First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France

  1. Philippe Colson
  2. Jérémy Delerce
  3. Mamadou Beye
  4. Anthony Levasseur
  5. Céline Boschi
  6. Linda Houhamdi
  7. Hervé Tissot‐Dupont
  8. Nouara Yahi
  9. Matthieu Million
  10. Bernard La Scola
  11. Jacques Fantini
  12. Didier Raoult
  13. Pierre‐Edouard Fournier

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Abstract

The SARS‐CoV‐2 21K/BA.1, 21L/BA.2, and BA.3 Omicron variants have recently emerged worldwide. To date, the 21L/BA.2 Omicron variant has remained very minority globally but became predominant in Denmark instead of the 21K/BA.1 variant. Here, we describe the first cases diagnosed with this variant in south‐eastern France. We identified 13 cases using variant‐specific qPCR and next‐generation sequencing between 28/11/2021 and 31/01/2022, the first two cases being diagnosed in travelers returning from Tanzania. Overall, viral genomes displayed a mean (±standard deviation) number of 65.9 ± 2.5 (range, 61–69) nucleotide substitutions and 31.0 ± 8.3 (27–50) nucleotide deletions, resulting in 49.6 ± 2.2 (45–52) amino acid substitutions (including 28 in the spike protein) and 12.4 ± 1.1 (12–15) amino acid deletions. Phylogeny showed the distribution in three different clusters of these genomes, which were most closely related to genomes from England and South Africa, from Singapore and Nepal, or from France and Denmark. Structural predictions highlighted a significant enlargement and flattening of the surface of the 21L/BA.2 N‐terminal domain of the spike protein compared to that of the 21K/BA.1 Omicron variant, which may facilitate initial viral interactions with lipid rafts. Close surveillance is needed at global, country, and center scales to monitor the incidence and clinical outcome of the 21L/BA.2 Omicron variant.

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  1. Version published to 10.1002/jmv.27695
  2. ScreenIT

    SciScore for 10.1101/2022.02.08.22270495: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: This study was approved by the ethics committee of University Hospital Institute Méditerranée
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Mapping was cleaned with Samtools (https://www.htslib.org/).
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    The genomes the closest genetically to those obtained here were selected using Usher (https://genome.ucsc.edu/cgi-bin/hgPhyloPlace) and the GISAID BLAST tool (https://www.epicov.org/epi3/) then incorporated in phylogeny with all 21L/BA.2 Omicron variant genomes from France available in GISAID.
    GISAID BLAST tool
    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.
    • 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 10.1101/2022.02.08.22270495 on medRxiv