Deep sequencing and phylogenetic analysis of SARScov2 strains circulating in North Italy from February to April 2020

From February to April, 2020, Lombardy (Italy) was the area who worldwide registered the highest numbers of SARS-CoV-2 infection. By extensively analyzing 346 whole SARS-CoV-2 genomes, we demonstrated the presence in Lombardy of seven viral lineages likely derived from different introductions, occurring since the second half of January. Six single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. The seven lineages, and the presence of local transmission clusters inside three of them, revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy.