DisCVR: Rapid viral diagnosis from high-throughput sequencing data
Identifieur interne : 001191 ( Pmc/Curation ); précédent : 001190; suivant : 001192DisCVR: Rapid viral diagnosis from high-throughput sequencing data
Auteurs : Maha Maabar [Royaume-Uni] ; Andrew J. Davison [Royaume-Uni] ; Matej Vu Ak [Royaume-Uni] ; Fiona Thorburn [Royaume-Uni] ; Pablo R. Murcia [Royaume-Uni] ; Rory Gunson [Royaume-Uni] ; Massimo Palmarini [Royaume-Uni] ; Joseph Hughes [Royaume-Uni]Source :
- Virus Evolution [ 2057-1577 ] ; 2019.
Abstract
High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample
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DOI: 10.1093/ve/vez033
PubMed: 31528358
PubMed Central: 6735924
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Davison</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author><author><name sortKey="Vu Ak, Matej" sort="Vu Ak, Matej" uniqKey="Vu Ak M" first="Matej" last="Vu Ak">Matej Vu Ak</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author><author><name sortKey="Thorburn, Fiona" sort="Thorburn, Fiona" uniqKey="Thorburn F" first="Fiona" last="Thorburn">Fiona Thorburn</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff2">Microbiology Department, Glasgow Royal Infirmary, Glasgow G4 0SF, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Microbiology Department, Glasgow Royal Infirmary, Glasgow G4 0SF</wicri:regionArea></affiliation></author><author><name sortKey="Murcia, Pablo R" sort="Murcia, Pablo R" uniqKey="Murcia P" first="Pablo R" last="Murcia">Pablo R. Murcia</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author><author><name sortKey="Gunson, Rory" sort="Gunson, Rory" uniqKey="Gunson R" first="Rory" last="Gunson">Rory Gunson</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff3">West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow G4 0SF, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow G4 0SF</wicri:regionArea></affiliation></author><author><name sortKey="Palmarini, Massimo" sort="Palmarini, Massimo" uniqKey="Palmarini M" first="Massimo" last="Palmarini">Massimo Palmarini</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author><author><name sortKey="Hughes, Joseph" sort="Hughes, Joseph" uniqKey="Hughes J" first="Joseph" last="Hughes">Joseph Hughes</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31528358</idno><idno type="pmc">6735924</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735924</idno><idno type="RBID">PMC:6735924</idno><idno type="doi">10.1093/ve/vez033</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">001191</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001191</idno><idno type="wicri:Area/Pmc/Curation">001191</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001191</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">DisCVR: Rapid viral diagnosis from high-throughput sequencing data</title><author><name sortKey="Maabar, Maha" sort="Maabar, Maha" uniqKey="Maabar M" first="Maha" last="Maabar">Maha Maabar</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author><author><name sortKey="Davison, Andrew J" sort="Davison, Andrew J" uniqKey="Davison A" first="Andrew J" last="Davison">Andrew J. Davison</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author><author><name sortKey="Vu Ak, Matej" sort="Vu Ak, Matej" uniqKey="Vu Ak M" first="Matej" last="Vu Ak">Matej Vu Ak</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author><author><name sortKey="Thorburn, Fiona" sort="Thorburn, Fiona" uniqKey="Thorburn F" first="Fiona" last="Thorburn">Fiona Thorburn</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff2">Microbiology Department, Glasgow Royal Infirmary, Glasgow G4 0SF, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Microbiology Department, Glasgow Royal Infirmary, Glasgow G4 0SF</wicri:regionArea></affiliation></author><author><name sortKey="Murcia, Pablo R" sort="Murcia, Pablo R" uniqKey="Murcia P" first="Pablo R" last="Murcia">Pablo R. Murcia</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author><author><name sortKey="Gunson, Rory" sort="Gunson, Rory" uniqKey="Gunson R" first="Rory" last="Gunson">Rory Gunson</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff3">West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow G4 0SF, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow G4 0SF</wicri:regionArea></affiliation></author><author><name sortKey="Palmarini, Massimo" sort="Palmarini, Massimo" uniqKey="Palmarini M" first="Massimo" last="Palmarini">Massimo Palmarini</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author><author><name sortKey="Hughes, Joseph" sort="Hughes, Joseph" uniqKey="Hughes J" first="Joseph" last="Hughes">Joseph Hughes</name><affiliation wicri:level="1"><nlm:aff id="vez033-aff1">MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH</wicri:regionArea></affiliation></author></analytic><series><title level="j">Virus Evolution</title><idno type="eISSN">2057-1577</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample <italic>k</italic>-mers (twenty-two nucleotide sequences) to <italic>k</italic>-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.cvr.ac.uk/discvr.php">http://bioinformatics.cvr.ac.uk/discvr.php</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Altschul, S F" uniqKey="Altschul S">S. F. Altschul</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Audano, P" uniqKey="Audano P">P. Audano</name></author><author><name sortKey="Vannberg, F" uniqKey="Vannberg F">F. Vannberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Borozan, I" uniqKey="Borozan I">I. Borozan</name></author><author><name sortKey="Ferretti, V" uniqKey="Ferretti V">V. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Virus Evol</journal-id><journal-id journal-id-type="iso-abbrev">Virus Evol</journal-id><journal-id journal-id-type="publisher-id">vevolu</journal-id><journal-title-group><journal-title>Virus Evolution</journal-title></journal-title-group><issn pub-type="epub">2057-1577</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">31528358</article-id><article-id pub-id-type="pmc">6735924</article-id><article-id pub-id-type="doi">10.1093/ve/vez033</article-id><article-id pub-id-type="publisher-id">vez033</article-id><article-categories><subj-group subj-group-type="heading"><subject>Resources</subject></subj-group></article-categories><title-group><article-title>DisCVR: Rapid viral diagnosis from high-throughput sequencing data</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Maabar</surname><given-names>Maha</given-names></name><xref ref-type="aff" rid="vez033-aff1">1</xref><xref ref-type="corresp" rid="vez033-cor1"></xref><pmc-comment>Maha.Maabar@glasgow.ac.uk </pmc-comment>
</contrib><contrib contrib-type="author"><name><surname>Davison</surname><given-names>Andrew J</given-names></name><xref ref-type="aff" rid="vez033-aff1">1</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0002-3181-2808</contrib-id><name><surname>Vučak</surname><given-names>Matej</given-names></name><xref ref-type="aff" rid="vez033-aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Thorburn</surname><given-names>Fiona</given-names></name><xref ref-type="aff" rid="vez033-aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Murcia</surname><given-names>Pablo R</given-names></name><xref ref-type="aff" rid="vez033-aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Gunson</surname><given-names>Rory</given-names></name><xref ref-type="aff" rid="vez033-aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Palmarini</surname><given-names>Massimo</given-names></name><xref ref-type="aff" rid="vez033-aff1">1</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0003-2556-2563</contrib-id><name><surname>Hughes</surname><given-names>Joseph</given-names></name><xref ref-type="aff" rid="vez033-aff1">1</xref><xref ref-type="corresp" rid="vez033-cor1"></xref><pmc-comment>Joseph.Hughes@glasgow.ac.uk </pmc-comment>
</contrib></contrib-group><aff id="vez033-aff1"><label>1</label>MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK</aff><aff id="vez033-aff2"><label>2</label>Microbiology Department, Glasgow Royal Infirmary, Glasgow G4 0SF, UK</aff><aff id="vez033-aff3"><label>3</label>West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow G4 0SF, UK</aff><author-notes><corresp id="vez033-cor1">Corresponding authors: E-mails: <email>Joseph.Hughes@glasgow.ac.uk</email> (J.H.); <email>Maha.Maabar@glasgow.ac.uk</email> (M.M.)</corresp></author-notes><pub-date pub-type="collection"><month>7</month><year>2019</year></pub-date><pub-date pub-type="epub" iso-8601-date="2019-08-26"><day>26</day><month>8</month><year>2019</year></pub-date><pub-date pub-type="pmc-release"><day>26</day><month>8</month><year>2019</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>5</volume><issue>2</issue><elocation-id>vez033</elocation-id><permissions><copyright-statement>© The Author(s) 2019. Published by Oxford University Press.</copyright-statement><copyright-year>2019</copyright-year><license license-type="cc-by" 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 License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="vez033.pdf"></self-uri><abstract><title>Abstract</title><p>High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample <italic>k</italic>-mers (twenty-two nucleotide sequences) to <italic>k</italic>-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.cvr.ac.uk/discvr.php">http://bioinformatics.cvr.ac.uk/discvr.php</ext-link>.</p></abstract><kwd-group><kwd>virus</kwd><kwd>diagnosis</kwd><kwd>high-throughput sequencing</kwd><kwd>k-mer</kwd></kwd-group><funding-group><award-group award-type="grant"><funding-source><named-content content-type="funder-name">Medical Research Council</named-content><named-content content-type="funder-identifier">10.13039/501100000265</named-content></funding-source><award-id>MC_UU_12014/12</award-id></award-group></funding-group><counts><page-count count="8"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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