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Origin, Genetic Variation and Molecular Epidemiology of SARS-CoV-2 Strains Circulating in Sardinia (Italy) during the First and Second COVID-19 Epidemic Waves

Understanding how geography and human mobility shape the patterns and spread of infectious diseases such as COVID-19 is key to control future epidemics. An interesting example is provided by the second wave of the COVID-19 epidemic in Europe, which was facilitated by the intense movement of tourists...

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Published in:Viruses 2023-01, Vol.15 (2), p.277
Main Authors: Rocchigiani, Angela Maria, Ferretti, Luca, Ledda, Alice, Di Nardo, Antonello, Floris, Matteo, Bonelli, Piero, Loi, Federica, Idda, Maria Laura, Angioi, Pier Paolo, Zinellu, Susanna, Fiori, Mariangela Stefania, Bechere, Roberto, Capitta, Paola, Coccollone, Annamaria, Coradduzza, Elisabetta, Dettori, Maria Antonietta, Fattaccio, Maria Caterina, Gallisai, Elena, Maestrale, Caterina, Manunta, Daniela, Pedditzi, Aureliana, Piredda, Ivana, Palmas, Bruna, Salza, Sara, Sechi, Anna Maria, Tanda, Barbara, Madrau, Maria Paola, Sanna, Maria Luisa, Cherchi, Simonetta, Ponti, Nicoletta, Masala, Giovanna, Sirica, Roberto, Evangelista, Eloisa, Oggiano, Annalisa, Puggioni, Giantonella, Ligios, Ciriaco, Dei Giudici, Silvia
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cited_by cdi_FETCH-LOGICAL-c536t-763cf5da1461f90c9528bd00a36246a40d7d743c93fb48512c7da356132a96923
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container_start_page 277
container_title Viruses
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creator Rocchigiani, Angela Maria
Ferretti, Luca
Ledda, Alice
Di Nardo, Antonello
Floris, Matteo
Bonelli, Piero
Loi, Federica
Idda, Maria Laura
Angioi, Pier Paolo
Zinellu, Susanna
Fiori, Mariangela Stefania
Bechere, Roberto
Capitta, Paola
Coccollone, Annamaria
Coradduzza, Elisabetta
Dettori, Maria Antonietta
Fattaccio, Maria Caterina
Gallisai, Elena
Maestrale, Caterina
Manunta, Daniela
Pedditzi, Aureliana
Piredda, Ivana
Palmas, Bruna
Salza, Sara
Sechi, Anna Maria
Tanda, Barbara
Madrau, Maria Paola
Sanna, Maria Luisa
Cherchi, Simonetta
Ponti, Nicoletta
Masala, Giovanna
Sirica, Roberto
Evangelista, Eloisa
Oggiano, Annalisa
Puggioni, Giantonella
Ligios, Ciriaco
Dei Giudici, Silvia
description Understanding how geography and human mobility shape the patterns and spread of infectious diseases such as COVID-19 is key to control future epidemics. An interesting example is provided by the second wave of the COVID-19 epidemic in Europe, which was facilitated by the intense movement of tourists around the Mediterranean coast in summer 2020. The Italian island of Sardinia is a major tourist destination and is widely believed to be the origin of the second Italian wave. In this study, we characterize the genetic variation among SARS-CoV-2 strains circulating in northern Sardinia during the first and second Italian waves using both Illumina and Oxford Nanopore Technologies Next Generation Sequencing methods. Most viruses were placed into a single clade, implying that despite substantial virus inflow, most outbreaks did not spread widely. The second epidemic wave on the island was actually driven by local transmission of a single B.1.177 subclade. Phylogeographic analyses further suggest that those viral strains circulating on the island were not a relevant source for the second epidemic wave in Italy. This result, however, does not rule out the possibility of intense mixing and transmission of the virus among tourists as a major contributor to the second Italian wave.
doi_str_mv 10.3390/v15020277
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Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>Coronavirus Research Database</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Viruses</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Rocchigiani, Angela Maria</au><au>Ferretti, Luca</au><au>Ledda, Alice</au><au>Di Nardo, Antonello</au><au>Floris, Matteo</au><au>Bonelli, Piero</au><au>Loi, Federica</au><au>Idda, Maria Laura</au><au>Angioi, Pier Paolo</au><au>Zinellu, Susanna</au><au>Fiori, Mariangela Stefania</au><au>Bechere, Roberto</au><au>Capitta, Paola</au><au>Coccollone, Annamaria</au><au>Coradduzza, Elisabetta</au><au>Dettori, Maria Antonietta</au><au>Fattaccio, Maria Caterina</au><au>Gallisai, Elena</au><au>Maestrale, Caterina</au><au>Manunta, Daniela</au><au>Pedditzi, Aureliana</au><au>Piredda, Ivana</au><au>Palmas, Bruna</au><au>Salza, Sara</au><au>Sechi, Anna Maria</au><au>Tanda, Barbara</au><au>Madrau, Maria Paola</au><au>Sanna, Maria Luisa</au><au>Cherchi, Simonetta</au><au>Ponti, Nicoletta</au><au>Masala, Giovanna</au><au>Sirica, Roberto</au><au>Evangelista, Eloisa</au><au>Oggiano, Annalisa</au><au>Puggioni, Giantonella</au><au>Ligios, Ciriaco</au><au>Dei Giudici, Silvia</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Origin, Genetic Variation and Molecular Epidemiology of SARS-CoV-2 Strains Circulating in Sardinia (Italy) during the First and Second COVID-19 Epidemic Waves</atitle><jtitle>Viruses</jtitle><addtitle>Viruses</addtitle><date>2023-01-18</date><risdate>2023</risdate><volume>15</volume><issue>2</issue><spage>277</spage><pages>277-</pages><issn>1999-4915</issn><eissn>1999-4915</eissn><abstract>Understanding how geography and human mobility shape the patterns and spread of infectious diseases such as COVID-19 is key to control future epidemics. An interesting example is provided by the second wave of the COVID-19 epidemic in Europe, which was facilitated by the intense movement of tourists around the Mediterranean coast in summer 2020. The Italian island of Sardinia is a major tourist destination and is widely believed to be the origin of the second Italian wave. In this study, we characterize the genetic variation among SARS-CoV-2 strains circulating in northern Sardinia during the first and second Italian waves using both Illumina and Oxford Nanopore Technologies Next Generation Sequencing methods. Most viruses were placed into a single clade, implying that despite substantial virus inflow, most outbreaks did not spread widely. The second epidemic wave on the island was actually driven by local transmission of a single B.1.177 subclade. Phylogeographic analyses further suggest that those viral strains circulating on the island were not a relevant source for the second epidemic wave in Italy. This result, however, does not rule out the possibility of intense mixing and transmission of the virus among tourists as a major contributor to the second Italian wave.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>36851491</pmid><doi>10.3390/v15020277</doi><orcidid>https://orcid.org/0000-0001-9013-8203</orcidid><orcidid>https://orcid.org/0000-0001-5243-8977</orcidid><orcidid>https://orcid.org/0000-0001-7578-7301</orcidid><orcidid>https://orcid.org/0000-0002-1292-5022</orcidid><orcidid>https://orcid.org/0000-0003-0289-0716</orcidid><orcidid>https://orcid.org/0000-0003-4462-8257</orcidid><orcidid>https://orcid.org/0000-0001-6942-3296</orcidid><orcidid>https://orcid.org/0000-0002-3167-0942</orcidid><orcidid>https://orcid.org/0000-0003-0352-0039</orcidid><orcidid>https://orcid.org/0000-0003-1803-4666</orcidid><orcidid>https://orcid.org/0000-0003-4385-9336</orcidid><orcidid>https://orcid.org/0000-0002-2878-4682</orcidid><orcidid>https://orcid.org/0000-0003-3045-3150</orcidid><oa>free_for_read</oa></addata></record>
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identifier ISSN: 1999-4915
ispartof Viruses, 2023-01, Vol.15 (2), p.277
issn 1999-4915
1999-4915
language eng
recordid cdi_doaj_primary_oai_doaj_org_article_3217fe301f1c41f1be314935c6272b6b
source Access via ProQuest (Open Access); PubMed Central; Coronavirus Research Database
subjects Coronaviruses
COVID-19
COVID-19 - epidemiology
COVID-19 vaccines
Disease transmission
Epidemics
Epidemiology
Fatalities
Genetic diversity
Genetic Variation
Genomes
Health surveillance
Humans
Immunization
Infections
Infectious diseases
Influenza
Italy - epidemiology
Methods
Molecular Epidemiology
Mortality
Next-generation sequencing
Pandemics
Phylogeography
SARS-CoV-2
SARS-CoV-2 - genetics
Seasons
Severe acute respiratory syndrome coronavirus 2
Software
spike (S) protein
Strains (organisms)
Viruses
whole genome sequencing
Zoonoses
title Origin, Genetic Variation and Molecular Epidemiology of SARS-CoV-2 Strains Circulating in Sardinia (Italy) during the First and Second COVID-19 Epidemic Waves
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