Evidence map›Paper›PMID 39936851›Full record

ArticleJournal of medical virology2025

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 and 27 more

Abstract read
In one paragraph

Article in Journal of medical virology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Is early combination therapy associated with lower risk of respiratory failure in severely immunocompromised hosts with COVID-19? a target trial emulation study from the omicron-dominant era.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026
    Article
  2. Article
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

37 authors.

Annalisa BergnaDepartment of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.ORCID 0000-0003-1653-1917
Alessia LaiDepartment of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.ORCID 0000-0002-3174-5721
Fabio SagradiUnit of Infectious Diseases, Azienda Socio-Sanitaria Territoriale Cremona, Cremona, Italy.
Stefano MenzoDepartment of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy.
Nicasio ManciniDepartment of Medicine and Technological Innovation, University of Insubria, Varese, Italy.
Bianca BruzzoneHygiene Unit, IRCCS AOU San Martino-IST, Genoa, Italy.
Stefano RusconiDepartment of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.ORCID 0000-0002-0375-9990
Greta MarchegianiDepartment of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.
Nicola ClementiLaboratory of Microbiology and Virology, Università "Vita-Salute" San Raffaele, Milan, Italy.ORCID 0000-0002-1822-9861
Daniela FrancisciDepartment of Medicine and Surgery, Clinic of Infectious Diseases, "Santa Maria della Misericordia" Hospital, University of Perugia, Perugia, Italy.
Ilaria VicentiDepartment of Medical Biotechnologies, University of Siena, Siena, Italy.ORCID 0000-0002-4306-2960
Silvia RonchiadinIntesa Sanpaolo Innovation Center- Artificial Intelligence Lab, Turin, Italy.
Harcel Djaya MbissamDepartment of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
Carla Della VenturaDepartment of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
Leonardo LanfranchiUnit of Infectious Diseases, Azienda Socio-Sanitaria Territoriale Cremona, Cremona, Italy.
Sophie TestaUnit of Infectious Diseases, Azienda Socio-Sanitaria Territoriale Cremona, Cremona, Italy.
Sara CaucciDepartment of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy.
Carla AcciarriDepartment of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy.
Luca CariotiDepartment of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.ORCID 0000-0003-1713-8682
Alessandro OcchioneroClinic of Infectious Diseases - AOU delle Marche, Ancona, Italy.
Federica NovazziDepartment of Medicine and Technological Innovation, University of Insubria, Varese, Italy.ORCID 0000-0002-2741-8840
Angelo Paolo GenoniDepartment of Medicine and Technological Innovation, University of Insubria, Varese, Italy.
Francesca Drago FerranteDepartment of Medicine and Technological Innovation, University of Insubria, Varese, Italy.
Vanessa De PaceHygiene Unit, IRCCS AOU San Martino-IST, Genoa, Italy.
Monica FerrarisHygiene Unit, IRCCS AOU San Martino-IST, Genoa, Italy.
Matilde OgliastroDepartment of Health Sciences (DISSAL), University of Genoa, Genoa, Italy.
Arianna GabrieliDepartment of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
Massimo De PaschaleUnit of Microbiology, Legnano Hospital, ASST Ovest Milanese, Legnano, Italy.ORCID 0000-0002-4770-6399
Giada CanavesiOspedale Civile di Legnano ASST Ovest Milanese, University of Milan, Legnano, Italy.
Maria Concetta BellocchiDepartment of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.
Marco IannettaDepartment of System Medicine, Clinical Infectious Diseases, Tor Vergata University, Rome, Italy.
Loredana SarmatiDepartment of System Medicine, Clinical Infectious Diseases, Tor Vergata University, Rome, Italy.
Francesca Ceccherini-SilbersteinDepartment of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.
Agostino RivaDepartment of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.ORCID 0000-0003-3171-3049
Spinello AntinoriDepartment of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
Gianguglielmo ZehenderDepartment of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.ORCID 0000-0002-1886-2915
SARS‐CoV‐2 ITALIAN RESEARCH ENTERPRISE – collaborative Group

Funding

This work was supported by the European Union's Horizon Europe Research and Innovation Actions under grant no. 101046041, and from the Ministero dell'Università e della Ricerca (PRIN 202022GZEHE_01) and partly supported by EU funding within the NextGeneration EU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (Project no. PE00000007, INF-ACT).
6 · The paper itself

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). R

Indexed as

COVID-19SARS-CoV-2AdolescentAdultAgedAged, 80 and overCOVID-19 VaccinesFemaleGenome, ViralHumansItalyMaleMiddle AgedMolecular EpidemiologyPhylogenyYoung AdultCOVID-19 VaccinesCOVID‐19 clinical aspectsgenomic epidemiologyOmicronphylogenySARS‐CoV‐2 variants

Identifiers

PMID39936851
PMCPMC11816846

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.