SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing

  1. Ana Rita Goncalves Cabecinhas
  2. Tim Roloff
  3. Madlen Stange
  4. Claire Bertelli
  5. Michael Huber
  6. Alban Ramette
  7. Chaoran Chen
  8. Sarah Nadeau
  9. Yannick Gerth
  10. Sabine Yerly
  11. Onya Opota
  12. Trestan Pillonel
  13. Tobias Schuster
  14. Cesar M. J. A. Metzger
  15. Jonas Sieber
  16. Michael Bel
  17. Nadia Wohlwend
  18. Christian Baumann
  19. Michel C. Koch
  20. Pascal Bittel
  21. Karoline Leuzinger
  22. Myrta Brunner
  23. Franziska Suter-Riniker
  24. Livia Berlinger
  25. Kirstine K. Søgaard
  26. Christiane Beckmann
  27. Christoph Noppen
  28. Maurice Redondo
  29. Ingrid Steffen
  30. Helena M. B. Seth-Smith
  31. Alfredo Mari
  32. Reto Lienhard
  33. Martin Risch
  34. Oliver Nolte
  35. Isabella Eckerle
  36. Gladys Martinetti Lucchini
  37. Emma B. Hodcroft
  38. Richard A. Neher
  39. Tanja Stadler
  40. Hans H. Hirsch
  41. Stephen L. Leib
  42. Lorenz Risch
  43. Laurent Kaiser
  44. Alexandra Trkola
  45. Gilbert Greub
  46. Adrian Egli

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Abstract

The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.

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    SciScore for 10.1101/2021.02.11.21251589: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: In addition, the study was approved as a multi-center study by the leading ethical committee (Ethik Kommission Nordwest-und Zentralschweiz, EKNZ; Approval number 2019-01291).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your code and 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.

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  2. Version published to 10.3390/microorganisms9040677
  3. Version published to 10.1101/2021.02.11.21251589 on medRxiv