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Phylogenetic analysis of SARS-CoV-2 genomes in Turkey

Ogün ADEBALİ; Aylin BİRCAN; Defne ÇİRCİ; Burak İŞLEK; Zeynep KILINÇ; Berkay SELÇUK; Berk TURHAN


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  <identifier identifierType="URL">https://aperta.ulakbim.gov.tr//record/97865</identifier>
  <creators>
    <creator>
      <creatorName>Ogün ADEBALİ</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-9213-4070</nameIdentifier>
      <affiliation>Molecular Biology, Genetics and Bioengineering, Faculty of Natural Sciences and Engineering, Sabancı University, İstanbul, Turkey</affiliation>
    </creator>
    <creator>
      <creatorName>Aylin BİRCAN</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6663-6173</nameIdentifier>
      <affiliation>Molecular Biology, Genetics and Bioengineering, Faculty of Natural Sciences and Engineering, Sabancı University, İstanbul, Turkey</affiliation>
    </creator>
    <creator>
      <creatorName>Defne ÇİRCİ</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-5761-0198</nameIdentifier>
      <affiliation>Molecular Biology, Genetics and Bioengineering, Faculty of Natural Sciences and Engineering, Sabancı University, İstanbul, Turkey</affiliation>
    </creator>
    <creator>
      <creatorName>Burak İŞLEK</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-2700-9884</nameIdentifier>
      <affiliation>Molecular Biology, Genetics and Bioengineering, Faculty of Natural Sciences and Engineering, Sabancı University, İstanbul, Turkey</affiliation>
    </creator>
    <creator>
      <creatorName>Zeynep KILINÇ</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1906-0391</nameIdentifier>
      <affiliation>Molecular Biology, Genetics and Bioengineering, Faculty of Natural Sciences and Engineering, Sabancı University, İstanbul, Turkey</affiliation>
    </creator>
    <creator>
      <creatorName>Berkay SELÇUK</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-3206-4749</nameIdentifier>
      <affiliation>Molecular Biology, Genetics and Bioengineering, Faculty of Natural Sciences and Engineering, Sabancı University, İstanbul, Turkey</affiliation>
    </creator>
    <creator>
      <creatorName>Berk TURHAN</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-6471-0357</nameIdentifier>
      <affiliation>Molecular Biology, Genetics and Bioengineering, Faculty of Natural Sciences and Engineering, Sabancı University, İstanbul, Turkey</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Phylogenetic Analysis Of Sars-Cov-2 Genomes In Turkey</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>SARS-CoV-2</subject>
    <subject>COVID-19</subject>
    <subject>phylogenetics</subject>
    <subject>evolution</subject>
    <subject>genome sequence</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-06-23</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Text">Journal article</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://aperta.ulakbim.gov.tr//record/97865</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.3906/biy-2005-35-sup</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://www.opendefinition.org/licenses/cc-by-sa">Creative Commons Attribution Share-Alike</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;COVID-19 has effectively spread worldwide. As of May 2020, Turkey is among the top ten countries with the most cases. A comprehensive genomic characterization of the virus isolates in Turkey is yet to be carried out. Here, we built a phylogenetic tree with globally obtained 15,277 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes. We identified the subtypes based on the phylogenetic clustering in comparison with the previously annotated classifications. We performed a phylogenetic analysis of the first 30 SARS-CoV-2 genomes isolated and sequenced in Turkey. We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection. Virus genomes isolated from Turkey are dispersed among most types in the phylogenetic tree. We find 2 of the seventeen subclusters enriched with the isolates of Turkey, which likely have spread expansively in the country. Finally, we traced virus genomes based on their phylogenetic placements. This analysis suggested multiple independent international introductions of the virus and revealed a hub for the inland transmission. We released a web application to track the global and interprovincial virus spread of the isolates from Turkey in comparison to thousands of genomes worldwide.&lt;/p&gt;</description>
  </descriptions>
</resource>
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