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

Viruses. 2020 Jul 24;12(8):798. doi: 10.3390/v12080798.

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.

Keywords: Phylodynamic analyses; SARS-CoV2 circulation in Italy; molecular tracing; whole genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bayes Theorem
  • Betacoronavirus / classification*
  • Betacoronavirus / genetics*
  • Betacoronavirus / isolation & purification
  • COVID-19
  • Coronavirus Infections / epidemiology*
  • Coronavirus Infections / virology*
  • Epidemiological Monitoring
  • Genome, Viral
  • Humans
  • Italy / epidemiology
  • Likelihood Functions
  • Molecular Epidemiology
  • Molecular Typing
  • Mutation
  • Pandemics*
  • Phylogeny
  • Pneumonia, Viral / epidemiology*
  • Pneumonia, Viral / virology*
  • SARS-CoV-2
  • Time Factors
  • Whole Genome Sequencing