Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 to January 2022

  1. Paola Stefanelli
  2. Filippo Trentini
  3. Daniele Petrone
  4. Alessia Mammone
  5. Luigina Ambrosio
  6. Mattia Manica
  7. Giorgio Guzzetta
  8. Valeria d'Andrea
  9. Valentina Marziano
  10. Agnese Zardini
  11. Carla Molina Grane’
  12. Marco Ajelli
  13. Angela Di Martino
  14. Flavia Riccardo
  15. Antonino Bella
  16. Monica Sane Schepisi
  17. Francesco Maraglino
  18. Piero Poletti
  19. Anna Teresa Palamara
  20. Silvio Brusaferro
  21. Giovanni Rezza
  22. Patrizio Pezzotti
  23. Stefano Merler
  24. the Genomic SARS–CoV–2 National Surveillance Working Group
  25. the Italian Integrated Surveillance of COVID–19 Study Group

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Abstract

The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021.

Aim

To comprehensively describe Omicron spread in Italy in the 2 subsequent months and its impact on the overall SARS-CoV-2 circulation at population level.

Methods

We analyse data from four genomic surveys conducted across the country between December 2021 and January 2022. Combining genomic sequencing results with epidemiological records collated by the National Integrated Surveillance System, the Omicron reproductive number and exponential growth rate are estimated, as well as SARS-CoV-2 transmissibility.

Results

Omicron became dominant in Italy less than 1 month after its first detection, representing on 3 January 76.9–80.2% of notified SARS-CoV-2 infections, with a doubling time of 2.7–3.3 days. As of 17 January 2022, Delta variant represented < 6% of cases. During the Omicron expansion in December 2021, the estimated mean net reproduction numbers respectively rose from 1.15 to a maximum of 1.83 for symptomatic cases and from 1.14 to 1.36 for hospitalised cases, while remaining relatively stable, between 0.93 and 1.21, for cases needing intensive care. Despite a reduction in relative proportion, Delta infections increased in absolute terms throughout December contributing to an increase in hospitalisations. A significant reproduction numbers’ decline was found after mid-January, with average estimates dropping below 1 between 10 and 16 January 2022.

Conclusion

Estimates suggest a marked growth advantage of Omicron compared with Delta variant, but lower disease severity at population level possibly due to residual immunity against severe outcomes acquired from vaccination and prior infection.

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  1. Version published to 10.2807/1560-7917.es.2022.27.45.2200125
  2. ScreenIT

    SciScore for 10.1101/2022.01.27.22269949: (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 10.1101/2022.01.27.22269949v1 on medRxiv