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Prevalence of SARS-CoV-2 variants in Italy (ISS report n. 15 and December 20th 2021 ISS Flash Survey)

Prevalence of SARS-CoV-2 variants of concern in Italy (adapted from the 15th ISS genomic surveillance report and from the ISS Flash Survey of December 20th 2021)

Published: 14 January 2022

The I-Co-Gen platform developed by the Italian National Institute of Health (ISS), and released in April 2021, is currently the most up to date and reliable system for the collection and analysis of SARS-CoV-2 genome sequencing data in Italy. Based on the data incorporated in I-Co-Gen, the Italian National Institute of Health (ISS), supported by the Bruno Kessler Foundation and in collaboration with the Italian Ministry of Health, the Regional administrations and the Autonomous Provinces (PPAA), have started an ongoing and coordinated effort for the accurate mapping of the spread of SARS-CoV-2 variants in Italy. Results are released periodically in the form of brief reports (further details here).
This highlight provides a brief overview of the main results presented in the most recent reports (data from December 6th and December 20th 2021). Data from the previous report (September 28th 2021) are also included to facilitate the comparison.
ISS decided to perform two different Flash Surveys in December, to monitor more carefully the spread of the Omicron variant in Italy. This highlight includes both.
Prevalence of SARS-CoV-2 variants in Italy (ISS report n. 15 and December 20th 2021 ISS Flash Survey)
The table reports the prevalence of the four Variants of Concern (VOCs) of SARS-CoV-2 currently recognized by international health authorities: Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529). Additional information concerning the nomenclature and features of these variants can be found here, in a paper by the World Health Organization (WHO).
Prevalence data are stratified by Region/Autonomous Province, the total number of genomic sequences included in the analysis is reported as well. Aggregated data are also reported to offer an overview of the current situation in Italy. A total of 7572 genomes were sequenced in Italy in December 2021; of these 2127 and 2139 have been included in the Flash Survey of December 6th and December 20th respectively.
Matched data from the previous report are included for the sake of comparison (September 28th 2021).

According to the most recent ISS report (genomic data from December 6th 2021) and the subsequent Flash Survey of December 20th 2021, the Delta variant of the virus (lineage B.1.617.2 and derivative lineages AY.n) still is the most prevalent variant in Italy. However, the prevalence of Delta has steadily decreased from 100% (genomic data from September 28th 2021), to 99,53% on December 6th and, finally, reaching a value equal to 79,0% on December 20th 2021.
The most likely hypothesis is that this rapid decrease in the prevalence of the Delta variant correlates with the detection in Italy of the new Variant of Concern (VOC) identified for the first time in South Africa in November 2021 and named Omicron (lineage B.1.1.529 and derivative lineages BA.n) by the World Health Organization (WHO). Additional information about this new variant is available from the dedicated update on the COVID-19 Data Portal Italy. Data collected on December 6th and December 20th, infact, highlight a rapid increase in the prevalence of the Omicron variant, which increased from 0,32% to 21,0% in the span of two weeks. However, considering the fast rate of transmission of Omicron [1] and the recent surge in the number of cases of COVID-19 in Italy a further increase of the prevalence of this variant is expected in the near future.
Finally, no cases of COVID-19 associated with other VOC (either Beta (B.1.351) or Gamma (P.1)) have been reported.

To obtain detailed information concerning the data included in the report, the methods applied and the technical limitations of the survey, please refer to the complete report as available on the ISS website at the following links (italian only):

The previous report is available at the following links (italian only):

Sources:
ISS (prevalence data),
[1] “ECDC publishes new risk assessment on further emergence of Omicron variant”, ECDC