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231 results for “Avian influenza”
Data complementing the Avian influenza overview March - June 2024
<p>Data complementing the Avian influenza overview March - June 2024</p> <p> </p> <p><strong>Annex A – Data on birds and mammals</strong></p> <p>The annex contains tables and figures on birds and mammals, including HPAI virus detections in these species.</p> <p> </p> <p><strong>Annex B – Characteristics of the HPAI A(H5Nx)-affected poultry establishments</strong></p> <p>The annex contains a table with the characteristics of the HPAI A(H5Nx)-affected poultry establishments by affected European country submitted to ADIS between 16 March and 14 June 2024.</p> <p> </p> <p><strong>Annex C – Data on virus sequences</strong></p> <p>The annex contains information on authors, originating and submitting laboratories of the sequences from GISAID's EpiFlu™ Database on which this research is based. All data submitters may be contacted directly via <a title="https://eur03.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.gisaid.org%2f&data=05%7c02%7c%7cbccd5bb40f5e4a4ccee508dbfbeb3823%7c406a174be31548bdaa0acdaddc44250b%7c1%7c0%7c638380763212264062%7cunknown%7ctwfpbgzsb3d8eyjwijoimc4wljawmdailcjqijoiv2lumziilcjbtii6ik1hawwilcjxvci6mn0%3d%7c3000%7c%7c%7c&sdata=yxkh9bn0bh3m4pak8dja4mkdj1ptc6%2fyqioei05qg1m%3d&reserved=0" href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gisaid.org%2F&data=05%7C02%7C%7Cbccd5bb40f5e4a4ccee508dbfbeb3823%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C638380763212264062%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Yxkh9bN0bH3m4Pak8DJa4Mkdj1PTc6%2FYqIoei05qg1M%3D&reserved=0" target="_blank" rel="noreferrer noopener">www.gisaid.org</a>.</p> <p> </p> <p><span> </span></p>
Extra tables and fastq files for "Virome Sequencing Identifies H5N1 Avian Influenza in Wastewater from Nine Cities."
<p>Tables:</p> <p>"mutation_analysis.xlsx" = detailed notes on variant analysis of H5N1 reads.</p> <p>"TEPHI_samples_H5N1_status1.xlsx" = Table of samples with metadata and H5N1 status</p> <p>"BioSampleObjects.txt" = Table from SRA mapping BioSample IDs to library (sample) IDs</p> <p> </p> <p>H5N1_reads_thru_p1858:</p> <p>Paired-end Illumina read files (.fastq) from all samples. Includes automated H5N1 called reads from iav_serotype tool from samples that were manually validated to have H5N1 specific reads.</p>
Data complementing the Avian influenza overview June - September 2024
<p>Data complementing the Avian influenza overview June - September 2024</p> <p> </p> <p><strong>Annex A – Data on birds</strong></p> <p>The annex contains figures and tables on HPAI virus detections in birds in Europe as well as a description of the vaccination campaign implemented in France in 2023–2024.</p> <p><strong>Annex B – Characteristics of the HPAI-affected poultry establishments</strong></p> <p>The annex contains a table with the characteristics of the HPAI-affected poultry establishments by affected European country submitted to ADIS between 15 June and 20 September 2024.</p> <p><strong>Annex C – Data on virus sequences</strong></p> <p>The annex contains information on authors, originating and submitting laboratories of the sequences from GISAID's EpiFlu™ Database on which this research is based. All data submitters may be contacted directly via <a title="https://eur03.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.gisaid.org%2f&data=05%7c02%7c%7cbccd5bb40f5e4a4ccee508dbfbeb3823%7c406a174be31548bdaa0acdaddc44250b%7c1%7c0%7c638380763212264062%7cunknown%7ctwfpbgzsb3d8eyjwijoimc4wljawmdailcjqijoiv2lumziilcjbtii6ik1hawwilcjxvci6mn0%3d%7c3000%7c%7c%7c&sdata=yxkh9bn0bh3m4pak8dja4mkdj1ptc6%2fyqioei05qg1m%3d&reserved=0" href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gisaid.org%2F&data=05%7C02%7C%7Cbccd5bb40f5e4a4ccee508dbfbeb3823%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C638380763212264062%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Yxkh9bN0bH3m4Pak8DJa4Mkdj1PTc6%2FYqIoei05qg1M%3D&reserved=0" target="_blank" rel="noreferrer noopener">www.gisaid.org</a>.</p>
Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union in 2020 - high quality maps
<p>Here you can find the high quality maps published in 'Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union in 2020' by EFSA.</p>
Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union in 2020 - monthly maps
<p>Here you can find monthly maps referred in publication 'Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union in 2020' by EFSA.</p> <p>Figure legend for all figures:<br> Monthly observations and samples from wild birds on the EFSA list of target species for 2020 by NUTS3 region. The green colour scale represents the number of wild bird observations from the target species, as per data provided by the EuroBirdPortal project. The black dots represent the number of wild bird samples from target species tested within the countries' AI passive surveillance programmes. Wild bird samples reported at NUTS2 level are not shown on these maps.</p>
Dataset and R Code for Species-level Avian Influenza Phylogenetic Generalized Least Squares Regression
<p>Dataset for Species-level Avian Influenza Phylogenetic Generalized Least Squares (PGLS) Regression:<br> Variables include taxonomic information for each species, # of IAV-positive individuals, # of IAV-tested individuals, the prevalence of IAV, the proportion of diet made up of different food types, the proportion of foraging time spent in different strata (below water, water surface, ground, understory, etc), sampling-related variables (mean latitude, mean date, the proportion of hatch year individuals), migration and territoriality category, climatologic variables, mean clutch size, and mating system.</p> <p>R Code for PGLS and Avian Influenza Prevalence ContMap.</p>
Data complementing the Avian influenza overview June-September 2023
<p>Annex A – Data on wild bird species and HPAI virus detections in birds</p> <p>The annex contains tables and figures on wild bird species and HPAI virus detections in birds.</p> <p> </p> <p>Annex B – Applied prevention and control measures on avian influenza</p> <p>The annex contains an overview of specific prevention and control measures applied in Austria, Belgium, Bulgaria, Czechia, Denmark, Finland, France, Iceland, Italy, Latvia, Lithuania, Luxembourg, Netherlands, Norway, Poland, Slovakia, Spain, Sweden and Switzerland in relation to recent avian influenza outbreaks in poultry, wild birds or mammals.</p> <p> </p> <p>Annex C – Characteristics of the HPAI A(H5N1)-positive poultry establishments</p> <p>The annex contains a table with the characteristics of the HPAI A(H5N1)-positive poultry establishments by affected EU Member State from 9 June to 18 August 2023. </p> <p> </p> <p>Annex D- Data on virus sequences</p> <p>The annex contains information on authors, originating and submitting laboratories of the sequences from GISAID’s EpiFlu™ Database on which this research is based. All submitters of data may be contacted directly via <a href="https://www.gisaid.org./">www.gisaid.org.</a></p>
Vaccination of poultry against highly pathogenic avian influenza – part 1. Available vaccines and vaccination strategies. Annex A–Supplementary information on ToR 1 data
<p>Table A.1 - Available vaccines for HPAI in poultry. The table includes information on vaccine characteristics such as HA seed strain, vaccine dosage and administration route, target species, authorisation status, challenge strain, duration of immunity and source of information.</p> <p>Table A.2 - Challenge experiments. The table includes data extracted from 28 selected studies from literature on challenge experiments. The data was used to quantify VE<sub>S</sub>, VE<sub>m</sub>, VE<sub>sh </sub>and VE<sub>s,sh </sub>for each vaccine assessed within each study. For each value of VE<sub>s,sh</sub> the probability R<sub>vac</sub> < 1 was estimated to infer the probability of the vaccine to potentially stop transmission in vaccinated birds (VE<sub>T</sub>).</p> <p>Table A.3 - Transmission experiments. The table includes data extracted from 12 studies from the literature, data was used from the unvaccinated and vaccinated groups to quantify VE<sub>S</sub>, VE<sub>m</sub>, VE<sub>sh</sub> and VE<sub>s,sh</sub> for each vaccine assessed within each study; the estimated R values for the unvaccinated (R<sub>unv</sub>) and vaccinated (R<sub>vac</sub>) groups were also extracted. The R<sub>vac</sub> values were used to create a binomial variable classifying whether the vaccine could stop transmission (R < 1) or not.</p>
Data from: Utilising citizen science data to rapidly assess changing associations between wild birds and avian influenza outbreaks in poultry
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Polymerase trapping as mechanism of H5 highly pathogenic avian influenza virus genesis
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AI results complementing the Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Denmark
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2019, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Austria
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2019, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
Avian influenza virus data sets
<p>FASTA files containing AIV data sets.</p>
Data complementing the Avian influenza overview December 2021 – March 2022
<p>The Annexes contain data and information on highly pathogenic avian influenza outbreaks in poultry and detections in wild birds in Europe</p> <p>Annex A – Characteristics of the HPAI A(H5Nx)-positive poultry establishments</p> <p>Annex B – Applied prevention and control measures on avian influenza</p> <p>Annex C – Data on wild birds</p>
Excel mapping tool for 2019 avian influenza data reporting
<p>Data collection is an important task of the European Food Safety Authority (EFSA) and a fundamental component of risk assessment (Articles 22 and 23 of Regulation (EC) No 178/2002). EFSA receives a large volume of data from Member States (MSs) that is used in support of its risk assessment mission.</p> <p>Council Directive 2005/94/EC and Commission Decision 2010/367/EU lay down the guidelines for monitoring and reporting avian influenza surveillance data on poultry and wild birds by European Union (EU) MSs. EFSA has been assigned the task of collating, validating, analysing, and summarising in an annual report the results from the avian influenza surveillance programmes in poultry and wild birds. For the reporting of data, EFSA provides a Data Collection Framework that allows data providers to submit data in eXtensible Markup Language (XML) format through a web interface or a web service. Here, a data model describing the format, and the content requested when submitting data through the DCF, is provided.</p> <p>The data model supports the reporting of laboratory testing results for avian influenza in both wild birds, and poultry. The use of this reporting standard ensures that reported results are comparable between reporting countries. Data reported in this format will be used to generate epidemiological updates on the avian influenza surveillance testing carry out in Europe, and to provide scientific advice to the European Commission.</p>
Out of the blue: Detection of a unique highly pathogenic avian influenza virus of subtype H7N5 in Germany: Data sets on phylogenetic analyses
<div> <p><span>In June 2024, a highly pathogenic avian influenza virus of subtype H7N5 was detected in a single laying hen holding in Germany. Closest relatives of the eight viral genome segments were among recent low pathogenic (LP) viruses from Asia and Europe. No further detections of this unique virus or its presumed LP precursor have been made in poultry or wild birds.</span></p> </div>
Avian influenza markers
<p><span>The spreadsheets summarizing the identified AIV zoonotic markers </span></p>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Cyprus
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Iceland
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Estonia
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.