Date (Creation)

2023-04-24

Date (Publication)

2026-05-21

Identifier

FR-330-715-368-00032-IFR_BIOINFO_SEARSE_METABARCODING

Credit

Laboratoire Sante Environnement Microbiologie

GEMET - INSPIRE themes, version 1.0

• Habitats and biotopes

Thèmes Sextant

• /Biological Environment/Bioinformatics

ODATIS aggregation parameters and Essential Variable names

• Bioinformatics

Type de jeux de donnée ODATIS

• Analysis data

Use limitation

CC-BY (Creative Commons - Attribution)

Access constraints

License

Use constraints

License

Spatial representation type

grid Grid

Metadata language

English

Character set

utf8 UTF8

Reference system identifier

EPSG / WGS 84 (EPSG:4326) / 8.6

Number of dimensions

0

Cell geometry

Area

Transformation parameter availability

No

Distribution format

• ( )

OnLine resource

/home/ref-bioinfo-public/ifremer/sg2m/capture-environmental-virome ( NETWORK:LINK )

OnLine resource

ENA Publication ( WWW:LINK )

OnLine resource

Download link ( WWW:DOWNLOAD )

Hierarchy level

Dataset

Statement

Human sewage is the main source of contamination of environmental waters with human enteric viruses, that can contaminate food such as shellfish. Metagenomic represents a new way of analyzing viral diversity through an a priori massive parallel sequencing approach. However, the precise identification of enteric viruses in sewage or shellfish matrices, is still challenging due to the low viral load, large diversity of viral genera and the large amounts of matrix masking viral sequences. This work compared three commercial kits using capture-based enrichment during the library preparation, for the diversity of detected enteric viruses and for the identification of viral strains in sewage and shellfish samples, focusing on four families impacting human health. Triplicate libraries were prepared for each sample and each kit. All three kits allowed the characterization of a variety of viral genera. In sewage samples, a large number of long contigs was obtained allowing a precise identification of more than 35 strains. In shellfish samples, long contigs were rarer but allowed the identification of one human astrovirus and one norovirus strains. Of the tested kits, one displayed lower variation between replicates, allowed to sequence a higher diversity of viruses from the four families of interest and yielded a higher number of nearlywhole genomes.

File identifier

eb3302a8-2405-499c-8854-f7cb8e372859 XML

Metadata language

English

Character set

UTF8

Hierarchy level

Non geographic dataset

Date stamp

2026-06-25T14:38:57.701938Z

Metadata standard name

ISO 19115-3 - SEXTANT

Metadata standard version

1.0