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Prevalence of SARS-CoV-2 variants in Italy (ISS Report n. 26 and November 8th 2022 ISS Flash Survey)

Prevalence of variants of concern of SARS-CoV-2 in Italy, according to the 26th genomic surveillance report and the Flash Survey of November 8th 2022 by ISS

Published: 20 December 2022

The I-Co-Gen platform by the Italian National Institute of Health (ISS) is the reference point for the collection and analysis of SARS-CoV-2 genome sequencing data in Italy. By periodic analysis of the data processed through I-Co-Gen, the Italian National Institute of Health (ISS), in collaboration with the Bruno Kessler Foundation and with the Italian Ministry of Health, the Regional administrations and the Autonomous Provinces (PPAA), have undertaken a coordinated effort to monitor the spread of SARS-CoV-2 variants in Italy. Data are released periodically in the form of brief reports (further details here, Italian only).
This highlight provides a brief overview of the main results from the most recent report (November 8th 2022). Data from the previous report (October 4th 2022) are also included for the sake of comparison.
Prevalence of SARS-CoV-2 variants in Italy (ISS Report n. 26 and November 8th 2022 ISS Flash Survey)
The table reports the prevalence of the Omicron (B.1.1.529, derivative lineages BA.n and recombinant lineages) Variant of Concern (VOC) of SARS-CoV-2 in Italy. Additional information concerning the nomenclature and genomic features of this and other variants can be found here, in a paper by the World Health Organization (WHO).
Data are aggregated by Region/Autonomous Province and the total number of genome sequences considered in the analysis is reported as well. Cumulative data are also reported to present an overview of the current situation in Italy.
Matched data from the previous report (October 4th 2022) are included.

According to the results of the November 8th 2022 ISS Flash Survey, the Omicron variant (B.1.1.529, its derivative lineages BA.n and recombinant lineages) is the dominant variant in Italy and its prevalence at National level is 99,84%.
With an average prevalence of 91,53% in the Peninsula, the BA.5 sublineage and its descendants are the dominant family of SARS-CoV-2 lineages in Italy; indeed the cumulative prevalence of BA.5 and its child lineages is 81,8% or above in all Regions/PPAA analysed. About 30,7% of the total number of genomes assigned to BA.5 belongs to the BQ.1.n sublineage and 14,7% to BF.7.n (as stated in Report n. 26).
Interestingly, a slight increase in the prevalence of the BA.2 sub-lineage from 2,33% in the previous update (data from October 4th 2022) to 3,98% in the current update (data from November 8th 2022) is observed. Data also includes sequences assigned to BA.2.75 (and sublineages), an Omicron sublineage under international monitoring.
On the contrary, the prevalence of the BA.4 sublineage decreased from 4,27% to 1,95% in the current update.
Finally, all of the Omicron/Omicron recombinant lineages identified during the survey belong to the XBB.1 lineage and their cumulative prevalence equals to 2,39%.
To conclude, we highlight that the remaining 0,16% of sequences collected during the November 8th Flash Survey and not assigned to the Omicron variant or its sublineages belong to the Omicron/Delta recombinant XAY.1.

Please refer to the report as provided on the ISS website at the following links (italian only) for a complete reference:

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

Source: ISS (prevalence data)