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Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic.
Viruses. 2020 07 24; 12(8)V

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.

Authors+Show Affiliations

Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy.Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy.Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, 60131 Ancona, Italy.Microbiology and Virology Unit, "Vita-Salute" San Raffaele University, 20132 Milan, Italy.Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy.Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy.Infectious Diseases Unit, Department of Internal Medicine, Azienda Ospedaliera-Universitaria di Padova, 35128 Padua, Italy.Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, 60131 Ancona, Italy.Infectious Diseases, ASST Cremona, 26100 Cremona, Italy.Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy.Section of Legal Medicine, Universita Politecnica delle Marche, 60126 Ancona, Italy.Microbiology Unit, Department of Molecular and Translational Medicine, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy.Microbiology Unit, Department of Molecular and Translational Medicine, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy.Intesa Sanpaolo Innovation Center-AI LAB, 10138 Turin, Italy.Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy.Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy.Medical Oncology and Immune-related Tumors, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy.Microbiology and Virology Unit, "Vita-Salute" San Raffaele University, 20132 Milan, Italy.Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy.Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32722343

Citation

Lai, Alessia, et al. "Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic." Viruses, vol. 12, no. 8, 2020.
Lai A, Bergna A, Caucci S, et al. Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic. Viruses. 2020;12(8).
Lai, A., Bergna, A., Caucci, S., Clementi, N., Vicenti, I., Dragoni, F., Cattelan, A. M., Menzo, S., Pan, A., Callegaro, A., Tagliabracci, A., Caruso, A., Caccuri, F., Ronchiadin, S., Balotta, C., Zazzi, M., Vaccher, E., Clementi, M., Galli, M., & Zehender, G. (2020). Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic. Viruses, 12(8). https://doi.org/10.3390/v12080798
Lai A, et al. Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic. Viruses. 2020 07 24;12(8) PubMed PMID: 32722343.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic. 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, Y1 - 2020/07/24/ PY - 2020/07/03/received PY - 2020/07/17/revised PY - 2020/07/21/accepted PY - 2020/7/30/entrez PY - 2020/7/30/pubmed PY - 2020/8/7/medline KW - Phylodynamic analyses KW - SARS-CoV2 circulation in Italy KW - molecular tracing KW - whole genome sequencing JF - Viruses JO - Viruses VL - 12 IS - 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. SN - 1999-4915 UR - https://www.unboundmedicine.com/medline/citation/32722343/Molecular_Tracing_of_SARS_CoV_2_in_Italy_in_the_First_Three_Months_of_the_Epidemic_ L2 - https://www.mdpi.com/resolver?pii=v12080798 DB - PRIME DP - Unbound Medicine ER -