Surveillance Open Access
Like 0



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


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.


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.


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.


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.


Article metrics loading...

Loading full text...

Full text loading...



  1. European Centre for Disease Prevention and Control (ECDC). Assessment of the further emergence and potential impact of the SARS-CoV-2 Omicron variant of concern in the context of ongoing transmission of the Delta variant of concern in the EU/EEA, 18th update. Stockholm: ECDC; December 2021. Available from: https://www.ecdc.europa.eu/sites/default/files/documents/covid–19–assessment–further–emergence–omicron–18th–risk–assessment–december–2021.pdf
  2. Cereda D, Manica M, Tirani M, Rovida F, Demicheli V, Ajelli M, et al. The early phase of the COVID–19 epidemic in Lombardy, Italy. Epidemics. 2021;37:100528.  https://doi.org/10.1016/j.epidem.2021.100528  PMID: 34814093 
  3. Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, et al. Assessing transmissibility of SARS–CoV–2 lineage B.1.1.7 in England. Nature. 2021;593(7858):2669.  https://doi.org/10.1038/s41586-021-03470-x  PMID: 33767447 
  4. Griffin J, Casey M, Collins Á, Hunt K, McEvoy D, Byrne A, et al. Rapid review of available evidence on the serial interval and generation time of COVID–19. BMJ Open. 2020;10(11):e040263.  https://doi.org/10.1136/bmjopen-2020-040263  PMID: 33234640 
  5. Hu S, Wang W, Wang Y, Litvinova M, Luo K, Ren L, et al. Infectivity, susceptibility, and risk factors associated with SARS–CoV–2 transmission under intensive contact tracing in Hunan, China. Nat Commun. 2021;12(1):1533.  https://doi.org/10.1038/s41467-021-21710-6  PMID: 33750783 
  6. Kremer C, Ganyani T, Chen D, Torneri A, Faes C, Wallinga J, et al. Authors’ response: Estimating the generation interval for COVID–19 based on symptom onset data. Euro Surveill. 2020;25(29):2001269.  https://doi.org/10.2807/1560-7917.ES.2020.25.29.2001269  PMID: 32720639 
  7. Pezzotti P, Punzo O, Bella A, Del Manso M, Urdiales AM, Fabiani M, et al. The challenges of the outbreak: the Italian COVID–19 integrated surveillance system. Eur J Public Health. 2020;30(Supplement_5);ckaa165.356.  https://doi.org/10.1093/eurpub/ckaa165.356 
  8. Manica M, Litvinova M, De Bellis A, Guzzetta G, Mancuso P, Vicentini M, et al. Estimation of the incubation period and generation time of SARS–CoV–2 Alpha and Delta variants from contact tracing data. arXiv.2203.07063. 2022Mar11.  https://doi.org/10.48550/arXiv.2203.07063 
  9. Manica M, De Bellis A, Guzzetta G, Mancuso P, Vicentini M, Venturelli F, et al. , Reggio Emilia COVID-19 Working Group. Intrinsic generation time of the SARS-CoV-2 Omicron variant: An observational study of household transmission. Lancet Reg Health Eur. 2022;19:100446.  https://doi.org/10.1016/j.lanepe.2022.100446  PMID: 35791373 
  10. Monitoraggio delle varianti del virus SARS–CoV–2 di interesse in sanità pubblica in Italia [Monitoring of SARS-CoV-2 variants of public health interest in Italy]. [Accessed 21 Jan 2022]. Available from: https://www.epicentro.iss.it/coronavirus/sars–cov–2–monitoraggio–varianti
  11. Ferguson N. Report 49: Growth and immune escape of the Omicron SARS–CoV–2 variant of concern in England. Imperial College London; 2021 Dec. [Accessed 19 Jan 2022]. Available from: http://spiral.imperial.ac.uk/handle/10044/1/93038
  12. Grabowski F, Kochańczyk M, Lipniacki T. The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0-3.3 Days Can Be Explained by Immune Evasion. Viruses. 2022;14(2):294.  https://doi.org/10.3390/v14020294  PMID: 35215887 
  13. Official Gazette of the Italian Republic. Decree of Italian President of Council of Ministers of 24 December 2021. Italian. [Accessed 7 Oct 2021]. Available from: https://www.gazzettaufficiale.it/eli/id/2021/12/24/21G00244/sg
  14. Official Gazette of the Italian Republic. Decree of Italian President of Council of Ministers of 30 December 2021. Italian. [Accessed 7 October 2021]. Available from: https://www.gazzettaufficiale.it/eli/id/2021/12/30/21G00258/sg
  15. Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, et al. , PITCH Consortium, COVID-19 Genomics UK (COG-UK) Consortium. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat Microbiol. 2022;7(8):1161-79.  https://doi.org/10.1038/s41564-022-01143-7  PMID: 35798890 
  16. Rössler A, Riepler L, Bante D, von Laer D, Kimpel J. SARS-CoV-2 Omicron Variant Neutralization in Serum from Vaccinated and Convalescent Persons. N Engl J Med. 2022;386(7):698-700.  https://doi.org/10.1056/NEJMc2119236  PMID: 35021005 
  17. Pearson CAB, Silal SP, Li MWZ, Dushoff J, Bolker BM, Abbott S, et al. Bounding the levels of transmissibility & immune evasion of the Omicron variant in South Africa. MedRxiv. .  https://doi.org/10.1101/2021.12.19.21268038 
  18. Planas D, Saunders N, Maes P, Guivel-Benhassine F, Planchais C, Buchrieser J, et al. Considerable escape of SARS-CoV-2 Omicron to antibody neutralization. Nature. 2022;602(7898):671-5.  https://doi.org/10.1038/s41586-021-04389-z  PMID: 35016199 
  19. Menegale F, Manica M, Zardini A, Guzzetta G, Marziano V, d’Andrea V, et al. Waning of SARS–CoV–2 vaccine–induced immunity: A systematic review and secondary data analysis. medRxiv. 2022.07.04.22277225; doi:  https://doi.org/10.1101/2022.07.04.22277225 
  20. Kirsebom FCM, Andrews N, Stowe J, Toffa S, Sachdeva R, Gallagher E, et al. COVID-19 vaccine effectiveness against the omicron (BA.2) variant in England. Lancet Infect Dis. 2022;22(7): S1473–3099(22)00309–7.  https://doi.org/10.1016/S1473-3099(22)00309-7  PMID: 35623379 
  21. Björk J, Bonander C, Moghaddassi M, Rasmussen M, Malmqvist U, Inghammar M, et al. COVID–19 vaccine effectiveness against severe disease from SARS–CoV–2 Omicron BA.1 and BA.2 subvariants–surveillance results from southern Sweden, December 2021 to March 2022. Euro Surveill. 2022;27(18):2200322.  https://doi.org/10.2807/1560-7917.ES.2022.27.18.2200322  PMID: 35514304 
  22. Davies MA, Kassanjee R, Rousseau P, Morden E, Johnson L, Solomon W, et al. Outcomes of laboratory–confirmed SARS–CoV–2 infection in the Omicron–driven fourth wave compared with previous waves in the Western Cape Province, South Africa. Trop Med Int Health. 2022;27(6):56473.  https://doi.org/10.1111/tmi.13752  PMID: 35411997 
  23. Lauring AS, Tenforde MW, Chappell JD, Gaglani M, Ginde AA, McNeal T, et al. , Influenza and Other Viruses in the Acutely Ill (IVY) Network. Clinical severity of, and effectiveness of mRNA vaccines against, covid–19 from omicron, delta, and alpha SARS–CoV–2 variants in the United States: prospective observational study. BMJ. 2022;376:e069761.  https://doi.org/10.1136/bmj-2021-069761  PMID: 35264324 
  24. Marziano V, Guzzetta G, Menegale F, Sacco C, Petrone D, Urdiales AM, et al. The decline of COVID–19 severity and lethality over two years of pandemic. medRxiv2022.07.01.22277137; doi:  https://doi.org/10.1101/2022.07.01.22277137 

Data & Media loading...

Supplementary data

Submit comment
Comment moderation successfully completed
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error