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Virosaurus A Reference to Explore and Capture Virus Genetic Diversity

The huge genetic diversity of circulating viruses is a challenge for diagnostic assays for emerging or rare viral diseases. High-throughput technology offers a new opportunity to explore the global virome of patients without preconception about the culpable pathogens. It requires a solid reference d...

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Autores principales: Gleizes, Anne, Laubscher, Florian, Guex, Nicolas, Iseli, Christian, Junier, Thomas, Cordey, Samuel, Fellay, Jacques, Xenarios, Ioannis, Kaiser, Laurent, Mercier, Philippe Le
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693494/
https://www.ncbi.nlm.nih.gov/pubmed/33139591
http://dx.doi.org/10.3390/v12111248
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author Gleizes, Anne
Laubscher, Florian
Guex, Nicolas
Iseli, Christian
Junier, Thomas
Cordey, Samuel
Fellay, Jacques
Xenarios, Ioannis
Kaiser, Laurent
Mercier, Philippe Le
author_facet Gleizes, Anne
Laubscher, Florian
Guex, Nicolas
Iseli, Christian
Junier, Thomas
Cordey, Samuel
Fellay, Jacques
Xenarios, Ioannis
Kaiser, Laurent
Mercier, Philippe Le
author_sort Gleizes, Anne
collection PubMed
description The huge genetic diversity of circulating viruses is a challenge for diagnostic assays for emerging or rare viral diseases. High-throughput technology offers a new opportunity to explore the global virome of patients without preconception about the culpable pathogens. It requires a solid reference dataset to be accurate. Virosaurus has been designed to offer a non-biased, automatized and annotated database for clinical metagenomics studies and diagnosis. Raw viral sequences have been extracted from GenBank, and cleaned up to remove potentially erroneous sequences. Complete sequences have been identified for all genera infecting vertebrates, plants and other eukaryotes (insect, fungus, etc.). To facilitate the analysis of clinically relevant viruses, we have annotated all sequences with official and common virus names, acronym, genotypes, and genomic features (linear, circular, DNA, RNA, etc.). Sequences have been clustered to remove redundancy at 90% or 98% identity. The analysis of clustering results reveals the state of the virus genetic landscape knowledge. Because herpes and poxviruses were under-represented in complete genomes considering their potential diversity in nature, we used genes instead of complete genomes for those in Virosaurus.
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spelling pubmed-76934942020-11-28 Virosaurus A Reference to Explore and Capture Virus Genetic Diversity Gleizes, Anne Laubscher, Florian Guex, Nicolas Iseli, Christian Junier, Thomas Cordey, Samuel Fellay, Jacques Xenarios, Ioannis Kaiser, Laurent Mercier, Philippe Le Viruses Article The huge genetic diversity of circulating viruses is a challenge for diagnostic assays for emerging or rare viral diseases. High-throughput technology offers a new opportunity to explore the global virome of patients without preconception about the culpable pathogens. It requires a solid reference dataset to be accurate. Virosaurus has been designed to offer a non-biased, automatized and annotated database for clinical metagenomics studies and diagnosis. Raw viral sequences have been extracted from GenBank, and cleaned up to remove potentially erroneous sequences. Complete sequences have been identified for all genera infecting vertebrates, plants and other eukaryotes (insect, fungus, etc.). To facilitate the analysis of clinically relevant viruses, we have annotated all sequences with official and common virus names, acronym, genotypes, and genomic features (linear, circular, DNA, RNA, etc.). Sequences have been clustered to remove redundancy at 90% or 98% identity. The analysis of clustering results reveals the state of the virus genetic landscape knowledge. Because herpes and poxviruses were under-represented in complete genomes considering their potential diversity in nature, we used genes instead of complete genomes for those in Virosaurus. MDPI 2020-11-01 /pmc/articles/PMC7693494/ /pubmed/33139591 http://dx.doi.org/10.3390/v12111248 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Gleizes, Anne
Laubscher, Florian
Guex, Nicolas
Iseli, Christian
Junier, Thomas
Cordey, Samuel
Fellay, Jacques
Xenarios, Ioannis
Kaiser, Laurent
Mercier, Philippe Le
Virosaurus A Reference to Explore and Capture Virus Genetic Diversity
title Virosaurus A Reference to Explore and Capture Virus Genetic Diversity
title_full Virosaurus A Reference to Explore and Capture Virus Genetic Diversity
title_fullStr Virosaurus A Reference to Explore and Capture Virus Genetic Diversity
title_full_unstemmed Virosaurus A Reference to Explore and Capture Virus Genetic Diversity
title_short Virosaurus A Reference to Explore and Capture Virus Genetic Diversity
title_sort virosaurus a reference to explore and capture virus genetic diversity
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693494/
https://www.ncbi.nlm.nih.gov/pubmed/33139591
http://dx.doi.org/10.3390/v12111248
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