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

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...

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Autores principales: Di Giallonardo, Francesca, Duchene, Sebastian, Puglia, Ilaria, Curini, Valentina, Profeta, Francesca, Cammà, Cesare, Marcacci, Maurilia, Calistri, Paolo, Holmes, Edward C., Lorusso, Alessio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7765063/
https://www.ncbi.nlm.nih.gov/pubmed/33327566
http://dx.doi.org/10.3390/v12121438
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author Di Giallonardo, Francesca
Duchene, Sebastian
Puglia, Ilaria
Curini, Valentina
Profeta, Francesca
Cammà, Cesare
Marcacci, Maurilia
Calistri, Paolo
Holmes, Edward C.
Lorusso, Alessio
author_facet Di Giallonardo, Francesca
Duchene, Sebastian
Puglia, Ilaria
Curini, Valentina
Profeta, Francesca
Cammà, Cesare
Marcacci, Maurilia
Calistri, Paolo
Holmes, Edward C.
Lorusso, Alessio
author_sort Di Giallonardo, Francesca
collection PubMed
description 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.
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spelling pubmed-77650632020-12-27 Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy Di Giallonardo, Francesca Duchene, Sebastian Puglia, Ilaria Curini, Valentina Profeta, Francesca Cammà, Cesare Marcacci, Maurilia Calistri, Paolo Holmes, Edward C. Lorusso, Alessio Viruses Article 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. MDPI 2020-12-14 /pmc/articles/PMC7765063/ /pubmed/33327566 http://dx.doi.org/10.3390/v12121438 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Di Giallonardo, Francesca
Duchene, Sebastian
Puglia, Ilaria
Curini, Valentina
Profeta, Francesca
Cammà, Cesare
Marcacci, Maurilia
Calistri, Paolo
Holmes, Edward C.
Lorusso, Alessio
Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy
title Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy
title_full Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy
title_fullStr Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy
title_full_unstemmed Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy
title_short Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy
title_sort genomic epidemiology of the first wave of sars-cov-2 in italy
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7765063/
https://www.ncbi.nlm.nih.gov/pubmed/33327566
http://dx.doi.org/10.3390/v12121438
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