Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein

  1. Philippe Colson
  2. Jérémy Delerce
  3. Emilie Burel
  4. Jordan Dahan
  5. Agnès Jouffret
  6. Florence Fenollar
  7. Nouara Yahi
  8. Jacques Fantini
  9. Bernard La Scola
  10. Didier Raoult

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Abstract

SARS-CoV-2 variants have become a major virological, epidemiological, and clinical concern, particularly with regard to the risk of escape from vaccine-induced immunity. Here, we describe the emergence of a new variant, with the index case returning from travel in Cameroon. For 13 SARS-CoV-2-positive patients living in the same geographical area of southeastern France, a qPCR test for screening variant-associated mutations showed an atypical combination. The genome sequences were obtained by next-generation sequencing with Oxford Nanopore Technologies on GridION instruments within about 8 h. Analysis revealed 46 nucleotide substitutions and 37 deletions, resulting in 30 amino acid substitutions and 12 deletions. Fourteen of the amino acid substitutions, including N501Y and E484K, and nine deletions are located in the spike protein. This genotype pattern led to the establishment of a new Pangolin lineage, named B.1.640.2, that is a phylogenetic sister group to the old B.1.640 lineage, which has now been renamed B.1.640.1. The lineages differ by 25 nucleotide substitutions and 33 deletions. The combination of mutations in these isolates and their phylogenetic position indicate, based on our previous definition, that they represent a new variant, which we have named “IHU”. These data are a further example of the unpredictability of the emergence of SARS-CoV-2 variants, and of their possible introduction into a given geographical area from abroad.

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  1. Version published to 10.1007/s00705-022-05385-y
  2. ScreenIT

    SciScore for 10.1101/2021.12.24.21268174: (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

    No key resources detected.

    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.

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  3. Version published to 10.1101/2021.12.24.21268174v1 on medRxiv