A 21L/BA.2-21K/BA.1 “MixOmicron” SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis

  1. Philippe Colson
  2. Jeremy Delerce
  3. Elise Marion-Paris
  4. Jean-Christophe Lagier
  5. Anthony Levasseur
  6. Pierre-Edouard Fournier
  7. Bernard La Scola
  8. Didier Raoult

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Abstract

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  1. Version published to 10.1016/j.meegid.2022.105360
  2. ScreenIT

    SciScore for 10.1101/2022.03.28.22273010: (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
    (Illumina Inc.)], mapping was carried out using the bwa-mem2 tool (v2.2.1; https://github.com/bwa-mem2/bwa-mem2) on the Wuhan-Hu-1 isolate genome (GenBank accession no. NC_045512.2) before cleaning with the SAMtools program (v. 1.13; https://www.htslib.org/) (Danecek et al., 2021).
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Variant calling was performed using FreeBayes (v1.3.5; https://github.com/freebayes/freebayes) (Garrison et al., 2012), and consensus genomes were built with the Bcftools program (v1.13; https://samtools.github.io/bcftools/bcftools.html).
    FreeBayes
    suggested: (FreeBayes, RRID:SCR_010761)
    Phylogenetic analyses were performed the MEGA X software (v10.2.5; https://www.megasoftware.net/) (Kumar et al., 2018) following sequence alignment with MAFFT (https://mafft.cbrc.jp/alignment/server/)
    MEGA X
    suggested: None
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    (Katoh et al., 2002), and trees were visualized with MEGA X.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    The 10 genomes the most similar to these sequences among genomes of the Omicron 21L/BA.2 and 21K/BA.1 variants of the sequence database of our institute were selected by a BLAST search (Altschul et al., 1990) then incorporated in the phylogenies together with the sequence of the Wuhan-Hu-1 isolate.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Genome sequences obtained and analyzed here were deposited in the NCBI GenBank nucleotide sequence database (https://www.ncbi.nlm.nih.gov/genbank/) (Sayers et al., 2022) (
    NCBI GenBank
    suggested: (NCBI GenBank via FTP, RRID:SCR_010535)

    Results from OddPub: Thank you for sharing your 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 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 10.1101/2022.03.28.22273010v1 on medRxiv