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.

The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Here, the authors use whole genome sequencing and show that there were multiple introductions into the region, with transmission occurring before the first case was detected.

Details

Title
Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy
Author
Alteri, Claudia 1   VIAFID ORCID Logo  ; Cento Valeria 1 ; Piralla Antonio 2   VIAFID ORCID Logo  ; Costabile Valentino 3   VIAFID ORCID Logo  ; Tallarita Monica 2 ; Luna, Colagrossi 4 ; Renica Silvia 1 ; Giardina Federica 2 ; Novazzi Federica 2 ; Gaiarsa Stefano 2 ; Matarazzo Elisa 5 ; Antonello, Maria 1 ; Vismara Chiara 6 ; Fumagalli, Roberto 7 ; Epis, Oscar Massimiliano 8 ; Puoti Massimo 9 ; Perno, Carlo Federico 4   VIAFID ORCID Logo  ; Baldanti Fausto 10 

1  University of Milan, Department of Oncology and Hemato-oncology, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822) 
2  Fondazione IRCCS Policlinico San Matteo, Molecular Virology Unit, Microbiology and Virology Department, Pavia, Italy (GRID:grid.419425.f) (ISNI:0000 0004 1760 3027) 
3  University of Milan, Department of Pathophysiology and Transplantation, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822) 
4  Bambino Gesù Children’s Hospital, IRCCS, Microbiology and Diagnostic Immunology Unit, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809) 
5  University of Milan, Residency in Microbiology and Virology, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822) 
6  ASST Grande Ospedale Metropolitano Niguarda, Chemico-clinical and Microbiological Analyses, Milan, Italy (GRID:grid.4708.b) 
7  Department of Anesthesiology, Critical Care and Pain Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy (GRID:grid.4708.b) 
8  Rheumatology Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy (GRID:grid.4708.b) 
9  ASST Grande Ospedale Metropolitano Niguarda, Infectious Diseases Unit, Milan, Italy (GRID:grid.4708.b) 
10  Fondazione IRCCS Policlinico San Matteo, Molecular Virology Unit, Microbiology and Virology Department, Pavia, Italy (GRID:grid.419425.f) (ISNI:0000 0004 1760 3027); University of Pavia, Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, Pavia, Italy (GRID:grid.8982.b) (ISNI:0000 0004 1762 5736) 
Publication year
2021
Publication date
2021
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41467-020-20688-x
ProQuest document ID
2478868841
Copyright
© The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.