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.

Details

Title
Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020
Author
Lai, Alessia 1 ; Bergna Annalisa 2 ; Toppo Stefano 3 ; Morganti, Marina 4 ; Menzo Stefano 5 ; Ghisetti Valeria 6 ; Bruzzone Bianca 7 ; Codeluppi Mauro 8 ; Fiore, Vito 9 ; Rullo Emmanuele Venanzi 10 ; Antonelli Guido 11 ; Sarmati Loredana 12 ; Brindicci Gaetano 13 ; Callegaro Annapaola 14 ; Sagnelli Caterina 15 ; Francisci Daniela 16 ; Vicenti Ilaria 17 ; Miola Arianna 18 ; Tonon Giovanni 19 ; Cirillo, Daniela 20 ; Menozzi Ilaria 4 ; Caucci, Sara 5 ; Cerutti, Francesco 6 ; Orsi, Andrea 21 ; Schiavo, Roberta 22 ; Babudieri Sergio 9 ; Nunnari Giuseppe 10 ; Mastroianni, Claudio M 23 ; Andreoni Massimo 12 ; Monno, Laura 13 ; Guarneri Davide 14 ; Coppola, Nicola 15 ; Crisanti, Andrea 24 ; Galli Massimo 2 ; Zehender Gianguglielmo 25 ; Balotta Claudia 2 ; Ventura, Carla della 2 ; Schiuma Marco 2 ; Lavezzo Enrico 26 ; Fontana, Paolo 27 ; Bianco, Luca 28 ; Bertolotti Luigi 28 ; Manuto Laura 26 ; Grazioli, Marco 26 ; Federico, Bianca 26 ; Del Vecchio Claudia 26 ; Franchin Elisa 26 ; Onelia Francesco 26 ; Spitaleri Andrea 29 ; Saluzzo Francesca 29 ; Lorenzin Giovanni 29 ; Pongolini Stefano 4 ; Scaltriti Erika 4 ; Soliani, Laura 4 ; Bagnarelli Patrizia 5 ; Turchi Chiara 5 ; Onofri Valerio 5 ; Melchionda Filomena 5 ; Tagliabracci Adriano 5 ; Burdino Elisa 6 ; Milia, Maria Grazia 6 ; Caligiuri Patrizia 7 ; De Pace Vanessa 7 ; Ricucci Valentina 7 ; Domnich Alexander 7 ; Boccotti Simona 21 ; Cristina Leoni Maria 30 ; Cascio Giuliana Lo 30 ; Rubino Salvatore 31 ; Lai, Vincenzo 31 ; Rocca Giulia 31 ; Govoni Rosalba 31 ; Mancuso Giuseppe 32 ; Campagna, Roberta 11 ; Mazzuti Laura 11 ; Oliveto Giuseppe 11 ; Turriziani Ombretta 11 ; Campogiani Laura 12 ; Compagno Mirko 12 ; Coppola Luigi 12 ; Crea Angela Maria Antonia 12 ; De, Simone Giuseppe 12 ; Di Lorenzo Andrea 12 ; Ferrari Ludovica 12 ; Iannetta, Marco 12 ; Malagnino Vincenzo 12 ; Mulas Tiziana 12 ; Rossi, Benedetta 12 ; Spalliera Ilaria 12 ; Tedde Simona 12 ; Teti Elisabetta 12 ; Vitale Pietro 12 ; Zordan Marta 12 ; Milano Eugenio 13 ; Lagioia Antonella 13 ; Gallitelli Rosa 14 ; Starace, Mario 15 ; Minichini Carmine 15 ; Alessia, Di Fraia 15 ; Schioppa Maddalena 33 ; Greco, Rita 33 ; Gidari, Anna 16 ; Zazzi Maurizio 17 ; Dragoni Filippo 17 ; Puma Laura Li 18 ; Ronchiadin Silvia 18 ; Ruggerone Luigi 18 ; Russignaga Dario 34 

1  University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822); University of Milan, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822) 
2  University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822) 
3  University of Padova, Department of Molecular Medicine, Padua, Italy (GRID:grid.5608.b) (ISNI:0000 0004 1757 3470); CRIBI Biotech Center, University of Padova, Padua, Italy (GRID:grid.5608.b) (ISNI:0000 0004 1757 3470) 
4  Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Risk Analyses and Genomic Epidemiology Unit, Parma, Italy (GRID:grid.419583.2) (ISNI:0000 0004 1757 1598) 
5  Virology Unit, Polytechnic University of Marche, Department of Biomedical Sciences and Public Health, Ancona, Italy (GRID:grid.7010.6) (ISNI:0000 0001 1017 3210) 
6  Amedeo di Savoia, ASL Città di Torino, Laboratory of Microbiology and Virology, Torino, Italy (GRID:grid.7010.6) 
7  Hygiene Unit, IRCCS AOU San Martino-IST, Genoa, Italy (GRID:grid.410345.7) (ISNI:0000 0004 1756 7871) 
8  Guglielmo da Saliceto Hospital, AUSL Piacenza, UOC of Infectious Diseases, Department of Oncology and Hematology, Piacenza, Italy (GRID:grid.410345.7) 
9  University of Sassari, Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, Sassari, Italy (GRID:grid.11450.31) (ISNI:0000 0001 2097 9138) 
10  University of Messina, Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, Messina, Italy (GRID:grid.10438.3e) (ISNI:0000 0001 2178 8421) 
11  University Hospital Policlinico Umberto I, Sapienza University of Rome, Department of Molecular Medicine, Rome, Italy (GRID:grid.7841.a) 
12  Tor Vergata University, Infectious Diseases, Rome, Italy (GRID:grid.6530.0) (ISNI:0000 0001 2300 0941) 
13  University of Bari, Infectious Diseases Unit, Bari, Italy (GRID:grid.7644.1) (ISNI:0000 0001 0120 3326) 
14  ASST Papa Giovanni XXIII, Microbiology and Virology Laboratory, Bergamo, Italy (GRID:grid.460094.f) (ISNI:0000 0004 1757 8431) 
15  University of Campania “Luigi Vanvitelli”, Department of Mental Health and Public Medicine, Naples, Italy (GRID:grid.9841.4) (ISNI:0000 0001 2200 8888) 
16  “Santa Maria della Misericordia” Hospital, University of Perugia, Department of Medicine and Surgery, Clinic of Infectious Diseases, Perugia, Italy (GRID:grid.9027.c) (ISNI:0000 0004 1757 3630) 
17  University of Siena, Department of Medical Biotechnologies, Siena, Italy (GRID:grid.9024.f) (ISNI:0000 0004 1757 4641) 
18  Intesa San Paolo Innovation Center-AI LAB, Turin, Italy (GRID:grid.9024.f) 
19  IRCCS Ospedale San Raffaele, Center for Omics Sciences, Milan, Italy (GRID:grid.18887.3e) (ISNI:0000000417581884); IRCCS Ospedale San Raffaele, Division of Experimental Oncology, Milan, Italy (GRID:grid.18887.3e) (ISNI:0000000417581884) 
20  IRCCS Ospedale San Raffaele, Division of Immunology, Transplantation and Infectious Disease, Milan, Italy (GRID:grid.18887.3e) (ISNI:0000000417581884) 
21  University of Genoa, Department of Health Sciences (DISSAL), Genoa, Italy (GRID:grid.5606.5) (ISNI:0000 0001 2151 3065) 
22  Guglielmo da Saliceto Hospital, AUSL Piacenza, UOC of Microbiology, Department of Clinical Pathology, Piacenza, Italy (GRID:grid.5606.5) 
23  University Hospital Policlinico Umberto I, Sapienza University of Rome, Department of Public Health and Infectious Diseases, Rome, Italy (GRID:grid.7841.a) 
24  Padua University Hospital, Microbiology and Virology Diagnostic Unit, Padua, Italy (GRID:grid.411474.3) (ISNI:0000 0004 1760 2630); Imperial College London, Department of Life Science, London, UK (GRID:grid.7445.2) (ISNI:0000 0001 2113 8111) 
25  University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822); University of Milan, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822); University of Milan, CRC-Coordinated Research Center “EpiSoMI”, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822) 
26  University of Padova, Department of Molecular Medicine, Padua, Italy (GRID:grid.5608.b) (ISNI:0000 0004 1757 3470) 
27  San Michele All’Adige, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy (GRID:grid.424414.3) (ISNI:0000 0004 1755 6224) 
28  University of Studies of Torino, Department of Veterinary Science, Turin, Italy (GRID:grid.424414.3) 
29  Emerging Bacterial Pathogens Unit IRCCS Ospedale San Raffaele, Milan, Italy (GRID:grid.18887.3e) (ISNI:0000000417581884) 
30  Guglielmo da Saliceto Hospital, AUSL Piacenza, UOC of Infectious Diseases, Department of Oncology and Hematology, Piacenza, Italy (GRID:grid.5606.5) 
31  University of Sassari, Department of Biomedical Science, Sassari, Italy (GRID:grid.11450.31) (ISNI:0000 0001 2097 9138) 
32  University of Messina, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi” Division of Microbiology, Messina, Italy (GRID:grid.10438.3e) (ISNI:0000 0001 2178 8421) 
33  AORN S. Anna E S. Sebastiano Caserta, Caserta, Italy (GRID:grid.9841.4) 
34  INTESA s.p.a., Prevention and Protection Service, Milan, Italy (GRID:grid.9024.f) 
Publication year
2022
Publication date
2022
Publisher
Nature Publishing Group
e-ISSN
20452322
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41598-022-09738-0
ProQuest document ID
2647482737
Copyright
© The Author(s) 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.