Abstract
From February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. 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 within three of them, revealed that sustained community transmission was underway before the first COVID-19 case had been detected in Lombardy.
Highlights
From February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide
In Italy, the first case of evident SARS-CoV-2 transmission emerged on February 20, in Codogno, Lombardy, when a young man affected by interstitial pneumonia was diagnosed for SARSCoV-2
From February 22 through April 4, 2020, nasopharyngeal swabs taken from a total of 25,082 patients were screened for SARS-CoV-2 infection at two major hospitals in Lombardy (Supplementary Fig. 1)
Summary
From February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. Two months later, reported COVID19 cases in Italy dropped to ~600 per day, indicating the first wave of epidemic was nearing containment. Milan is the largest metropolitan area in Italy and the third most densely populated functional urban area in Europe[3], with well-established economical and transportation links to Europe and beyond. This scenario creates the conditions to host and favor the spread of a highly transmissible virus such as SARS-CoV-2. The main aim of this study was to trace local transmission chains and the temporal and geographical evolution of the virus in Lombardy in relation to epidemiological data and measures implemented to contain the outbreak
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