Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020

  1. Antonin Bal
  2. Gregory Destras
  3. Alexandre Gaymard
  4. Karl Stefic
  5. Julien Marlet
  6. Sébastien Eymieux
  7. Hadrien Regue
  8. Quentin Semanas
  9. Constance d’Aubarede
  10. Geneviève Billaud
  11. Frédéric Laurent
  12. Claudia Gonzalez
  13. Yahia Mekki
  14. Martine Valette
  15. Maude Bouscambert
  16. Catherine Gaudy-Graffin
  17. Bruno Lina
  18. Florence Morfin
  19. Laurence Josset
  20. the COVID-Diagnosis HCL Study Group

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Abstract

We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69–V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.

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  1. Version published to 10.2807/1560-7917.es.2021.26.3.2100008
  2. Version published to 10.1101/2020.11.10.20228528v3 on medRxiv
  3. Version published to 10.1101/2020.11.10.20228528v2 on medRxiv
  4. ScreenIT

    SciScore for 10.1101/2020.11.10.20228528: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot 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.

    About SciScore

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  5. Version published to 10.1101/2020.11.10.20228528v1 on medRxiv