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. 2025 Feb;97(2):e70215.
doi: 10.1002/jmv.70215.

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

Annalisa Bergna  1 , Alessia Lai  1 , Fabio Sagradi  2 , Stefano Menzo  3 , Nicasio Mancini  4   5 , Bianca Bruzzone  6 , Stefano Rusconi  1   7 , Greta Marchegiani  8 , Nicola Clementi  9   10 , Daniela Francisci  11 , Ilaria Vicenti  12 , Silvia Ronchiadin  13 , Harcel Djaya Mbissam  1 , Carla Della Ventura  1 , Leonardo Lanfranchi  2 , Sophie Testa  2 , Sara Caucci  3 , Carla Acciarri  3 , Luca Carioti  8 , Alessandro Occhionero  14 , Federica Novazzi  4   5 , Angelo Paolo Genoni  4   5 , Francesca Drago Ferrante  4   5 , Vanessa De Pace  6 , Monica Ferraris  6 , Matilde Ogliastro  15 , Arianna Gabrieli  1   16 , Massimo De Paschale  16 , Giada Canavesi  7 , Maria Concetta Bellocchi  8 , Marco Iannetta  17 , Loredana Sarmati  17 , Francesca Ceccherini-Silberstein  8 , Agostino Riva  1 , Spinello Antinori  1 , Gianguglielmo Zehender  1 ; SARS‐CoV‐2 ITALIAN RESEARCH ENTERPRISE – collaborative Group
Collaborators, Affiliations

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

Annalisa Bergna et al. J Med Virol. 2025 Feb.

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.

Keywords: COVID‐19 clinical aspects; Omicron; SARS‐CoV‐2 variants; genomic epidemiology; phylogeny.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Dynamics of the SARS‐CoV‐2 epidemic in Italy, in term of lineages, during 2022.
Figure 2
Figure 2
(A) Bayesian Skygrid plot of BA.1 variant. The y‐axis indicates the effective population (Ne), the x‐axis shows the time expressed in dates. The thick line in the graph indicates the median of the value of the estimate, while the blue area indicates 95% HPD. (B) Birth‐death skyline plot of BA.1 variant, in relation to time (x‐axis) and the effective reproduction rate (R e) (y‐axis).
Figure 3
Figure 3
(A) Bayesian Skygrid plot of BA.2 variant. The y‐axis indicates the effective population (Ne), the x‐axis shows the time expressed in dates. The thick line in the graph indicates the median of the value of the estimate, while the blue area indicates 95% HPD. (B) Birth‐death skyline plot of BA.2 variant, in relation to time (x‐axis) and the effective reproduction rate (R e) (y‐axis).
Figure 4
Figure 4
(A) Bayesian Skygrid plot of BA.5 variant. The y‐axis indicates the effective population (Ne), the x‐axis shows the time expressed in dates. The thick line in the graph indicates the median of the value of the estimate, while the blue area indicates 95% HPD. (B) Birth‐death skyline plot of BA.5 variant, in relation to time (x‐axis) and the effective reproduction rate (R e) (y‐axis).
See this image and copyright information in PMC

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