Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic

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 li...

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Bibliographic Details
Published in:Viruses Vol. 12; no. 8; p. 798
Main Authors: Lai, Alessia, Bergna, Annalisa, Caucci, Sara, Clementi, Nicola, Vicenti, Ilaria, Dragoni, Filippo, Cattelan, Anna, Menzo, Stefano, Pan, Angelo, Callegaro, Annapaola, Tagliabracci, Adriano, Caruso, Arnaldo, Caccuri, Francesca, Ronchiadin, Silvia, Balotta, Claudia, Zazzi, Maurizio, Vaccher, Emanuela, Clementi, Massimo, Galli, Massimo, Zehender, Gianguglielmo
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 24.07.2020
MDPI
Subjects:
Bayes Theorem
Betacoronavirus - classification
Betacoronavirus - genetics
Betacoronavirus - isolation & purification
Coronavirus Infections - epidemiology
Coronavirus Infections - virology
Coronaviruses
COVID-19
COVID-19 infection
Datasets
Disease transmission
Epidemics
Epidemiological Monitoring
epidemiology
Genetic drift
genome
Genome, Viral
Genomes
genomics
Humans
Italy
Italy - epidemiology
Likelihood Functions
Molecular Epidemiology
molecular tracing
Molecular Typing
monitoring
Mutation
Pandemics
patients
Phylodynamic analyses
Phylogenetics
Phylogeny
Pneumonia, Viral - epidemiology
Pneumonia, Viral - virology
SARS-CoV-2
SARS-CoV2 circulation in Italy
Severe acute respiratory syndrome coronavirus 2
Software
Time Factors
virus replication
viruses
Whole Genome Sequencing
Italy
United States > US
Massachusetts
Germany
whole genome sequencing
SARS-CoV2 circulation in Italy
Phylodynamic analyses
molecular tracing
ISSN:1999-4915, 1999-4915
Online Access:Get full text
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Summary: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.
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ISSN:1999-4915
1999-4915
DOI:10.3390/v12080798