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684 results for “Influenza A virus”
Iceland as stepping stone for intercontinental spread of highly pathogenic avian influenza H5N1 virus between Europe and North America: data set on phylogeographic analysis
<p>Highly pathogenic avian influenza viruses (HPAIV) subtype H5 clade 2.3.4.4b have widely spread within the northern hemisphere since 2020 and threaten wild bird populations as well as poultry production. For the very first time, HPAIV were detected in wild birds and, subsequently, in poultry holdings in Iceland.</p> <p>Here, we present phylogeographic evidence that Iceland has been used as a stepping stone for HPAIV translocation from Northern Europe to North America in 2021 and describe two independent incursions of HPAI H5N1 clade 2.3.4.4b viruses of two different genotypes to Iceland in 2021 and 2022.</p>
Diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice
<p>Data and analysis files for diallel analysis of weight loss in 8-12 week old male and female mice (n=1,043), mock treated or infected with influenza A virus (H1N1, PR8) across 4 days post-infection, as well as founder haplotype effect analysis at Mx1 for pre-CC and CC-RIX.</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>
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>
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 from: Sequence-based detection of emerging antigenically novel influenza A viruses
Open the record for dataset details and reuse information.
Polymerase trapping as mechanism of H5 highly pathogenic avian influenza virus genesis
Open the record for dataset details and reuse information.
1918 influenza A virus alignments
<p>This dataset includes nucleotide alignments for 8 viral segments from five 1918 influenza A virus strains.</p>
Avian influenza virus data sets
<p>FASTA files containing AIV data sets.</p>
Supplemental Material: High serological barriers may contribute to restricted Influenza-A-virus transmission between pigs and humans
<p>Human-to-swine (reverse zoonotic) transmission of seasonal and pandemic human influenza A viruses (IAV) to pigs primarily replenishes the vast reservoir of genetically and antigenically heterogeneous swine (sw) IAV maintained in domestic pigs worldwide. Sporadic but regularly observed cases of pig-to-human (zoonotic) infections with swIAV tend to be discovered by chance, with children being affected disproportionately often.</p> <p>Here, a total of 3070 porcine and 333 human nasal swab samples from 135 swine farms in Germany were investigated for IAV by real time RT-PCR and full genome sequencing. In addition, swIAV sequences generated in the frame of this study were analyzed to determine potential mutations for human MxA and BTN3A3 escape. </p> <div> <p><strong>01_Table S1: </strong>Summary of information of swine holdings and RT-qPCR results. 1 indicates applicable; 0 indicates not applicable; n.d. indicates not determined.</p> <p><strong>02_Table S2</strong>: Summary of information about human samples and. 1 indicates applicable; 0 indicates not applicable; n.d. indicates not determined.</p> <p><strong>03_Table S3: A.</strong> Comparison of relevant mutations in the genome of MWP/21, swine-MWP/21, and NRW/22 generated by Flusurver (http://flusurver.bii.a-star.edu.sg). 1 indicates the presence of mutation(s), 0 indicates the absence of those mutation(s).<strong> B.</strong> Visualization of the AA differences of affected segments of the zoonotic case MWP/21 and the corresponding sequence (sw-MWP/21) generated from pigs of the related herd. </p> <p><strong>04_Table S4: </strong>Accession number (EPI_ISL) of sequences analyzed in the frame of this study. All sequences are available on GISAID EpiFLU.</p> <p><strong>05_Table S5: </strong>Amino acids on positions in the nucleoprotein (NP) sequence associated with MxA resistance and BTN3A3 resistance of selected swIAV NP sequences. "av) indicates genome segments phylogenetically associated with the avian-derived H1 (1C), "pdm" indicates those of the human pandemic A/H1N1 2009 lineage (1A). </p> <p><strong>06_Figure S1: </strong>Phylogenic tree of swIAV H1 HA gene of the clades 1A, 1B and 1C annotated by global H1-lineage nomenclature by Anderson et al. (2016). Swine derived swIAV sequences generated in the frame of this study are colored in red, zoonotic cases MWP/21 and NRW/22 are colored in green. The reverse-zoonotic case is highlighted in violet with its closest related human sequence colored in green.<strong> </strong></p> <p><strong>07_Material and Methods:</strong> Description of material used and specification of applied methods in the frame of this study.</p> <p><strong>08_Questinonaire human participants:</strong> Questionaire used in the frame of this study.</p> <p><strong>09_Questinonaire swine farms:</strong> Questionaire used in the frame of this study.</p> </div> <p> </p>
Global dissemination of Influenza A virus is driven by wild bird migration through arctic and subarctic zones
<p><span>Influenza A viruses (IAV) circulate endemically among many wild aquatic bird populations that seasonally migrate between wintering grounds in southern latitudes to breeding ranges along the perimeter of the circumpolar arctic. </span>Arctic and subarctic zones are hypothesized to serve as ecologic drivers of the intercontinental movement and reassortment of IAVs <span>due to high densities of disparate populations of long distance migratory and native bird species present during breeding season</span>s. <span>Iceland</span> is a staging ground that connects <span>the East Atlantic and </span><span>North Atlantic</span><span> American flyways, providing a unique study system for characterizing viral flow between eastern and western hemispheres. Using Bayesian phylodynamic analyses, we sought to evaluate the </span><span>viral connectivity of Iceland to proximal regions and how inter-species transmission and reassortment dynamics in this region influence the geographic spread of low and highly pathogenic IAVs. </span><span>Findings demonstrate that IAV movement in the arctic and subarctic follows seabird migration around the perimeter of the circumpolar north, favoring short-distance flights between proximal regions rather than long distance flights over the polar interior. Iceland connects virus movement between mainland Europe and North America, particularly due to the westward migration of wild birds from mainland Europe to Northeastern Canada and Greenland. Though virus diffusion rates were similar among avian taxonomic groups in Iceland, g</span>ulls act as recipients and not sources of IAVs to other avian hosts prior to onward migration. <span>These data identify patterns of virus movement in northern latitudes and inform future surveillance strategies related to seasonal and emergent IAVs with pandemic potential</span>.</p>
Influenza A virus liquid condensates can undergo pharmacological hardening
<p>Data generated and codes used for the publication titled "Influenza A virus liquid condensates can undergo pharmacological hardening"</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>
Inhibition of cellular RNA methyltransferase abrogates influenza virus capping and replication
<p>Raw data of the paper titled "Inhibition of cellular RNA methyltransferase abrogates influenza virus capping and replication".</p>
Data from: Postnatal administration of S-adenosylmethionine restores developmental AHR activation-induced deficits in CD8+ T cell function during influenza A virus infection
<p>Abstract Developmental exposures can influence life-long health; yet, counteracting negative consequences is challenging due to poor understanding of cellular mechanisms. The aryl hydrocarbon receptor (AHR) binds many small molecules, including numerous pollutants. Developmental exposure to the signature environmental AHR ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) significantly dampens adaptive immune responses to influenza A virus (IAV) in adult offspring. CD8+ cytotoxic T lymphocytes (CTL) are crucial for successful infection resolution, which depends on the number generated and the complexity of their functionality. Prior studies showed developmental AHR activation significantly reduced the number of virus-specific CD8+ T cells, but impact on their functions is less clear. Other studies showed developmental exposure was associated with differences in DNA methylation in CD8+ T cells. Yet, empirical evidence that differences in DNA methylation are causally related to altered CD8+ T cell function is lacking. The two objectives were to ascertain whether developmental AHR activation affects CTL function, and whether differences in methylation contribute to reduced CD8+ T cell responses to infection. Developmental AHR triggering significantly reduced CTL polyfunctionality, and modified the transcriptional program of CD8+ T cells. S-adenosylmethionine (SAM), which increases DNA methylation, but not Zebularine, which diminishes DNA methylation, restored polyfunctionality and boosted the number of virus-specific CD8+ T cells. These findings suggest that diminished methylation, initiated by developmental exposure to an AHR-binding chemical, contributes to durable changes in antiviral CD8+ CTL functions later in life. Thus, deleterious consequence of development exposure to environmental chemicals are not permanently fixed, opening the door for interventional strategies to improve health.</p>
Primer sequences for H3N2 canine influenza virus full-length amplification, polymerase activity assay, and rescue
<p><span>Influenza A viruses in animal reservoirs repeatedly cross species barriers to infect humans. Once an animal-borne virus with novel antigenicity acquired the efficient human-to-human transmissibility, it will become epidemic in the population. Dogs are the closest animal companions to humans, and canine respiratory tract expresses both SAα2,3-(avian type) and α2,6-Gal (human type) receptors. However, the role of dogs in the ecology of influenza viruses is unclear. H3N2 avian influenza viruses were transmitted to dogs around 2006 and have formed stable lineages. The long-term epidemic of avian-origin H3N2 virus in canines offers the best models to investigate the effect of dogs on the evolution of influenza viruses. Here, we carried out a systematic and comparative identification of the biological characteristics of H3N2 canine influenza viruses (CIVs) isolated in worldwide</span> <span>over 10 years. We found that during the adaptation of H3N2 CIVs to dogs, H3N2 CIVs became to recognize the human-like SAα2,6-Gal receptor, gradually increased HA acid stability and replication ability in human airway epithelial cells, and acquired a 100% transmission rate via respiratory droplet in ferret model, which were essential hallmarks of being adapted to humans. We also identified that the frequency of substitutions related to human adaptation has gradually increased in H3N2 CIVs and determined four cumulative molecular changes responsible for the increased airborne transmission ability in ferrets. Our results suggested that canines may serve as an intermediate for the adaptation of avian influenza virus to humans. Continuous surveillance coordinated with risk assessment for CIVs is necessary.</span></p>
Supporting data and code for: Phylogenetic identification of influenza virus candidates for seasonal vaccines
<p>The seasonal influenza (flu) vaccine is designed to protect against those influenza viruses predicted to circulate during the upcoming flu season, but identifying which viruses are likely to circulate is challenging. We use features from phylogenetic trees reconstructed from hemagglutinin (HA) and neuraminidase (NA) sequences, together with a support vector machine, to predict future circulation. We obtain accuracies of 0.75–0.89 (Area under the curve AUC 0.83–0.91) over 2016–2020. We explore ways to select potential candidates for a seasonal vaccine and find that the machine learning model has a moderate ability to select strains that are close to future populations. However, consensus sequences among the most recent three years also do well at this task. We identify similar candidate strains to those proposed by the World Health Organization, suggesting that this approach can help inform vaccine strain selection.</p>
ATG9A regulates dissociation of recycling endosomes from microtubules leading to formation of influenza A virus liquid condensates - MAIN FIGURES
<p>Metadata for the manuscript entitled "ATG9A regulates dissociation of recycling endosomes from microtubules leading to formation of influenza A virus liquid inclusions" - MAIN FIGURES</p>
Limited outbreak of highly pathogenic influenza A(H5N1) virus in a Herring Gull colony, Canada, 2022
<p class="MsoNormal">In summer 2022, highly pathogenic influenza A(H5N1) virus reached the Herring Gull (<em>Larus argentatus</em>) breeding colony on Kent Island, New Brunswick, Canada. Real-time monitoring revealed a self-limiting outbreak with low mortality. Proactive seabird surveillance is crucial for monitoring such limited outbreaks, protecting vulnerable seabirds, and tracing potential zoonotic transmission routes.</p>
Safety Study of CSL Limited's Influenza Virus Vaccine in the Paediatric Population Aged >= 6 Months to < 18 Years
ClinicalTrials.gov study NCT00825162. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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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.