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

被引：0

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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