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Phylogenetic analysis of SARS-CoV-2 data is difficult.

Identifieur interne : 000394 ( Main/Exploration ); précédent : 000393; suivant : 000395

Phylogenetic analysis of SARS-CoV-2 data is difficult.

Auteurs : Benoit Morel [Allemagne] ; Pierre Barbera [Allemagne] ; Lucas Czech [États-Unis] ; Ben Bettisworth [Allemagne] ; Lukas Hübner [Allemagne] ; Sarah Lutteropp [Allemagne] ; Dora Serdari [Allemagne] ; Evangelia-Georgia Kostaki [Grèce] ; Ioannis Mamais ; Alexey M. Kozlov [Allemagne] ; Pavlos Pavlidis [Grèce] ; Dimitrios Paraskevis [Grèce] ; Alexandros Stamatakis [Allemagne]

Source :

RBID : pubmed:33316067

Abstract

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.

DOI: 10.1093/molbev/msaa314
PubMed: 33316067
PubMed Central: PMC7798910


Affiliations:


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<ELocationID EIdType="doi" ValidYN="Y">10.1093/molbev/msaa314</ELocationID>
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<AbstractText>Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.</AbstractText>
<CopyrightInformation>© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Morel</LastName>
<ForeName>Benoit</ForeName>
<Initials>B</Initials>
<AffiliationInfo>
<Affiliation>Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Barbera</LastName>
<ForeName>Pierre</ForeName>
<Initials>P</Initials>
<AffiliationInfo>
<Affiliation>Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Czech</LastName>
<ForeName>Lucas</ForeName>
<Initials>L</Initials>
<AffiliationInfo>
<Affiliation>Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Bettisworth</LastName>
<ForeName>Ben</ForeName>
<Initials>B</Initials>
<AffiliationInfo>
<Affiliation>Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Hübner</LastName>
<ForeName>Lukas</ForeName>
<Initials>L</Initials>
<AffiliationInfo>
<Affiliation>Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Lutteropp</LastName>
<ForeName>Sarah</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Serdari</LastName>
<ForeName>Dora</ForeName>
<Initials>D</Initials>
<AffiliationInfo>
<Affiliation>Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Kostaki</LastName>
<ForeName>Evangelia-Georgia</ForeName>
<Initials>EG</Initials>
<AffiliationInfo>
<Affiliation>Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Mamais</LastName>
<ForeName>Ioannis</ForeName>
<Initials>I</Initials>
<AffiliationInfo>
<Affiliation>Department of Health Sciences, European University Cyprus, Nicosia-Cyprus.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Kozlov</LastName>
<ForeName>Alexey M</ForeName>
<Initials>AM</Initials>
<AffiliationInfo>
<Affiliation>Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Pavlidis</LastName>
<ForeName>Pavlos</ForeName>
<Initials>P</Initials>
<AffiliationInfo>
<Affiliation>Institute of Computer Science, Foundation for Research and Technology-Hellas, Crete, Greece.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Paraskevis</LastName>
<ForeName>Dimitrios</ForeName>
<Initials>D</Initials>
<AffiliationInfo>
<Affiliation>Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Stamatakis</LastName>
<ForeName>Alexandros</ForeName>
<Initials>A</Initials>
<AffiliationInfo>
<Affiliation>Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2020</Year>
<Month>12</Month>
<Day>15</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>United States</Country>
<MedlineTA>Mol Biol Evol</MedlineTA>
<NlmUniqueID>8501455</NlmUniqueID>
<ISSNLinking>0737-4038</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<KeywordList Owner="NOTNLM">
<Keyword MajorTopicYN="N">SARS-CoV-2</Keyword>
<Keyword MajorTopicYN="N">outgroups</Keyword>
<Keyword MajorTopicYN="N">phylogenetic inference</Keyword>
<Keyword MajorTopicYN="N">phylogeny rooting</Keyword>
<Keyword MajorTopicYN="N">strain classification</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="received">
<Year>2020</Year>
<Month>08</Month>
<Day>08</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised">
<Year>2020</Year>
<Month>11</Month>
<Day>26</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2020</Year>
<Month>11</Month>
<Day>28</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>2020</Year>
<Month>12</Month>
<Day>14</Day>
<Hour>17</Hour>
<Minute>14</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed">
<Year>2020</Year>
<Month>12</Month>
<Day>15</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2020</Year>
<Month>12</Month>
<Day>15</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>aheadofprint</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">33316067</ArticleId>
<ArticleId IdType="pii">6030946</ArticleId>
<ArticleId IdType="doi">10.1093/molbev/msaa314</ArticleId>
<ArticleId IdType="pmc">PMC7798910</ArticleId>
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<list>
<country>
<li>Allemagne</li>
<li>Grèce</li>
<li>États-Unis</li>
</country>
<region>
<li>Attique (région)</li>
<li>Bade-Wurtemberg</li>
<li>Californie</li>
<li>District de Karlsruhe</li>
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<settlement>
<li>Athènes</li>
<li>Heidelberg</li>
<li>Karlsruhe</li>
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<name sortKey="Morel, Benoit" sort="Morel, Benoit" uniqKey="Morel B" first="Benoit" last="Morel">Benoit Morel</name>
</region>
<name sortKey="Barbera, Pierre" sort="Barbera, Pierre" uniqKey="Barbera P" first="Pierre" last="Barbera">Pierre Barbera</name>
<name sortKey="Bettisworth, Ben" sort="Bettisworth, Ben" uniqKey="Bettisworth B" first="Ben" last="Bettisworth">Ben Bettisworth</name>
<name sortKey="Hubner, Lukas" sort="Hubner, Lukas" uniqKey="Hubner L" first="Lukas" last="Hübner">Lukas Hübner</name>
<name sortKey="Hubner, Lukas" sort="Hubner, Lukas" uniqKey="Hubner L" first="Lukas" last="Hübner">Lukas Hübner</name>
<name sortKey="Kozlov, Alexey M" sort="Kozlov, Alexey M" uniqKey="Kozlov A" first="Alexey M" last="Kozlov">Alexey M. Kozlov</name>
<name sortKey="Lutteropp, Sarah" sort="Lutteropp, Sarah" uniqKey="Lutteropp S" first="Sarah" last="Lutteropp">Sarah Lutteropp</name>
<name sortKey="Serdari, Dora" sort="Serdari, Dora" uniqKey="Serdari D" first="Dora" last="Serdari">Dora Serdari</name>
<name sortKey="Stamatakis, Alexandros" sort="Stamatakis, Alexandros" uniqKey="Stamatakis A" first="Alexandros" last="Stamatakis">Alexandros Stamatakis</name>
<name sortKey="Stamatakis, Alexandros" sort="Stamatakis, Alexandros" uniqKey="Stamatakis A" first="Alexandros" last="Stamatakis">Alexandros Stamatakis</name>
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<country name="États-Unis">
<region name="Californie">
<name sortKey="Czech, Lucas" sort="Czech, Lucas" uniqKey="Czech L" first="Lucas" last="Czech">Lucas Czech</name>
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<region name="Attique (région)">
<name sortKey="Kostaki, Evangelia Georgia" sort="Kostaki, Evangelia Georgia" uniqKey="Kostaki E" first="Evangelia-Georgia" last="Kostaki">Evangelia-Georgia Kostaki</name>
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<name sortKey="Paraskevis, Dimitrios" sort="Paraskevis, Dimitrios" uniqKey="Paraskevis D" first="Dimitrios" last="Paraskevis">Dimitrios Paraskevis</name>
<name sortKey="Pavlidis, Pavlos" sort="Pavlidis, Pavlos" uniqKey="Pavlidis P" first="Pavlos" last="Pavlidis">Pavlos Pavlidis</name>
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