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2,992 results for “influenza”
Data complementing the Avian influenza overview March – June 2022
<p>Annex A – Characteristics of the HPAI A(H5Nx)-positive poultry establishments</p> <p>The Annex contains table with the characteristics of the HPAI A(H5Nx)-positive poultry establishments by affected EU Member State from 4 March to 1 June 2022.</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 Albania, Belgium, Bulgaria, Czechia, France, Hungary, Iceland, Italy, Moldova, Kosovo, The Netherlands, Poland, Romania, Slovakia, Spain from 1 December 2021 to 4 March 2022 in relation to HPAI outbreaks in poultry and in wild birds.</p> <p>Annex C – Data on wild birds</p> <p>The Annex contains tables and plots on HPAI notifications in wild birds in Europe.</p>
Weekly Standardized Counts of Influenza Positive Isolates in 4 Region in China Mainland
<p><strong>The data include weekly standardized counts of influenza positive isolates in 4 region in China mainland that covers 30 provinces.More details about the method of standardization and division of regions can be seen in "Characterization of influenza seasonality in China, 2010-2018: implications for seasonal influenza vaccination timing".</strong></p>
Data complementing the Avian influenza overview June – September 2022
<p>Annex A – Characteristics of the HPAI A(H5Nx)-positive poultry establishments</p> <p>The Annex contains table with the characteristics of the HPAI A(H5Nx)-positive poultry establishments by affected EU Member State from 2 June to 2 September 2022.</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 Bulgaria, Croatia, France, Hungary, Germany, Moldova, the Netherlands, Poland, Portugal, Spain from 2 June to 2 September 2022 in relation to HPAI outbreaks in poultry and in wild birds.</p> <p>Annex C – Data on wild birds</p> <p>The Annex contains tables and plots on HPAI virus notifications in wild birds in Europe.</p>
Data for: Schaub et al., Impact of Organic Compounds on the Stability of Influenza A Virus in deposited 1-µl droplets
<p><strong>Experimental data</strong></p> <p>This folder contains the experimental data to the figures shown in the main manuscript and Supporting Information.</p> <p>Figure 1: inactivation data after 0 and 60 min for 1-μl droplet experiments at various RH in PBS, SLF and nasal mucus (infectivity titer and genomic copy enumeration).</p> <p>Figure 3: inactivation data after 0 and 60 min for 1-μl droplet experiments at 60% RH in SLF derivatives (infectivity titer and genomic copy enumeration).</p> <p>Figure 4: inactivation data after 0 and 60 min for 1-μl droplet experiments at 60% RH in various albumin:NaCl mass ratios (infectivity titer and genomic copy enumeration).</p> <p>Figure 5: inactivation data after 0 and 60 min for 1-μl droplet experiments at 60% RH with various proteins (infectivity titer and genomic copy enumeration).</p> <p>Figure S1: Control in bulk for data from Figure 1 (infectivity titer).</p> <p>Figure S2: Recovery fraction for data from Figure 1 (GC/GC<sub>0</sub>). </p> <p> </p> <p><strong>Abbrevations used:</strong></p> <p>GC = Genomic Copies</p> <p>LoQ = Limit of Quantification</p> <p>PFU = Plaque Forming Unit</p> <p>ul = microliter</p>
Raman spectra collected from influenza A strains at 785 and 532 nm
<p>This composite contains Raman spectra of a strain of Influenza A subtype H1N1 (A/nebraska/14/2019) and subtype H3N2 (A/hawaii/47/2014) collected at an incident wavelenght of 785 nm and 532 nm. The spectra were collected at 100x magnification for 5 seconds per spectrum.</p>
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>
Data from: Sequence-based detection of emerging antigenically novel influenza A viruses
<p>The detection of evolutionary transitions in influenza A (H3N2) viruses' antigenicity is a major obstacle to effective vaccine design and development. In this study, we describe NIAViD, an unsupervised machine learning tool, adept at identifying these transitions, using HA1 sequence and associated physicochemical properties. NIAViD, performed with 88.9% (95% CI, 56.5%–98.0%) and 72.7% (95% CI,43.4%– 90.3%) sensitivity in training and validation respectively, outperforming the uncalibrated null model – 33.3% (95% CI,12.1%–64.6%) and does not require the need for potentially biased, time-consuming and costly laboratory assays. The pivotal role of Boman's index, indicative of the virus's cell surface binding potential, is underscored, enhancing the precision of detecting antigenic transitions. NIAViD's efficacy is not only in identifying influenza isolates that belong to novel antigenic clusters, but also in pinpointing potential sites driving significant antigenic changes, without the reliance on explicit modeling of hemagglutinin inhibition titers. Our approach holds immense promise to augment existing surveillance networks, offering timely insights for the development of updated, effective influenza vaccines. Consequently, NIAViD, in conjunction with other resources, could be used to support surveillance efforts and inform the development of updated influenza vaccines.</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>
Emergenet models for HA/NA sequences of Influenza A strains
<p>Models emergent dependencies between mutational variations of key viral proteins in Influenza A.</p> <p>Models can be read using the emergenet package available on pypi. (https://pypi.org/project/emergenet/)</p>
Datasets and Scripts associated with "Transposable elements are associated with the variable response to influenza infection"
<p>Scripts and datasets included here were used for the main analyses in the article "Transposable elements are associated with the variable response to influenza infection" (BioRxiv doi: <a href="https://doi.org/10.1101/2022.05.10.491101">https://doi.org/10.1101/2022.05.10.491101</a>).</p> <p>Study Summary:</p> <p>Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Given that the regulation of transposable elements (TEs) contributes to the activation of innate immunity, we wanted to explore their potential role in this variability. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using ATAC-seq we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators (e.g., BATFs, FOSs/JUNs, IRFs, STATs, NFkBs, NFYs, and RELs) in stably enriched TE families and with other factors in variable families, including KRAB-ZNFs. We also observed a strong association between basal TE transcripts and viral load post infection and showed that TEs, and host factors regulating TEs, were predictive of the response. Our findings shed light on the variable transcriptional and epigenetic response to infection and the role TEs and KRAB-ZNFs may play in inter-individual variation in immunity.</p> <p> </p> <p> </p> <p> </p> <p> </p>
All cause mortality and morbidity from Influenza in the City and the Canton of Zurich, 1910-1970
<p><strong>Contact:</strong> PD Dr. Kaspar Staub <a href="mailto:kaspar.staub@iem.uzh.ch">kaspar.staub@iem.uzh.ch</a></p> <p>For the <a href="http://leaddata.ch">LEAD Hub</a> we digitized and analyzed the following historical demographic and epidemiological data for the city and the canton of Zurich the first time: Since the end of the 19th century, the Federal Health Office (Eidgenössisches Gesundheitsamt) published a <a href="https://swisscovery.slsp.ch/permalink/41SLSP_NETWORK/gp9v4j/alma991049771079705501">weekly bulletin</a> on vital statistics, newly reported cases of notifiable infectious diseases, and hospitalisations. For the period January 1910 to December 1970, we have digitized and transcribed the following weekly series: </p> <ol> <li>Weekly deaths for residents and non-residents of the city of Zurich. The quality of these historical vital statistics is assessed to be very good in the literature, incompleteness and migration are no longer a problem as compared to earlier years. However, age-, sex- and cause-specific death numbers were not available on the weekly level. </li> <li>Weekly newly reported cases of influenza-like-illness for the canton and the city of Zurich. This series begins with the introduction of the reporting obligation for influenza in the canton of Zürich in mid-July 1918. As these figures do not include mild cases not treated by a doctor and misdiagnoses, they are probably underestimates, but can still track pandemic and seasonal waves. The reporting system and obligation did not change in the observed time period.</li> <li>Weekly new hospitalisation due to influenza in the canton of Zurich. This series ends in 1938. </li> </ol> <p>The original data format in the weekly bulletins are printed, aggregated tables that have been converted into PDFs using a professional book scanner. Transcription of the data was performed by student assistants using a software and running extended quality-controls. The original tables were in German and French, the digitised data set was annotated in English.</p> <p>The digitized data are organized as a spreadsheet and stored in csv format. The data are organized as rows (representing reporting weeks) and columns (see variable list below). For a few weeks, information in the original sources was missing (indicated by 1 in the “interpolated” variable). In these cases, the missing values were interpolated by averaging the numbers of the week before and the week afterwards. </p> <p><strong>Codebook:</strong></p> <p><em>Worksheet "Data"</em></p> <ul> <li>StartReportingPeriod = Start date of the reporting week (dd.mm.yyyy)</li> <li>EndReportingPeriod = End date of reporting week (dd.mm.yyyy)</li> <li>Interpolated: 1=value for this week has been interpolated; 0=not interpolated</li> <li>CityDeathsTotal = Total absolute number of deaths (all-causes) in the City of Zurich (residents and non-residents)</li> <li>CityDeathsResidents = Absolute number of deaths (all-causes) in the City of Zurich for residents</li> <li>CityDeathsNonresidents = Absolute number of deaths (all-causes) in the City of Zurich for non-residents</li> <li>CantonCases = Absolute number of reported new influenza-like-illness cases by physicians in the Canton of Zurich (including the City)</li> <li>CityCases = Absolute number of reported new influenza-like-illness cases by physicians in the City of Zurich</li> <li>CantonHospitalisationsFluInfections = Absolute number of new hospitalisations due to influenza-like-illness in the Canton of Zurich (including the City)</li> </ul> <p><em>Worksheet "Population"</em></p> <ul> <li>Yearly population numbers for the City and the Canton of Zurich (<a href="https://hsso.ch">source</a>)</li> </ul>
Mortality and morbidity from Influenza in Swiss cantons, 1953-1958
<p><strong>Contact: </strong>PD Dr. Kaspar Staub <a href="mailto:kaspar.staub@iem.uzh.ch">kaspar.staub@iem.uzh.ch</a></p> <p><strong>Description:</strong></p> <p>For the <a href="http://leaddata.ch"><strong>LEAD Hub</strong></a>, we digitized and analyzed the following historical demographic and epidemiological data for all Swiss cantons the first time: Since the end of the 19th century, the Federal Health Office (Eidgenössisches Gesundheitsamt) published a <a href="https://swisscovery.slsp.ch/permalink/41SLSP_NETWORK/gp9v4j/alma991049771079705501">weekly bulletin</a>. For the period January 1953 to December 1958, we have digitized and transcribed the following monthly series: Monthly deaths from influenza and all causes for all Swiss cantons; Weekly reported new cases of Influenza-like-Illness for all cantons; Yearly population numbers for all cantons (<a href="https://hsso.ch">source</a>). There was no change in the obligation to report new influenza cases during the observation period. </p> <p><strong>Codebook:</strong></p> <p><em>Worksheet «MonthlyDeaths”</em></p> <ul> <li>Month = Reporting month</li> <li>Year = Reporting year</li> <li>Parameter = Variable description (here “Deaths influenza” and “Deaths total”)</li> <li>ZH to CH = <a href="https://en.wikipedia.org/wiki/Cantons_of_Switzerland">Official abbreviations of the Swiss cantons</a></li> </ul> <p><em>Worksheet “WeeklyInfluenzaCases”</em></p> <ul> <li>Start week = Start date of the reporting week</li> <li>End week = End date of the reporting week</li> <li>Parameter: Variable description (here “Newly reported Influenza cases”)</li> <li>ZH to CH = <a href="https://en.wikipedia.org/wiki/Cantons_of_Switzerland">Official abbreviations of the Swiss cantons</a></li> </ul> <p><em>Worksheet “Population”</em></p> <ul> <li>ZH to CH = <a href="https://en.wikipedia.org/wiki/Cantons_of_Switzerland">Official abbreviations of the Swiss cantons</a></li> </ul>
Prospects for a sequence-based taxonomy of influenza A virus subtypes
<p>This dataset comprises the multiple sequence alignments (*.fasta) and maximum likelihood phylogenies (Newick tree strings, *.nwk) for all available protein sequences corresponding to the eight genome segments of influenza A virus from the NCBI Genbank database. </p> <p>Each sequence is labelled with the Genbank accession number (e.g., "CY103884"), WHO strain identifier ("A/little yellow-shouldered bat/Guatemala/164/2009"), subtype label ("H17N10"), host species ("Sturnira lilium; gender M"), sampling location ("Guatemala: El Jobo"), and sample collection date ("May-2009"). These fields are separated by underscore characters.</p> <p>These data are provided under a Creative Commons license in support of a manuscript in progress, "Prospects for a sequence-based taxonomy of influenza A virus subtypes".</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>
A Multicenter Study to Assess Response to Influenza Vaccine in Multiple Sclerosis Participants Treated With Ofatumumab
ClinicalTrials.gov study NCT04667117. IPD Sharing: YES. Countries: 1. Publications: 1.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.