Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.
Identifieur interne : 000969 ( PubMed/Curation ); précédent : 000968; suivant : 000970Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.
Auteurs : Sara Cleemput [Belgique] ; Wim Dumon [Belgique] ; Vagner Fonseca [Afrique du Sud] ; Wasim Abdool Karim [Afrique du Sud] ; Marta Giovanetti [Brésil] ; Luiz Carlos Alcantara [Brésil] ; Koen Deforche [Belgique] ; Tulio De Oliveira [Afrique du Sud]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2020.
Abstract
Genome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS) related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease.
DOI: 10.1093/bioinformatics/btaa145
PubMed: 32108862
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Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.</title><author><name sortKey="Cleemput, Sara" sort="Cleemput, Sara" uniqKey="Cleemput S" first="Sara" last="Cleemput">Sara Cleemput</name><affiliation wicri:level="1"><nlm:affiliation>Emweb bv, Herent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Emweb bv, Herent</wicri:regionArea></affiliation></author><author><name sortKey="Dumon, Wim" sort="Dumon, Wim" uniqKey="Dumon W" first="Wim" last="Dumon">Wim Dumon</name><affiliation wicri:level="1"><nlm:affiliation>Emweb bv, Herent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Emweb bv, Herent</wicri:regionArea></affiliation></author><author><name sortKey="Fonseca, Vagner" sort="Fonseca, Vagner" uniqKey="Fonseca V" first="Vagner" last="Fonseca">Vagner Fonseca</name><affiliation wicri:level="1"><nlm:affiliation>KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban</wicri:regionArea></affiliation></author><author><name sortKey="Karim, Wasim Abdool" sort="Karim, Wasim Abdool" uniqKey="Karim W" first="Wasim Abdool" last="Karim">Wasim Abdool Karim</name><affiliation wicri:level="1"><nlm:affiliation>KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban</wicri:regionArea></affiliation></author><author><name sortKey="Giovanetti, Marta" sort="Giovanetti, Marta" uniqKey="Giovanetti M" first="Marta" last="Giovanetti">Marta Giovanetti</name><affiliation wicri:level="1"><nlm:affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ</wicri:regionArea></affiliation></author><author><name sortKey="Alcantara, Luiz Carlos" sort="Alcantara, Luiz Carlos" uniqKey="Alcantara L" first="Luiz Carlos" last="Alcantara">Luiz Carlos Alcantara</name><affiliation wicri:level="1"><nlm:affiliation>Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte</wicri:regionArea></affiliation></author><author><name sortKey="Deforche, Koen" sort="Deforche, Koen" uniqKey="Deforche K" first="Koen" last="Deforche">Koen Deforche</name><affiliation wicri:level="1"><nlm:affiliation>Emweb bv, Herent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Emweb bv, Herent</wicri:regionArea></affiliation></author><author><name sortKey="De Oliveira, Tulio" sort="De Oliveira, Tulio" uniqKey="De Oliveira T" first="Tulio" last="De Oliveira">Tulio De Oliveira</name><affiliation wicri:level="1"><nlm:affiliation>KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban</wicri:regionArea></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Genome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS) related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32108862</PMID><DateRevised><Year>2020</Year><Month>02</Month><Day>28</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Feb</Month><Day>28</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">btaa145</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btaa145</ELocationID><Abstract><AbstractText Label="SUMMARY" NlmCategory="CONCLUSIONS">Genome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS) related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">https://www.genomedetective.com/app/typingtool/cov.</AbstractText><AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText><CopyrightInformation>© The Author(s) 2020. Published by Oxford University Press.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cleemput</LastName><ForeName>Sara</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Emweb bv, Herent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dumon</LastName><ForeName>Wim</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Emweb bv, Herent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fonseca</LastName><ForeName>Vagner</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS) Brasília, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Karim</LastName><ForeName>Wasim Abdool</ForeName><Initials>WA</Initials><AffiliationInfo><Affiliation>KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giovanetti</LastName><ForeName>Marta</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alcantara</LastName><ForeName>Luiz Carlos</ForeName><Initials>LC</Initials><AffiliationInfo><Affiliation>Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Deforche</LastName><ForeName>Koen</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Emweb bv, Herent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>de Oliveira</LastName><ForeName>Tulio</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Global Health, University of Washington, Seattle, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>01</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>02</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>02</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32108862</ArticleId><ArticleId IdType="pii">5766118</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btaa145</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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