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

Viruses

Sebastian Duchene¹  Paolo Calistri²  Valentina Curini²  Maurilia Marcacci²  Francesca Profeta²  Alessio Lorusso²  Cesare Cammಠ Ilaria Puglia²  EdwardC. Holmes³  FrancescaDi Giallonardo⁴ 

[1] Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity at The University of Melbourne, Melbourne 3010, Australia;Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 641000 Teramo, Italy;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;The Kirby Institute, the University of New South Wales (UNSW), Sydney 2052, Australia;

关键词: SARS-Cov-2;    Italy;    lockdown;    phylogeny;    transmission;   

DOI  :  10.3390/v12121438

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown