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These data support a paired USGS publication and document the use of retention ponds on commercial poultry farms by wild waterfowl.
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Raw sequencing data as generated by the five different methods used are provided for each of the three samples used in the comparison. The files are in FASTQ format as exported from the Oxford Nanopore’s MK1C using MinION flowcells. Files are labeled according to the method (as described in the paper) and the Sample ID). The MK1C exports data in blocks of 6000 reads per FASTQ file and all the FASTQ files from each method and sample are grouped in a common folder.
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WHISPers stands for Wildlife Health Information Sharing Partnership - event reporting system. It is a web-based repository for sharing basic information about historic and ongoing wildlife mortality (death) and morbidity (illness) events. The system possesses a searchable archive of wildlife mortality and morbidity event data that is available to the public. The information is opportunistically collected and does not reflect all the mortality events that occur in North America.
Types: Citation; Tags: Alabama, Alaska, American Samoa, Arizona, Arkansas, All tags...
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Data consist of flow cytometry files that were generated in the analysis of white blood cells from kestrel blood. Thus, data are in standard format that allows files created by one type of acquisition hardware and software to be analyzed by any other type.
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These data, which support a paired USGS publication, document the movement and infection status of mallards captured, marked, and tested at a wintering site in Tennessee. Data document differences in movement ecology between mallards infected and not infected with HPAI H5N1.
Influenza A viruses are one of the most significant viral groups globally with substantial impacts on human, domestic animal and wildlife health. Wild birds are the natural reservoirs for these viruses, and active surveillance within wild bird populations provides critical information about viral evolution forming the basis of risk assessments and counter measure development. Unfortunately, active surveillance programs are often resource-intensive, and thus enhancing programs for increased efficiency is paramount. Machine learning, a branch of artificial intelligence applications, provides statistical learning procedures that can be used to gain novel insights into disease surveillance systems. We use a form of...
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These data describe the results of virus isolation from oropharyngeal/cloacal swabs and testing of sera by a commercial blocking enzyme-linked immunosorbent assay (bELISA) and hemagglutinin (HA) specific testing by microneutralization (MN) and hemagglutination inhibition (HI) for Lesser Scaup in both the Atlantic and Pacific Flyways and Greater Scaup in the Pacific Flyway. These data support a USGS published manuscript.
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This data release provides the predicted proportion of influenza-positive birds testing positive for H5 and H7 subtypes of IAV for each species at monthly intervals for each county centroid in the continental United States. This data supports a paired USGS publication.
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From 2010-2018 we investigated the occurrence of avian influenza virus in wild birds in Iceland. A total of 6635 swabs samples were collected from wild birds or fecal material directly associated with wild birds. We screened all samples by a real time - polymerase chain reaction (RT-PCR) test with 381 testing positive. Further testing of all RT-PCR positive samples and all negative samples collected in 2012 by virus isolation yielded 120 positives, with 92 of those testing positive by RT-PCR for avian influenza virus.
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These data describe the creation, execution, and results of an effort to model the risk of avian influenza transmission across the wild waterfowl - domestic poultry interface at weekly intervals for the contiguous United States.
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This data release provides the predicted proportion of birds testing positive for IAV for each species at weekly intervals for each county centroid in the continental United States. This data supports a paired USGS publication.
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Data were collected as part of an investigation developed by Leetown Science Center to investigate the comparative detection of avian influenza viruses from waterfowl and potential environmental reservoirs such as aquatic sediment from waterfowl habitat. This dataset identifies positive or negative test results for qRT-PCR (quantitative reverse transcriptase polymerase chain reaction) for avian influenza virus through identification of the Type A influenza virus matrix gene from aquatic sediment samples. Sediment samples were collected from waterfowl habitat so as to determine if temporal and spatial differences in virus detection by qRT-PCR were evident among test sites.
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From 2010-2018 we investigated the occurrence of avian influenza antibody in wild birds in Iceland. A total of 2453 serum samples were collected from wild birds. We tested all samples by enzyme-linked immunosorbent assay (ELISA) for evidence of previous exposure to avian influenza virus with 1302 testing positive.
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Zoonotic diseases are of considerable concern to the human population and viruses such as avian influenza (AIV) threaten food security, wildlife conservation and human health. Wild waterfowl and the natural wetlands they use, are known AIV reservoirs, with birds capable of virus transmission to domestic poultry populations. While infection risk models have linked migration routes and AIV outbreaks, there is a limited understanding of wild waterfowl presence on commercial livestock facilities, and movement patterns linked to natural wetlands. In this dataset, records (rows) represent all analyzed locations of individual waterfowl relative to locations of commercial livestock facilities and habitats. Each row has...
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A compilation of previously published results exploring the pathogenesis of avian influenza viruses in wild avian species in North America.
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Wild lesser scaup from the Chesapeake Bay, captured and implanted with satellite transmitters for a separate ecology study, were opportunistically sampled for avian influenza. These data detail the virological sampling results, obtained post release, which include a single positive for clade 2.3.4.4 H5N1 virus of the A/goose/Guangdong/1/1996 (Gs/GD) H5N1 lineage of highly pathogenic IAV. These data also include the movements of the infected bird from release until death as well as four conspecifics marked and released concurrent with the HPAI positive bird. These data support a paired publication.
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Laboratory analysis of innate American kestrel, Falco sparverius, immune response after exposure to flame retardant, isopropylphenyl phosphate (ITP) through 21 days post hatch. Data consist of flow cytometry files that were generated in the analysis of white blood cells from kestrel blood. Thus, data are in standard format that allows files created by one type of acquisition hardware and software to be analyzed by any other type.
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This data set represents an ecological and laboratory-based experiment to understand influenza virus viability in surface water. Data tables included in this release consist of 1) daily mean water temperature, 2) viability of viruses maintained in water, 3) influenza detection in duck samples, 4) viral titers of experimentally inoculated water samples, and 5) water chemistry.
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Emergence of avian influenza viruses with high lethality to humans, such as the currently circulating highly pathogenic A(H5N1) and A(H7N9) cause serious concern for the global economic and public health sectors. To improve our understanding of the spatial and temporal trends in transmission risk we developed a model that predicts hotspots of novel virus emergence between domestic and wild birds and incorporates H5N1 risk factors. Models were produced at 30 km spatial resolution across two temporal seasons. Files are named using a TransmisisonDirection_Season_DataType format such that Transmission direction can end in a (poultry to waterfowl) or b (waterfowl to poultry), Season can be breeding (br) or wintering...
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This data release details the results of avian influenza sampling of dabbling ducks in Maine and Maryland. These data support an associated USGS publication.


map background search result map search result map Wildlife Health Information Sharing Partnership-event reporting system (WHISPers) Molecular detection of avian influenza virus from sediment samples in waterfowl habitats on the Delmarva Peninsula, USA Discerning innate immunity in American kestrels, Falco sparverius, through 21 days post-hatch Laboratory analysis assessing immune response after flame retardant exposure in American kestrels, Falco sparverius, through 21 days post-hatch Dataset: Surveillance for Avian Influenza Virus in Iceland, 2010 – 2018 Data concerning maintenance and dissemination of avian-origin influenza A virus within the Northern Atlantic Flyway of North America Predicted Avian Influenza Prevalence for Wild Waterfowl Species Across the Continental United States Locations of Pacific Flyway Ducks in and near Commercial Livestock Facilities of the Western USA (2015-2021) Telemetry data of a Lesser Scaup (Aythya affinis) positive for 2.3.4.4 Highly Pathogenic H5N1 Spatial models indicating avian influenza transmission risk at the interface of domestic poultry and wild birds in China Predicted H5 and H7 subtype Avian Influenza Prevalence for Wild Waterfowl Species Across the Continental United States Raw MinION FASTQ datafiles corresponding to the paper “A comparison of avian influenza virus whole genome sequencing approaches using nanopore technology” Data showing similar movement ecology between mallards infected and not infected with highly pathogenic avian influenza H5N1 Data describing the use of retention ponds on commercial poultry facilities on Delmarva by wild waterfowl Estimates of avian influenza transmission risk across the wild waterfowl - domestic poultry interface (ver. 2.0, May 2024) Database collating previous laboratory investigations into the pathogenesis of avian influenza viruses in wild avifauna of North America Dataset: Sero-surveillance for avian influenza exposure in wild birds in Iceland, 2012-2017 Data for Infectivity of Wild-Bird Origin Influenza A Viruses in Minnesota Wetlands Across Seasons Results of Virus Isolation and Serology testing on Influenza A Virus Samples from Lesser Scaup (Aythya affinis) and Greater Scaup (Aythya Marila) Raw MinION FASTQ datafiles corresponding to the paper “A comparison of avian influenza virus whole genome sequencing approaches using nanopore technology” Molecular detection of avian influenza virus from sediment samples in waterfowl habitats on the Delmarva Peninsula, USA Telemetry data of a Lesser Scaup (Aythya affinis) positive for 2.3.4.4 Highly Pathogenic H5N1 Data describing the use of retention ponds on commercial poultry facilities on Delmarva by wild waterfowl Dataset: Surveillance for Avian Influenza Virus in Iceland, 2010 – 2018 Dataset: Sero-surveillance for avian influenza exposure in wild birds in Iceland, 2012-2017 Data for Infectivity of Wild-Bird Origin Influenza A Viruses in Minnesota Wetlands Across Seasons Locations of Pacific Flyway Ducks in and near Commercial Livestock Facilities of the Western USA (2015-2021) Data concerning maintenance and dissemination of avian-origin influenza A virus within the Northern Atlantic Flyway of North America Data showing similar movement ecology between mallards infected and not infected with highly pathogenic avian influenza H5N1 Predicted Avian Influenza Prevalence for Wild Waterfowl Species Across the Continental United States Estimates of avian influenza transmission risk across the wild waterfowl - domestic poultry interface (ver. 2.0, May 2024) Results of Virus Isolation and Serology testing on Influenza A Virus Samples from Lesser Scaup (Aythya affinis) and Greater Scaup (Aythya Marila) Spatial models indicating avian influenza transmission risk at the interface of domestic poultry and wild birds in China Predicted H5 and H7 subtype Avian Influenza Prevalence for Wild Waterfowl Species Across the Continental United States Wildlife Health Information Sharing Partnership-event reporting system (WHISPers) Database collating previous laboratory investigations into the pathogenesis of avian influenza viruses in wild avifauna of North America Discerning innate immunity in American kestrels, Falco sparverius, through 21 days post-hatch Laboratory analysis assessing immune response after flame retardant exposure in American kestrels, Falco sparverius, through 21 days post-hatch