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355 results for “RNA viruses”
VirHunter: a deep learning-based method for detection of novel RNA viruses in plant sequencing data
<p>This storage contains 2 archives: toy datasets to test the training of the VirHunter and weights of the fully trained VirHunter models for 3 host species (peach, grapevine, sugar beet) and for fragment sizes 500 and 1000. .</p> <p>The toy dataset consists of 3 archived files: 'viruses.fasta', 'host.fasta', 'bacteria.fasta'.</p> <p>'viruses.fasta' contains 10000 randomly selected plant viruses from the virus dataset described in the paper.</p> <p>'host.fasta' consists of peach chromosome 2.</p> <p>'bacteria.fasta' consists of 10 bacterial genomes selected randomly: GCF_000284415, GCF_000590555, GCF_001548055, GCF_002795265, GCF_003330825, GCF_003957805, GCF_005845345, GCF_009176625, GCF_010748935, GCF_014681765</p> <p> </p>
Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of (RNA) viruses
<p>Fasta file (blackfly_viral_genomes.fasta) with identified virus sequences in Cameroonian blackflies and a corresponding table with their taxonomy when possible (taxonomy_data.tsv). Viruses were identified with geNomad v1.7.0 and Diamond blastx v2.0.11 with the NCBI nr database (accessed 23-03-2023).</p> <p>We also included a fata file with all assembled sequences across all blackfly samples (blackfly.all.fasta)</p>
CRISPR-based engineering of RNA viruses
<p>CRISPR RNA-guided endonucleases have enabled precise editing of DNA. However, options for editing RNA remain limited. Here, we combine sequence-specific RNA cleavage by CRISPR ribonucleases with programmable RNA repair to make precise deletions and insertions in RNA. This work establishes a new recombinant RNA technology with immediate applications for the facile engineering of RNA viruses.</p> <p> </p> <p>This dataset contains code for analyzing sequencing data and generating figures in the manuscript.</p>
Host developmental stages shape the evolution of a plant RNA virus
<p>Datasets used in the generation of figures 1 and 2 of:</p> <p>Melero, I., González, R., Elena, S.F. 2022. Host developmental stages shape the evolution of a plant RNA Virus. Philos. Trans. R. Soc. B doi: 10.1098/rtsb.2022.0005</p>
Raw data to: "Persistent RNA virus infection is short-lived at the single cell level but leaves transcriptomic footprints"
<p>Raw data underlying the publication by Reuther and Martin et al. entitled "Persistent RNA virus infection is short-lived at the single cell level but leaves transcriptomic footprints"</p>
RNA sequences for Aedes species, Dengue, and Chikungunya viruses
<p>There are arthropod-borne disease outbreaks as a result of pathogen influx including arboviruses which are transmitted by strains of <em>Aedes</em> species that occur periodically in varying spots on the globe. The aim of this study was to determine phylogenetic relationship of <em>Aedes</em> mosquitoes, Dengue, and Chikungunya viruses along the Coastline of Kenya based on sequences of:</p> <ol> <li>mitochondria nicotinamide adenine dehydrogenase sub unit 4 gene for Aedes species.</li> <li>non-structural protein 5 gene for Dengue virus</li> <li>non-structural protein 1 gene for Chikungunya virus</li> </ol>
Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus
<p><strong>Rotaviruses transcribe eleven distinct protein-coding RNAs that must be stoichiometrically co-packaged prior to their replication to make an infectious virion. During infection, </strong><strong>rotavirus transcripts accumulate in cytoplasmic ribonucleoprotein (RNP) condensates, termed viroplasms. </strong><strong>Understanding the mechanisms of viroplasm assembly and RNA enrichment within is crucial to gaining greater insight into their function and stoichiometric assortment of individual transcripts.</strong> <strong>We analysed the subcellular distribution of individual RV transcripts and viroplasm transcriptome by combining multiplexed DNA-barcoded single-molecule RNA FISH of infected cells. Using DNA-PAINT microscopy, we provide evidence of the early onset of viral transcript oligomerisation that occurs prior to the formation of viroplasms. We demonstrate that viral sequences lacking the conserved terminal regions fail to undergo enrichment in rotavirus RNP condensates. We show that individual viral transcripts exhibit variable propensities to partition into viroplasms, irrespective of their absolute numbers in cells, suggesting a selective RNA enrichment mechanism distinct from other known cellular RNP granules. </strong><strong>We suggest that rotavirus replication factories represent unique RNP condensates enriched in eleven types of cognate transcripts that may facilitate the assembly of a multi-segmented RNA genome.</strong></p>
Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches
<p><strong>Supplementary Data</strong></p> <p><strong>Tables</strong></p> <p><strong>Table S1:</strong> Virus characteristics including abbreviation, family, order, tax id, sequence length threshold (for nearly complete genomes), vaccination status, mode of transmission, circulation (human or human/zoonotic), available treatment, and disease progression (acute or chronic).</p> <p><strong>Table S2:</strong> Sequence IDs of outgroup constituents.</p> <p><strong>Table S3:</strong> GISAID acknowledgements for the SARS-CoV-2 sequences used in this study.</p> <p><strong>Table S4:</strong> Summary of manual sequence curation indicating lab- or vaccine-related keywords used to prune sequences.</p> <p><strong>Table S5:</strong> Sequence IDs for EVA and H3N2 e10, e100, d10, and d100 subtrees.</p> <p><strong>Table S6:</strong> Sequence IDs for ML and GL lineages.</p> <p><strong>Table S7:</strong> Sequence IDs for the H3N2 “new” and “old” subtrees.</p> <p><strong>Table S8:</strong> Mutation rates (in units of nucleotide substitutions per site per year) and estimated dates for the last common ancestor of all tree/subtrees. Negative dates represent years prior to 0 CE.</p> <p><strong>Table S9:</strong> Mean dN/dS values.</p> <p><strong>Table S10:</strong> Yearly viral cases and generation time estimations (with references).</p> <p><strong>Table S11:</strong> Metadata including the sequence ID, host, date of isolation, location of isolation, and subtype.</p> <p><strong>Table S12:</strong> Overview of key parameters including number of GLs N, Ne, and MRCA for each virus species as well as the mean over all species.</p> <p><strong>Directories</strong></p> <p><strong>Alignments</strong> ORFeome alignments (excluding stop codons) with the exception of SARS-CoV-2.</p> <p><strong>Correlated Subtrees</strong> Subtrees representing all correlated-clades (genealogical lineages; GL) in Newick format.</p> <p><strong>Diversity TMRCA and Skyline Plots</strong> .png files.</p> <p><strong>e/d/n/o Subtrees</strong> EVA and H3N2 subtrees, evenly and diversely sampled as well as “early” and “late” subtrees for H3N2.</p> <p><strong>Genealogical Trees</strong> Including global topologies (.main), subtrees, and grafted trees (.grafted).</p> <p><strong>Maximally Diverse Subtrees:</strong> Genealogical trees sampled to contain the same number of leaves as each respective tree in the Simulated Trees directory.</p> <p><strong>ORF References</strong> The first and last nucleotide of each ORF in the reference sequence.</p> <p><strong>Redundancy Tables</strong> List of all redundant isolates and the corresponding representative in the ORFeome-unique alignment.</p> <p><strong>Reference Sequences</strong> Genbank page for all reference sequences.</p> <p><strong>Rooted Trees</strong> Global topologies for each virus.</p> <p><strong>Simulated Trees:</strong> Neutral models, based on Yule-Harding, for each virus.<br> Ultrametric Trees For each global topology.</p> <p><strong>Ultrametric Trees </strong>For each global topology.</p>
Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome
<div class="page"> <div class="layoutArea"> <div class="column"> <p>Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are relatively understudied outside disease settings. Here, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogues and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of new phyla<span> </span><em>"Taraviricota"</em><span>, </span>a missing link in early RNA virus evolution, and<span> </span><em>"Arctiviricota"</em><span> </span>are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.</p> </div> </div> </div>
An aphid symbiont confers protection against a specialized RNA virus, another increases vulnerability to the same pathogen
<p>Insects often harbor heritable symbionts that provide defense against specialized natural enemies, yet little is known about symbiont protection when hosts face simultaneous threats. In pea aphids (Acyrthosiphon pisum), the facultative endosymbiont Hamiltonella defensa confers protection against the parasitoid, Aphidius ervi, and Regiella insecticola protects against aphid-specific fungal pathogens, including Pandora neoaphidis. Here we investigated whether these two common aphid symbionts protect against a specialized virus A. pisum virus (APV), and whether their anti-fungal and anti-parasitoid services are impacted by APV infection. We found that APV imposed large fitness costs on symbiont-free aphids and these costs were elevated in aphids also housing H. defensa. In contrast, APV titers were significantly reduced and costs to APV infection were largely eliminated in aphids with R. insecticola. To our knowledge, R. insecticola is the first aphid symbiont shown to protect against a viral pathogen, and only the second arthropod symbiont reported to do so. In contrast, APV infection did not impact the protective services of either R. insecticola or H. defensa. To better understand APV biology, we produced five genomes and examined transmission routes. We found that moderate rates of vertical transmission, combined with horizontal transfer through food plants, were the major route of APV spread, although lateral transfer by parasitoids also occurred. Transmission was unaffected by facultative symbionts. In summary, the presence and species identity of facultative symbionts resulted in highly divergent outcomes for aphids infected with APV, while not impacting defensive services that target other enemies. These findings add to the diverse phenotypes conferred by aphid symbionts, and to the growing body of work highlighting extensive variation in symbiont-mediated interactions.</p>
A longitudinal study of DNA and RNA viruses plasma detection in allogeneic hematopoietic stem cell transplant recipients
<p><span><strong>Background:</strong> </span><span>Viral infections are among the most common complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT) and can be associated with transient or sustained viremia. Besides viruses that are common causes of infection, metagenomics revealed the presence of several novel viruses and variants that are overlooked in clinical routine and represent potential sources of unrecognized systemic infections</span><span>. Our aim was to describe the prevalence and the dynamics of 17 DNA and 3 RNA viral infections using (r(RT-)PCR) assays on plasma samples of adult allo-HSCT recipients over a one-year period after HSCT.</span></p> <p><strong><span>Methods:</span></strong><span> 109 adult patients that received a first allo-HSCT from 1<sup>st</sup> March 2017 to 31<sup>st</sup> January 2019 we included in this</span> <span>longitudinal observational monocentric cohort study</span><span>.</span> <span>17 DNA and 3 RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays performed on plasma samples </span><span>collected at five time-points (day 0 and 30 days, 3 months, 6 months and one year after HSCT). </span></p> <p><strong><span>Results: </span></strong><span>TTV was the most prevalent with an increasing prevalence to 96% of patients at 3 months. HPgV-1 prevalence ranged from 26 to 36% of patients. TTV and HPgV-1 plasma viral load peaked at month 3 (TTV: median 3.29E5 copies/ml [range, 3.37E2 to 4.06E9 copies/ml]; HPgV-1: median 1.18E6 copies/ml [range, 2.61E3 to 4.49E7 copies/ml]). Among <em>Polyomaviridae</em>, BKPyV, JCPyV, MCPyV, HPyV6 and 7 were detected in ≥10% of patients at ≥1 time-point. HPyV6 and HPyV7 prevalence reached 27% and 12% of patients at month 3. Among those, 41% and 63% had quantifiable viral loads, with median viral loads above 1E3copies/ml and results may suggest HPyV6 sustained viremia. Co-detections were frequent, in particular at 3 months with ≥2 viruses detected in 72% of patients. </span></p> <p><strong><span>Conclusion: </span></strong><span>Our study confirms that TTV and HPgV-1 infections are highly prevalent and that infection may be sustained up to one year after allo-HSCT. Our systematic and large strategy of screening also revealed diverse and numerous co-detections, and that several novel <em>Polyomaviridae</em> (MCPyV, HPyV6/7) that are overlooked in clinical routine are as or more frequently detected compared to classical culprits. Our results underscores the need for further studies investigating the clinical impact of classical culprits together with other viruses in particular novel <em>Polyomaviridae</em> and HPgV-1. </span></p>
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>
The Aedes aegypti RNA interference response against Zika virus in the context of co-infection with dengue and chikungunya viruses
<p>This is the corresponding data of the Publication in Plos Neglected tropical diseases.</p> <p>Zika virus (ZIKV) is a mosquito-borne human-pathogenic arbovirus of the <em>Flaviviridae</em> family, genus <em>Flavivirus</em>. Other arboviruses, including dengue (DENV) or chikungunya (CHIKV) virus, can occur in the same regions as ZIKV and are also transmitted by <em>Aedes aegypti</em>. Notably, it has been shown that these viruses can co-infect this mosquito, andco-transmission occurs. Such processes may add to the serious public health issues already linked to those pathogens. Arbovirus infections in mosquitoes are controlled through an immune response called RNA interference (RNAi). It is however unknown whether immune responses changs when a mosquito is exposed to a co-infection of ZIKV with either DENV or CHIKV. In this study, we provide evidence that ZIKV co-infections with CHIKV or DENV are similarly well controlled by RNAi as single infections. These findings give new insights into the dynamics of arboviral co-infections in mosquito vectors that increase our understanding of co-infection scenarios during arbovirus outbreaks.</p>
A longitudinal study of DNA and RNA viruses plasma detection in allogeneic hematopoietic stem cell transplant recipients
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G-quadruplex-forming small RNA inhibits coronavirus and influenza A virus replication
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Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
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An aphid symbiont confers protection against a specialized RNA virus, another increases vulnerability to the same pathogen
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RNA sequences for Aedes species, Dengue, and Chikungunya viruses
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Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment
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Data from: Distinct spread of DNA and RNA viruses among mammals amid prominent role of domestic species
<p><b>Aim:</b> Emerging infectious diseases arising from pathogen spillover from mammals to humans comprise a substantial health threat. Tracing virus origin and predicting the most likely host species for future spillover events are major objectives in One Health disciplines.</p> <p>We assessed patterns of virus sharing among a large diversity of mammals, including humans and domestic species.</p> <p><b>Location:</b> Global.</p> <p><b>Time period:</b> Current.</p> <p><b>Major taxa studied:</b> Mammals and associated viruses.</p> <p><b>Methods:</b> We used network centrality analysis and trait-based Bayesian hierarchical models to explore patterns of virus sharing among mammals. We analysed a global database that compiled the associations between 1,785 virus species and 725 mammalian host species as sourced from automatic screening of meta-data accompanying published nucleotide sequences between 1950 – 2019.</p> <p><b>Results:</b> We show that based on current evidence, domesticated mammals hold the most central positions in networks of known mammal-virus associations. Among entire host-virus networks, Carnivora and Chiroptera hold central positions for mainly sharing RNA viruses, while Ungulates hold central positions for sharing both RNA and DNA viruses with other host species. We revealed strong evidence that DNA viruses were phylogenetically more host specific than RNA viruses. RNA viruses exhibited low functional host specificity despite an overall tendency to infect phylogenetically related species, signifying high potential to shift across hosts with different ecological niches. The frequencies of sharing viruses among hosts and the proportion of zoonotic viruses in hosts were larger for RNA than DNA viruses.</p> <p><b>Main conclusions:</b> Acknowledging the role of domestic species in addition to host and virus traits in patterns of virus sharing is necessary to improve our understanding of virus spread and spillover in times of global change. Understanding multi-host virus sharing pathways adds focus to curtail disease spread.</p>
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.