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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| Format: | Article |
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MDPI AG
2020-12-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/12/12/1438 |
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| author | Francesca Di Giallonardo Sebastian Duchene Ilaria Puglia Valentina Curini Francesca Profeta Cesare Cammà Maurilia Marcacci Paolo Calistri Edward C. Holmes Alessio Lorusso |
| author_facet | Francesca Di Giallonardo Sebastian Duchene Ilaria Puglia Valentina Curini Francesca Profeta Cesare Cammà Maurilia Marcacci Paolo Calistri Edward C. Holmes Alessio Lorusso |
| author_sort | Francesca Di Giallonardo |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T14:05:13Z |
| format | Article |
| id | doaj.art-be33ffdc0be04521b27f62dc5cb2f29b |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T14:05:13Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-be33ffdc0be04521b27f62dc5cb2f29b2023-11-21T00:46:03ZengMDPI AGViruses1999-49152020-12-011212143810.3390/v12121438Genomic Epidemiology of the First Wave of SARS-CoV-2 in ItalyFrancesca Di Giallonardo0Sebastian Duchene1Ilaria Puglia2Valentina Curini3Francesca Profeta4Cesare Cammà5Maurilia Marcacci6Paolo Calistri7Edward C. Holmes8Alessio Lorusso9The Kirby Institute, The University of New South Wales (UNSW), Sydney 2052, AustraliaDepartment of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne 3010, AustraliaIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, ItalyIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, ItalyIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, ItalyIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, ItalyIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, ItalyIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, ItalyMarie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney 2006, AustraliaIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, ItalyItaly 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.https://www.mdpi.com/1999-4915/12/12/1438SARS-Cov-2Italylockdownphylogenytransmission |
| spellingShingle | Francesca Di Giallonardo Sebastian Duchene Ilaria Puglia Valentina Curini Francesca Profeta Cesare Cammà Maurilia Marcacci Paolo Calistri Edward C. Holmes Alessio Lorusso Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy Viruses SARS-Cov-2 Italy lockdown phylogeny transmission |
| 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 | SARS-Cov-2 Italy lockdown phylogeny transmission |
| url | https://www.mdpi.com/1999-4915/12/12/1438 |
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