Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy

Abstract

Abstract 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 simultaneous circulation in Lombardy of two major viral lineages, likely derived from multiple introductions, occurring since the second half of January. Seven single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. These two lineages, and the presence of two well defined clusters inside Lineage 1, revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy.