Migratory Bird Avian Influenza Sampling; Yukon Kuskokwim Delta, Alaska, 2015

Metadata:

Identification_Information:
Citation:
Citation_Information:
Originator: Andrew M. Ramey
Publication_Date: 20160609
Title:
Migratory Bird Avian Influenza Sampling; Yukon Kuskokwim Delta, Alaska, 2015
Geospatial_Data_Presentation_Form: spreadsheet
Publication_Information:
Publication_Place: Anchorage, AK
Publisher: U.S. Geological Survey, Alaska Science Center
Online_Linkage: http://dx.doi.org/10.5066/F7SB43V5
Larger_Work_Citation:
Citation_Information:
Originator: Andrew M. Ramey
Publication_Date: 201603
Title:
Testing for highly pathogenic avian influenza viruses through a tribal health network in western Alaska
Geospatial_Data_Presentation_Form: website
Publication_Information:
Publication_Place: Anchorage, Alaska
Publisher: U.S. Geological Survey, Alaska Science Center
Online_Linkage: http://alaska.usgs.gov/portal/project.php?project_id=368
Description:
Abstract:
Data set containing avian influenza sampling information for spring and summer waterbirds on the Yukon Kuskokwim Delta, 2015. Data contains sample ID, species common name, age and sex, collection data and location, and laboratory specific data used to identify presence and absence of avian influenza viruses.
Purpose:
The purpose of this project was to sample migratory birds in western Alaska on the Yukon Kuskokwim Delta to determine the presence of avian influenza viruses and the role of migratory birds in the dispersal and maintenance of avian influenza viruses. Specific objectives were to provide: (1) a timely collection of an otherwise unavailable sample of wide spectrum avian influenza specimens; (2) an assessment of whether the highly pathogenic H5 virus strains are circulating in wild birds in Alaska, (3) an evaluation of how the virus has mutated since the last detections of highly pathogenic H5 in the lower U.S., and (4) an indication of where the virus may spread during the southerly, fall migration to the lower U.S (based on return migration patterns).
Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2015
Currentness_Reference: ground condition
Status:
Progress: Complete
Maintenance_and_Update_Frequency: None planned
Spatial_Domain:
Description_of_Geographic_Extent:
Study area is comprised of 10 Alaska native villages on the Yukon-Kuskokwim Delta, Alaska
Bounding_Coordinates:
West_Bounding_Coordinate: -166.09620
East_Bounding_Coordinate: -161.41861
North_Bounding_Coordinate: 63.03583
South_Bounding_Coordinate: 59.75333
Keywords:
Theme:
Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC55
Theme:
Theme_Keyword_Thesaurus: ISO 19115
Theme_Keyword: biota
Theme:
Theme_Keyword_Thesaurus: NASA GCMD Earth Science Keywords Thesaurus
Theme_Keyword: Earth Science
Theme_Keyword: Biological Classification
Theme_Keyword: Animals/Vertebrates
Theme_Keyword: Birds
Theme:
Theme_Keyword_Thesaurus: USGS Geographic Names Information System
Theme_Keyword: Alaska
Theme_Keyword: Yukon Delta
Theme_Keyword: Yukon Delta National Wildlife Refuge
Taxonomy:
Keywords/Taxon:
Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: single species
Taxonomic_Keywords: animals
Taxonomic_Keywords: vertebrates
Taxonomic_Keywords: bird
Taxonomic_System:
Classification_System/Authority:
Classification_System_Citation:
Citation_Information:
Originator:
M. Ruggiero & D. Gordon, eds. 2013. Consensus Management Hierarchy for the ITIS & Species2000 Catalogue of Life. Contributors: Nicolas Bailly, Thierry Bourgoin, Richard Brusca, Thomas Cavalier-Smith, Daphne Fautin, Dennis Gordon, Gerald Guala, Michael Guiry, Paul Kirk, Elliot Lefkowitz, David Mabberly, David Maddison, Alan Paton, Michael Ruggiero, Peter Stevens, and Brian Tyndall
Publication_Date: Unpublished material
Title: Integrated Taxonomic Information System
Geospatial_Data_Presentation_Form: database
Series_Information:
Series_Name: Integrated Taxonomic Classification System
Issue_Identification: TSN 174371
Publication_Information:
Publication_Place: online
Publisher: ITIS-North America
Other_Citation_Details:
Retrieved on April 27, 2016, from the Integrated Taxonomic Information System on-line database http://www.itis.gov
Online_Linkage:
http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=174371
Identification_Reference:
Citation_Information:
Originator: National Geographic
Publication_Date: Unknown
Title: Field Guide to the Birds of North America
Edition: 4th
Geospatial_Data_Presentation_Form: document
Publication_Information:
Publication_Place: Washington, D.C., USA
Publisher: National Geographic Society
Taxonomic_Procedures:
Avian species sampled were identified by field technicians/volunteers using field guides such as, but not limited to: National Geographic Field Guide to the Birds of North America, fourth edition.
Taxonomic_Completeness:
Taxonomy may not be complete for all samples. For these, "Unknown species" appears under the attribute "Common Name," and "Class Aves" appears under the attribute scientific name.
Vouchers:
Specimen: Cloacal swab sample in viral transport media
Repository:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: Southeastern Cooperative Wildlife Disease Study
Contact_Person: Rebecca Poulson
Contact_Address:
Address_Type: mailing
Address: Department of Population Health,
Address: College of Veterinary Medicine, University of Georgia
City: Athens
State_or_Province: Georgia
Postal_Code: 30602
Country: USA
Contact_Voice_Telephone: 706.542.3473
Taxonomic_Classification:
Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Applicable_Common_Name: Animal
Applicable_Common_Name: animaux
Applicable_Common_Name: animals
Taxonomic_Classification:
Taxon_Rank_Name: Subkingdom
Taxon_Rank_Value: Bilateria
Taxonomic_Classification:
Taxon_Rank_Name: Infrakingdom
Taxon_Rank_Value: Deuterostomia
Taxonomic_Classification:
Taxon_Rank_Name: Phylum
Taxon_Rank_Value: Chordata
Applicable_Common_Name: cordés
Applicable_Common_Name: cordado
Applicable_Common_Name: chordates
Taxonomic_Classification:
Taxon_Rank_Name: Subphylum
Taxon_Rank_Value: Vertebrata
Applicable_Common_Name: vertebrado
Applicable_Common_Name: vertébrés
Applicable_Common_Name: vertebrates
Taxonomic_Classification:
Taxon_Rank_Name: Infraphylum
Taxon_Rank_Value: Gnathostomata
Taxonomic_Classification:
Taxon_Rank_Name: Superclass
Taxon_Rank_Value: Tetrapoda
Taxonomic_Classification:
Taxon_Rank_Name: Class
Taxon_Rank_Value: Aves
Applicable_Common_Name: Birds
Applicable_Common_Name: oiseaux
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Gaviiformes
Applicable_Common_Name: Loons
Applicable_Common_Name: huarts
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Gaviidae
Applicable_Common_Name: Loons
Applicable_Common_Name: Divers
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Gavia
Applicable_Common_Name: Loons
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Gavia pacifica
Applicable_Common_Name: Pacific Loon
Applicable_Common_Name: Colimbo pacífico
Applicable_Common_Name: Plongeon du Pacifique
Applicable_Common_Name: Pacific Diver
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Anseriformes
Applicable_Common_Name: Ducks
Applicable_Common_Name: Geese
Applicable_Common_Name: Screamers
Applicable_Common_Name: Swans
Applicable_Common_Name: Waterfowl
Applicable_Common_Name: canards
Applicable_Common_Name: cygnes
Applicable_Common_Name: oies
Applicable_Common_Name: sauvagine
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Anatidae
Applicable_Common_Name: Ducks
Applicable_Common_Name: Geese
Applicable_Common_Name: Swans
Applicable_Common_Name: canards
Applicable_Common_Name: cygnes
Applicable_Common_Name: oies
Taxonomic_Classification:
Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Anserinae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Cygnus
Applicable_Common_Name: Swans
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Cygnus columbianus
Applicable_Common_Name: Cisne de tundra
Applicable_Common_Name: Tundra Swan
Applicable_Common_Name: cygne siffleur
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Branta
Applicable_Common_Name: Brent Geese
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Branta bernicla
Applicable_Common_Name: Brant Goose
Applicable_Common_Name: Brent Goose
Applicable_Common_Name: Ganso de collar
Applicable_Common_Name: Brant
Applicable_Common_Name: bernache cravant
Taxonomic_Classification:
Taxon_Rank_Name: Subspecies
Taxon_Rank_Value: Branta bernicla nigricans
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Branta hutchinsii
Applicable_Common_Name: Cackling Goose
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Anser
Applicable_Common_Name: Bean Geese
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Anser albifrons
Applicable_Common_Name: Ganso careto-mayor
Applicable_Common_Name: Greater White-fronted Goose
Applicable_Common_Name: oie rieuse
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Chen
Applicable_Common_Name: Snow Geese
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Chen caerulescens
Applicable_Common_Name: Blue Goose
Applicable_Common_Name: Ganso blanco
Applicable_Common_Name: Snow Goose
Applicable_Common_Name: oie des neiges
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Chen canagica
Applicable_Common_Name: Emperor Goose
Taxonomic_Classification:
Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Anatinae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Anas
Applicable_Common_Name: Dabbling Ducks
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Anas platyrhynchos
Applicable_Common_Name: Pato de collar
Applicable_Common_Name: Mallard
Applicable_Common_Name: canard colvert
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Anas strepera
Applicable_Common_Name: Pato friso
Applicable_Common_Name: Gadwall
Applicable_Common_Name: canard chipeau
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Anas acuta
Applicable_Common_Name: Pato golondrino
Applicable_Common_Name: Northern Pintail
Applicable_Common_Name: canard pilet
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Anas crecca
Applicable_Common_Name: Eurasian Teal
Applicable_Common_Name: Cerceta ala verde
Applicable_Common_Name: Green-winged Teal
Applicable_Common_Name: sarcelle d'hiver
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Anas americana
Applicable_Common_Name: Pato chalcuán
Applicable_Common_Name: American Wigeon
Applicable_Common_Name: canard d'Amérique
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Anas clypeata
Applicable_Common_Name: Pato cucharón-norteño
Applicable_Common_Name: Northern Shoveler
Applicable_Common_Name: canard souchet
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Aythya
Applicable_Common_Name: Diving Ducks
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Aythya marila
Applicable_Common_Name: Pato boludo-mayor
Applicable_Common_Name: Greater Scaup
Applicable_Common_Name: fuligule milouinan
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Aythya affinis
Applicable_Common_Name: Pato boludo-menor
Applicable_Common_Name: Lesser Scaup
Applicable_Common_Name: petit fuligule
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Bucephala
Applicable_Common_Name: Goldeneyes
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Bucephala clangula
Applicable_Common_Name: Pato chillón
Applicable_Common_Name: Common Goldeneye
Applicable_Common_Name: garrot à oeil d'or
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Clangula
Applicable_Common_Name: Oldsquaws
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Clangula hyemalis
Applicable_Common_Name: Long-tailed Duck
Applicable_Common_Name: Pato cola larga
Applicable_Common_Name: Oldsquaw
Applicable_Common_Name: harelde kakawi
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Melanitta
Applicable_Common_Name: Scoters
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Melanitta fusca
Applicable_Common_Name: Velvet Scoter
Applicable_Common_Name: Negreta ala blanca
Applicable_Common_Name: macreuse brune
Applicable_Common_Name: White-winged Scoter
Taxonomic_Classification:
Taxon_Rank_Name: Subspecies
Taxon_Rank_Value: Melanitta fusca deglandi
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Melanitta perspicillata
Applicable_Common_Name: Negreta nuca blanca
Applicable_Common_Name: Surf Scoter
Applicable_Common_Name: macreuse à front blanc
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Melanitta nigra
Applicable_Common_Name: Negreta negra
Applicable_Common_Name: Black Scoter
Applicable_Common_Name: macreuse noire
Taxonomic_Classification:
Taxon_Rank_Name: Subspecies
Taxon_Rank_Value: Melanitta nigra americana
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Mergus
Applicable_Common_Name: Greater Mergansers
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Mergus merganser
Applicable_Common_Name: Mergo mayor
Applicable_Common_Name: Common Merganser
Applicable_Common_Name: grand harle
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Galliformes
Applicable_Common_Name: Fowls
Applicable_Common_Name: Gallinaceous Birds
Applicable_Common_Name: gallinacées
Applicable_Common_Name: volaille
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Phasianidae
Applicable_Common_Name: Partridges
Applicable_Common_Name: Turkeys
Applicable_Common_Name: Grouse
Applicable_Common_Name: Pheasants
Applicable_Common_Name: Quail
Applicable_Common_Name: cailles
Applicable_Common_Name: faisans
Taxonomic_Classification:
Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Tetraoninae
Applicable_Common_Name: Grouse
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Lagopus
Applicable_Common_Name: Ptarmigans
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Lagopus lagopus
Applicable_Common_Name: Willow Grouse
Applicable_Common_Name: Willow Ptarmigan
Applicable_Common_Name: lagopède des saules
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Gruiformes
Applicable_Common_Name: Cranes
Applicable_Common_Name: Rails
Applicable_Common_Name: grues
Applicable_Common_Name: râles
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Gruidae
Applicable_Common_Name: Cranes
Taxonomic_Classification:
Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Gruinae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Grus
Applicable_Common_Name: Cranes
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Grus canadensis
Applicable_Common_Name: Grulla gris
Applicable_Common_Name: Sandhill Crane
Applicable_Common_Name: grue du Canada
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Charadriiformes
Applicable_Common_Name: Shore Birds
Applicable_Common_Name: Gulls
Applicable_Common_Name: Alcids
Applicable_Common_Name: Plovers
Applicable_Common_Name: Oystercatchers
Applicable_Common_Name: goélands
Applicable_Common_Name: alcidés
Applicable_Common_Name: Auks
Applicable_Common_Name: huîtriers
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Scolopacidae
Applicable_Common_Name: Sandpipers
Applicable_Common_Name: bécasseaux
Applicable_Common_Name: Snipes
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Arenaria
Applicable_Common_Name: Turnstones
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Arenaria melanocephala
Applicable_Common_Name: Black Turnstone
Applicable_Common_Name: Vuelvepiedras negro
Applicable_Common_Name: Tournepierre noir
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Calidris
Applicable_Common_Name: Stints
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Calidris ptilocnemis
Applicable_Common_Name: Rock Sandpiper
Applicable_Common_Name: Bécasseau des Aléoutiennes
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Calidris acuminata
Applicable_Common_Name: Sharp-tailed Sandpiper
Applicable_Common_Name: Bécasseau à queue pointue
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Calidris melanotos
Applicable_Common_Name: Playero pectoral
Applicable_Common_Name: Pectoral Sandpiper
Applicable_Common_Name: Bécasseau à poitrine cendrée
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Calidris alpina
Applicable_Common_Name: Playero dorso rojo
Applicable_Common_Name: Dunlin
Applicable_Common_Name: Bécasseau variable
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Limnodromus
Applicable_Common_Name: Dowitchers
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Limnodromus scolopaceus
Applicable_Common_Name: Costurero pico largo
Applicable_Common_Name: Long-billed Dowitcher
Applicable_Common_Name: Bécassin à long bec
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Limosa
Applicable_Common_Name: Godwits
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Limosa lapponica
Applicable_Common_Name: Picopando cola barrada
Applicable_Common_Name: Bar-tailed Godwit
Applicable_Common_Name: Barge rousse
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Gallinago
Applicable_Common_Name: Snipes
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Gallinago delicata
Applicable_Common_Name: Wilson's Snipe
Applicable_Common_Name: Bécassine de Wilson
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Phalaropus
Applicable_Common_Name: Phalaropes
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Phalaropus lobatus
Applicable_Common_Name: Red-necked Phalarope
Applicable_Common_Name: Falaropo cuello rojo
Applicable_Common_Name: Phalarope à bec étroit
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Laridae
Applicable_Common_Name: Gulls
Applicable_Common_Name: Terns
Applicable_Common_Name: becs-en-ciseaux
Applicable_Common_Name: goélands
Applicable_Common_Name: labbes
Applicable_Common_Name: mouettes
Applicable_Common_Name: Skimmers
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Larus
Applicable_Common_Name: Gulls
Applicable_Common_Name: Ivory Gulls
Applicable_Common_Name: Kittiwakes
Applicable_Common_Name: Ross' Gulls
Applicable_Common_Name: Sabine's Gulls
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Larus canus
Applicable_Common_Name: Gaviota cana
Applicable_Common_Name: Mew Gull
Applicable_Common_Name: Goéland cendré
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Xema
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Xema sabini
Applicable_Common_Name: Gaviota cola hendida
Applicable_Common_Name: Sabine's Gull
Applicable_Common_Name: Mouette de Sabine
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Sterna
Applicable_Common_Name: Typical Terns
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Sterna paradisaea
Applicable_Common_Name: Charrán ártico
Applicable_Common_Name: Arctic Tern
Applicable_Common_Name: Sterne arctique
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Passeriformes
Applicable_Common_Name: Perching Birds
Applicable_Common_Name: passereaux
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Calcariidae
Applicable_Common_Name: Longspurs
Applicable_Common_Name: Snow Buntings
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Calcarius
Applicable_Common_Name: Longspurs
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Calcarius lapponicus
Applicable_Common_Name: Escribano ártico
Applicable_Common_Name: Lapland Longspur
Applicable_Common_Name: bruant lapon
Access_Constraints: None
Use_Constraints:
It is requested that the authors and the USGS Alaska Science Center be cited for any subsequent publications referenced to this dataset. It is strongly recommended that careful attention be paid to the contents of the metadata file associated with these data to evaluate data set limitations, restrictions or intended use.
Point_of_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey, Alaska Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 4210 University Dr.
City: Anchorage
State_or_Province: Alaska
Postal_Code: 99503
Country: USA
Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov
Data_Set_Credit: U.S. Geological Survey, Alaska Science Center, Anchorage, AK
Security_Information:
Security_Classification_System: None
Security_Classification: Unclassified
Security_Handling_Description: None
Cross_Reference:
Citation_Information:
Originator: Ramey, A.M.
Originator: Pearce, J.M.
Originator: Reeves, A.B.
Originator: Poulson, R.L.
Originator: Dobson, J.
Originator: Lefferts, B.
Originator: Spragens, K.
Originator: Stallknecht, D.
Publication_Date: 20160405
Title:
Surveillance for Eurasian-origin and intercontinental reassotant highly pathogenic influenza A viruses in Alaska, spring and summer 2015
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Virology Journal
Issue_Identification: 13
Other_Citation_Details: RameyDOI: 10.1186/s12985-016-0511-9
Online_Linkage:
http://virologyj.biomedcentral.com/articles/10.1186/s12985-016-0511-9
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
Attributes were spot checked and values were sorted to assess possible outliers or errors. Data were peer-reviewed for accuracy.
Logical_Consistency_Report:
Data were spot checked during a formal peer review of the data and metadata files. Data omissions for particular entities are explained in the Entity and Attribute definitions.
Completeness_Report:
Users are advised to read the rest of the metadata record carefully for additional details, particularly the Entity and Attribute definitions for specifics on each entity and data within those entities. Data omissions for particular entities are explained in the Entity and Attribute definitions.
Lineage:
Methodology:
Methodology_Type: Field
Methodology_Description:
Hunter-harvested birds were sampled for IAVs at ten villages within the Yukon-Kuskokwim Delta, Alaska during May 2015 as part of the subsistence season, a traditional harvest period for native people living in this region. Subsistence hunters brought intact harvested birds for viral sampling to health clinic sampling stations located in each village: Chefornak, Eek, Emmonak, Hooper Bay, Kipnuk, Kotlik, Kwethluk, Pilot Station, Quinhagak, and Toksook Bay. At sampling stations for each village, swab samples for viral screening were collected from each bird by applying a polyester-tipped applicator to each the orophranx/trachea and the cloaca and swabbing. Paired samples were then combined in a single cryovial with 2.0 ml of chilled viral transport media supplemented with antibiotics. Samples were then placed directly in dewars charged with liquid nitrogen and transferred to -80˚ C freezers until testing. In summer, cackling geese (Branta hutchinsii) were sampled at remote sites near the Anerkochik River during 16–19 July as part of banding efforts conducted by the Yukon Delta National Wildlife Refuge. Geese were captured during the flightless molting period in drives using lead fences to guide birds into a capture pen with assistance from a helicopter and 6-person ground crew to encourage directionality of bird movements (United States Department of the Interior federal bird banding permit # 09811; USFWS-Region 7 IACUC #2015-009). After capture, and application of a metal tarsal band, paired oropharyngeal and cloacal swabs were collected as previously explained for hunter-harvested birds (United States Department of the Interior federal bird banding permit #20022; USGS Alaska Science Center ACUC #2015-13). Samples were kept cool/frozen upon collection until transfer to -80˚ C freezers within approximately one week of collection.
Methodology:
Methodology_Type: Lab
Methodology_Description:
In the laboratory, all paired swab samples were screened using rRT-PCR targeting gene products for the influenza A virus matrix gene. All spring samples yielding Ct values < 41 for the IAV matrix gene and all summer samples (regardless of Ct value for the IAV matrix gene) were inoculated into specific pathogen-free embryonated chicken eggs for virus isolation. Amnio-allantoic fluids were collected after 120 hours, and tested via hemagglutination assay. RNAs extracted from hemagglutination assay positive amnio-allantoic fluids were screened for the influenza A virus matrix gene by rRT-PCR and resultant isolates were genomically sequenced
Process_Step:
Process_Description:
Samples that were genomically sequenced were submitted to the National Center for Biotechnology Information (NCBI) GenBank website for public release (http://www.ncbi.nlm.nih.gov/genbank/).
Process_Date: Unknown
Spatial_Data_Organization_Information:
Direct_Spatial_Reference_Method: Point
Spatial_Reference_Information:
Horizontal_Coordinate_System_Definition:
Geographic:
Latitude_Resolution: 0.00001
Longitude_Resolution: 0.00001
Geographic_Coordinate_Units: Degrees and decimal minutes
Geodetic_Model:
Horizontal_Datum_Name: World Geodetic System of 1984
Ellipsoid_Name: World Geodetic System of 1984
Semi-major_Axis: 6378137
Denominator_of_Flattening_Ratio: 298.25722210088
Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label: Avian Influenza Sampling Data
Entity_Type_Definition:
Table of bird samples and test results for avian influenza viruses
Entity_Type_Definition_Source: Author defined
Attribute:
Attribute_Label: Age
Attribute_Definition:
Definition: Age (year Class) Codes specified by the USGS, Bird Banding Laboratory, Patuxent Wildlife Research Center. Age codes and definitions: UNK – Unknown age AHY – After hatching year. A bird known to have hatched before the calendar year of banding; year of hatch otherwise unknown. HY – Hatching year. A bird capable of sustained flight and known to have hatched during the calendar year in which it was banded. L – Local. A young bird incapable of sustained flight. After a young bird achieves sustained flight it becomes an "HY" until December 31. SY – Second year. A bird known to have hatched in the calendar year preceding the year of banding and in its second calendar year of life. Example: Banded 1997 - Hatched 1996. ASY – After second year. A bird known to have hatched earlier than the calendar year preceeding the year of banding; year of hatch otherwise unknown. Example: Banded 1997 - Hatched 1995 or earlier. TY – Third year. A bird known to have hatched in the calendar year two years prior to the year of banding, now in its third calendar year of life. Example: Banded 1997 - Hatched 1995. ATY – After third year. A bird known to have hatched prior to two years prior to the year of banding, now in at least its fourth calendar year of life. Example: Banded 1997 - Hatched 1994 or earlier.
Attribute_Definition_Source:
USGS, Bird Banding Laboratory, Patuxent Wildlife Research Center.
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: AHY
Enumerated_Domain_Value_Definition:
A bird known to have hatched before the calendar year of banding; year of hatch otherwise unknown. Example: Banded 1997 - Hatched before January 1, 1997. Birds that would have been coded "U" on December 31 "graduate" to class "AHY" on January 1. [Also referred to as adult or Ad.]
Enumerated_Domain_Value_Definition_Source:
USGS, Bird Banding Laboratory, Patuxent Wildlife Research Center, https://www.pwrc.usgs.gov/BBL/index.cfm
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: HY
Enumerated_Domain_Value_Definition:
A bird capable of sustained flight and known to have hatched during the calendar year in which it was banded. Example: Banded 1997 - Hatched 1997.
Enumerated_Domain_Value_Definition_Source:
USGS, Bird Banding Laboratory, Patuxent Wildlife Research Center, https://www.pwrc.usgs.gov/BBL/index.cfm
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ASY
Enumerated_Domain_Value_Definition:
A bird known to have hatched earlier than the calendar year preceding the year of banding; year of hatch otherwise unknown. Example: Banded 1997 - Hatched 1995 or earlier
Enumerated_Domain_Value_Definition_Source:
USGS, Bird Banding Laboratory, Patuxent Wildlife Research Center, https://www.pwrc.usgs.gov/BBL/index.cfm
Attribute:
Attribute_Label: Sex
Attribute_Definition: Sex as determined by plumage
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: F
Enumerated_Domain_Value_Definition: Female
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: M
Enumerated_Domain_Value_Definition: Male
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: U
Enumerated_Domain_Value_Definition: Unknown
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Collection Sample ID#
Attribute_Definition:
Six or nine character individualized identification provided for each sample collected. For samples collected from villages, the first three letters correspond to a three-letter abbreviation of the respective village (e.g. CYF 001 = sample #1 from Chefornak, Alaska, EMO 083 = sample #83 from Emmonak, Alaska). For collection sample IDs with nine characters, the first four letters correspond to the AOU alpha code of the species being sampled followed by a two digit code defining the year of collection (e.g. CACG-15-005 = sample #5 of cackling goose collected in year 2015).
Attribute_Definition_Source: Author defined.
Attribute_Domain_Values:
Unrepresentable_Domain: None
Attribute:
Attribute_Label: Lab ID#
Attribute_Definition:
The laboratory number is assigned by the laboratory at the University of Georgia where the original samples are processed. The prefix: UG indicates the samples were processed at the University of Georgia, followed by AI to indicate the samples are screened for avian influenza, lastly there is a two-character code for the year of collection (15=2015). Each sample is assigned a unique number separated by the prefix by a "-".
Attribute_Definition_Source: Author defined.
Attribute_Domain_Values:
Unrepresentable_Domain: Lab ID from UGA
Attribute:
Attribute_Label: Common name
Attribute_Definition:
Common name of avian species sampled as identified by field technicians/volunteers using field guides such as, but not limited to: National Geographic Field Guide to the Birds of North America, fourth edition.
Attribute_Definition_Source: Author Defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Unknown species
Enumerated_Domain_Value_Definition:
species identification was not recorded, lost, or otherwise compromised.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Collection date
Attribute_Definition:
Date of collection event (e.g. day samples were collected from live or dead birds or day fecal sample was taken.(Month/Day/Year).
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 5/7/2015
Range_Domain_Maximum: 7/19/2015
Attribute_Units_of_Measure: Date
Attribute:
Attribute_Label: Scientific name
Attribute_Definition:
Scientific names are assigned post collection by uploading common names identified by field technicians/volunteers to the Integrated Taxonomic Information System (ITIS).
Attribute_Definition_Source: http://www.itis.gov/
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Class Aves
Enumerated_Domain_Value_Definition:
The taxonomic class "Class Aves" was assigned under the domain: "Scientific Name" if the "Common Name" was given as "Unknown species."
Enumerated_Domain_Value_Definition_Source: Author Defined
Attribute:
Attribute_Label: Latitude
Attribute_Definition:
Latitude of site location as captured by hand held GPS. Coordinates are expressed as North latitude, decimal degrees, WGS84 datum.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 59.75333
Range_Domain_Maximum: 63.03583
Attribute:
Attribute_Label: Longitude
Attribute_Definition:
Longitude of site location as captured by hand held GPS. Coordinates are expressed as West longitude, decimal degrees, WGS84 datum.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: -166.09620
Range_Domain_Maximum: -161.41861
Attribute:
Attribute_Label: Location
Attribute_Definition:
Location of wild bird sampling defined as either a western Alaska village name (e.g. Eek, Alaska) or a description of a remote sampling site (e.g. Anerkochik River 1)
Attribute_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Chefornak, Y-K Delta
Enumerated_Domain_Value_Definition: Chefornak, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Eek, Y-K Delta
Enumerated_Domain_Value_Definition: Eek, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Emmonak, Y-K Delta
Enumerated_Domain_Value_Definition: Emmonak, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Hooper Bay, Y-K Delta
Enumerated_Domain_Value_Definition: Hooper Bay, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Kipnuk, Y-K Delta
Enumerated_Domain_Value_Definition: Kipnuk, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Kotlik, Y-K Delta
Enumerated_Domain_Value_Definition: Kotlik, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Kwethluk, Y-K Delta
Enumerated_Domain_Value_Definition: Kwethluk, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Pilot Station, Y-K Delta
Enumerated_Domain_Value_Definition: Pilot Station, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Quinhagak, Y-K Delta
Enumerated_Domain_Value_Definition: Quinhagak, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Toksook Bay, Y-K Delta
Enumerated_Domain_Value_Definition: Toksook Bay, Y-K Delta, Alaska
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anerkochik River 1
Enumerated_Domain_Value_Definition: Anerkochik River sampling site #1
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anerkochik River 2
Enumerated_Domain_Value_Definition: Anerkochik River sampling site #2
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anerkochik River 3
Enumerated_Domain_Value_Definition: Anerkochik River sampling site #3
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anerkochik River 4
Enumerated_Domain_Value_Definition: Anerkochik River sampling site #4
Enumerated_Domain_Value_Definition_Source: author defined
Attribute:
Attribute_Label: RT-PCR Ct Values
Attribute_Definition:
The number of cycles required for the fluorescent signal of a molecular probe for the influenza A matrix gene target to exceed background levels in a real-time reverse transcriptase polymerase chain reaction (rRT-PCR) applied to swab samples stored in viral transport media as described by Spackman et al. (2002). The RT-PCR is run for up to 45 cycles using reaction conditions described in the previous reference. Samples with no value did not exceed background levels.
Attribute_Definition_Source:
author defined with reference to: Spackman E, Senne DA, Myers TJ, Bulaga LL, Garber LP, Perdue ML, Lohman K, Daum LT, Suarez DL. Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. J Clin Microbiol. 2002;40:3256–60
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0.00000
Range_Domain_Maximum: 44.02000
Attribute:
Attribute_Label: AIVM VI(+)
Attribute_Definition:
The detection of the influenza A matrix gene target in RNA extracted from amnio-allantoic fluids using real-time reverse transcriptase polymerase chain reaction (rRT-PCR) as described by Fouchier et al. (2000). Only samples put into eggs have a reported result of either NEG (negative) or POS (positive); blank fields indicate eggs were not inoculated with a given sample.
Attribute_Definition_Source:
author defined with reference to Fouchier RAM, Bestebroer TM, Herfst S, Van Der Kemp L, Rimmelzwaan GF, Osterhaus ADME. Detection of influenza A viruses from different species by PCR amplification of conserved sequences in the matrix gene. J Clin Microbiol. 2000;38:4096–101.
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: POS
Enumerated_Domain_Value_Definition: Assay result positive
Enumerated_Domain_Value_Definition_Source: author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: NEG
Enumerated_Domain_Value_Definition: Assay result negative
Enumerated_Domain_Value_Definition_Source: author defined
Attribute:
Attribute_Label: Strain Name
Attribute_Definition:
Strain names follows an internationally accepted naming convention for influenza viruses. This convention was accepted by WHO in 1979 and published in February 1980 in the Bulletin of the World Health Organization, 58(4):585-591 (1980) (see A revision of the system of nomenclature for influenza viruses: a WHO Memorandum[854 KB, 7 pages]). The approach uses the following components: The antigenic type (e.g., A, B, C) The host of origin (e.g., swine, equine, chicken, etc. For human-origin viruses, no host of origin designation is given.) Geographical origin (e.g., Denver, Taiwan, etc.) Strain number (e.g., 15, 7, etc.) Year of isolation (e.g., 57, 2009, etc.) For influenza A viruses, the hemagglutinin and neuraminidase antigen description in parentheses (e.g., (H1N1), (H5N1) For example: A/duck/Alberta/35/76 (H1N1) for a virus from duck origin
Attribute_Definition_Source: Centers for Disease Control and Prevention
Attribute_Domain_Values:
Unrepresentable_Domain: None
Attribute:
Attribute_Label: Band Number
Attribute_Definition:
USGS band number on metal tarsus (leg) band. Each band has a unique number assigned by the Bird Banding Lab, Patuxent Wildlife Research Center, Patuxent, Maryland. Bands generally begin with a 3-4 digit prefix followed by a 5 digit suffix, e.g., 1347.59381. The initial capture and banding event and associated band number are reported to the USGS Bird Banding Laboratory in the year of banding and all banding data can be access through the Bird Banding Laboratory.
Attribute_Definition_Source:
Source: USGS Bird Banding Laboratory, Patuxent Wildlife Research Center
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 2047-26401
Range_Domain_Maximum: 2047-29018
Attribute:
Attribute_Label: Notes
Attribute_Definition:
Comments field associated with the sample collection record. These have no strict structure and usually have no relevance for interpretation of these data. Frequently they were used to remind field observers of things in the field.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain: None
Attribute:
Attribute_Label: GenBank Accession number
Attribute_Definition:
a unique identifier given to a nucleotide sequence or other biological polymer sequence (DNA, protein) when it is submitted to NCBI GenBank database
Attribute_Definition_Source: author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: KU310452
Range_Domain_Maximum: KU310492
Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey, Alaska Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 4210 University Drive
City: Anchorage
State_or_Province: AK
Postal_Code: 99508
Country: United States
Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov
Distribution_Liability:
Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display 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.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: Zip
Format_Version_Number: 19.0
Format_Information_Content:
Zip file containing the data in CSV file format and FGDC metadata in XML and HTML formats.
File_Decompression_Technique: Winzip legacy compression applied.
Transfer_Size: 1
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name: http://dx.doi.org/10.5066/F7SB43V5
Fees: None
Metadata_Reference_Information:
Metadata_Date: 20201125
Metadata_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey, Alaska Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 4210 University Drive
City: Anchorage
State_or_Province: AK
Postal_Code: 99508
Country: United States
Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov
Metadata_Standard_Name:
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001.1-1999
Metadata_Security_Information:
Metadata_Security_Classification_System: None
Metadata_Security_Classification: Unclassified
Metadata_Security_Handling_Description: None
Generated by mp version 2.9.33 on Mon Jul 25 18:55:19 2016