Reeves, A.B. (ORCID: 0000-0002-7526-0726)
Ramey, A.M. (ORCID: 0000-0002-3601-8400)
Lagassé, B.J.
Patil, V. (ORCID: 0000-0002-9357-194X)
Hubbard, L.E. (ORCID: 0000-0003-3813-1500)
Kolpin, D.W. (ORCID: 0000-0002-3529-6505)
McCleskey, R.B. (ORCID: 0000-0002-2521-8052)
Repert, D.A. (ORCID: 0000-0001-7284-1456)
Poulson, R.L. (ORCID: 0000-0002-8087-3295)
Stallknecht, D.E.
20210830
Temporal Viral Viability Data from Avian Influenza A Viruses Maintained in Alaska Wetlands Under Experimental and Environmental Conditions
tabular digital data
Anchorage, Alaska
U.S. Geological Survey, Alaska Science Center
Suggested Citation: Reeves, A.B., Ramey, A.M., Lagassé, B.J., Patil, V., Hubbard, L.E., Kolpin, D.W., McCleskey, R.B., Repert, D.A., Poulson, R.L., Stallknecht, D.E., 2021, Temporal viral viability data from avian influenza A viruses maintained in Alaska wetlands under experimental and environmental conditions: U.S. Geological Survey data release, https://doi.org/10.5066/P98L6ASV
https://doi.org/10.5066/P98L6ASV
U.S. Geological Survey, Alaska Science Center
2011
Assessment of wildlife health and disease in Alaska and adjacent regions
website
Alaska Science Portal
321
Anchorage, Alaska
U.S. Geological Survey, Alaska Science Center
This is a link to the broader USGS Alaska Science Center research project supported by these data. Users will find a description of the research project and links to associated reports, publications, and data products.
https://alaska.usgs.gov/portal/project.php?project_id=321
Data sets containing: (1) sample collection and influenza A virus (IAV) screening information for wild ducks, (2) water temperature data from four wetlands within the Izembek National Wildlife Refuge in Alaska, USA (3) water quality measurement from four wetlands within the Izembek National Wildlife Refuge in Alaska, USA, (4) genetic sequence data for IAVs recovered from replicate samples of wild ducks.
The data were collected to investigate the duration of viability of avian influenza viruses maintained in Alaska wetlands and to understand environmental conditions that contribute to the maintenance of IAVs.
2019
2020
observed
None planned
Study sites were located in Southwestern Alaska, USA
-163.455
-162.372
55.516
54.937
USGS Metadata Identifier
USGS:ASC402
ISO 19115 Topic Category
Biota
Environment
NASA GCMD Earth Science Keyword Thesaurus
Animals/Vertebrates
Birds
Ducks/Geese/Swans
Lakes
Waterfowl
Viruses
USGS CSA Biocomplexity Thesaurus
Migratory birds
Disease reservoirs
Disease detection
USGS Thesaurus
Wildlife
Wetland ecosystems
Health and disease
Wildlife disease
Disease vectors
Avian influenza
NIH MeSH Thesaurus
Virus Diseases
Influenza A virus
None
Influenza A virus
Mallard
Northern Pintail
Gadwall
American Wigeon
Eurasian Wigeon
Green-winged Teal
USGS Geographic Names Information System (GNIS)
Alaska
Izembek National Wildlife Refuge
None
Animals
Vertebrates
Birds
Viruses
ITIS Integrated Taxonomic Information System
Unknown
ITIS Integrated Taxonomic Information System
online database
online
ITIS-North America
Taxonomic details retrieved February 3, 2020, from the Integrated Taxonomic Information System online database https://www.itis.gov
https://www.itis.gov
International Committee on Taxonomy of Viruses (ICTV)
Unknown
International Committee on Taxonomy of Viruses
database
online
International Committee on Taxonomy of Viruses
Taxonomic details for influenza A virus were retrieved November 11, 2020, from the International Committee on Taxonomy of Viruses online database https://talk.ictvonline.org/
https://talk.ictvonline.org/
Influenza A viruses were identified by the successful amplification of an RNA influenza A matrix gene-target using real-time reverse transcriptase polymerase chain reaction (rRT-PCR).
Life
Life
Kingdom
Animalia
Subkingdom
Bilateria
Infrakingdom
Deuterostomia
Phylum
Chordata
Subphylum
Vertebrata
Infraphylum
Gnathostomata
Superclass
Tetrapoda
Class
Aves
Order
Anseriformes
Family
Anatidae
Subfamily
Anatinae
Genus
Anas
Species
Anas platyrhynchos
Mallard
TSN: 175063
Species
Anas acuta
Northern Pintail
TSN: 175074
Species
Anas strepera
Gadwall
TSN: 175073
Species
Anas americana
American Wigeon
TSN: 175094
Species
Anas penelope
Eurasian Wigeon
TSN: 175092
Species
Anas crecca
Eurasian Teal
Green-winged Teal
TSN: 175081
Realm
Riboviria
Phylum
Negarnaviricota
Subphylum
Polyploviricotina
Class
Insthoviricetes
Order
Articulavirales
Family
Orthomyxoviridae
Genus
Alphainfluenzavirus
Species
Influenza A virus
None
It is requested that the authors and the USGS Alaska Science Center be cited for any subsequent publications that reference this dataset.
U.S. Geological Survey, Alaska Science Center
Mailing and Physical
4210 University Drive
Anchorage
Alaska
99508
USA
907-786-7000
ascweb@usgs.gov
U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, Alaska 99508, USA; Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, USA; U.S Geological Survey, Upper Midwest Water Science Center, 8505 Research Way, Middleton, Wisconsin 53562,USA
Ramey, A.M. (ORCID: 0000-0002-3601-8400)
Reeves, A.B. (ORCID: 0000-0002-7526-0726)
Lagassé, B.J.
Patil, V. (ORCID: 0000-0002-9357-194X)
Hubbard, L.E. (ORCID: 0000-0003-3813-1500)
Kolpin, D.W. (ORCID: 0000-0002-3529-6505)
McCleskey, R.B. (ORCID: 0000-0002-2521-8052)
Repert, D.A. (ORCID: 0000-0001-7284-1456)
Stallknecht, D.E.
Poulson, R.L. (ORCID: 0000-0002-8087-3295
2021
Evidence for interannual persistence of infectious influenza A viruses in Alaska wetlands
journal article
Science of the Total Environment
TBD
online
Elsevier
Ramey, A.M., Reeves, A.B., Lagassé, B.J., Patil, V., Hubbard, L.E., Kolpin, D.W., McCleskey, R.B., Repert, D.A., Stallknecht, D.E., Poulson, R.L. 2021. Evidence for interannual persistence of infectious influenza A viruses in Alaska wetlands. Science of the Total Environment TBD
https://doi.org/TBD
Individual sample IDs, collection dates, sampling locations, and other values were cross-checked and verified with field worksheets. Positive and negative controls were included in all rRT-PCR assays from which Ct values were reported. Genomic RNA from replicate samples that were not in >99% nucleotide identity at all gene segments with other replicates of the same paired swab samples were sequenced at least one additional time from newly extracted RNA to reduce the possibility of contamination within the extraction and sequencing pipeline. The water quality probe was calibrated daily prior to measurement of conductance, pH, and specific conductance. The water quality probe was calibrated within one week to measurements of turbidity.
Attribute values fall within expected ranges and data were proofed for the presence of duplication and omission. N/A, N/D, N/T indicate that no data are available for a particular sample (see Attribute Definitions for details).
Data were omitted for samples collected from a source other than directly from wild ducks. Virus isolation data was omitted for samples determined to be avian paramyxovirus positive and influenza A virus negative. All data for one sample (#67) was removed because there was insufficient quantity of sample material to be aliquoted across all replicate samples and therefore could not be tested to completeness. Blank cells indicate data were not collected or not provided (see Attribute Definitions for details).
Field
Sample collection from wild birds: Swab samples for viral screening were collected by applying a polyester-tipped applicator to the cloaca and oropharynx of hunter harvested wild birds. All swabs were placed in 4 ml of distilled water. 20 sub-samples were made from each sample. Each sub-sample was created by adding 0.2 ml aliquot of the initial sample to 1.8 ml of either distilled water or 0.22-micron filtered water from four unique wetlands within Izembek National Wildlife Refuge, Alaska, USA. Four sub-samples were made for each of the 5 water treatment types.
All of the sub-samples in distilled water and one of four sub-samples of each filtered surface water type including negative controls were shipped as quickly as possible to the University of Georgia for initial influenza A virus (IAV) screening and storage. The other sub-samples were submerged in steel drums in approximately one meter of water within each of the four wetlands. Sample tubes were sorted and submerged in the corresponding wetland from which the filtered water in each tube was collected.
Lab
Sample IAV screening: All swab samples were initially screened at the University of Georgia using real-time reverse transcriptase polymerase chain reaction (rRT-PCR) targeting gene products for the influenza A virus matrix gene (Spackman et al. 2002). All samples were also inoculated into specific pathogen-free embryonated chicken eggs for virus isolation (Fouchier el al. 2000). Amnio-allantoic fluids were collected after 120 hours and tested via hemagglutination assay. RNAs extracted from hemagglutination assay positive amnio-allantoic fluids were tested for the IAV matrix gene by rRT-PCR and resultant isolates were genomically sequenced at the Alaska Science Center using next-generation sequencing technology (Illumina platform, Illumina Inc., San Diego, CA).
Field
Wetland water temperature: During September 2019, a perforated steel drum containing a Hobo® TidbiT® temperature logger (Onset Computer Corp; Bourne, Massachusetts) was anchored within each of the four field sites at a depth of approximately 0.5–1.0 m as measured from substrate to the top of the water column. The temperature loggers were programed to record temperature in degrees Celsius every hour on the hour for the duration of the study. Once retrieved (September 2020), the data was uploaded to a mobile device and downloaded as a comma-separated values (CSV) file.
Field
Wetland water measurements and collections: We used a YSI (Yellow Springs, OH) EXO water quality meter (calibrated daily) to determine pH, dissolved oxygen, specific conductance, temperature, barometric pressure, and turbidity of water at each field site. All other water metrics were measured by collecting water samples directly from each wetland in air-tight acid-washed plastic bottles. In addition to the untreated samples collected, surface water was collected from each field site and pre-filtered through 100 micron and 1 micron pour-through filters (Duda Energy LLC; Decatur, Alabama) and finally filtered through a 0.22 µm vacuum filter (Corning®; Corning, New York). All water samples were sent immediately on ice packs to the U.S. Geological Redox Chemistry Laboratory in Boulder, Colorado for testing.
Lab
Water sample testing and characterization: Standard techniques were used at the U.S. Geological Redox Chemistry Laboratory in Boulder, Colorado to characterize chemical concentrations of surface waters (alkalinity, aluminum, ammonium, antimony, arsenic, barium, beryllium, boron, bromine, calcium, chlorine, cobalt , dissolved organic carbon, fluorine, iron, lead, lithium, manganese, magnesium, molybdenum, nickel, nitrite, phosphorous, potassium, rubidium, silicon dioxide, sodium, strontium, sulfate, total dissolved nitrogen, tungsten, uranium, vanadium)(U.S. Environmental Protection Agency 1993, U.S. Environmental Protection Agency 1994, Brinton et al. 1996, Barringer et al. 1996).
Lab
Genomic Sequencing: Total RNA was also extracted from isolates using MagMAX™-96 AI/ND Viral RNA Isolation Kits. Complementary DNA was amplified from virus RNA extracts, visualized, and purified using methods reported in Reeves et al. (2018) at the USGS Alaska Science Center. Using a Nextera XT DNA library preparation kit (Illumina, Inc., San Diego, CA), indexed libraries were pooled and sequenced on an Illumina MiSeq using either 500 or 600-cycle reagent kits with paired-end reads. Sequence reads were assembled using a customized workflow on Geneious R11 (Biomatters Ltd. Auckland, New Zealand) using reference data for IAVs obtained from GenBank (Clark et al. 2016).
Spackman, E.
Senne, D.A.
Myers, T.J.
Bulaga, L.L.
Garber, L.P.
Perdue, M.L.
Lohman, K.
Daum, L.T.
Suarez, D.L.
2002
Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes
journal article
Journal of Clinical Microbiology
40(9):3256–32602
online
American Society for Microbiology
Spackman, E., Senne, D.A., Myers, T.J., Bulaga, L.L., Garber, L.P., Perdue, M.L., Lohman, K., Daum, L.T., Suarez, D.L. 2002. Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. Journal of Clinical Microbiology 40(9):3256–32602. doi:10.1128/JCM.40.9.3256-3260.2002
https://doi.org/10.1128/JCM.40.9.3256-3260.2002
publication
2002
publication date
Spackman et al 2002
Methods used for detecting IAV in a sample using rRT-PCR
Fouchier, R.A.M.
Bestebroer, T.M.
Herfst, S.
Van Der Kemp, L.
Rimmelzwaan, G.F.
Osterhaus, A.D.M.E..
2000
Detection of influenza A viruses from different species by PCR amplification of conserved sequences in the matrix gene. Journal of Clinical Microbiology.
journal article
Journal of Clinical Microbiology
38(11):4096–4101
online
American Society for Microbiology
Fouchier, R.A.M., Bestebroer, T.M., Herfst, S., Van Der Kemp, L., Rimmelzwaan, G.F., Osterhaus, A.D.M.E. 2000. Detection of influenza A viruses from different species by PCR amplification of conserved sequences in the matrix gene. Journal of Clinical Microbiology. Journal of Clinical Microbiology 38(11):4096–4101 doi:10.1128/JCM.38.11.4096-4101.2000
https://doi.org/10.1128/JCM.38.11.4096-4101.2000
publication
2000
publication date
Fouchier et al 2000
Methods used for detecting IAV in a sample using rRT-PCR and viral isolation methods
Reeves, A. B.
Hall, J. S.
Poulson, R. L.
Donnelly, T.
Stallknecht, D. E.
Ramey, A. M.
2018
Influenza A virus recovery, diversity, and intercontinental exchange: A multi-year assessment of wild bird sampling at Izembek National Wildlife Refuge, Alaska
journal article
Plos One
13(4):e0195327
online
Plos
Reeves, A.B., Hall, J.S., Poulson, R.L., Donnelly, T., Stallknecht, D.E., and Ramey, A.M. 2018. Influenza A virus recovery, diversity, and intercontinental exchange: A multi-year assessment of wild bird sampling at Izembek National Wildlife Refuge, Alaska. Plos One 13(4):e0195327 doi:10.1371/journal.pone.0195327
https://doi.org/10.1371/journal.pone.0195327
publication
2018
publication date
Reeves et al. 2018
Lab techniques; describing detailed methods used for the sequencing of IAVs
Clark, K.
Karsch-Mizrachi, I.
Lipman, D.J.
Ostell, J.
Sayers, E.W.
2016
GenBank
journal article
Nucleic Acids Research
44(D1):D67-D72
online
Oxford Academic Journals
Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Sayers, E.W. 2016. GenBank. Nucleic Acids Research, 44(D1):D67-D72. doi: 10.1093/nar/gkv1276
https://doi.org/10.1093/nar/gkv1276
publication
2016
publication date
Clark et al. 2016
GenBank was the source for IAV genomes used in sequence assembly.
U.S. Environmental Protection Agency
1993
Determination of Inorganic Anions in Drinking Water by Ion Chromatography
document
Selected Analytical Methods for Environmental Remediation and Recovery (SAM)
Method 300.1, Revision 1.0
U.S. Environmental Protection Agency. 1993. : Determination of Inorganic Anions in Drinking Water by Ion Chromatography. Selected Analytical Methods for Environmental Remediation and Recovery (SAM): EPA Method 300.1, Revision 1.0. 39pp
publication
1993
publication date
U.S. Environmental Protection Agency 1993
Laboratory techniques for water analysis.
U.S. Environmental Protection Agency
1994
EPA Method 200.7, Revision 4.4: Determination of Metals and Trace Elements in Water and Wastes by Inductively Coupled Plasma-Atomic Emission Spectrometry
document
Selected Analytical Methods for Environmental Remediation and Recovery (SAM).
Method 200.7, Revision 4.4
U.S. Environmental Protection Agency. 1994. Determination of Metals and Trace Elements in Water and Wastes by Inductively Coupled Plasma-Atomic Emission Spectrometry. Selected Analytical Methods for Environmental Remediation and Recovery (SAM): Method 200.7, Revision 4.4. 58pp
publication
1994
publication date
U.S. Environmental Protection Agency 1994
Laboratory techniques for water analysis.
Brinton, T.I.
Antweiler, R.C.
Taylor, H.E.
U.S. Geological Survey
1996
Method for the Determination of Dissolved Chloride, Nitrate, and Sulphate in Natural Water Using Ion Chromatography
document
Open file report
95-426A
Brinton, T.I., Antweiler, R.C., Taylor, H.E. 1996. Method for the Determination of Dissolved Chloride, Nitrate, and Sulphate in Natural Water Using Ion Chromatography. U.S. Geological Survey, Open file report: 95-426A, 16pp doi:10.3133/ofr95426a
https://doi.org/10.3133/ofr95426a
publication
1996
publication date
Brinton et al 1996
Laboratory techniques for water analysis.
Barringer, J.
Johnsson, P.
U.S. Geological Survey
1996
Theoretical Considerations and a Simple Method for Measuring Alkalinity and Acidity in Low-PH Waters by Gran Titration.
document
Water-Resources Investigations Report
89-4029
Barringer, J.; Johnsson, P. 1996. Theoretical Considerations and a Simple Method for Measuring Alkalinity and Acidity in Low-PH Waters by Gran Titration. U.S. Geological Survey, Water-Resources Investigations Report:89-4029, 36pp doi:10.3133/wri894029
https://doi.org/10.3133/wri894029
publication
1996
publication date
Barringer et al 1996
Laboratory techniques for water analysis.
Water temperature data was adjusted to the local time for each location (Alaska = AKDT UTC-8 and AKST UTC-9 after it was collected (downloaded) from the Hobo® TidbiT® data loggers.
2020
Field data sheets were transcribed into digital spreadsheets.
Unknown
Waterbody names are the proper or common names of the lakes, pools, etc. used in the study. They do not describe precise geographic points.
Point
0.001
0.001
Decimal degrees
World Geodetic System of 1984
World Geodetic System of 1984
6378137
298.257223563
avianFlu_collectionVIResults_alaska_reeves_2019-2020.csv
Table of samples collected from ducks and influenza A virus screening result data. Presented in a Comma Separated Value (CSV) formatted table.
Author defined
SAMPLE_ID
Individualized identification provided for each original cloacal and oropharyngeal swab sample collected. Although each sample was collected only once, the sample ID numbers here may appear more than once because each sample was originally aliquoted into 20 sub-samples with various water as media and in replicates to be analyzed at different time periods. A sample ID number not appearing more than once in this column indicates a sample that tested negative for the presence of IAVs in the initial screen of a sub-sample in distilled water.
Author defined
Unique identifier for each original cloacal and oropharyngeal swab sample collected.
A_NegCTRL
Negative control using a mix of 10% distilled water and 90% filtered water collected from Bluebill Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
B_NegCTRL
Negative control using a mix of 10% distilled water and 90% filtered water collected from Rescue Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
C_NegCTRL
Negative control using a mix of 10% distilled water and 90% filtered water collected from Proxy pond, an unnamed body of water within Izembek National Wildlife Refuge, Alaska, USA.
Author defined
D_NegCTRL
Negative control using a mix of 10% distilled water and 90% filtered water collected from Red Salmon Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
E_NegCTRL
Negative control using 100% distilled water
Author defined
DATE_OF_INITIAL_SAMPLE_COLLECTION
Date of collection event (e.g. day samples were collected from hunter-harvested or live captured birds)
Author defined
2019-09-06
2019-10-01
Date (YYYY-MM-DD)
N/A
Not applicable; water or control sample
Author defined
SPECIES
Common name of avian species; detailed in the Taxonomy of this metadata record sampled as identified by field technicians and or volunteers.
Author defined
Common name of avian species; detailed in the Taxonomy of this metadata record
N/A
Not applicable; water or control sample
Author defined
AGE
Age (class code) of the bird when captured or sampled.
Author defined
AHY
After Hatch Year. A bird known to have hatched before the year of capture or sampling; year of hatch otherwise unknown.
Author defined
HY
Hatch Year. A bird known to have hatched during the year of capture or sampling.
Author defined
Unknown
Unknown, Age not determined because plumage was inconclusive or sample was from the environment and individual could not be identified.
Author defined
N/A
Not applicable; water or control sample
Author defined
Sex
Sex of duck as determined by plumage and/or cloacal inversion by trained field observers
Author defined
F
Female
Author defined
M
Male
Author defined
N/A
Not applicable; water or control sample
Author defined
DATE_OF_ALIQUOTING_TO_SUBSAMPLES
The date that initial sample was aliquoted into the 20 subtypes. 'N/A' signifies not applicable (i.e., sample was not frozen)
Author defined
2019-09-10
2019-10-02
Date (YYYY-MM-DD)
WATER_TREATMENT_TYPE_OF_SUBSAMPLES
A letter used to define a distinct type of distilled or filtered water treatment used as media in subsamples (e.g. water type B indicates 0.2 ml of the original sample was aliquoted into 1.8 ml of filtered water from Rescue Lake).
Author defined
A
Bluebill Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
B
Rescue Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
C
Proxy pond, an unnamed body of water within Izembek National Wildlife Refuge, Alaska, USA.
Author defined
D
Red Salmon Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
E
Distilled water
Author defined
DATE_SUBSAMPLES_PLACED_IN_UGA_REFRIGERATOR
The date a subsample was received at the University of Georgia laboratory and placed into refrigeration. All of the subsamples in distilled water (E) were shipped and stored in refrigeration, as were all subsamples with filtered water from each waterbody (A-D) for the initial (T1) time point.
Author defined
2019-09-25
2019-10-09
Date (YYYY-MM-DD)
N/A
Not applicable
Author defined
DATE_SUBSAMPLES_PLACED_IN_WETLAND
The date a subsample in filtered surface water was placed in the respective wetland (A-D) from where the water was collected. Only samples intended to be collected at the later time points (T2-T4) were submerged in the wetlands.
Author defined
2019-10-03
2019-10-03
Date (YYYY-MM-DD)
N/A
Not applicable, subsamples in water treatment of distilled water (type E) were not submerged in wetlands.
Author defined
DATE_RNA_EXTRACTION_T1
The date that RNA was extracted from the primary subsample for time point 1 (T1).
Author defined
2019-09-26
2019-10-15
Date (YYYY-MM-DD)
MA_RRT-PCR_CT_VALUE_T1
The number of cycles required for the fluorescent signal of a molecular probe for the influenza A matrix (MA) 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 in Spackman et al (2002). The rRT-PCR is run for up to 45 cycles using reaction conditions described in the previous reference.
Author defined, with reference to: Spackman et al 2002.
26.69
44.49
No Ct
The sample was tested but did not exceed the background levels and therefore no Ct value was reported.
Author defined.
N/A
Not applicable
Author defined
DATE_VIRUS_ISOLATION_T1
The date that a swab sample was inoculated into the chorioallantoic sac of embryonating chicken eggs.
Author defined
2019-09-26
2019-10-17
Date (YYYY-MM-DD)
N/A
Not applicable
Author defined
IAV_VI_RESULT_SAMPLE_A_T1
Final result of viral isolation (VI) determined by 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) methods described in Fouchier et al 2000. Only samples put into eggs have a reported result; blank fields indicate eggs were not inoculated with a given sample.
Author defined
NEG
Assay result negative
Author defined
POS
Assay result positive
Author defined
DATE_SUBSAMPLE_REMOVED_FROM_WETLAND_T2
The date that a sub-sample was removed from the waterbody for a specific Time Point (T2).
Author defined
2019-12-04
2019-12-04
Date (YYYY-MM-DD)
N/A
Not applicable
Author defined
DATE_RNA_EXTRACTION_T2
The date that RNA was extracted from the primary subsample for time point 1 (T1).
Author defined
2019-12-10
2019-12-10
Date (YYYY-MM-DD)
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
MA_RRT-PCR_CT_VALUE_T2
The number of cycles required for the fluorescent signal of a molecular probe for the influenza A matrix (MA) 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 in Spackman et al (2002). The rRT-PCR is run for up to 45 cycles using reaction conditions described in the previous reference.
Author defined, with reference to: Spackman et al 2002.
29.34
39.50
No Ct
The sample was tested but did not exceed the background levels and therefore no Ct value was reported.
Author defined.
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
N/A
Not applicable
Author defined
DATE_VIRUS_ISOLATION_T2
The date that a swab sample was inoculated into the chorioallantoic sac of embryonating chicken eggs.
Author defined
2019-12-12
2019-12-12
Date (YYYY-MM-DD)
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
IAV_VI_RESULT_SAMPLE_A_T2
Final result of viral isolation (VI) determined by 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) methods described in Fouchier et al 2000. Only samples put into eggs have a reported result; blank fields indicate eggs were not inoculated with a given sample.
Author defined
NEG
Assay result negative
Author defined
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
POS
Assay result positive
Author defined
DATE_SUBSAMPLE_REMOVED_FROM_WETLAND_T3
The date that a sub-sample was removed from the waterbody for a specific Time Point (T3).
Author defined
2020-02-20
2020-02-21
Date (YYYY-MM-DD)
N/A
Not applicable
Author defined
DATE_RNA_EXTRACTION_T3
The date that RNA was extracted from the primary subsample for time point 1 (T1).
Author defined
2020-20-26
2020-02-26
Date (YYYY-MM-DD)
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
MA_RRT-PCR_CT_VALUE_T3
The number of cycles required for the fluorescent signal of a molecular probe for the influenza A matrix (MA) 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 in Spackman et al (2002). The rRT-PCR is run for up to 45 cycles using reaction conditions described in the previous reference.
Author defined, with reference to: Spackman et al 2002.
30.25
43.30
No Ct
The sample was tested but did not exceed the background levels and therefore no Ct value was reported.
Author defined.
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
DATE_VIRUS_ISOLATION_T3
The date that a swab sample was inoculated into the chorioallantoic sac of embryonating chicken eggs.
Author defined
2020-02-27
2020-02-27
Date (YYYY-MM-DD)
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
IAV_VI_RESULT_SAMPLE_A_T3
Final result of viral isolation (VI) determined by 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) methods described in Fouchier et al 2000. Only samples put into eggs have a reported result; blank fields indicate eggs were not inoculated with a given sample.
Author defined
NEG
Assay result negative
Author defined
POS
Assay result positive
Author defined
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
DATE_SUBSAMPLE_REMOVED_FROM_WETLAND_T4
The date that a sub-sample was removed from the waterbody for a specific Time Point (T4).
Author defined
2020-09-10
2020-09-16
Date (YYYY-MM-DD)
N/A
Not applicable
Author defined
DATE_RNA_EXTRACTION_T4
The date that RNA was extracted from the primary subsample for time point 1 (T1).
Author defined
2020-10-05
2020-10-08
Date (YYYY-MM-DD)
NT
The sample was not tested.
Author defined.
MA_RRT-PCR_CT_VALUE_T4
The number of cycles required for the fluorescent signal of a molecular probe for the influenza A matrix (MA) 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 in Spackman et al (2002). The rRT-PCR is run for up to 45 cycles using reaction conditions described in the previous reference.
Author defined, with reference to: Spackman et al 2002.
32.07
36.95
No Ct
The sample was tested but did not exceed the background levels and therefore no Ct value was reported.
Author defined.
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
DATE_VIRUS_ISOLATION_T4
The date that a swab sample was inoculated into the chorioallantoic sac of embryonating chicken eggs.
Author defined
2020-10-08
2020-10-16
Date (YYYY-MM-DD)
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
IAV_VI_RESULT_SAMPLE_A_T4
Final result of viral isolation (VI) determined by 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) methods described in Fouchier et al 2000. Only samples put into eggs have a reported result; blank fields indicate eggs were not inoculated with a given sample.
Author defined
NEG
Assay result negative
Author defined
POS
Assay result positive
Author defined
NT
The sample was not tested. No additional subsamples were tested at time points 2-4 if the subsamples with water treatment E (distilled water) was negative at the initial screening (time point 1).
Author defined.
avianFlu_wetlandWaterTemperature_alaska_reeves_2019-2020.csv
Temperature of wetland water recorded by a Hobo® TidbiT® temperature logger from inside a perforated steel drum. Presented in a Comma Separated Value (CSV) formatted table.
Author defined
Waterbody
The proper or common name of a waterbody (e.g. lake, pool, etc.) from which water temperature data were collected.
Author defined
Bluebill Lake
Bluebill Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
Red Salmon Lake
Red Salmon Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
Rescue Lake
Rescue Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
Proxy pond
Proxy pond, an unnamed body of water within Izembek National Wildlife Refuge, Alaska, USA.
Author defined
Date_Time
The date and time of each temperature recording. Date and time data correspond to local time zones of the wetlands from which the temperatures were recorded.
Author defined
2019-10-04 00:00
2020-09-15 23:00
Date and time (YYYY-MM-DD hh:mm)
Temp_C
Temperature recorded in Celsius (C)
Author defined
-0.10
21.38
Degrees Celsius
Average_Daily
Average daily temperature (in Celsius) calculated for each wetland using data adjusted to the local time zone. Average daily temperature values are only presented once a day for each wetland, at the midnight 00:00 (HH:MM). The remaining values corresponding to each date are intentionally left blank. Adjustments to calculations based on daylight savings time changes (November 4, 2018 and March 10, 2019) were made and factored into the values presented.
Author defined
0.01
18.73
degrees celsius
avianFlu_wetlandWaterMeasurment_alaska_reeves_2019-2020.csv
Table of water samples collected from various wetlands and testing results. Presented in a Comma Separated Value (CSV) formatted table.
Author defined
H2O_SAMPLE_ID
Unique identification number applied to each water sample tested
Author defined
Unique identifier for each water sample
Name_Description
The proper or common name of a waterbody (e.g. lake, pool, etc.) from which water samples were collected
Author defined
Bluebill Lake
Bluebill Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
Red Salmon Lake
Red Salmon Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
Rescue Lake
Rescue Lake, Izembek National Wildlife Refuge, Alaska, USA
Author defined
Proxy pond
Proxy pond, an unnamed body of water within Izembek National Wildlife Refuge, Alaska, USA.
Author defined
Waterbody_latitude
Approximate Latitude in decimal degrees of the waterbody as determined by hand held GPS.
Author defined
55.25
55.28
Decimal degrees (WGS84)
Waterbody_longitude
Approximate longitude in decimal degrees of the waterbody as determined by hand held GPS.
Author defined
-162.86
-162.78
Decimal degrees (WGS84)
USGS_Station
Unique identification number applied by the U.S. Geological Survey to each collection site or waterbody.
Author defined
Unique identifier for each sample collection site or body of water
Date_water_collected
The date (YYYY-MM-DD) that a water sample was collected from the wetland environment
Author defined
2019-09-05
2020-02-21
Date (YYYY-MM-DD)
Time_water_collected
The local time that a water sample was collected from the wetland environment
Author defined
1005
1600
Local time (mmss)
pH
pH measured from wetland water samples, measured in the field
Author defined
6.15
8.01
Specific_conductance
specific conductance measured from wetland water samples, measured in the field
Author defined
78
564
µS/cm
Temperature_C_measured_on_site
The temperature of the water in degrees Celsius (C) at time of measurement, taken on-site directly from the waterbody
Author defined
-0.05
13.39
Degrees Celsius
Dissolved_Oxygen
Dissolved oxygen mg/L, measured in the field
Author defined
4.20
16.78
mg/L
Turbidity
Turbidity of water, measured in the field
Author defined
-2
78.1
NTU
60-80
turbidity value between 60 - 80 NTU
Author defined
Ca through Be
These 28 columns represent elements or molecules measured in collected water samples as mg/L. Element and molecule: Ca (Calcium), Mg (Magnesium), Na (Sodium), K (Potassium), Cl (Chlorine), SO4 (Sulfate), HCO3 (Bicarbonate; alkalinity), SiO2 (Silicon dioxide), B (Boron), P (Phosphorus), Al (Aluminum), F (Fluorine), Li (lithium), Sr (Strontium), Ba (Barium), Rb (Rubidium), Br (Bromine), Mn (Manganese), Mo (Molybdenum), Cd (Cadmium), Co (Cobalt), Ni (Nickel), V (Vanadium), W (Tungsten), Sb (Antimony), U (Uranium), Be (Beryllium)
Author defined
measurements in mg/L
Pb through DOC
These 4 columns represent elements or molecules measured in collected water samples as µg/L. Element and molecule: Pb (lead), As (Arsenic), Cr (Chromium), DOC (Dissolved Organic Carbon)
Author defined
measurements in µg/L
Nitrite through Total_dissolved_nitrogen
These 3 columns represent molecules measured in collected water samples as mg N/L. Element and molecule: Nitrite (NO2), Ammonium (NH4), Total dissolved nitrogen (N)
Author defined
measurements in mg N/L
avianFlu_IAVgeneticSequence_alaska_reeves_2019-2020.csv
This table provides the nucleotide sequence for each IAV gene segment coding region that was sequenced from sub-samples. IAV genomic sequences resultant from T1 samples stored in distilled water are available on GenBank accession numbers MW874296 - MW874409. Presented in a Comma Separated Value (CSV) formatted table. Sequence_ID from this table corresponds to the SAMPLE_ID found in the table "avianFlu_collectionVIResults_alaska_reeves_2019-2020.csv" included with this data package.
Author defined
Sequence_ID
Unique identifier for each sub-sample cDNA sequence.
Author defined
Unique identifier for each cDNA sequence.
SAMPLE_ID
Individualized identification provided for each original cloacal and oropharyngeal swab sample collected. Although each sample was collected only once, the sample ID numbers here may appear more than once because each sample was originally aliquoted into 20 sub-samples with various water as media and in replicates to be analyzed at different time periods. The numerical portion of the Sample_ID here correspond to the Sample_ID provided in the table "avianFlu_collectionVIResults_alaska_reeves_2019-2020." The word clone will appear in the sample ID if there are multiple sequences for a given gene segment from the same subsample. This is a technical term that does not refer to the method of cloning in the traditional sense, but rather a way to distinguish multiple sequences from mixed infections (more than one virus, or 'quasispecies') in a single sample.
Author defined
Unique identifier for each sample
Water_ID
a simple code for the type of water treatment used in a given subsample as media, and from which viral RNA was tested for and extracted.
Author defined
A
filtered water from Bluebill Lake
Author defined
B
filtered water from Rescue Lake
Author defined
C
filtered water from Proxy Pond
Author defined
D
filtered water from Red Salmon Lake
Author defined
E
distilled water
Author defined
Time_ID
Unique identifier for sub-sample with respect to a time period of the study (T1-T4).
Author defined
T1
T4
time period
Segment
The number corresponding to the IAV genome segment
Author defined
1
Segment 1, also known as PB2
Author defined
2
Segment 2, also known as PB1
Author defined
3
Segment 3, also known as PA
Author defined
4
Segment 4, also known as HA
Author defined
5
Segment 5, also known as NP
Author defined
6
Segment 6, also known as NA
Author defined
7
Segment 7, also known as MA
Author defined
8
Segment 8, also known as NS
Author defined
cDNA_sequence
The complete coding region nucleotide sequence (cDNA) for a given IAV gene segment using standard IUPAC nucleotide codes. When sequencing methods failed to produce confidence in base calling (e.g. insufficient depth of reads, less than 10x) for a given site "?" was used to denote an unknown nucleotide.
Author defined
cDNA nucleotide sequence
U.S. Geological Survey, Alaska Science Center
Mailing and Physical
4210 University Drive
Anchorage
Alaska
99508
USA
907-786-7000
ascweb@usgs.gov
The U.S. Geological Survey, Alaska Science Center is the authoritative source and distributor of these data.
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, no warranty expressed or implied is made regarding the display or utility of the data for other purposes or on all computer systems, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
CSV
Data are distributed in a Zip package containing data in CSV format and FGDC metadata in XML and HTML formats.
Compression applied by the 7-Zip utility using default compression (5). The Zip package can be decompressed and unpacked by open source or commercially available unzip tools.
https://doi.org/10.5066/P98L6ASV
None
20210830
U.S. Geological Survey, Alaska Science Center
Mailing and Physical
4210 University Drive
Anchorage
Alaska
99508
USA
907-786-7000
ascweb@usgs.gov
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (CSDGM)
FGDC-STD-001.1-1999