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Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy.
Alteri, Claudia; Cento, Valeria; Piralla, Antonio; Costabile, Valentino; Tallarita, Monica; Colagrossi, Luna; Renica, Silvia; Giardina, Federica; Novazzi, Federica; Gaiarsa, Stefano; Matarazzo, Elisa; Antonello, Maria; Vismara, Chiara; Fumagalli, Roberto; Epis, Oscar Massimiliano; Puoti, Massimo; Perno, Carlo Federico; Baldanti, Fausto.
  • Alteri C; Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.
  • Cento V; Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.
  • Piralla A; Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
  • Costabile V; Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.
  • Tallarita M; Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
  • Colagrossi L; Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
  • Renica S; Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.
  • Giardina F; Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
  • Novazzi F; Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
  • Gaiarsa S; Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
  • Matarazzo E; Residency in Microbiology and Virology, University of Milan, Milan, Italy.
  • Antonello M; Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.
  • Vismara C; Chemico-clinical and Microbiological Analyses, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy.
  • Fumagalli R; Department of Anesthesiology, Critical Care and Pain Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy.
  • Epis OM; Rheumatology Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy.
  • Puoti M; Infectious Diseases Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy.
  • Perno CF; Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy. cf.perno@uniroma2.it.
  • Baldanti F; Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
Nat Commun ; 12(1): 434, 2021 01 19.
Article in English | MEDLINE | ID: covidwho-1038209
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Polymorphism, Single Nucleotide / Genomics / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Limits: Adult / Aged / Female / Humans / Male / Middle aged Country/Region as subject: Europa Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2021 Document Type: Article Affiliation country: S41467-020-20688-x

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Polymorphism, Single Nucleotide / Genomics / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Limits: Adult / Aged / Female / Humans / Male / Middle aged Country/Region as subject: Europa Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2021 Document Type: Article Affiliation country: S41467-020-20688-x