Culture and identification of a “Deltamicron” SARS‐CoV‐2 in a three cases cluster in southern France

  1. Philippe Colson
  2. Pierre‐Edouard Fournier
  3. Jeremy Delerce
  4. Matthieu Million
  5. Marielle Bedotto
  6. Linda Houhamdi
  7. Nouara Yahi
  8. Jeremy Bayette
  9. Anthony Levasseur
  10. Jacques Fantini
  11. Didier Raoult
  12. Bernard La Scola

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Abstract

Multiple SARS‐CoV‐2 variants have successively, or concomitantly spread worldwide since the summer of 2020. A few co‐infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co‐detection of signature mutations of different variants in a given genome. Here we report three infections in southern France with a Delta 21J_AY.4‐Omicron 21K/BA.1 “Deltamicron” recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1163–1421 reads and a mean nucleotide diversity of 0.1%–0.6%. It is composed of the near full‐length spike gene (from codons 156–179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening quantitative polymerase chain reaction (qPCR), we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.

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  1. Version published to 10.1002/jmv.27789
  2. ScreenIT

    SciScore for 10.1101/2022.03.03.22271812: (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.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    SARS-CoV-2 culture isolation was performed by inoculating 200 µL of respiratory sample on Vero E6 cells as previously described (La Scola et al., 2020).
    Vero E6
    suggested: None
    Software and Algorithms
    SentencesResources
    (Illumina Inc.)], mapping was performed with the bwa-mem2 tool (https://github.com/bwa-mem2/bwa-mem2) on the Wuhan-Hu-1 isolate genome (GenBank accession no. NC_045512.2) then cleaned with Samtools (https://www.htslib.org/), variant calling was carried out with freebayes (https://github.com/freebayes/freebayes) and consensus genomes were built using Bcftools (
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)

    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.

    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 10.1101/2022.03.03.22271812 on medRxiv