Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.
Identifieur interne : 000726 ( Main/Exploration ); précédent : 000725; suivant : 000727Genome 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
Affiliations:
- Afrique du Sud, Belgique, Brésil
- Minas Gerais, État de Rio de Janeiro
- Belo Horizonte
- Université fédérale du Minas Gerais
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Le document en format XML
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Herent</wicri:regionArea><wicri:noRegion>Herent</wicri:noRegion></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><wicri:noRegion>Durban</wicri:noRegion></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><affiliations><list><country><li>Afrique du Sud</li><li>Belgique</li><li>Brésil</li></country><region><li>Minas Gerais</li><li>État de Rio de Janeiro</li></region><settlement><li>Belo Horizonte</li></settlement><orgName><li>Université fédérale du Minas Gerais</li></orgName></list><tree><country name="Belgique"><noRegion><name sortKey="Cleemput, Sara" sort="Cleemput, Sara" uniqKey="Cleemput S" first="Sara" last="Cleemput">Sara Cleemput</name></noRegion><name sortKey="Deforche, Koen" sort="Deforche, Koen" uniqKey="Deforche K" first="Koen" last="Deforche">Koen Deforche</name><name sortKey="Dumon, Wim" sort="Dumon, Wim" uniqKey="Dumon W" first="Wim" last="Dumon">Wim Dumon</name></country><country name="Afrique du Sud"><noRegion><name sortKey="Fonseca, Vagner" sort="Fonseca, Vagner" uniqKey="Fonseca V" first="Vagner" last="Fonseca">Vagner Fonseca</name></noRegion><name sortKey="De Oliveira, Tulio" sort="De Oliveira, Tulio" uniqKey="De Oliveira T" first="Tulio" last="De Oliveira">Tulio De Oliveira</name><name sortKey="Karim, Wasim Abdool" sort="Karim, Wasim Abdool" uniqKey="Karim W" first="Wasim Abdool" last="Karim">Wasim Abdool Karim</name></country><country name="Brésil"><region name="État de Rio de Janeiro"><name sortKey="Giovanetti, Marta" sort="Giovanetti, Marta" uniqKey="Giovanetti M" first="Marta" last="Giovanetti">Marta Giovanetti</name></region><name sortKey="Alcantara, Luiz Carlos" sort="Alcantara, Luiz Carlos" uniqKey="Alcantara L" first="Luiz Carlos" last="Alcantara">Luiz Carlos Alcantara</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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