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Prevalence of SARS-CoV-2 variants in Italy (ISS Report n. 21 and June 7th 2022 ISS Flash Survey)

Prevalence of Variants of Concern of SARS-CoV-2 in Italy (according to the 21st ISS genomic surveillance Report and the ISS Flash Survey of June 7th 2022)

Published: 15 July 2022

The I-Co-Gen platform by the Italian National Institute of Health (ISS) is the most up to date system 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), supported by the Bruno Kessler Foundation and in collaboration 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. Results 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 (data from June 7th 2022). Data from the previous report (data from May 3rd 2022) are also included for the sake of comparison.
Prevalence of SARS-CoV-2 variants in Italy (ISS Report n. 21 and June 7th 2022 ISS Flash Survey)
The table reports the prevalence of the Omicron (B.1.1.529, derivative lineages BA.n and BA.1/BA.2 recombinant lineages) Variant of Concern (VOC) of SARS-CoV-2 in Italy. Additional information concerning the nomenclature and genomic features of this kind of variants can be found here, in a paper by the World Health Organization (WHO).
Prevalence data are aggregated by Region/Autonomous Province, the total number of genome sequences included 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 (May 3rd 2022) are included.

According to data collected during the Flash Survey performed by ISS on June 7th 2022, the Omicron variant (B.1.1.529, derivative lineages BA.n and BA.1/BA.2 recombinant lineages) is the only circulating SARS-CoV-2 variant in Italy, with an estimated prevalence of 100% at National level. However a shift in the prevalence of Omicron sublineages is observed: a substantial reduction of the prevalence of BA.2, from 93,83% on May 3rd to 62,98% on June 7th 2022 and a concomitant increase in the prevalence of the BA.4 and BA.5 sublineages from 0,47% to 11,41% and from 0,41% to 23,15% respectively. Finally, sequences related to BA.1/BA.2 recombinant lineages decreased as well, specifically, from a prevalence of 0,66% to 0,06% for XJ and from 0,59% to 0,12% for XM.

Please refer to the reports 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)