Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus

Highlights

• Sequences alignment of a high-quality dataset of Sars-CoV-2 genomes showed some highly conserved genes.

• Phylogenetic analysis revealed six clusters. The distribution of the clusters was associated with specific geographic areas.

• The SARS-CoV-2 strain detected in the first COVID-19 case diagnosed in Northern Italy was already circulating outside the country.

Abstract

A high-quality dataset of 3289 complete SARS-CoV-2 genomes collected in Europe and European Economic Area (EAA) in the early phase of the first wave of the pandemic was analyzed. Among all single nucleotide mutations, 41 had a frequency ≥ 1%, and the phylogenetic analysis showed at least 6 clusters with a specific mutational profile. These clusters were differentially distributed in the EU/EEA, showing a statistically significant association with the geographic origin. The analysis highlighted that the mutations C¹⁴⁴⁰⁸T and C¹⁴⁸⁰⁵T played an important role in clusters selection and further virus spread. Moreover, the molecular analysis suggests that the SARS-CoV-2 strain responsible for the first Italian confirmed COVID-19 case was already circulating outside the country.