Filters: Tags: avian influenza (X)25 results (9ms)
Raw MinION FASTQ datafiles corresponding to the paper “A comparison of avian influenza virus whole genome sequencing approaches using nanopore technology”
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.
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.
Avian Influenza Virus Test Results from Active Surveillance of North American Wild Birds Collected by Department of Interior from 2006-2011
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...
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.
Data showing similar movement ecology between mallards infected and not infected with highly pathogenic avian influenza H5N1
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.
Predicted H5 and H7 subtype Avian Influenza Prevalence for Wild Waterfowl Species Across the Continental United States
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.
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.
Molecular detection of avian influenza virus from sediment samples in waterfowl habitats on the Delmarva Peninsula, USA
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.
Predicted Avian Influenza Prevalence for Wild Waterfowl Species Across the Continental United States
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.
Locations of Pacific Flyway Ducks in and near Commercial Livestock Facilities of the Western USA (2015-2021)
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...
Laboratory analysis assessing immune response after flame retardant exposure in American kestrels, Falco sparverius, through 21 days post-hatch
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.
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 220.127.116.11 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.
Spatial models indicating avian influenza transmission risk at the interface of domestic poultry and wild birds in China
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...
Data concerning maintenance and dissemination of avian-origin influenza A virus within the Northern Atlantic Flyway of North America
This data release details the results of avian influenza sampling of dabbling ducks in Maine and Maryland. These data support an associated USGS publication.
This data set includes information pertaining to 300 bivalve mollusk tissue samples collected from mollusk specimens from waters in eastern Maryland on the Delmarva Peninsula. Data includes source location, species, morphometric data, and IAV matrix gene detection status for the bivalve samples collected and analyzed in the associated study.
Spatial Models of Wild Bird Risk Factors for Highly Pathogenic A(H5N1) Avian Influenza Virus Transmission
Wild waterfowl (family Anatidae) are reported as secondary transmitters of HPAIV and primary reservoirs for low-pathogenic avian influenza viruses, yet spatial inputs for disease risk modeling for this group have been lacking. Using geographic information software and Monte Carlo simulations, we developed geospatial indices of waterfowl abundance at 1 km resolutions for the breeding and wintering seasons for China, the epicenter of H5N1. Two types of spatial layers were developed: cumulative waterfowl abundance (WAB), a measure of predicted abundance by species, and cumulative abundance weighted by H5N1 prevalence (WPR), whereby abundance for each species was adjusted based on species specific prevalence values....
Weekly estimates of the risk of avian influenza transmission from wild waterfowl to domestic poultry - Initial phase models
This data layer depicts the weekly estimates of the relative risk of avian influenza transmission from wild waterfowl to domestic poultry. These data represent an early phase of ongoing model development and the inclusion of additional parameters is upcoming.
Waterfowl occurrence and residence time as indicators of H5 and H7 avian inﬂuenza in North American Poultry
This data release contains model outputs depicting the probability of an H5 or H7 avian influenza outbreak at any given point in the continental United States for each week of the year.
Water bodies within 500 meters of poultry feeding operations on the Delmarva Peninsula in 2016 and 2017
Data release contains 1710 polygons representing small bodies of water within 500 meters of poultry feeding operations on the Delmarva Peninsula. Ponds were identified using the USDA's National Agriculture Imagery Program's 2016 and 2017 products. Poultry feeding operations were described in location by Soroka and Duren (2020).
USGS National Wildlife Health Center necropsy results to determine cause of illness/death for seabirds collected in Alaska from January 1, 2017 through December 31, 2021
Summary of Bering and Chukchi Seas seabird necropsies, 2017-2021. More than 14,000 dead seabirds were reported and a total of 117 carcasses were examined. 92 cases had emaciation identified as the Cause Of Death (COD), seven cases where COD was undetermined, and 17 cases where COD was determined as "Other", which included predation, trauma, encephalitis, peritonitis, and bacterial infection. Low Pathogenic Avian Influenza (n=4) and saxitoxin (n=15) were also detected; however, the virus and biotoxin were not determined to be the COD except for one case in 2020 where saxitoxin toxicosis was suspected.