# features_pathogen

sample_name: 07_164_16
genbank_id: SAMN36736022
strain: NA
host: Ostrea edulis
collection_date: 2007-05-22
country_sample: France
geo_loc_name: Baie de quiberon
latitude: 47.538
longitude: -3.075
nature_coordinates: Unknown
host_stage: Larvae
isolation_source: Larvae
pool_individual: Pool
sample_conservation_method: Ethanol
sequencing_technology: Illumina
sequencer: NovaSeq 6000
additional_info_sequencing: Fasteris, 2022
viral_charge: 49100
assembly: Spades
genome_type: Non-redundant
structure: Unknown
first_name: Camille
last_name: Pelletier
email: camille.pelletier@ifremer.fr
collected_by: Unknown
organization: Ifremer
department: ASIM
country_organization: France
city: La Tremblade
street: Avenue du Mus de Loup
postal_code: 17390
project_data_type: Raw sequence reads
public_description:
  In the present study, we used high-throughput deep sequencing to characterize the genetic diversity of OsHV-1 found in both O. edulis and M. gigas in France and Sweden. To this end, we sequenced and assembled 40 new OsHV-1 genomes. Using these data and previously gathered information about genotypes circulating in different host species, our aims were to (i) describe OsHV-1 genomic diversity patterns in both species, (ii) estimate the genetic isolation between viruses infecting both species and (iii) determine if OsHV-1 cross-species transmission occur and at which frequency. To do so, we applied a combination of comparative and population genomic, phylogenetic and phylodynamic approaches and discussed results in the context of current knowledge of OsHV-1 molecular epidemiology. 


sample_name: 01-032
genbank_id: GCF_944738075.1
strain: 01-032
host: Magallana gigas
country_sample: France
geo_loc_name: Argenton Brittany
nature_coordinates: Unknown
host_stage: Unknown
isolation_source: Oyster hemolymph
pool_individual: Individual
sample_conservation_method: -80°C
sequencing_technology: Unknown
sequencer: Unknown
additional_info_sequencing: Unknown
assembly: Unknown
genome_type: Partial
structure: Unknown
first_name: Unknown
last_name: Unknown
email: Unknown
collected_by: GV team (IFREMER)
organization: STATION BIOLOGIQUE DE ROSCOFF
department: Unknown
country_organization: France
city: Roscoff
street: Pl. Georges Teissier
postal_code: 29683
project_data_type: Genome sequencing and assembly
sample_score: Unknown
ncbi_project: Yes
bioproject_id: PRJEB5902
biosample_id: SAMEA110138227
project_title:
  Recent Vibrio aestuarianus-associated mortality outbreaks of the Pacific oyster (Crassostrea gigas) in France.

public_description:
  High throughput sequencing (HTS)-based genome comparison and phylogenetic analysis of 15 strains allowed the grouping of virulent strains within two lineages independently of the isolation date. This result was confirmed using a larger collection of strains genotyped using a specific marker and challenged by experimental infection. The bacterial lethal dose was not different between strains isolated before or during the recent outbreaks excluding the hypothesis of the emergence a new genotype. However our results highlight an increase of the host sensitivity to V. aestuarianus.

project_name:
  Recent Vibrio aestuarianus-associated mortality outbreaks of the Pacific oyster (Crassostrea gigas) in France.


sample_name: 03_008T
genbank_id: GCF_011090235.1
strain: 03/008t
host: Crassostrea sp.
country_sample: USA
geo_loc_name: Oregon, Yaquina Bay
nature_coordinates: Unknown
host_stage: Unknown
isolation_source: Oyster
pool_individual: Unknown
sample_conservation_method: Unknown
sequencing_technology: Illumina
sequencer: MiSeq
additional_info_sequencing: Unknown
assembly: SPAdes v. 3.11
genome_type: Partial
structure: Unknown
first_name: Aurelie
last_name: Mesnil
email: aurelie.mesnil@ifremer.fr
collected_by: Unknown
organization: IFREMER
department: Unknown
country_organization: France
city: Unknown
street: Unknown
postal_code: Unknown
project_data_type: Genome sequencing and assembly
sample_score: Unknown
project_title: V. aestuarianus subsp cardi
public_description: Description of a new subspecies affecting cockles
ncbi_project: Yes
isolate:
  03/008 T= OY-0-002 = ATCC35048 = CAIM 592 = CCUG 28583 = CIP 102971 = NBRC 15629 = LMG 7909  = DSM 19606


sample_name: S_02_10
genbank_id: GCA_029890865.1
strain: S/02/10
host: Magallana gigas
country_sample: Ireland
geo_loc_name: Poularone Creek
nature_coordinates: Unknown
host_stage: 0 year
isolation_source: Gill
pool_individual: Unknown
sample_conservation_method: -80°C
sequencing_technology: Illumina
sequencer: Miseq
additional_info_sequencing: Unknown
assembly: SPAdes v. 3.13.1
genome_type: Partial
structure: Unknown
first_name: David
last_name: Ryder
email: david.ryder@cefas.co.uk
collected_by: Unknown
organization: Cefas
department: Unknown
country_organization: United Kingdom
city: Weymouth
street: Barrack Road
postal_code: DT4 8UB
project_data_type: Genome sequencing and assembly
sample_score: Unknown
ncbi_project: Yes
bioproject_id: PRJNA797372
biosample_id: SAMN25002015
project_title:
  Vibrio aestuarianus Clade A and Clade B isolates are associated with Pacific oyster (Crassostrea gigas) disease outbreaks across Ireland

public_description:
  Bacteria from the Vibrionaceae family have been implicated in mortalities of farmed Pacific oysters (Crassostrea gigas) from multiple locations particularly France. However evidence of their role in outbreaks in the UK and Ireland has to date been limited. Forty-three Vibrio isolates recovered from Pacific oyster summer mass mortality episodes in Ireland from 2008-2015 were sequenced and characterised.

project_name:
  Vibrio aestuarianus Clade A and Clade B isolates are associated with Pacific oyster (Crassostrea gigas) disease outbreaks across Ireland


