Raw deep-sequencing data of targeted metagenomics to study the diversity of norovirus GII in shellfish
A metagenomics approach targetting the capsid and polymerase genes of genotype norovirus (NoV GII) was tested on artificial samples and shellfish samples associated to confirmed norovirus outbreaks. This technique aims at assessing the diversity of NoV GII in environmentally-contaminated foods such as shellfish.
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Citation proposal
Desdouits Marion (IFREMER) - Wacrenier Candice (IFREMER) - Ollivier Joanna (IFREMER) - Schaeffer Julien (IFREMER) - Le Guyader Soizick (IFREMER) (2020) . Raw deep-sequencing data of targeted metagenomics to study the diversity of norovirus GII in shellfish. IFREMER https://services.mspdata.eu:/geonetwork/srv/api/records/6e0c6687-22fe-47e0-bc67-81dde633d25b |
Simple
- Date ( Creation )
- 2019-12-02
- Date ( Publication )
- 2020-09-02
- Identifier
- FR-330-715-368-00032-IFR_BIOINFO_MD1904_ARTIFICIAL_SAMPLES
- Identifier
- DOI:10.12770/6e0c6687-22fe-47e0-bc67-81dde633d25b
- Credit
- Ifremer - Laboratoire Santé Environnement et Microbiologie
Author
IFREMER
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Desdouits Marion
Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03
Nantes
France
Author
IFREMER
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Wacrenier Candice
Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03
Nantes
France
Author
IFREMER
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Ollivier Joanna
Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03
Nantes
France
Author
IFREMER
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Schaeffer Julien
Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03
Nantes
France
Author
IFREMER
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Le Guyader Soizick
Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03
Nantes
France
Publisher
- GEMET - INSPIRE themes, version 1.0 ( Theme )
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- Habitats and biotopes
- Thèmes Sextant ( Theme )
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- /Biological Environment/Bioinformatics
- Access constraints
- Copyright
- Use constraints
- Copyright
- Other constraints
- Metadata language
- French
- Character set
- UTF8
- Topic category
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- Environment
- Distribution format
-
- ( )
- OnLine resource
- /home/ref-bioinfo-public/ifremer/sg2m/targeted_metagenomics_norovirus_shellfish_2016
- OnLine resource
- Download link
- OnLine resource
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DOI of the dataset
DOI of the dataset
- Hierarchy level
- Dataset
- Statement
- Targeted metagenomics of genotype II norovirus (NoV GII) in artificial samples and shellfish linked to NoV outbreaks. The 8 artificial samples combine nucleic acid from 10 different viral strains into 4 different compositions (A, B, C, D) at two different concentrations (100 and 10 NoV GII genome copies /µl). The 10 naturally contaminated shellfish samples were linked to eight NoV outbreaks, and nucleic acid were extracted using the ISO-15216 method. For each sample, segments of the capsid (VP1) and polymerase (RdRp) viral genes were amplified by semi-nested PCRs, and the amplicon were deep-sequenced using Illumina MiSeq 2x150 or 2x300. The negative control (NC) used water in place of nucleic acid matrix and was processed in parallel with the other samples.
Metadata
- File identifier
- 6e0c6687-22fe-47e0-bc67-81dde633d25b XML
- Metadata language
- English
- Character set
- UTF8
- Hierarchy level
- Non geographic dataset
- Date stamp
- 2021-08-11T17:01:01
- Metadata standard name
- ISO 19115:2003/19139 - SEXTANT
- Metadata standard version
- 1.0
Point of contact
IFREMER
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Desdouits Marion
Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03
Nantes
France