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.
 
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

  02 40 37 40 27 

  Author

  Author

  02 40 37 40 27 

  Author

  Author

  02 40 37 40 27 

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GEMET - INSPIRE themes, version 1.0 ( Theme )
  • Habitats and biotopes
Thèmes Sextant ( Theme )
  • /Biological Environment/Bioinformatics
Access constraints
Copyright
Use constraints
Copyright
Other constraints
Metadata language
French
Character set
UTF8
Topic category
  • Environment
Distribution format
  • ( )

OnLine resource
/home/ref-bioinfo-public/ifremer/sg2m/targeted_metagenomics_norovirus_shellfish_2016  
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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

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  02 40 37 40 27 
 
 

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