TY - JOUR
T1 - Molecular tracing of SARS-CoV-2 in Italy in the first three months of the epidemic
AU - SARS-CoV-2 ITALIAN RESEARCH ENTERPRISE-(SCIRE) Collaborative Group
AU - Lai, Alessia
AU - Bergna, Annalisa
AU - Caucci, Sara
AU - Clementi, Nicola
AU - Vicenti, Ilaria
AU - Dragoni, Filippo
AU - Cattelan, Anna Maria
AU - Menzo, Stefano
AU - Pan, Angelo
AU - Callegaro, Annapaola
AU - Tagliabracci, Adriano
AU - Caruso, Arnaldo
AU - Caccuri, Francesca
AU - Ronchiadin, Silvia
AU - Balotta, Claudia
AU - Zazzi, Maurizio
AU - Vaccher, Emanuela
AU - Clementi, Massimo
AU - Galli, Massimo
AU - Zehender, Gianguglielmo
N1 - Funding Information:
Funding: This research was funded by Fondo straordinario di Ateneo per lo Studio del Covid-19, University of Milan.
Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2020/8
Y1 - 2020/8
N2 - The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly-characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.
AB - The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly-characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.
KW - Molecular tracing
KW - Phylodynamic analyses
KW - SARS-CoV2 circulation in Italy
KW - Whole genome sequencing
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U2 - 10.3390/v12080798
DO - 10.3390/v12080798
M3 - Article
C2 - 32722343
AN - SCOPUS:85088811603
VL - 12
JO - Viruses
JF - Viruses
SN - 1999-4915
IS - 8
M1 - 798
ER -