Date (Creation)

2023-06-06

Date (Publication)

2025-02-01

Identifier

FR-330-715-368-00032-IFR_BIOINFO_SARS_RATVAR

Identifier

DOI:10.12770/89c89669-b64a-4753-a70b-1e44312fc4bd

Credit

Ifremer - Laboratoire Sante Environnement Microbiologie (projet RATVAR du réseau Obepine)

GEMET - INSPIRE themes, version 1.0

• Habitats and biotopes

Thèmes Sextant

• /Biological Environment/Bioinformatics

Theme

ODATIS aggregation parameters and Essential Variable names

• Bioinformatics

Use limitation

CC-BY (Creative Commons - Attribution)

Access constraints

License

Use constraints

License

Spatial representation type

Grid

Metadata language

English

Character set

UTF8

Begin date

2022-04-01

End date

2022-05-31

Reference system identifier

EPSG / WGS 84 (EPSG:4326) / 8.6

Number of dimensions

0

Cell geometry

Area

Distribution format

• ( )

OnLine resource

/home/ref-bioinfo/ifremer/masae/ratvar ( NETWORK:LINK )

OnLine resource

Publication ENA ( WWW:LINK )

Publication ENA

OnLine resource

Digital Object Identifier (DOI) ( WWW:LINK-1.0-http--metadata-URL )

Hierarchy level

Dataset

Statement

The aim of this study was to adapt a protocol for amplifying and sequencing the complete SARS-CoV-2 genome, and to compare the diversity of variants observed following passive and grab sampling. Passive sampling and grab sampling of wastewater were carried out in parallel in the sewers of two French cities in April and May 2022, in regions with contrasting incidence rates. The devices were immersed for 24 hours at eleven sites, and sampling was repeated once at two-day intervals. The complete genome was amplified by ARTIC multiplex PCR and sequenced by Illumina MiSeq. Bioinformatics analysis was performed using the ASPICov pipeline. Sequencing of the SARS-CoV-2 genome from both types of sample showed that the circulating omicron variant sublineage BA2.1 was in the majority, and that sublineages B1.1, B.1.1.529, B.1.1.161 and BA.2.3 were poorly represented. Multiple mutations with varying frequencies were observed. The total number of reads and the percentage of mapped reads were similar for both sampling procedures. The protocol developed allowed the first sequencing of the SARS-CoV-2 genome in wastewater samples collected by passive sampling.

File identifier

89c89669-b64a-4753-a70b-1e44312fc4bd XML

Metadata language

English

Character set

UTF8

Hierarchy level

Dataset

Date stamp

2025-01-31T15:03:36.707897Z

Metadata standard name

ISO 19115:2003/19139 - SEXTANT

Metadata standard version

1.0