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

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

Ilaria Vicenti, Maurizio Zazzi, Alessia Lai, Annalisa Bergna, Sara Caucci, Nicola Clementi, Filippo Dragoni, Anna Maria Cattelan, Stefano Menzo, Angelo Pan, Annapaola Callegaro, Adriano Tagliabracci, Arnaldo Caruso, Francesca Caccuri, Silvia Ronchiadin, Claudia Balotta, Emanuela Vaccher, Massimo Clementi, Massimo Galli, Gianguglielmo Zehender

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.

2020

whole-genome sequencing, molecular tracing, Phylodynamic analyses, SARS-CoV2 circulation in Italy

10.3390/v12080798

Epidemiology and Health

Korean Society of Epidemiology

Microbiology