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90 results for “virus detection”
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>
Evaluation of two 4th generation point-of-care assays for the detection of Human Immunodeficiency Virus infection.
<p>Background. Fourth generation assays detect simultaneously antibodies for HIV and the p24 antigen, identifying HIV infection earlier than previous generation tests. Previous studies have shown that the Alere Determine HIV-1/2 Combo has lower than anticipated performance in detecting antibodies for HIV and the p24 antigen. Furthermore, there are currently very few studies evaluating the performance of Standard Diagnostics BIOLINE HIV Ag/Ab Combo.</p> <p>Objective: To evaluate the performance of the Alere Determine HIV-1/2 Combo and the Standard Diagnostics BIOLINE HIV Ag/Ab Combo in a panel of frozen serum samples.</p> <p>Study Design: The testing panel included 133 previously frozen serum specimens from the UCLA Clinical Microbiology & Immunoserology laboratory. Reference testing included testing for HIV antibodies by a 3<sup>rd</sup> generation enzyme immunoassay followed by HIV RNA detection. Antibody negative and RNA positive sera were also tested by a laboratory 4<sup>th</sup> generation HIV Ab/Ag enzyme immunoassay.</p> <p>Results: Reference testing yielded 97 positives for HIV infection and 36 negative samples. Sensitivity of the Alere test was 95% (88-98%), while the SD Bioline sensitivity was 91% (83-96%). Both assays showed 100% (90-100%) specificity. No indeterminate or invalid results were recorded. Among 13 samples with acute infection (HIV RNA positive, HIV antibody negative), 12 were found positive by the first assay and 8 by the second. The antigen component of the Alere assay detected 10 acute samples, while the SD Bioline assay detected only one.</p> <p>Conclusions: Both rapid assays showed very good overall performance in detecting HIV infection in frozen serum samples, but further improvements are required to improve the performance in acute infection.</p>
Supplementary Material from: Suppression of Pituitary Hormone Genes in Subjects Who Died From COVID-19 Independently of Virus Detection in the Gland
<p>Supplementary Table S1A. List of target genes analysed by the Human Host Response.</p> <p>Supplementary Table S1B. List of target genes analysed by the Coronavirus Panel Plus.</p> <p>Supplementary Table S1C. List of target genes analysed by the custom panel.</p> <p>Supplementary Table S2A. Differential gene expression analysis. Virus-positive vs control adenohypophyses.</p> <p>Supplementary Table S2B. Differential gene expression analysis. Virus-negative vs control adenohypophyses.</p>
A DNA biosensors-based microfluidic platform for attomolar real-time detection of unamplified SARS-CoV-2 virus
<p>Raw data associated to the study entitled:</p> <p><em>A DNA biosensors-based microfluidic platform for attomolar real-time detection of unamplified SARS-CoV-2 virus</em><strong> </strong></p> <p><em>- </em>Metadata file</p> <p>- Computational data</p> <p>- Extraction data</p> <p>- Fluorescence detection</p> <p>- Fluorescence imaging</p> <p>- Labbooks</p> <p>- Surface characterization</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>
Fig. 1 in The detection of Japanese encephalitis virus in Megachiropteran bats in West Kalimantan, Indonesia: A potential enzootic transmission pattern in the absence of pig holdings
Fig. 1. Buffer map overlaying estimated flight range of Culex mosquitoes and hunting ranges of bats.
Datasets of the manuscript "Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons"
<p><strong>DATASETS</strong></p> <p>Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons</p> <p>Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh and Arthur Gruber<sup>*</sup></p> <p>* Correspondence: <a href="mailto:argruber@usp.br">argruber@usp.br</a> (AG); Tel. +55 11 3091 7274</p> <p> </p> <p>Here we provide different data of <em>Microviridae</em>, <em>Flavivirus</em> and casposons used throughout the work:</p> <ul> <li>Microviridae folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for <em>Microviridae</em></li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for <em>Microviridae</em></li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Microviridae_113-seq_training_set.fasta - 113 VP1 sequences covering diversity of the <em>Microviridae</em> family</li> <li>Microviridae_113-seq.aln – multiple sequence alignment of the 113-protein dataset</li> <li>Microviridae_1836-seq_testset.fasta - 1,836 sequence dataset covering 1,836 sequences of the major capsid protein (VP1) comprising 501 <em>Alpavirinae</em> sequences, 1,040 <em>Gokushovirinae</em> sequences and 295 <em>Pichovirinae</em> sequences</li> <li>Microviridae_1866-seq.aln - multiple sequence alignment of the 1,866-protein <em>Microviridae</em> dataset used in the experiment of Figure 4</li> </ul> </li> </ul> </li> <li>Flavivirus folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for <em>Flavivirus</em></li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for <em>Flavivirus</em> <ul> <li>full-length – models constructed from full-length protein sequences</li> <li>short - models constructed from selected short alignment blocks of the protein sequences</li> </ul> </li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Flavivirus_127-seq_training_set.fasta - 127 polyprotein sequences covering species diversity of the genus <em>Flavivirus</em></li> <li>Flavivirus_127-seq.aln – multiple sequence alignment of the 127-protein dataset</li> <li>Flavivirus_6364-seq_testset.fasta - 6,364 sequence dataset covering species diversity of <em>Flavivirus</em>, including 3,919 of dengue virus (DENV), 327 of Zika virus (ZIKV), 63 of yellow fever virus (YFV), and the remaining 2,055 sequences covering other available flaviviruses</li> <li>Flavivirus_6364-seq.aln - multiple sequence alignment of the 6,364-protein <em>Flavivirus</em> dataset</li> </ul> </li> </ul> </li> <li>Casposons folder <ul> <li>casposon_generic_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the generic detection of all casposons and discrimination from CRISPRs.</li> <li>casposon_family_discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the specific discrimination among casposon families and from CRISPRs.</li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>casposons_crisprs.fasta – 106 Cas1 <em>bona fide</em> sequences derived from 52 CRISPRs and 54 casposons</li> <li>casposon_family_discrimination.aln - multiple sequence alignment of 52 <em>bona fide</em> CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for the discrimination of each casposon family.</li> <li>casposons_crisprs_discrimination.aln - multiple sequence alignment of 52 <em>bona fide</em> CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for discrimination of CRISPRs and casposons.</li> </ul> </li> </ul> </li> </ul>
Data from: Sequence-based detection of emerging antigenically novel influenza A viruses
Open the record for dataset details and reuse information.
A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs.
<p>The spectra were provided as unprocessed raw data in the manufacturers data format (Bruker), as labelled two zip archives with SARS CoV 2 positives and negative, according to the reviewer's recommendation.</p> <p>This information belongs to the publication (in review in <em>Journal of Virological Methods</em>)<br> "A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs"<br> All the information belongs to the National Reference Institute, INEI-ANLIS DR CARLOS G MALBRAN, BUENOS AIRES, ARGENTINA.</p>
Molecular characterisation of Crimean-Congo haemorrhagic fever virus detected in African blue ticks feeding on cattle in a Ugandan abattoir
<p>CCHFV multiple sequence alignments and maximum likelihood phylogeny treefiles.</p>
Fig1. Gel electrophoresis 2 in Promising use of Polymerase Chain Reaction Associated to Reverse Transcription for the Detection ofthe America-1 Lineage of Canine Distemper Virus
Fig1. Gel electrophoresis 2% agarose
Fig2. Gel electrophoresis Agarose 2 in Promising use of Polymerase Chain Reaction Associated to Reverse Transcription for the Detection ofthe America-1 Lineage of Canine Distemper Virus
Fig2. Gel electrophoresis Agarose 2%.
Underlying data for 'Rapid molecular assays for the detection of the four dengue viruses in infected mosquitoes'
<p>The pantropic emergence of severe dengue disease can partly be attributed to the co-circulation of different dengue viruses (DENVs) in the same geographical location. Effective monitoring for circulation of each of the four DENVs is critical to inform disease mitigation strategies. In low resource settings, this can be effectively achieved by utilizing inexpensive, rapid, sensitive and specific assays to detect viruses in mosquito populations. In this study, we developed four rapid DENV tests with direct applicability for low-resource virus surveillance in mosquitoes. The test protocols utilize a novel sample preparation step, a single-temperature isothermal amplification, and a simple lateral flow detection. Analytical sensitivity testing demonstrated tests could detect down to 1,000 copies/µL of virus-specific DENV RNA, and analytical specificity testing indicated tests were highly specific for their respective virus, and did not detect closely related flaviviruses. All four DENV tests showed excellent diagnostic specificity and sensitivity when used for detection of both individually infected mosquitoes and infected mosquitoes in pools of uninfected mosquitoes. With individually infected mosquitoes, the rapid DENV-1, -2 and -3 tests showed 100% diagnostic sensitivity (95% CI = 69% to 100%, n=8 for DENV-1; n=10 for DENV 2,3) and the DENV-4 test showed 92% diagnostic sensitivity (CI: <span>62% to 100%, n=12</span>) along with 100% diagnostic specificity (CI: 48–100%) for all four tests. Testing infected mosquito pools, the rapid DENV-2, -3 and -4 tests showed 100% diagnostic sensitivity (95% CI = 69% to 100%, n=10) and the DENV-1 test showed 90% diagnostic sensitivity (<span>55.50% to 99.75%, n=10</span>) together with 100% diagnostic specificity (CI: 48–100%). Our tests reduce the operational time required to perform mosquito infection status surveillance testing from > two hours to only 35 minutes, and have potential to improve accessibility of mosquito screening, improving monitoring and control strategies in low-income countries most affected by dengue outbreaks.</p>
Figure 1 in Detection of respiratory viruses and expression of inflammatory cytokines in patients with acute exacerbation chronic obstructive pulmonary disease in Mongolia China
Figure 1. Distribution of Viruses.
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>
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>
Safety, Tolerability and Efficacy of Molnupiravir (EIDD-2801) to Eliminate Infectious Virus Detection in Persons With COVID-19
ClinicalTrials.gov study NCT04405570. IPD Sharing: NO. Countries: 1. Publications: 4.
VircapSeq Virus Detection in Sézary Syndrome
ClinicalTrials.gov study NCT02836886. IPD Sharing: NO. Countries: 1. Publications: 8.
A longitudinal study of DNA and RNA viruses plasma detection in allogeneic hematopoietic stem cell transplant recipients
Open the record for dataset details and reuse information.
Underlying data for 'Rapid molecular assays for the detection of the four dengue viruses in infected mosquitoes'
Open the record for dataset details and reuse information.
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International Brain Laboratory public data
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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.