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

  1. Claudia Alteri
  2. Valeria Cento
  3. Antonio Piralla
  4. Valentino Costabile
  5. Monica Tallarita
  6. Luna Colagrossi
  7. Silvia Renica
  8. Federica Giardina
  9. Federica Novazzi
  10. Stefano Gaiarsa
  11. Elisa Matarazzo
  12. Maria Antonello
  13. Chiara Vismara
  14. Roberto Fumagalli
  15. Oscar Massimiliano Epis
  16. Massimo Puoti
  17. Carlo Federico Perno
  18. Fausto Baldanti
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Abstract

From February to April, 2020, Lombardy (Italy) was the area who worldwide registered the highest numbers of SARS-CoV-2 infection. By extensively analyzing 346 whole SARS-CoV-2 genomes, we demonstrated the simultaneous circulation in Lombardy of two major viral lineages, likely derived from multiple introductions, occurring since the second half of January. Seven single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. These two lineages, and the presence of two well defined clusters inside Lineage 1, revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy.

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