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

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作者：
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
Fausto Baldanti
机构：
[1] University of Milan,Department of Oncology and Hemato
[2] Fondazione IRCCS Policlinico San Matteo,oncology
[3] University of Milan,Molecular Virology Unit, Microbiology and Virology Department
[4] Bambino Gesù Children’s Hospital,Department of Pathophysiology and Transplantation
[5] IRCCS,Microbiology and Diagnostic Immunology Unit
[6] University of Milan,Residency in Microbiology and Virology
[7] ASST Grande Ospedale Metropolitano Niguarda,Chemico
[8] Department of Anesthesiology,clinical and Microbiological Analyses
[9] Critical Care and Pain Medicine,Infectious Diseases Unit
[10] ASST Grande Ospedale Metropolitano Niguarda,Department of Clinical, Surgical, Diagnostic and Paediatric Sciences
[11] Rheumatology Unit,undefined
[12] ASST Grande Ospedale Metropolitano Niguarda,undefined
[13] ASST Grande Ospedale Metropolitano Niguarda,undefined
[14] University of Pavia,undefined
来源：
Nature Communications | / 12卷
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摘要：
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.
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