SentencesResources
    The Wuhan-Hu-1 strain genome (NCBI accession ID: NC_045512.2) was added as reference sequence All the sampled sequences were merged and aligned with mafft v7.490 (Katoh and Standley, 2013), configured for closely related viral genomes as suggested by the authors.
    mafft
    suggested: (MAFFT, RRID:SCR_011811)
    The Augur pipeline (Huddleston et al., 2021) was then used to produce the sampling date-refined phylogenetic tree, with the Wuhan-Hu-1 genome set as a reference for rooting.
    Augur
    suggested: None

    Results from OddPub: Thank you for sharing your code.

    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.
    • No funding statement was detected.
    • 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 10.1101/2022.04.11.487924v1 on bioRxiv