Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020.

Autor: Lai A; Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy.; Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy., Bergna A; Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy., Toppo S; Department of Molecular Medicine, University of Padova, Padua, Italy.; CRIBI Biotech Center, University of Padova, Padua, Italy., Morganti M; Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy., Menzo S; Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy., Ghisetti V; Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy., Bruzzone B; Hygiene Unit, IRCCS AOU San Martino-IST, Genoa, Italy., Codeluppi M; UOC of Infectious Diseases, Department of Oncology and Hematology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy., Fiore V; Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy., Rullo EV; Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy., Antonelli G; Department of Molecular Medicine, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy., Sarmati L; Infectious Diseases, Tor Vergata University, Rome, Italy., Brindicci G; Infectious Diseases Unit, University of Bari, Bari, Italy., Callegaro A; Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy., Sagnelli C; Department of Mental Health and Public Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy., Francisci D; Department of Medicine and Surgery, Clinic of Infectious Diseases, 'Santa Maria della Misericordia' Hospital, University of Perugia, Perugia, Italy., Vicenti I; Department of Medical Biotechnologies, University of Siena, Siena, Italy., Miola A; Intesa San Paolo Innovation Center-AI LAB, Turin, Italy., Tonon G; Center for Omics Sciences, IRCCS Ospedale San Raffaele, Milan, Italy.; Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy., Cirillo D; Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy., Menozzi I; Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy., Caucci S; Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy., Cerutti F; Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy., Orsi A; Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy., Schiavo R; UOC of Microbiology, Department of Clinical Pathology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy., Babudieri S; Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy., Nunnari G; Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy., Mastroianni CM; Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy., Andreoni M; Infectious Diseases, Tor Vergata University, Rome, Italy., Monno L; Infectious Diseases Unit, University of Bari, Bari, Italy., Guarneri D; Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy., Coppola N; Department of Mental Health and Public Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy., Crisanti A; Microbiology and Virology Diagnostic Unit, Padua University Hospital, Padua, Italy.; Department of Life Science, Imperial College London, South Kensington Campus Imperial College Road, London, SW7 AZ, UK., Galli M; Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy., Zehender G; Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy. gianguglielmo.zehender@unimi.it.; Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy. gianguglielmo.zehender@unimi.it.; CRC-Coordinated Research Center 'EpiSoMI', University of Milan, Milan, Italy. gianguglielmo.zehender@unimi.it.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2022 Apr 06; Vol. 12 (1), pp. 5736. Date of Electronic Publication: 2022 Apr 06.
DOI: 10.1038/s41598-022-09738-0
Abstrakt: 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.
(© 2022. The Author(s).)
Databáze: MEDLINE
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