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

Claudia Alteri, Valeria Cento, Antonio Piralla, Valentino Costabile, Monica Tallarita, Luna Colagrossi, Silvia Renica, Federica Giardina, Federica Novazzi, Stefano Gaiarsa, Elisa Matarazzo, Maria Antonello, Chiara Vismara, Roberto Fumagalli, Oscar Massimiliano Epis, Massimo Puoti, Carlo Federico Perno () and Fausto Baldanti
Additional contact information
Claudia Alteri: University of Milan
Valeria Cento: University of Milan
Antonio Piralla: Fondazione IRCCS Policlinico San Matteo
Valentino Costabile: University of Milan
Monica Tallarita: Fondazione IRCCS Policlinico San Matteo
Luna Colagrossi: Bambino Gesù Children’s Hospital, IRCCS
Silvia Renica: University of Milan
Federica Giardina: Fondazione IRCCS Policlinico San Matteo
Federica Novazzi: Fondazione IRCCS Policlinico San Matteo
Stefano Gaiarsa: Fondazione IRCCS Policlinico San Matteo
Elisa Matarazzo: University of Milan
Maria Antonello: University of Milan
Chiara Vismara: ASST Grande Ospedale Metropolitano Niguarda
Roberto Fumagalli: Department of Anesthesiology, Critical Care and Pain Medicine, ASST Grande Ospedale Metropolitano Niguarda
Oscar Massimiliano Epis: Rheumatology Unit, ASST Grande Ospedale Metropolitano Niguarda
Massimo Puoti: ASST Grande Ospedale Metropolitano Niguarda
Carlo Federico Perno: Bambino Gesù Children’s Hospital, IRCCS
Fausto Baldanti: Fondazione IRCCS Policlinico San Matteo

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-020-20688-x

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