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Genomic Epidemiology of the Main SARS-CoV-2 Variants Circulating in Italy During the Omicron Era.

Annalisa Bergna·Alessia Lai·Fabio Sagradi·Stefano Menzo·Nicasio Mancini·Bianca Bruzzone·Stefano Rusconi·Greta Marchegiani·Nicola Clementi·Daniela Francisci·Ilaria Vicenti·Silvia Ronchiadin·Harcel Djaya Mbissam·Carla Della Ventura·Leonardo Lanfranchi·Sophie Testa·Sara Caucci·Carla Acciarri·Luca Carioti·Alessandro Occhionero·Federica Novazzi·Angelo Paolo Genoni·Francesca Drago Ferrante·Vanessa De Pace·Monica Ferraris·Matilde Ogliastro·Arianna Gabrieli·Massimo De Paschale·Giada Canavesi·Maria Concetta Bellocchi·Marco Iannetta·Loredana Sarmati·Francesca Ceccherini-Silberstein·Agostino Riva·Spinello Antinori·Gianguglielmo Zehender·SARS‐CoV‐2 ITALIAN RESEARCH ENTERPRISE – collaborative Group
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Abstract

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). Re 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.

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HumansItalyCOVID-19SARS-CoV-2PhylogenyMiddle AgedMaleFemaleAdultAgedGenome, ViralMolecular EpidemiologyYoung AdultCOVID-19 VaccinesAged, 80 and overAdolescentCOVID‐19 clinical aspectsOmicronSARS‐CoV‐2 variantsgenomic epidemiologyphylogenyJournal ArticleResearch Support, Non-U.S. Gov't

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Annalisa Bergna, Alessia Lai, Fabio Sagradi, Stefano Menzo, Nicasio Mancini, Bianca Bruzzone, Stefano Rusconi, Greta Marchegiani, Nicola Clementi, Daniela Francisci, Ilaria Vicenti, Silvia Ronchiadin, Harcel Djaya Mbissam, Carla Della Ventura, Leonardo Lanfranchi, Sophie Testa, Sara Caucci, Carla Acciarri, Luca Carioti, Alessandro Occhionero, Federica Novazzi, Angelo Paolo Genoni, Francesca Drago Ferrante, Vanessa De Pace, Monica Ferraris, Matilde Ogliastro, Arianna Gabrieli, Massimo De Paschale, Giada Canavesi, Maria Concetta Bellocchi, Marco Iannetta, Loredana Sarmati, Francesca Ceccherini-Silberstein, Agostino Riva, Spinello Antinori, Gianguglielmo Zehender, SARS‐CoV‐2 ITALIAN RESEARCH ENTERPRISE – collaborative Group. 2025. Genomic Epidemiology of the Main SARS-CoV-2 Variants Circulating in Italy During the Omicron Era.. https://doi.org/10.1002/jmv.70215

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