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...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-11-01
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| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/12/11/1248 |
| _version_ | 1797549086017060864 |
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| author | Anne Gleizes Florian Laubscher Nicolas Guex Christian Iseli Thomas Junier Samuel Cordey Jacques Fellay Ioannis Xenarios Laurent Kaiser Philippe Le Mercier |
| author_facet | Anne Gleizes Florian Laubscher Nicolas Guex Christian Iseli Thomas Junier Samuel Cordey Jacques Fellay Ioannis Xenarios Laurent Kaiser Philippe Le Mercier |
| author_sort | Anne Gleizes |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T15:09:38Z |
| format | Article |
| id | doaj.art-18768f6cf35948759a93fbeb7c228c57 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T15:09:38Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-18768f6cf35948759a93fbeb7c228c572023-11-20T19:25:52ZengMDPI AGViruses1999-49152020-11-011211124810.3390/v12111248Virosaurus A Reference to Explore and Capture Virus Genetic DiversityAnne Gleizes0Florian Laubscher1Nicolas Guex2Christian Iseli3Thomas Junier4Samuel Cordey5Jacques Fellay6Ioannis Xenarios7Laurent Kaiser8Philippe Le Mercier9Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, SwitzerlandDivision of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, SwitzerlandBioinformatics Competence Center, University of Lausanne, 1015 Lausanne, SwitzerlandBioinformatics Competence Center, University of Lausanne, 1015 Lausanne, SwitzerlandVital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, SwitzerlandDivision of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, SwitzerlandUnité de Médecine de Précision, CHUV, 1015 Lausanne, SwitzerlandCenter for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, SwitzerlandDivision of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, SwitzerlandSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1011 Geneva, SwitzerlandThe 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.https://www.mdpi.com/1999-4915/12/11/1248databasecomplete genomebioinformaticsHTSdiagnosticssequencing |
| spellingShingle | Anne Gleizes Florian Laubscher Nicolas Guex Christian Iseli Thomas Junier Samuel Cordey Jacques Fellay Ioannis Xenarios Laurent Kaiser Philippe Le Mercier Virosaurus A Reference to Explore and Capture Virus Genetic Diversity Viruses database complete genome bioinformatics HTS diagnostics sequencing |
| 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 | database complete genome bioinformatics HTS diagnostics sequencing |
| url | https://www.mdpi.com/1999-4915/12/11/1248 |
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