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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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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. |
format | Online Article Text |
id | pubmed-7765063 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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