Evolutionary Dynamics of SARS-CoV-2 in Space and Time During the First Phase of the Epidemic in Italy

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

doi:10.20944/preprints202107.0654.v1

How to cite: Lai, A.; Bergna, A.; Toppo, S.; Morganti, M.; Menzo, S.; Ghisetti, V.; Bruzzone, B.; Codeluppi, M.; Fiore, V.; Venanzi Rullo, E.; Antonelli, G.; Sarmati, L.; Brindicci, G.; Callegaro, A.; Sagnelli, C.; Francisci, D.; Vicenti, I.; Miola, A.; Tonon, G.; Cirillo, D.; Menozzi, I.; Caucci, S.; Cerutti, F.; Orsi, A.; Schiavo, R.; Babudieri, S.; Nunnari, G.; Mastroianni, C.M.; Andreoni, M.; Monno, L.; Guarneri, D.; Coppola, N.; Crisanti, A.; Galli, M.; Zehender, G. Evolutionary Dynamics of SARS-CoV-2 in Space and Time During the First Phase of the Epidemic in Italy. Preprints 2021, 2021070654. https://doi.org/10.20944/preprints202107.0654.v1. Lai, A.; Bergna, A.; Toppo, S.; Morganti, M.; Menzo, S.; Ghisetti, V.; Bruzzone, B.; Codeluppi, M.; Fiore, V.; Venanzi Rullo, E.; Antonelli, G.; Sarmati, L.; Brindicci, G.; Callegaro, A.; Sagnelli, C.; Francisci, D.; Vicenti, I.; Miola, A.; Tonon, G.; Cirillo, D.; Menozzi, I.; Caucci, S.; Cerutti, F.; Orsi, A.; Schiavo, R.; Babudieri, S.; Nunnari, G.; Mastroianni, C.M.; Andreoni, M.; Monno, L.; Guarneri, D.; Coppola, N.; Crisanti, A.; Galli, M.; Zehender, G. Evolutionary Dynamics of SARS-CoV-2 in Space and Time During the First Phase of the Epidemic in Italy. Preprints 2021, 2021070654. https://doi.org/10.20944/preprints202107.0654.v1.

Abstract

The aim of this study was the reconstruction of SARS-CoV-2 evolutionary dynamics in time and space in Italy and Europe between February and June 2020. The cluster analysis showed that 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 most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 entered Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, the reconstructed ancestral scenario suggests a central 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.

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Evolutionary Dynamics of SARS-CoV-2 in Space and Time During the First Phase of the Epidemic in Italy

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