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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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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. |
format | Online Article Text |
id | pubmed-7693494 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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