Scientific Reports (Apr 2022)
Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020
- Alessia Lai,
- Annalisa Bergna,
- Stefano Toppo,
- Marina Morganti,
- Stefano Menzo,
- Valeria Ghisetti,
- Bianca Bruzzone,
- Mauro Codeluppi,
- Vito Fiore,
- Emmanuele Venanzi Rullo,
- Guido Antonelli,
- Loredana Sarmati,
- Gaetano Brindicci,
- Annapaola Callegaro,
- Caterina Sagnelli,
- Daniela Francisci,
- Ilaria Vicenti,
- Arianna Miola,
- Giovanni Tonon,
- Daniela Cirillo,
- Ilaria Menozzi,
- Sara Caucci,
- Francesco Cerutti,
- Andrea Orsi,
- Roberta Schiavo,
- Sergio Babudieri,
- Giuseppe Nunnari,
- Claudio M. Mastroianni,
- Massimo Andreoni,
- Laura Monno,
- Davide Guarneri,
- Nicola Coppola,
- Andrea Crisanti,
- Massimo Galli,
- Gianguglielmo Zehender,
- SCIRE-SARS-CoV-2 Italian Research Enterprise-Collaborative Group
Affiliations
- Alessia Lai
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan
- Annalisa Bergna
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan
- Stefano Toppo
- Department of Molecular Medicine, University of Padova
- Marina Morganti
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna
- Stefano Menzo
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche
- Valeria Ghisetti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino
- Bianca Bruzzone
- Hygiene Unit, IRCCS AOU San Martino-IST
- Mauro Codeluppi
- UOC of Infectious Diseases, Department of Oncology and Hematology, Guglielmo da Saliceto Hospital, AUSL Piacenza
- Vito Fiore
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari
- Emmanuele Venanzi Rullo
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina
- Guido Antonelli
- Department of Molecular Medicine, University Hospital Policlinico Umberto I, Sapienza University of Rome
- Loredana Sarmati
- Infectious Diseases, Tor Vergata University
- Gaetano Brindicci
- Infectious Diseases Unit, University of Bari
- Annapaola Callegaro
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII
- Caterina Sagnelli
- Department of Mental Health and Public Medicine, University of Campania “Luigi Vanvitelli”
- Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, “Santa Maria della Misericordia” Hospital, University of Perugia
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena
- Arianna Miola
- Intesa San Paolo Innovation Center-AI LAB
- Giovanni Tonon
- Center for Omics Sciences, IRCCS Ospedale San Raffaele
- Daniela Cirillo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele
- Ilaria Menozzi
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna
- Sara Caucci
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche
- Francesco Cerutti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino
- Andrea Orsi
- Department of Health Sciences (DISSAL), University of Genoa
- Roberta Schiavo
- UOC of Microbiology, Department of Clinical Pathology, Guglielmo da Saliceto Hospital, AUSL Piacenza
- Sergio Babudieri
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari
- Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina
- Claudio M. Mastroianni
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome
- Massimo Andreoni
- Infectious Diseases, Tor Vergata University
- Laura Monno
- Infectious Diseases Unit, University of Bari
- Davide Guarneri
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII
- Nicola Coppola
- Department of Mental Health and Public Medicine, University of Campania “Luigi Vanvitelli”
- Andrea Crisanti
- Microbiology and Virology Diagnostic Unit, Padua University Hospital
- Massimo Galli
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan
- Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan
- SCIRE-SARS-CoV-2 Italian Research Enterprise-Collaborative Group
- DOI
- https://doi.org/10.1038/s41598-022-09738-0
- Journal volume & issue
-
Vol. 12,
no. 1
pp. 1 – 12
Abstract
Abstract The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including < 80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 (20B) most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 (20D) developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.
