Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe
Identifieur interne : 001003 ( Pmc/Curation ); précédent : 001002; suivant : 001004Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe
Auteurs : Paola Stefanelli [Italie] ; Giovanni Faggioni [Italie] ; Alessandra Lo Presti [Italie] ; Stefano Fiore [Italie] ; Antonella Marchi [Italie] ; Eleonora Benedetti [Italie] ; Concetta Fabiani [Italie] ; Anna Anselmo [Italie] ; Andrea Ciammaruconi [Italie] ; Antonella Fortunato [Italie] ; Riccardo De Santis [Italie] ; Silvia Fillo [Italie] ; Maria Rosaria Capobianchi [Italie] ; Maria Rita Gismondo [Italie] ; Alessandra Ciervo [Italie] ; Giovanni Rezza [Italie] ; Maria Rita Castrucci [Italie] ; Florigio Lista [Italie]Source :
- Eurosurveillance [ 1025-496X ] ; 2020.
Abstract
Whole genome sequences of SARS-CoV-2 obtained from two patients, a Chinese tourist visiting Rome and an Italian, were compared with sequences from Europe and elsewhere. In a phylogenetic tree, the Italian patient’s sequence clustered with sequences from Germany while the tourist’s sequence clustered with other European sequences. Some additional European sequences in the tree segregated outside the two clusters containing the patients’ sequences. This suggests multiple SARS-CoV-2 introductions in Europe or virus evolution during circulation.
Url:
DOI: 10.2807/1560-7917.ES.2020.25.13.2000305
PubMed: 32265007
PubMed Central: 7140597
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Rome</wicri:regionArea></affiliation></author><author><name sortKey="De Santis, Riccardo" sort="De Santis, Riccardo" uniqKey="De Santis R" first="Riccardo" last="De Santis">Riccardo De Santis</name><affiliation wicri:level="1"><nlm:aff id="aff2">Scientific Department Army Medical Center, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Scientific Department Army Medical Center, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Fillo, Silvia" sort="Fillo, Silvia" uniqKey="Fillo S" first="Silvia" last="Fillo">Silvia Fillo</name><affiliation wicri:level="1"><nlm:aff id="aff2">Scientific Department Army Medical Center, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Scientific Department Army Medical Center, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Capobianchi, Maria Rosaria" sort="Capobianchi, Maria Rosaria" uniqKey="Capobianchi M" first="Maria Rosaria" last="Capobianchi">Maria Rosaria Capobianchi</name><affiliation wicri:level="1"><nlm:aff id="aff4">Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Gismondo, Maria Rita" sort="Gismondo, Maria Rita" uniqKey="Gismondo M" first="Maria Rita" last="Gismondo">Maria Rita Gismondo</name><affiliation wicri:level="1"><nlm:aff id="aff5">Clinical Microbiology, Virology and Bioemergency, L. Sacco University Hospital, Milan, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Clinical Microbiology, Virology and Bioemergency, L. Sacco University Hospital, Milan</wicri:regionArea></affiliation></author><author><name sortKey="Ciervo, Alessandra" sort="Ciervo, Alessandra" uniqKey="Ciervo A" first="Alessandra" last="Ciervo">Alessandra Ciervo</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Rezza, Giovanni" sort="Rezza, Giovanni" uniqKey="Rezza G" first="Giovanni" last="Rezza">Giovanni Rezza</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Castrucci, Maria Rita" 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Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Faggioni, Giovanni" sort="Faggioni, Giovanni" uniqKey="Faggioni G" first="Giovanni" last="Faggioni">Giovanni Faggioni</name><affiliation wicri:level="1"><nlm:aff id="aff2">Scientific Department Army Medical Center, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Scientific Department Army Medical Center, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Lo Presti, Alessandra" sort="Lo Presti, Alessandra" uniqKey="Lo Presti A" first="Alessandra" last="Lo Presti">Alessandra Lo Presti</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Fiore, Stefano" sort="Fiore, Stefano" uniqKey="Fiore S" first="Stefano" last="Fiore">Stefano Fiore</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation><affiliation><nlm:aff id="aff3">These authors contributed equally to the work</nlm:aff></affiliation></author><author><name sortKey="Marchi, Antonella" sort="Marchi, Antonella" uniqKey="Marchi A" first="Antonella" last="Marchi">Antonella Marchi</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation><affiliation><nlm:aff id="aff3">These authors contributed equally to the work</nlm:aff></affiliation></author><author><name sortKey="Benedetti, Eleonora" sort="Benedetti, Eleonora" uniqKey="Benedetti E" first="Eleonora" last="Benedetti">Eleonora Benedetti</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation><affiliation><nlm:aff id="aff3">These authors contributed equally to the work</nlm:aff></affiliation></author><author><name sortKey="Fabiani, Concetta" sort="Fabiani, Concetta" uniqKey="Fabiani C" first="Concetta" last="Fabiani">Concetta Fabiani</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation><affiliation><nlm:aff id="aff3">These authors contributed equally to the work</nlm:aff></affiliation></author><author><name sortKey="Anselmo, Anna" sort="Anselmo, Anna" uniqKey="Anselmo A" first="Anna" last="Anselmo">Anna Anselmo</name><affiliation wicri:level="1"><nlm:aff id="aff2">Scientific Department Army Medical Center, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Scientific Department Army Medical Center, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Ciammaruconi, Andrea" sort="Ciammaruconi, Andrea" uniqKey="Ciammaruconi A" first="Andrea" last="Ciammaruconi">Andrea Ciammaruconi</name><affiliation wicri:level="1"><nlm:aff id="aff2">Scientific Department Army Medical Center, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Scientific Department Army Medical Center, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Fortunato, Antonella" sort="Fortunato, Antonella" uniqKey="Fortunato A" first="Antonella" last="Fortunato">Antonella Fortunato</name><affiliation wicri:level="1"><nlm:aff id="aff2">Scientific Department Army Medical Center, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Scientific Department Army Medical Center, Rome</wicri:regionArea></affiliation></author><author><name sortKey="De Santis, Riccardo" sort="De Santis, Riccardo" uniqKey="De Santis R" first="Riccardo" last="De Santis">Riccardo De Santis</name><affiliation wicri:level="1"><nlm:aff id="aff2">Scientific Department Army Medical Center, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Scientific Department Army Medical Center, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Fillo, Silvia" sort="Fillo, Silvia" uniqKey="Fillo S" first="Silvia" last="Fillo">Silvia Fillo</name><affiliation wicri:level="1"><nlm:aff id="aff2">Scientific Department Army Medical Center, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Scientific Department Army Medical Center, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Capobianchi, Maria Rosaria" sort="Capobianchi, Maria Rosaria" uniqKey="Capobianchi M" first="Maria Rosaria" last="Capobianchi">Maria Rosaria Capobianchi</name><affiliation wicri:level="1"><nlm:aff id="aff4">Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Gismondo, Maria Rita" sort="Gismondo, Maria Rita" uniqKey="Gismondo M" first="Maria Rita" last="Gismondo">Maria Rita Gismondo</name><affiliation wicri:level="1"><nlm:aff id="aff5">Clinical Microbiology, Virology and Bioemergency, L. Sacco University Hospital, Milan, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Clinical Microbiology, Virology and Bioemergency, L. Sacco University Hospital, Milan</wicri:regionArea></affiliation></author><author><name sortKey="Ciervo, Alessandra" sort="Ciervo, Alessandra" uniqKey="Ciervo A" first="Alessandra" last="Ciervo">Alessandra Ciervo</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Rezza, Giovanni" sort="Rezza, Giovanni" uniqKey="Rezza G" first="Giovanni" last="Rezza">Giovanni Rezza</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Castrucci, Maria Rita" sort="Castrucci, Maria Rita" uniqKey="Castrucci M" first="Maria Rita" last="Castrucci">Maria Rita Castrucci</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome</wicri:regionArea></affiliation></author><author><name sortKey="Lista, Florigio" sort="Lista, Florigio" uniqKey="Lista F" first="Florigio" last="Lista">Florigio Lista</name><affiliation wicri:level="1"><nlm:aff id="aff2">Scientific Department Army Medical Center, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Scientific Department Army Medical Center, Rome</wicri:regionArea></affiliation></author></analytic><series><title level="j">Eurosurveillance</title><idno type="ISSN">1025-496X</idno><idno type="eISSN">1560-7917</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Whole genome sequences of SARS-CoV-2 obtained from two patients, a Chinese tourist visiting Rome and an Italian, were compared with sequences from Europe and elsewhere. In a phylogenetic tree, the Italian patient’s sequence clustered with sequences from Germany while the tourist’s sequence clustered with other European sequences. Some additional European sequences in the tree segregated outside the two clusters containing the patients’ sequences. This suggests multiple SARS-CoV-2 introductions in Europe or virus evolution during circulation.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wu, P" uniqKey="Wu P">P Wu</name></author><author><name sortKey="Hao, X" uniqKey="Hao X">X Hao</name></author><author><name sortKey="Lau, Ehy" uniqKey="Lau E">EHY Lau</name></author><author><name sortKey="Wong, Jy" uniqKey="Wong J">JY Wong</name></author><author><name sortKey="Leung, Ksm" uniqKey="Leung K">KSM Leung</name></author><author><name sortKey="Wu, Jt" uniqKey="Wu J">JT Wu</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Kearse, M" uniqKey="Kearse M">M Kearse</name></author><author><name sortKey="Moir, R" uniqKey="Moir R">R Moir</name></author><author><name sortKey="Wilson, A" uniqKey="Wilson A">A Wilson</name></author><author><name sortKey="Stones Havas, S" uniqKey="Stones Havas S">S Stones-Havas</name></author><author><name sortKey="Cheung, M" uniqKey="Cheung M">M Cheung</name></author><author><name sortKey="Sturrock, S" uniqKey="Sturrock S">S Sturrock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Edgar, Rc" uniqKey="Edgar R">RC Edgar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, S" uniqKey="Kumar S">S Kumar</name></author><author><name sortKey="Stecher, G" uniqKey="Stecher G">G Stecher</name></author><author><name sortKey="Li, M" uniqKey="Li M">M Li</name></author><author><name sortKey="Knyaz, C" uniqKey="Knyaz C">C Knyaz</name></author><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Phan, T" uniqKey="Phan T">T Phan</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Euro Surveill</journal-id><journal-id journal-id-type="iso-abbrev">Euro Surveill</journal-id><journal-id journal-id-type="publisher-id">eurosurveillance</journal-id><journal-title-group><journal-title>Eurosurveillance</journal-title></journal-title-group><issn pub-type="ppub">1025-496X</issn><issn pub-type="epub">1560-7917</issn><publisher><publisher-name>European Centre for Disease Prevention and Control (ECDC)</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">32265007</article-id><article-id pub-id-type="pmc">7140597</article-id><article-id pub-id-type="publisher-id">2000305</article-id><article-id pub-id-type="doi">10.2807/1560-7917.ES.2020.25.13.2000305</article-id><article-id pub-id-type="publisher-id">2000305</article-id><article-categories><subj-group subj-group-type="heading"><subject>Rapid Communication</subject></subj-group></article-categories><title-group><article-title>Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Stefanelli</surname><given-names>Paola</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Faggioni</surname><given-names>Giovanni</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lo Presti</surname><given-names>Alessandra</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fiore</surname><given-names>Stefano</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Marchi</surname><given-names>Antonella</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Benedetti</surname><given-names>Eleonora</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fabiani</surname><given-names>Concetta</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Anselmo</surname><given-names>Anna</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ciammaruconi</surname><given-names>Andrea</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fortunato</surname><given-names>Antonella</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>De Santis</surname><given-names>Riccardo</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fillo</surname><given-names>Silvia</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Capobianchi</surname><given-names>Maria Rosaria</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gismondo</surname><given-names>Maria Rita</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ciervo</surname><given-names>Alessandra</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rezza</surname><given-names>Giovanni</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Castrucci</surname><given-names>Maria Rita</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lista</surname><given-names>Florigio</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><collab>on behalf of ISS COVID-19 study group</collab><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><aff id="aff1"><label>1</label>Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy</aff><aff id="aff2"><label>2</label>Scientific Department Army Medical Center, Rome, Italy</aff><aff id="aff3"><label>3</label>These authors contributed equally to the work</aff><aff id="aff4"><label>4</label>Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy</aff><aff id="aff5"><label>5</label>Clinical Microbiology, Virology and Bioemergency, L. Sacco University Hospital, Milan, Italy</aff><aff id="aff6"><label>6</label>The members of the ISS COVID-19 study group are acknowledged at the end of the article</aff></contrib-group><author-notes><fn id="afn1"><p>Correspondence: Paola Stefanelli (<email xlink:href="paola.stefanelli@iss.it">paola.stefanelli@iss.it</email>)</p></fn></author-notes><pub-date pub-type="ppub"><day>02</day><month>4</month><year>2020</year></pub-date><volume>25</volume><issue>13</issue><elocation-id>2000305</elocation-id><history><date date-type="received"><day>13</day><month>3</month><year>2020</year></date><date date-type="accepted"><day>02</day><month>4</month><year>2020</year></date></history><permissions><copyright-statement>This article is copyright of the authors or their affiliated institutions, 2020.</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>The authors or their affiliated institutions</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY 4.0) Licence. You may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence, and indicate if changes were made.</license-p></license></permissions><abstract><p>Whole genome sequences of SARS-CoV-2 obtained from two patients, a Chinese tourist visiting Rome and an Italian, were compared with sequences from Europe and elsewhere. In a phylogenetic tree, the Italian patient’s sequence clustered with sequences from Germany while the tourist’s sequence clustered with other European sequences. Some additional European sequences in the tree segregated outside the two clusters containing the patients’ sequences. This suggests multiple SARS-CoV-2 introductions in Europe or virus evolution during circulation.</p></abstract><kwd-group><title>Keywords: </title><kwd>SARS-CoV-2</kwd><kwd>Whole genome sequence</kwd><kwd>phylogenetic analysis</kwd><kwd>Europe</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>sequence</meta-name><meta-value>1</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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