Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic.
Bayes Theorem
Betacoronavirus
/ classification
COVID-19
Coronavirus Infections
/ epidemiology
Epidemiological Monitoring
Genome, Viral
Humans
Italy
/ epidemiology
Likelihood Functions
Molecular Epidemiology
Molecular Typing
Mutation
Pandemics
Phylogeny
Pneumonia, Viral
/ epidemiology
SARS-CoV-2
Time Factors
Whole Genome Sequencing
Phylodynamic analyses
SARS-CoV2 circulation in Italy
molecular tracing
whole genome sequencing
Journal
Viruses
ISSN: 1999-4915
Titre abrégé: Viruses
Pays: Switzerland
ID NLM: 101509722
Informations de publication
Date de publication:
24 07 2020
24 07 2020
Historique:
received:
03
07
2020
revised:
17
07
2020
accepted:
21
07
2020
entrez:
30
7
2020
pubmed:
30
7
2020
medline:
7
8
2020
Statut:
epublish
Résumé
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 (R
Identifiants
pubmed: 32722343
pii: v12080798
doi: 10.3390/v12080798
pmc: PMC7472216
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Università degli Studi di Milano
ID : Fondo straordinario di Ateneo
Pays : International
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