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2,489 results for “Sars-CoV-2”
Mass Spectrometry Datasets for "Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape"
<p>This repository contains mass spectrometry raw datasets for the research paper "<strong><em>Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape</em></strong>". An early version of the manuscript can be viewed on <a href="https://www.biorxiv.org/content/10.1101/2021.04.08.438911v1">bioRxiv</a>.</p> <p>The datasets include two parts:</p> <ol> <li>Identification of nanobodies targeting SARS-CoV-2 spikes.</li> <li>Chemical cross-linking of nanobody-spikes complexes.</li> </ol> <p>The included <strong>.raw</strong> files are Thermo Orbitrap Raw files, and can be assessed by various software such as <em>Thermo Xcalibur</em>, <em><a href="https://proteowizard.sourceforge.io/">ProteoWizard</a></em> and <em><a href="https://pypi.org/project/pymsfilereader/">pymsfilereader</a></em>.</p>
Nsp3 macrodomain of SARS-CoV-2 ; A Target Enabling Package
<p>The conserved macrodomain encoded as non-structural protein 3 (Nsp3 Mac1) is employed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to remove host-derived ribosylation, which is a post-translational modification involved in the production of antiviral cytokines. This TEP provides early tools to develop Nsp3 Mac1 inhibitors, including purification protocols of recombinant proteins, reproducible crystallisation condition suitable for X-ray crystallography fragment screening, biophysical (activity and binding) assays and over 200 fragment hits representing a wide range of chemotypes, that are a starting point for the development of more selective and potent compounds.</p>
Source data for Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum
<p>This dataset contains the source data used in the publication: "Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum" published in Nature communications on August 26, 2021 (10.1038/s41467-021-25479-6).</p>
Simulated wastewater sequencing data for benchmarking SARS-CoV-2 variant abundance estimation
<p>To evaluate the accuracy of variant abundance predictions from wastewater sequencing, we built a collection of benchmarking datasets that resemble real wastewater samples. For each variant (B.1.1.7, B.1.351, B.1.427, B.1.429, P.1) we created a series of 33 benchmarks by simulating sequencing reads from a variant genome, as well as a collection of background (non-variant of concern/interest) sequences, such that the variant abundance ranges from 0.05% to 100%. Analogously, we created a second series of benchmarks, simulating reads only from the Spike gene of each SARS-CoV-2 genome. We refer to the first set of benchmarks as "whole genome" (WG) and to the second set of benchmarks as "S-only". We repeated these simulations at different sequencing depths: 100x and 1000x coverage for the whole genome benchmarks, and 100x, 1000x, and 10,000x coverage for the S-only benchmarks.</p>
Source data for "Date of introduction and epidemiologic patterns of SARS-CoV-2 in Mogadishu, Somalia: estimates from transmission modelling of satellite-based excess mortality data in 2020"
<p>Source data for the model fitting code at https://doi.org/10.5281/zenodo.5525349, accompanying the article "<em>Date of introduction and epidemiologic patterns of SARS-CoV-2 in Mogadishu, Somalia: estimates from transmission modelling of satellite-based excess mortality data in 2020</em>"</p>
SARS-CoV-2–host proteome interactions for antiviral drug discovery
<p>Images and datasets used in Fig 6 and corresponding supplementary material Image analysis was performed with Harmony 4.9 software (PerkinElmer) with feature extraction and linear classification of N-protein positive cells from the total population as presented in the PlateResults file. Prism files (GraphPad Software) include the calculations for curve fits of drug testing data (4PL logistic regression) as well as area under the curve (AUC) of the fitted curves..</p>
OME-NGFF: EM image of SARS-CoV-2
<p>Section of a 30 GB EM image of SARS-CoV-2 in the human intestine from Lamers et al. (Science 2020; 10.1126/science.abc1669) available in the Image Data Resource under accession idr0083 and DOI 10.17867/10000135 under CC-BY 4.0.</p> <p>The original data in TIFF format was converted into the Zarr format following the 0.1 version of the OME-NGFF specification (https://ngff.openmicroscopy.org/0.1/)</p>
Primers for whole genome sequencing of the Sars-Cov-2 virus
<p>Here is the primer sequence for amplification and sequencing of the whole genome of the Sars-Cov-2 virus.</p>
A patient-centric modelling framework captures recovery from SARS-CoV-2 infection
<p>The biology driving individual patient responses to SARS-CoV-2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data and covering a year post-disease onset, from 215 SARS-CoV-2 infected subjects with differing disease severities. Our analyses revealed distinct “systemic recovery” profiles, with specific progression and resolution of the inflammatory, immune cell, metabolic and clinical responses. In particular, we found a strong inter- and intra-patient temporal covariation of innate immune cell numbers, kynurenine metabolites and lipid metabolites, which highlighted candidate immunologic and metabolic pathways influencing the restoration of homeostasis, the risk of death and that of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery at the patient level, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool <a href="https://aus01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fshiny.mrc-bsu.cam.ac.uk%2Fapps%2Fcovid-19-systemic-recovery-prediction-app&data=05%7C01%7CJulien.Wist%40murdoch.edu.au%7C117789e168814a13808a08dabcf18a3e%7Cc00d4c1bcf7b4e93b7c710113a9bc230%7C1%7C0%7C638030042858394016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=z7RJ8%2BGTWr84dYvWSoc%2F9Cj1zYRHV7%2BHfyr9MyCnX6M%3D&reserved=0">http://shiny.mrc-bsu.cam.ac.uk/apps/covid-19-systemic-recovery-prediction-app</a>, designed to test our findings prospectively.</p>
AMTraC-19 (v7.9) Dataset: Persistence of the Omicron variant of SARS-CoV-2 in Australia
<p>The paper describing scenarios which generated this dataset:</p> <p>S. L. Chang, Q. D. Nguyen, A. Martiniuk, V. Sintchenko, T. C. Sorrell, M. Prokopenko, Persistence of the Omicron variant of SARS-CoV-2 in Australia: The impact of fluctuating social distancing, <em>PLOS Global Public Health</em>, 3(4): e0001427, 2023.</p> <p>The AMTraC-19 source code (v7.9) is released on Zenodo: https://zenodo.org/record/7325675</p>
Evaluation of Ortho VITROS and Roche Elecsys S and NC immunoassays for SARS-CoV-2 serosurveillance applications
<p>SARS-CoV-2 seroprevalence studies are instrumental in monitoring epidemic activity and require <span>well-characterized, high-throughput assays, and appropriate testing algorithms.</span> The U.S. Nationwide Blood Donor Seroprevalence Study performed monthly cross-sectional serological testing from July 2020 to December 2021, implementing evolving testing algorithms in response to changes in pandemic activity. With high vaccine uptake, anti-Spike (S) reactivity rates reached > 80% by May 2021, and the study pivoted from reflex Roche anti-nucleocapsid (NC) testing of Ortho S-reactive specimens to parallel Ortho S/NC testing. We evaluated the performance of the Ortho NC assay as a replacement for the Roche NC assay and compared performance of parallel S/NC testing on both platforms. Qualitative and quantitative agreement of Ortho NC with Roche NC assays was evaluated on pre-selected S/NC concordant and discordant specimens. All 190 Ortho S+/Roche NC+ specimens were reactive on the Ortho NC assay; 34% of 367 Ortho S+/Roche NC- specimens collected prior to vaccine availability and 43% of 37 Ortho S-/Roche NC+ specimens were reactive on the Ortho NC assay. Performance of parallel S/NC testing using Ortho and Roche platforms was evaluated on 200 specimens collected in 2019 and 3,903 study specimens collected in 2021. All 200 pre-COVID 2019 specimens tested negative on the four assays. Agreement of S and NC reactivity on specimens was 96.4% (3,769/3,903); most discordant results had reactivity close to the cutoffs on the alternate assays. These findings, and higher efficiency and throughput, support use of parallel S/NC testing on either Roche or Ortho platforms for large serosurveillance studies.</p>
Detection of SARS-CoV-2 variants by genomic analysis of wastewater ampliconic samples (Galaxy Training Material)
<p>The tutorial aims to train how to run workflows to analyze lineages abundances in SAR-CoV-2 wastewater ampliconic samples. (https://training.galaxyproject.org/training-material/)</p>
Detection of SARS-CoV-2 variants by genomic analysis of wastewater metatranscriptomic samples (Galaxy Training Material)
<p>The tutorial aims to train how to run workflows to analyze lineages abundances in SAR-CoV-2 wastewater metatranscriptomic samples. (https://training.galaxyproject.org/training-material/)</p>
Data for: Oligonucleotide mapping via mass spectrometry to enable comprehensive primary structure characterization of an mRNA vaccine against SARS-CoV-2
<p>Oligonucleotide mapping via liquid chromatography mass spectrometry mass spectrometry (LC-MS/MS) was recently developed to support development of Comirnaty®, the world's first commercial mRNA vaccine which immunizes against the SARS-CoV-2 virus. Analogous to peptide mapping of therapeutic protein modalities, oligonucleotide mapping described here provides direct primary structure characterization of mRNA, through enzymatic digestion, accurate mass determinations, and optimized collisionally-induced fragmentation. Sample preparation for oligonucleotide mapping is a rapid, one-pot, one-enzyme digestion. The digest is analyzed via LC-MS/MS with an extended gradient and resulting data analysis employs semi-automated software. In a single method, oligonucleotide mapping readouts include a highly reproducible and completely annotated UV chromatogram with >98% sequence coverage and a microheterogeneity assessment of 5´ terminus capping and 3´ terminus poly(A) tail length. Oligonucleotide mapping was pivotal to ensure the quality, safety, and efficacy of mRNA vaccines by providing: confirmation of construct identity and primary structure and assessment of product comparability following manufacturing process changes. More broadly, this technique may be used to directly interrogate the primary structure of RNA molecules in general.</p>
Nature and well-being: The association of nature engagement and well-being during the SARS-CoV-2 pandemic
<p><span>1. </span><span>Numerous studies have shown the positive association between nature engagement and well-being. During the early phases of the SARS-CoV-2 pandemic, nature engagement changed dramatically as mental health and well-being declined across the globe.</span></p> <p><span>2. </span><span>This study examines how psychological connection to nature and engagement with nature in various forms is associated with well-being during the SARS-CoV-2 pandemic. Specifically, we examine which types of nature engagement (i.e., with nearby nature, through nature excursions, and media-based) are more strongly associated with well-being based on measures of loneliness, rumination, pandemic emotional impact, and mental health.</span></p> <p><span>3. </span><span>We employed a cross-sectional online survey of adults (N=3,282) residing in the United States, 25% of whom report seldom spending time in nature.</span></p> <p><span>4. </span><span>Our findings revealed that the psychological construct of connection to nature was associated with less loneliness and greater mental health. Overall, nature engagement was a consistent predictor of well-being, but different types of activities predicted varying outcomes on our four dependent variables. Greater engagement with nearby nature during the pandemic was associated with less rumination, less pandemic emotional impact, and better mental health while nature excursions (e.g., camping, backpacking) and media-based nature engagement were associated with greater loneliness, more emotional impact from the pandemic, and worse mental health. Additionally, nature engagement via media was associated with greater rumination.</span></p> <p><span>5. </span><span>Our findings suggest that promoting opportunities to increase engagement with and access to nearby nature is associated with better human well-being, especially during challenging events, and should be part of a </span>multi-pronged approach for coping with the next public health crisis<span>.</span></p>
Raw Data for the article: Analysis of the Specific Immune Response after the Third Dose of mRNA COVID-19 Vaccines in Organ Transplant Recipients: Possible Spike-S1 Reactive IgA Signature in Protection from SARS-CoV-2 Infection
<p><strong>Background:</strong> Several studies have indicated that anti-SARS-CoV-2 mRNA vaccinations are less effective in inducing robust immune responses among solid organ transplant recipients (SOTRs) compared with the immunocompetent. The third dose of vaccine in SOTRs showed promising results of immunogenicity, even though clinical studies have suggested that immunocompromised subjects are less likely to build a protective immune response against SARS-CoV-2 resulting in lower vaccine efficacy for the prevention of severe COVID-19. <strong>Methods:</strong> Serological IgG and IgA were analyzed through CLIA or ELISA, respectively, while Spike-specific T cells were detected by ELISpot assay after the second and third dose of vaccine in 43 SOTRs. <strong>Results:</strong> The third dose induced an improvement in antibody response against SARS-CoV-2. We also reported a strong correlation between specific humoral and cellular responses after the third dose, even though we did not see significant changes in the magnitude of the SARS-CoV-2-specific T cell response. SOTRs who contracted the SARS-CoV-2 infection after the third dose, despite eliciting a positive IgG response, failed to mount an anti-Spike-S1 IgA response, both after the third dose and after SARS-CoV-2 infection. <strong>Conclusions:</strong> We can conclude that serum IgA detection can be helpful, along with IgG detection, for the evaluation of vaccine efficacy, principally in fragile subjects at high risk of infection.</p>
Data for: Single versus serial dilution SARS-CoV-2 IgG
<p>Reliable and scalable seroepidemiology methods are needed to estimate SARS-CoV-2 incidence and monitor the dynamics of population-level immunity as the pandemic evolves. We aimed to evaluate the reliability of SARS-CoV-2 normalized ELISA optical density (nOD) at a single dilution compared to titers derived from serial dilutions. We conducted serial serosurveys within a community-based cohort in Salvador, Brazil. Anti-S IgG ELISA (Euroimmun AG) was performed with five serial 3-fold dilutions of paired sera from 54 participants. Changes in nOD reliably predicted increases and decreases in titers (98.1% agreement, <span>κ </span>= 95.8%). Fitting the relationship between nOD and interpolated titers to a log-log curve yields highly accurate predictions of titers (r<sup>2</sup> = 0.995) and changes in titers (r<sup>2</sup> = 0.975), using only one to two dilutions. This approach can significantly reduce the time, labor and resources needed for large-scale serosurveys to ascertain population-level changes in exposure and immunity.</p>
SARS-COV-2 genomic sequences used as references for the NASCarD method
<p>A set of 9 SARS-CoV-2 genome sequences used as reference in the NASCarD process.</p>
Data for: Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state
<p>All code and data necessary to reproduce results and figures in the publication "Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state".</p>
Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin
<p>The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub<sub>2</sub>) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub<sub>2</sub> combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub<sub>2</sub> are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub<sub>2</sub> modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.</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.