Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020
Authors: Lai Alessia , Bergna Annalisa , Toppo Stefano , Morganti Marina , Menzo Stefano , Ghisetti Valeria , Bruzzone Bianca , Codeluppi Mauro , Fiore Vito , Rullo Emmanuele Venanzi , Antonelli Guido , Sarmati Loredana , Brindicci Gaetano , Callegaro Annapaola , Sagnelli Caterina , Francisci Daniela , Vicenti Ilaria , Miola Arianna , Tonon Giovanni , Cirillo Daniela , Menozzi Ilaria , Caucci Sara , Cerutti Francesco , Orsi Andrea , Schiavo Roberta , Babudieri Sergio , Nunnari Giuseppe , Mastroianni Claudio M. , Andreoni Massimo , Monno Laura , Guarneri Davide , Coppola Nicola , Crisanti Andrea , Galli Massimo , Zehender Gianguglielmo ,   SCIRE-SARS-CoV-2 Italian Research Enterprise-Collaborative Group, Balotta Claudia , Ventura Carla della , Schiuma Marco , Lavezzo Enrico , Fontana Paolo , Bianco Luca , Bertolotti Luigi , Manuto Laura , Grazioli Marco , Bianca Federico , Del Vecchio Claudia , Franchin Elisa , Onelia Francesco , Spitaleri Andrea , Saluzzo Francesca , Lorenzin Giovanni , Pongolini Stefano , Scaltriti Erika , Soliani Laura , Bagnarelli Patrizia , Turchi Chiara , Onofri Valerio , Melchionda Filomena , Tagliabracci Adriano , Burdino Elisa , Milia Maria Grazia , Caligiuri Patrizia , De Pace Vanessa , Ricucci Valentina , Domnich Alexander , Boccotti Simona , Cristina Leoni Maria , Cascio Giuliana Lo , Rubino Salvatore , Lai Vincenzo , Rocca Giulia , Govoni Rosalba , Mancuso Giuseppe , Campagna Roberta , Mazzuti Laura , Oliveto Giuseppe , Turriziani Ombretta , Campogiani Laura , Compagno Mirko , Coppola Luigi , Crea Angela Maria Antonia , De Simone Giuseppe , Di Lorenzo Andrea , Ferrari Ludovica , Iannetta Marco , Malagnino Vincenzo , Mulas Tiziana , Rossi Benedetta , Spalliera Ilaria , Tedde Simona , Teti Elisabetta , Vitale Pietro , Zordan Marta , Milano Eugenio , Lagioia Antonella , Gallitelli Rosa , Starace Mario , Minichini Carmine , Di Fraia Alessia , Schioppa Maddalena , Greco Rita , Gidari Anna , Zazzi Maurizio , Dragoni Filippo , Puma Laura Li , Ronchiadin Silvia , Ruggerone Luigi , Russignaga Dario 
Published: April 2022

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.