Search the National Biological Information Infrastructure Metadata Clearinghouse for more biological information.

When you connect to the NBII Metadata Clearinghouse you will be able to search through metadata-based descriptions of biological data sets and information products from many different sources to identify those that meet your particular search criteria.

The NBII Metadata Clearinghouse: http://metadata.nbii.gov/

The NBII Home Page: http://www.nbii.gov/

WFRC - Infectious Hematopoietic Necrosis Virus (HNV) Database

Identification_Information:

Citation:

Citation_Information:

Originator: Evi Emmenegger and Gael Kurath

Publication_Date: 2006

Title: WFRC - Infectious Hematopoietic Necrosis Virus (HNV) Database

Geospatial_Data_Presentation_Form: maps data

Other_Citation_Details: Database Software: FileMaker Pro version 5.0

Online_Linkage: http://gis.nacse.org/

Description:

Abstract:: Infectious hematopoietic necrosis virus (IHNV) is a pathogen infecting primarily salmonid hosts and is endemic to the Pacific Northwest. Numerous IHNV isolations and IHN outbreaks have occurred since the early 1900's. We have characterized the midG sequence, a 303 nucleotide region in the middle of the glycoprotein (G) gene, of over 900 IHNV isolates through its endemic range. Genetic sequencing and phylogenetic analysis divided the isolates into three genogroups; U, M, and L. Generally, the genetic relatedness of the IHNV isolates correlates spatially with the site of isolation. The genogroup, spatial locale, temporal reference, and additional host traits associated with the viruses have been used to discern IHNV traffic patterns both on a broad scale (e.g. watersheds) and in discreet areas (e.g. hatchery outbreaks). In an effort to organize and disseminate the genetic, physical, and biological (GP Bio.) information for all the analyzed IHNV isolates we have catalogued them into a user-friendly searchable database that will be web-enabled and geo-referenced.

Purpose:: Each virus isolates biological profile data is divided into five fields: general information, host information, geographic information, sequence results, and biological results. The user can search for selected isolates with the same criteria (i.e. sockeye with the identical midG sequence type) and then also sort the selected isolates with other parameters (i.e. year of isolation and geographic region, etc.) It is our intent that database become a repository for data on future IHNV isolates with their corresponding profiles that can be utilized by other researchers, fish managers, and diagnosticians to facilitate decisions regarding fish management (e.g. stock transfers, stock isolation, disease quarantines, etc.).

Supplemental_Information: (previous geoform was 'Maps Data')

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates_Times:

Beginning_Date: 1970

Beginning_Time: Unknown

Ending_Date: Present

Ending_Time: Unknown

Currentness_Reference: ground condition

Status:

Progress: Complete

Maintenance_and_Update_Frequency:: Updates will be done to the in-house database by the scientists and an exported data file will be sent to Northwest Alliance for Computational Science & Engineering who will be maintaing the web-enabled database.

Spatial_Domain:

Description_of_Geographic_Extent:: The watersheds spanning the Pacific Northwest, from the coastal & inland water systems of Alaska, British Columbia (Canada), Washington state, Oregon coastal watersheds and inland into Idaho via the Columbia River.

Bounding_Coordinates:

West_Bounding_Coordinate: 160

East_Bounding_Coordinate: -120

North_Bounding_Coordinate: 80

South_Bounding_Coordinate: 35

Keywords:

Theme:

Theme_Keyword_Thesaurus: none

Theme_Keyword: Infectious hematopoietic necrosis virus (IHNV)

Theme_Keyword: genogroup

Theme_Keyword: rhabdovirus

Theme_Keyword: phylogeny

Theme_Keyword: fish

Theme_Keyword: salmon

Theme_Keyword: trout

Place:

Place_Keyword_Thesaurus: none

Place_Keyword: Pacific Northwest

Taxonomy:

Keywords_Taxon:

Taxonomic_Keyword_Thesaurus: none

Taxonomic_Keywords: infectious hematopoietic necrosis virus

Taxonomic_Keywords: rhabdoviridae

Taxonomic_System:

Classification_System_Authority:

Classification_System_Citation:

Citation_Information:

Originator: The International Committee on Taxonomy of Viruses (ICTV)

Publication_Date: Unknown

Title: International Committee on Taxonomy of Viruses

Geospatial_Data_Presentation_Form: Unknown

Classification_System_Modifications: None

Taxonomic_Procedures: Unknown

Taxonomic_Classification:

Taxon_Rank_Name: Domain

Taxon_Rank_Value: Acytota

Access_Constraints:: The data will be available to other researchers when the database is made available online. Some of the geographical locations (i.e. Where the virus was isolated) for political sensitive regions may be "fuzzy" for the web-enabled database.

Use_Constraints: Unknown

Point_of_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Evi Emmenegger and Gael Kurath

Contact_Organization:: National Biological Information Infrastructure / Pacific Information Node / Western Fisheries Research Center

Contact_Address:

Address_Type: mailing and physical

Address: 6505 NE 65th Street

City: Seattle

State_or_Province: Washington

Postal_Code: 98115

Contact_Voice_Telephone: (206) 526-6282, Ext. 276 (EE); (206) 526-6583 (GK)

Contact_Electronic_Mail_Address: evi_emmenegger@usgs.gov; gael_kurath@usgs.gov

Data_Set_Credit:: Judy Ranson, Ryan Troyer, Kyle Garver, Eric Anderson, and Katja Einer-Jensen

Cross_Reference:

Citation_Information:

Originator: Emmenegger, E.J., Meyers, T.R., Burton, T.O., and Kurath, G.

Publication_Date: 2000

Title:: Genetic Diversity and Epidemiology of Infectious Hematopoietic Necrosis Virus in Alaska

Geospatial_Data_Presentation_Form: publication

Series_Information:

Series_Name: Dis. Aquat. Org.

Issue_Identification: 40:163-176

Cross_Reference:

Citation_Information:

Originator: Troyer, R.M., LaPatra, S.E., and Kurath, G.

Publication_Date: 2001

Title:: Genetic Analyses Reveal Unusually High Diversity of Infectious Hematopoietic Necrosis Virus in Rainbow Trout Aquaculture.

Geospatial_Data_Presentation_Form: publication

Series_Information:

Series_Name: J. Gen. Virol.

Issue_Identification: 81:2823-2832

Cross_Reference:

Citation_Information:

Originator: Emmenegger, E.J., and Kurath, G.

Publication_Date: 2002

Geospatial_Data_Presentation_Form: publication

Title:: Genetic chacterization of infectious Hematopoietic Necrosis Virus of Coastal Salmonid Stocks in Washington State

Series_Information:

Series_Name: J. Aquat. Anim. Health

Issue_Identification: 14:25-34

Cross_Reference:

Citation_Information:

Originator:: Kurath, G., Garver, K.A., Troyer, R.M., Emmenegger, E. J., Einer-Jensen, K., and Anderson, E.D.

Publication_Date: 2003

Title:: Phylogeography of infectious hematopoietic necrosis virus in North America.

Geospatial_Data_Presentation_Form: publication

Series_Information:

Series_Name: J. Gen. Virol.

Issue_Identification: 84:803-814

Cross_Reference:

Citation_Information:

Originator: Kurath, G., Garver, K.A. Batts, W.N, and Emmenegger, E. (2005)

Publication_Date: 2005

Title:: article in Health and Diseases of Aquatic Organisms: Bilateral Perspectives. Proceedings of the Second Bilateral Conference between Russia and the United States 21 - 28 September 2003 Sheperdstown, West Virginia

Geospatial_Data_Presentation_Form: publication

Publication_Information:

Publication_Place: East Lansing, Michigan

Publisher: Michigan State University

Larger_Work_Citation:

Citation_Information:

Originator: Cipriano, R.C., Shchelkunoiv, I.S., and Faisal, M., editors

Publication_Date: 2005

Geospatial_Data_Presentation_Form: publication

Title:: Health and Diseases of Aquatic Organisms: Bilateral Perspectives. Proceedings of the Second Bilateral Conference between Russia and the United States 21 - 28 September 2003

Publication_Information:

Publication_Place: East Lansing, Michigan

Publisher: Michigan State University

Analytical_Tool:

Analytical_Tool_Description:: Sequencher software can edit and analyze raw nucleotide sequence data.

Tool_Access_Information:

Online_Linkage:: http://www.genecodes.com/?referrer=Google_US&gclid=CIWc4ZjbtIQCFRgvUAodUWQL-w

Tool_Access_Instructions:: http://www.genecodes.com/?referrer=Google_US&gclid=CIWc4ZjbtIQCFRgvUAodUWQL-w

Analytical_Tool:

Analytical_Tool_Description:: PAUP was used in the phylogenetic analyses utilizing the neighbor-joining and parsimony methodologies.

Tool_Access_Information:

Online_Linkage:: http://paup.csit.fsu.edu/about.html

Tool_Access_Instructions:: http://paup.csit.fsu.edu/downl.html

Tool_Computer_and_Operating_System: MacIntosh, PC

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:: One of the strengths of the database will be the search parameters offered. A user can search for a matching IHNV nucleotide sequence and request spatial outputs simultaneously.
We employed a technician to review the database records by exporting all the fields into an Excel spreadsheet and comparing the exported data for any outliers. In addition, we utilized the FileMaker Pro search feature to query the database for known genetic sequences and biological attributes to determine if the data was entered correctly.

Logical_Consistency_Report: unknown

Completeness_Report:: If multiple samples were taken during a disease outbreak and the diagnostic analyses indicated that the virus samples had the identical genetic sequences, we concluded that only one virus strain was responsible for the particular outbreak. Consequently, only one record was entered for that site at that time.

Lineage:

Methodology:

Methodology_Type: Lab

Methodology_Description: Genetic sequencing and phylogenetic analysis

Methodology_Citation:

Citation_Information:

Originator:: G. Kurath, K. A. Garver, R.M. Troyer, E.J. Emmenegger, K. Einer-Jensen, and E. Anderson.

Publication_Date: 2003

Geospatial_Data_Presentation_Form: publication

Title:: Phylogeography of infectious hematopoietic necrosis virus in North America

Series_Information:

Series_Name: Journal of General Virology

Issue_Identification: 84: 803-814

Process_Step:

Process_Description: unknown

Process_Date: Unknown

Cloud_Cover: 0

Spatial_Data_Organization_Information:

Indirect_Spatial_Reference:: All virus isolates have latitude and longitude coordinates based on their site of isolation

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: General information

Entity_Type_Definition: general information

Entity_Type_Definition_Source: Western Fisheries Research Center

Attribute:

Attribute_Label: Date isolated

Attribute_Definition: date isolated

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Study name

Attribute_Definition: study name

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Detailed_Description:

Entity_Type:

Entity_Type_Label: Host Information

Entity_Type_Definition: host information

Entity_Type_Definition_Source: None

Attribute:

Attribute_Label: age of fish

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: comments

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: disease status

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: epizootic

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: fish species

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: fish stock

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: life history

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: origin

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: sex

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: tissue source

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Detailed_Description:

Entity_Type:

Entity_Type_Label: Geographic Information

Entity_Type_Definition: geographic information

Entity_Type_Definition_Source: Western Fisheries Research Center

Attribute:

Attribute_Label: Isolation site

Attribute_Definition: unknown

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Latitude

Attribute_Definition: latitude

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Longitude

Attribute_Definition: longitude

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Region

Attribute_Definition: region

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Watershed

Attribute_Definition: watershed

Attribute_Definition_Source: unknown

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Detailed_Description:

Entity_Type:

Entity_Type_Label: Sequence Results

Entity_Type_Definition: history information

Entity_Type_Definition_Source: Western Fisheries Research Center

Attribute:

Attribute_Label: Address

Attribute_Definition: address

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: date received

Attribute_Definition: date received

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Isolate sent by

Attribute_Definition: isolate sent by

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Organization

Attribute_Definition: organization

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Phone number

Attribute_Definition: phone number

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Publication Reference

Attribute_Definition: publication reference

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: Virus alternate names

Attribute_Definition: virus alternate names

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: WFRC lab contact

Attribute_Definition: Western Fisheries Research Center lab contact

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Detailed_Description:

Entity_Type:

Entity_Type_Label: Results

Entity_Type_Definition: Biological results

Entity_Type_Definition_Source: Western Fisheries Research Center

Attribute:

Attribute_Label: Electropherotype

Attribute_Definition: unknown

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: In vivo data

Attribute_Definition: in vivo data

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Attribute:

Attribute_Label: MidG Clade

Attribute_Definition: unknown

Attribute_Definition_Source: Western Fisheries Research Center

Attribute_Domain_Values:

Unrepresentable_Domain: unknown

Overview_Description:

Entity_and_Attribute_Overview: Infectious hematopoietic necrosis virus

Entity_and_Attribute_Detail_Citation: Western Fisheries Research Center

Distribution_Information:

Distributor:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: Northwest Alliance for Computational Science and Engineering

Contact_Address:

Address_Type: mailing and physical address

Address: 2000 Kelley Engineering Center Oregon State University

City: Corvallis

State_or_Province: Oregon

Postal_Code: 97331-5501

Country: U.S.

Contact_Voice_Telephone: 541-737-6601

Distribution_Liability:: Although these data have been processed successfully on a computer system at the Northwest Alliance for Computational Science and Engineering, no warranty expressed or implied is made regarding the accuracy or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. This disclaimer applies both to individual use of the data and aggregate use with other data. It is strongly recommended that these data are directly acquired from a Northwest Alliance for Computational Science and Engineering server, and not indirectly through other sources which may have changed the data in some way. It is also strongly recommended that careful attention be paid to the contents of the metadata file associated with these data. The Northwest Alliance for Computational Science and Engineering shall not be held liable for improper or incorrect use of the data described and/or contained herein.

Metadata_Reference_Information:

Metadata_Date: 20060417

Metadata_Review_Date: 20070221

Metadata_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Arturo Restrepo

Contact_Organization: NASA-Global Change Master Directory (GCMD)

Contact_Position: Ecological Informatics Coordinator

Contact_Address:

Address_Type: mailing and physical address

Address: 7515 Mission Drive, Suite A1-C1

City: Lanham

State_or_Province: MD

Postal_Code: 20706

Country: United States

Contact_Voice_Telephone: 301-352-4616

Contact_Facsimile_Telephone: 301-352-0437

Contact_Electronic_Mail_Address: restrepo at gcmd.nasa.gov

Metadata_Standard_Name:: Content Standard for National Biological Information Infrastructure Metadata

Metadata_Standard_Version: FGDC-STD-001.1-1999