Genomic Epidemiology of the Main SARS‐CoV‐2 Variants Circulating in Italy During the Omicron Era
Since early 2022 the Omicron variant has rapidly spread worldwide, becoming the dominant variant to date. The study aimed to investigate the clinical and epidemiological characteristics of COVID-19 patients and reconstruct the genomic epidemiology of main SARS-CoV-2 Omicron sublineages in Italy in 2022. A total of 8970 SARS-CoV-2 samples were studied, and phylogenetic analyses were focused on BA.1, BA.2, and BA.5 subvariants. More than half of subjects received three doses of vaccine and experienced a reinfection. A significant larger proportion of unvaccinated subjects presented reinfection compared with vaccinated. Clusters presented a tMRCA between September-November 2021 (BA.1), November 2021-January 2022 (BA.2), and October 2021-May 2022 (BA.5). R<sub>e</sub> values showed the highest level between September-October, January-February 2022, and May 2022 for BA.1, BA.2 and BA.5, respectively. Limited number of studied variant sequences are included in clusters. The spread rate of the studied variant exceeded its evolutionary rate. No single sublineage had sufficient time to differentiate into large clusters, but only into small and fragmented groups sharing the same recent ancestor. These analyses dissect the epidemiological dynamics of Omicron sublineages in Italy over a period of great epidemiological changes in the COVID-19 epidemic.
Authors
- Arianna Gabrieli (ORCID: https://orcid.org/0000-0002-2657-8025)
- Matilde Ogliastro
- Vanessa De Pace (ORCID: https://orcid.org/0000-0002-9822-6520)
- Carla Della Ventura (ORCID: https://orcid.org/0009-0005-0055-1827)
- Fabio Sagradi
- Spinello Antinori (ORCID: https://orcid.org/0000-0003-0569-9407)
- Nicola Clementi (ORCID: https://orcid.org/0000-0002-1822-9861)
- Luca Carioti (ORCID: https://orcid.org/0000-0003-1713-8682)
- Marco Iannetta (ORCID: https://orcid.org/0000-0002-6938-8627)
- Gianguglielmo Zehender (ORCID: https://orcid.org/0000-0002-1886-2915)
- Carla Acciarri
- Loredana Sarmati (ORCID: https://orcid.org/0000-0003-1452-0333)
- Bianca Bruzzone (ORCID: https://orcid.org/0000-0002-3456-1899)
- Angelo Genoni (ORCID: https://orcid.org/0000-0001-9848-2981)
- Nicasio Mancini (ORCID: https://orcid.org/0000-0003-0637-0910)
- Ilaria Vicenti (ORCID: https://orcid.org/0000-0002-4306-2960)
- Sophie Testa
- Greta Marchegiani (ORCID: https://orcid.org/0009-0006-7878-2833)
- Alessia Lai (ORCID: https://orcid.org/0000-0002-3174-5721)
- Stefano Rusconi (ORCID: https://orcid.org/0000-0002-0375-9990)
- Annalisa Bergna (ORCID: https://orcid.org/0000-0003-1653-1917)
- Agostino Riva (ORCID: https://orcid.org/0000-0003-3171-3049)
- Francesca Ceccherini‐Silberstein (ORCID: https://orcid.org/0000-0002-6024-5101)
- Federica Novazzi (ORCID: https://orcid.org/0000-0002-2741-8840)
- Silvia Ronchiadin (ORCID: https://orcid.org/0000-0001-7169-3893)
- Francesca Drago Ferrante (ORCID: https://orcid.org/0000-0003-4950-0703)
- Alessandro Occhionero
- Monica Ferraris (ORCID: https://orcid.org/0000-0003-4449-4308)
- Maria Concetta Bellocchi (ORCID: https://orcid.org/0000-0001-7717-2343)
- Sara Caucci
- Stefano Menzo (ORCID: https://orcid.org/0000-0002-4425-3750)
- Massimo De Paschale (ORCID: https://orcid.org/0000-0002-4770-6399)
- G Canavesi
- Harcel Djaya Mbissam
- Leonardo Lanfranchi
- Daniela Francisci
Institutions
- University of Siena (IT)
- University of Insubria (IT)
- University of Rome Tor Vergata (IT)
- Marche Polytechnic University (IT)
- Vita-Salute San Raffaele University (IT)
- University of Milan (IT)
- University of Perugia (IT)
- Ospedale di Circolo e Fondazione Macchi (IT)
- Ospedale Policlinico San Martino (IT)
- Istituti di Ricovero e Cura a Carattere Scientifico (IT)
- Azienda Ospedaliera Ospedale Civile di Legnano (IT)
- Istituti Ospitalieri di Cremona (IT)
- Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele (IT)
- Aziende Socio Sanitarie Territoriale Ovest Milanese
- University of Genoa (IT)
Publication Details
- Journal
- Journal of Medical Virology
- Published
- 2025-02-01
- DOI
- https://doi.org/10.1002/jmv.70215
- Citations
- 2
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 2.79
Funders
- Università degli Studi di Milano
- European Commission
- Ministero dell'Università e della Ricerca
- HORIZON EUROPE Framework Programme