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2,489 results for “Sars-CoV-2”
Multiplexed On-Yeast Serological Assay for Immune Escape Screening of SARS-CoV-2 Variants
<p>Experimental data and scripts used for the development of a Yeast-based serological Assay:</p> <ol> <li>The<strong> Python scripts</strong> folder includes all scripts used in this study to analyze sera titers and plotting data.</li> <li>The<strong> Raw data</strong> folder includes: <ol> <li>The Y<strong>east Immunoassay development</strong> folder includes the flow cytometric data for serum depletion and reduction of ligand depletion effects.</li> <li>The <strong>Yeast serological data folder</strong> includes the raw data of all tested sera and related data for their analyses.</li> </ol> </li> <li>The <strong>Snapgene plasmid maps </strong>folder includes the plasmid maps for the three SARS-CoV-2 VOCs for Snapgene.</li> </ol> <p> </p> <p> </p>
SARS-CoV-2 vaccine breakthrough infections by Omicron and Delta variants in healthcare workers
<p>An observational prospective cohort study was conducted in vaccinated employees with acute SARS-CoV-2 infection between October 2021 and February 2022. Serological and molecular testing was performed to determine SARS-CoV-2 viral load, lineage, antibody levels, and neutral-ising antibody titres. A total of 571 (9.7%) employees experienced SARS-CoV-2 breakthrough infections during the enrolment period, of which 81 were included. The majority (n=79, 97.5%) was symptomatic and most (n=75, 92.6%) showed Ct-values < 30 in RT-PCR assays. Twenty-four (30%) remained PCR-positive for > 15 days. Neutralizing antibody titres were strongest for the wildtype, intermediate for Delta and lowest for Omicron variants. Omicron infections occurred at higher anti-RBD-IgG serum levels (p= 0.00001) and showed a trend for higher viral loads (p=0.14, median Ct-difference 4.3, 95% CI [-2.5-10.5]). For both variants, viral loads were signifi-cantly higher in participants with lower anti-RBD-IgG serum levels (p=0.02). </p>
Supplementary Data for: "The principles of SARS-CoV-2 inter-variant competition are exemplified in the pre-Omicron era of the Colombian epidemic"
<p>Supplementary data files, including BEAST XMLs and logs from the study "The principles of SARS-CoV-2 inter-variant competition are exemplified in the pre-Omicron era of the Colombian epidemic".</p>
Data set: genetic variants related to SARS-CoV-2 viremia
<p>Data set generated to evaluate the association between SNPs from genes related to SARS-CoV-2 pathogenesis and the presence of viremia.</p>
Validation of a SARS-CoV-2 surrogate neutralization test detecting neutralizing antibodies against the major variants of concern
<p>SARS-CoV-2 infection and/or vaccination elicit a broad range of neutralizing antibody responses against the different variants of concern (VOC). We established a new variant-adapted surrogate neutralization test (sVNT) and assessed the neutralization activity against the ancestral B.1 (WT) as well as VOC Delta, Omicron BA.1, BA.2 and BA.5. Performances were compared to the reference virus neutralization test (VNT) against the respective VOC using three different cohorts collected during the COVID waves. Pre-COVID samples confirmed 100% specificity of the sVNT. Correlation analyses showed moderate to strong correlation for Omicron sub-variants (Spearman’s r=0.7081 for BA.1, r=0.7205 for BA.2 and r=0.6042 for BA.5), and for WT (r=0.8458) and Delta-sVNT (r=0.8158), respectively. Comparison of the WT-sVNT performance with two CE-IVD commercial kits “Icosagen SARS-CoV-2 Neutralizing Antibody ELISA kit” and “Genscript cPass kit” revealed an overall good correlation ranging from 0.8673 to -0.8773 and a midway profile between both commercial kits with 87.76% sensitivity and 90.48% clinical specificity resulting in a Youden Index of 78.24. This midway trend was further confirmed on 100 double-vaccinated individuals. The BA.2-sVNT performance was similar to that of the Genscript test. Finally, sVNT ability to assess neutralizing antibodies against Omicron BA.5 was validated on a double-vaccinated cohort (n=100) and an Omicron-breakthrough infection cohort (n=91). Correlation analysis revealed a strong association (r=0.8583) between BA.5-sVNT and VNT. Accurate classification was confirmed by receiving operating characteristic (ROC) analysis reporting an area under the curve (AUC) of 0.9543. In conclusion, the sVNT allows for efficient prediction of immune protection against the various VOCs.</p>
Dataset for a study:Clinical characteristics of SARS-CoV-2 delta variant infection in Xiamen
<p>This retrospective study aims to identify the clinical and demographic features of patients infected with the SARS-CoV-2 delta variant at a single institution in Xiamen, China.</p>
SARS-CoV-2 Viral Samples and Reference Genome for Galaxy Training Network SARS with Galaxy on AnVIL Tutorial
<p>In the lab activity, we'll see if there are genomic differences in the collected sample compared to the original SARS-CoV-2 genome (the reference). We need three files to do this:</p> <ul> <li><strong>SARS-CoV-2_reference_genome.fasta</strong> : the reference genome</li> <li><strong>VA_sample_forward_reads.fastq.gz</strong>: 1 of 2 raw read data files</li> <li><strong>VA_sample_reverse_reads.fastq.gz</strong>: 2 of 2 raw read data files</li> </ul> <p>The sample for this activity was derived from data collected at Virginia Commonwealth University in Richmond, VA. The researchers collected the sample with the goal of being able to track the spread and evolution of this virus state-wide, nationally, and internationally. You can download the original data <a href="https://www.ncbi.nlm.nih.gov/sra/?term=XGTK449087">here</a>.</p> <p>You can download the reference genome <a href="https://www.ncbi.nlm.nih.gov/nuccore/1798174254">here</a>.</p>
Data from: Serosurvey of SARS-COV-2 at a large public university
<p><strong>Objective</strong>: This study investigated the seroprevalence of SARS-CoV-2 antibodies among adults over 18 years.</p> <p><strong>Design</strong>: Prospective cohort study.</p> <p><strong>Settings</strong>: a population-based study among the big university community.</p> <p><strong>Participants</strong>: This study took volunteers over five days and recruited adult 1064 participants.</p> <p><strong>Primary outcome measures</strong>: We conducted a seroprevalence in our community with SARS-CoV-2-specific antibodies due to previous exposure to SARS-CoV-2 and/or vaccination.</p> <p><strong>Results</strong>: The seroprevalence of the anti-receptor binding domain (RBD) antibody was 90% by a lateral flow assay and 88% by a semi-quantitative chemiluminescent immunoassay. The seroprevalence for anti-nucleocapsid (NC) was 20%. In addition, individuals with previous natural COVID infection plus vaccination had higher anti-RBD antibody levels compared to those who had vaccination only or infection only. Individuals who had a breakthrough infection had the highest anti-RBD antibody levels.</p> <p><strong>Conclusion</strong>: Accurate estimates of the cumulative incidence of SARS-CoV-2 infection can inform the development of university risk mitigation protocols such as encouraging booster shots, extending mask mandates, or reverting to online classes. It could help us to have clear guidance to act at the first sign of the next surge as well, especially since there is a surge of COVID subvariant infections.</p>
Data from: Phenotypic evolution of SARS-CoV-2: A statistical inference approach
<p>Since its emergence in late 2019, the SARS-CoV-2 virus has spread globally, causing the ongoing COVID-19 pandemic. In the fall of 2020, the Alpha variant (lineage B.1.1.7) was detected in England and spread rapidly, outcompeting the previous lineage. Yet, very little is known about the underlying modifications of the infection process that can explain this selective advantage. Here, we try to quantify how the Alpha variant differed from its predecessor on two phenotypic traits: the transmission rate and the duration of infectiousness. To this end, we analysed the joint epidemiological and evolutionary dynamics as a function of the Stringency Index, a measure of the amount of Non-Pharmaceutical Interventions. Assuming that these control measures reduce contact rates and transmission, we developed a two-step approach based on SEIR models and the analysis of a combination of epidemiological and evolutionary information. First, we quantify the link between the Stringency Index and the reduction in viral transmission. Secondly, based on a novel theoretical derivation of the selection gradient in an SEIR model, we infer the phenotype of the Alpha variant from its frequency changes. We show that its selective advantage is more likely to result from a higher transmission than from a longer infectious period. Our work illustrates how the analysis of the joint epidemiological and evolutionary dynamics of infectious diseases can help understand the phenotypic evolution driving pathogen adaptation.</p>
Evaluation of oxidative stress markers in Rwanda during the SARS-CoV-2 pandemic: a cross-sectional study
<p>SARS-CoV-2 is mainly described as endothelial dysfunction, and due to the bidirectional link between oxidative stress and endothelial dysfunction, we initiated a program directed to the evaluation of the oxidative status of the population of Rwanda by measuring spectrophotometrically their plasma Reactive Oxygen Metabolites (dROMs) and Plasma Antioxidant Potential (PAT). The reference population was chosen to reflect the absence of actual or past SARS-CoV-2 infections as well as other clinically established infective status and reference intervals for d-ROM and PAT were identified.</p> <p>The average d-ROM was 378.6 UCARR with a standard deviation of 105.2. The average PAT value was 2853.6, with a standard deviation of 635.7 UCOR. On the basis of the published values for the Caucasian and East Asian populations, the average value of d-ROM obtained in Rwanda was significantly higher than expected. Conversely, the average PAT value was at the upper limit according to the averaged values for healthy Caucasian populations. The results of this study, the first so far reported on a sub-Saharan population, can effectively be used as a baseline value for clinical management of inflammatory conditions, for the stratification of at-risk individuals and to inform recommendations for effective use of public health resources.</p>
Raw data for " Unnatural evolutionary processes of SARS-CoV-2 variants and possibility of deliberate natural selection" DOI 10.5281/zenodo.8248320
<p>Compressed raw data for " Unnatural evolutionary processes of SARS-CoV-2 variants and possibility of deliberate natural selection" </p> <p>DOI 10.5281/zenodo.8248320</p>
SARS-CoV-2 spike protein complexes and their contacts
<p>This archive contains protein complex structures containing SARS-CoV-2 spike protein as well as derived data.</p>
Data for: A catalytic model for SARS-CoV-2 reinfections: Performing simulation-based validation and extending the model to include nth infections
<p>For code and more details see: </p> <ul> <li><code>inf_for_sbv.RDS</code> - simluated timeseries of primary infections used in the simulation-based validation of reinfections. </li> <li><code>inf_for_sbv_third.RDS</code> - simluated timeseries of primary infections used in the simulation-based validation of third infections. </li> <li><code>3_posterior_90_null_correctdata.RData</code> - posterior samples from the MCMC fitting procedure (as used in the manuscript) when not considering a second lambda parameter (to third infections)</li> <li><code>3_posterior_90_null_l2_correctdata.RData</code> - posterior samples from the MCMC fitting procedure (as used in the manuscript) when considering a second lambda parameter (to third infections)</li> <li><code>3_sim_90_null_correctdata.RDS</code> - simulation results when not considering a second lambda parameter for third infections (as used in the manuscript)</li> <li><code>3_sim_90_null_l2_correctdata.RDS</code> - simulation results when considering a second lambda parameter for third infections (as used in the manuscript)</li> </ul> <p> </p>
Proteomic profiling of survivors of SARS-CoV-2-induced ARDS
<p>Around 80% of patients who develop acute respiratory distress syndrome (ARDS) secondary to SARS-CoV-2 infection experience persistent lung dysfunction. The molecular factors that mediate pulmonary sequelae and recovery are unknown.<strong> </strong>In this context, we sought to comprehensively characterize the proteomic determinants of pulmonary diffusion impairment.<strong> </strong></p> <p>This was a prospective cohort study including eighty-seven SARS-CoV-2–induced ARDS survivors. A complete pulmonary function evaluation and chest computed tomography (CT) were performed 3 months after hospital discharge. Proteomic profiling (364 proteins) was performed in plasma samples using proximity extension assay (PEA) technology. Partial least squares-discriminant analysis (PLS-DA) and random forest (RF) methods were used to assess predictor importance.</p> <p>Thirty percent of patients presented moderate to severe impairment of lung diffusing capacity (D<sub>LCO</sub><60% predicted). In the univariate analysis, fifteen proteins showed high concentrations in patients with D<sub>LCO</sub><60% [false discovery rate (FDR)<0.05]. Pleiotrophin (PTN) displayed the highest differences: fold change=2.22 and FDR=0.001. Differentially detected proteins showed an inverse and independent dose–response relationship with D<sub>LCO</sub>. The multivariable approaches clustered proteins according to the severity of diffusion impairment. Clusters were composed of host mediators of cell proliferation and differentiation, tissue remodeling, angiogenesis, coagulation, inflammation, immune response and fibrosis signaling.</p> <p>In survivors of SARS-CoV-2–induced ARDS, lung diffusion impairment is associated with specific circulating factors implicated in multiple injury and repair mechanisms. The host protein signatures allow a better understanding of pulmonary sequelae and may constitute therapeutic targets and biomarkers. The long-term biological and clinical significance of these observations requires further investigation.</p>
Transcriptome of Peromyscus leucopus lungs infected with SARS-CoV-2
<p><em>Peromyscus leucopus</em> is a reservoir for numerous zoonoses and one of the most abundant mammals in North America. Since they live near humans we are interested in the possibility of SARS-CoV-2 infection in this animal model from a zoonoses standpoint. The experimental design for the first trial involves using adult male and female <em>P. leucopus</em> LL stock. Animals were dosed with nasal inhalation of either tissue culture medium (DMEM) alone (controls) or alpha variant, WA1 strain of SARS-CoV-2 virus. We dosed 8 animals with a virus (titer 2x104) and 6 with DMEM alone. Animals were euthanized at either 3 or 6 days post-infection. For a second trial, <em>P. leucopus</em> animals were 1-3 years old and we had 3 groups: control animals with nasal inhalation of media, control animals with nasal inhalation of the heat-treated virus, and infected animals. Each group has 4 animals euthanized on 3- or 6-days post-infection (DPI). Lung tissue was used for RNA isolation and further sequencing to obtain 40 x 106 PE150 reads.</p>
Delayed Heterologous SARS-CoV-2 Vaccine Dosing (Boost) After Receipt of EUA Vaccines
ClinicalTrials.gov study NCT04889209. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Dornase Alfa for ARDS in Patients With Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2)
ClinicalTrials.gov study NCT04402970. IPD Sharing: NO. Countries: 1. Publications: 6.
COVID-19: Longitudinal Study of Seroprevalence of SARS-CoV-2 Antibodies and Development of Immunity in School Children
ClinicalTrials.gov study NCT04448717. IPD Sharing: UNDECIDED. Countries: 1. Publications: 14.
Singapore SARS-CoV-2 Human Challenge Study
ClinicalTrials.gov study NCT06654973. IPD Sharing: NO. Countries: 1. Publications: 2.
Dose Finding Study to Evaluate The Safety, Tolerability and Immunogenicity of an Inactiviated, Adjuvanted SARS-CoV-2 Virus Vaccine Candidate Against Covid-19 in Healthy Subjects
ClinicalTrials.gov study NCT04671017. IPD Sharing: UNDECIDED. 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.
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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.