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.

Molecular tracing of SARS-CoV-2 in Italy in the first three months of the epidemic / A. Lai, A. Bergna, S. Caucci, N. Clementi, I. Vicenti, F. Dragoni, A.M. Cattelan, S. Menzo, A. Pan, A. Callegaro, A. Tagliabracci, A. Caruso, F. Caccuri, S. Ronchiadin, C. Balotta, M. Zazzi, E. Vaccher, M. Clementi, M. Galli, G. Zehender. - In: VIRUSES. - ISSN 1999-4915. - 12:8(2020 Jul 24), pp. 798.1-798.13. [10.3390/v12080798]

Molecular tracing of SARS-CoV-2 in Italy in the first three months of the epidemic

A. Lai
;
A. Bergna;F. Dragoni;A. Callegaro;F. Caccuri;C. Balotta;M. Galli;G. Zehender
2020-07-24

Abstract

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.
Molecular tracing; Phylodynamic analyses; SARS-CoV2 circulation in Italy; Whole genome sequencing
Settore MED/17 - Malattie Infettive
Settore MED/07 - Microbiologia e Microbiologia Clinica
Settore MED/42 - Igiene Generale e Applicata
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/773359
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