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

Author

Listed:
  • 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
    University of Pavia)

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.

Suggested Citation

  • Claudia Alteri & Valeria Cento & Antonio Piralla & Valentino Costabile & Monica Tallarita & Luna Colagrossi & Silvia Renica & Federica Giardina & Federica Novazzi & Stefano Gaiarsa & Elisa Matarazzo &, 2021. "Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20688-x
    DOI: 10.1038/s41467-020-20688-x
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    Cited by:

    1. Haogao Gu & Ruopeng Xie & Dillon C. Adam & Joseph L.-H. Tsui & Daniel K. Chu & Lydia D. J. Chang & Sammi S. Y. Cheuk & Shreya Gurung & Pavithra Krishnan & Daisy Y. M. Ng & Gigi Y. Z. Liu & Carrie K. C, 2022. "Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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