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Article

Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

1
The Kirby Institute, The University of New South Wales (UNSW), Sydney 2052, Australia
2
Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne 3010, Australia
3
Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, Italy
4
Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, 70010 Valenzano, Italy
5
Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney 2006, Australia
*
Author to whom correspondence should be addressed.
Academic Editor: Stefano Aquaro
Received: 17 November 2020 / Revised: 11 December 2020 / Accepted: 11 December 2020 / Published: 14 December 2020
(This article belongs to the Section SARS-CoV-2 and COVID-19)
Italy was one of the first countries to experience a major epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with >1000 cases confirmed by 1 March 2020. However, virus genome sequence data is sparse and there has been only limited investigation of virus transmission across the country. Here, we provide the most extensive study to date of the genomic epidemiology of SARS-CoV-2 in Italy covering the first wave of infection. We generated 191 new full-length genomes, largely sampled from central Italy (Abruzzo), before, during, and after the enforcement of a nationwide “lockdown” (8 March–3 June). These were combined with 460 published SARS-CoV-2 sequences sampled across Italy. Phylogenetic analysis including global sequence data revealed multiple independent introductions into Italy, with at least 124 instances of sequence clusters representing longer chains of transmission. Eighteen of these transmission clusters emerged before the nation-wide lockdown was implemented on 8 March, and an additional 18 had evidence for transmission between different Italian regions. Extended transmission periods between infections of up to 104 days were observed in five clusters. In addition, we found seven clusters that persisted throughout the lockdown period. Overall, we show how importations were an important driver of the first wave of SARS-CoV-2 in Italy. View Full-Text
Keywords: SARS-Cov-2; Italy; lockdown; phylogeny; transmission SARS-Cov-2; Italy; lockdown; phylogeny; transmission
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MDPI and ACS Style

Di Giallonardo, F.; Duchene, S.; Puglia, I.; Curini, V.; Profeta, F.; Cammà, C.; Marcacci, M.; Calistri, P.; Holmes, E.C.; Lorusso, A. Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy. Viruses 2020, 12, 1438. https://0-doi-org.brum.beds.ac.uk/10.3390/v12121438

AMA Style

Di Giallonardo F, Duchene S, Puglia I, Curini V, Profeta F, Cammà C, Marcacci M, Calistri P, Holmes EC, Lorusso A. Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy. Viruses. 2020; 12(12):1438. https://0-doi-org.brum.beds.ac.uk/10.3390/v12121438

Chicago/Turabian Style

Di Giallonardo, Francesca; Duchene, Sebastian; Puglia, Ilaria; Curini, Valentina; Profeta, Francesca; Cammà, Cesare; Marcacci, Maurilia; Calistri, Paolo; Holmes, Edward C.; Lorusso, Alessio. 2020. "Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy" Viruses 12, no. 12: 1438. https://0-doi-org.brum.beds.ac.uk/10.3390/v12121438

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