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Dataset results
19 results for “Variants of Concern”
MD simulations from "#GotGlycans: Role of N343 Glycosylation on the SARS-CoV-2 S RBD Structure and Co-Receptor Binding Across Variants of Concern
<p>This folder contains all the MD simulations (saved in frames of 1 ns in PDB format) analysed and discussed in the paper titled "#GotGlycans: Role of N343 Glycosylation on the SARS-CoV-2 S RBD Structure and Co-Receptor Binding Across Variants of Concern" DOI https://doi.org/10.1101/2023.12.05.570076. The naming reflects the specific variant and the presence ('g' or 'gly') or absence ('ng' or 'nogly') of glycosylation at N343 and N331 sites in the SARS-CoV-2 S RBD. Gaussian accelerated MD simulations are indicated with 'gamd', all others represent conventional (deteriministic) sampling. For all details please refer to the original manuscript.</p>
Interaction of Surface Glycoprotein of SARS-CoV-2 Variants of Concern with Potential Drug Candidates: A Molecular Docking Study
<p>This dataset contains additional docking images of SARS-CoV-2 Variants of Concern with drugs under study. It also contains a spreadsheet containing binding residues with different types of bonds. Further it includes the raw spike protein sequences, 3D model of spike proteins of VOCs (variant of concern) and potential drugs used in this study. </p>
Data for: Immunogenicity of SARS-CoV-2 spike antigens derived from Beta & Delta variants of concern
<p>Using our strongly immunogenic SmT1 SARS-CoV-2 spike antigen platform, we developed novel antigens based on the Beta & Delta variants of concern. These antigens elicited higher neutralizing antibody activity to the corresponding variant than comparable vaccine formulations based on the original reference strain, while a multivalent vaccine generated cross-neutralizing activity to all three variants. This suggests that while current vaccines may be effective at reducing severe disease to existing variants of concern, variant-specific antigens, whether in a mono- or multivalent vaccine, may be required to induce optimal immune responses and reduce infection against arising variants.</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>
Efficacy Study of COVID-19 mRNA Vaccine in Regions With SARS-CoV-2 Variants of Concern
ClinicalTrials.gov study NCT05168813. IPD Sharing: Not stated. Countries: 7. Publications: 1.
Data for: Immunogenicity of SARS-CoV-2 spike antigens derived from Beta & Delta variants of concern
Open the record for dataset details and reuse information.
Data and code for "SARS-CoV-2 correlates of protection from infection against variants of concern"
Open the record for dataset details and reuse information.
mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status
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SARS-CoV-2 Variant of Concern Fitness and Adaptation in Primary Human Airway Epithelia
GEO Series GSE253698. Homo sapiens. 13 samples. Type: Expression profiling by high throughput sequencing.
Identification of host dependency factors shared by multiple SARS-CoV-2 variants of concern
GEO Series GSE207981. Homo sapiens. 48 samples. Type: Expression profiling by high throughput sequencing.
Effects of Ancestral SARS-CoV-2 versus Variants of Concern Delta and Omicron on Megakaryocyte Activation and Transcriptome
GEO Series GSE277576. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Real-time quantitative PCR analysis of mouse lungs after exposure to SARS-CoV-2 and variants of concern (VOC)
GEO Series GSE183621. Mus musculus. 21 samples. Type: Expression profiling by RT-PCR.
Upper respiratory infection drives clinical signs and inflammatory responses in heterologous challenge of SARS-CoV-2 variants of concern
GEO Series GSE216048. Mus musculus. 131 samples. Type: Expression profiling by high throughput sequencing.
CRISPR screens for host factors critical for infection by SARS-CoV-2 variants of concern
GEO Series GSE197962. Homo sapiens; Severe acute respiratory syndrome coronavirus 2. 9 samples. Type: Other.
Primary SARS-CoV-2 variant of concern infections elicit broad antibody Fc-mediated effector functions and memory B cell responses
<p><span>Neutralization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by human sera is a strong correlate of protection against symptomatic and severe Coronavirus Disease 2019 (COVID-19). The emergence of antigenically distinct SARS-CoV-2 variants of concern (VOCs) and the relatively rapid waning of serum antibody titers, however, raises questions about the sustainability of serum protection. In addition to serum neutralization, other antibody functionalities and the memory B cell (MBC) response are suggested to help maintaining this protection. In this study, we investigate the breadth of spike (S) protein-specific serum antibodies that mediate effector functions by interacting with Fc-gamma receptor IIa (<span>FcγRIIa) and FcγRIIIa,</span> and of the receptor binding domain (RBD)-specific MBCs, following a primary SARS-CoV-2 infection with the D614G, Alpha, Beta, Gamma, Delta, Omicron BA.1 or BA.2 variant. Irrespectively of the variant causing the infection, the breadth of S protein-specific serum antibodies that interact with <span>FcγRIIa and FcγRIIIa and the RBD-specific MBC responses </span>exceeded the breadth of serum neutralization, although the Alpha-induced B cell response seemed more strain-specific<span>. Between VOC groups, both quantitative and qualitative differences in the immune responses were observed, suggesting differences in immunogenicity. Overall</span>, this study contributes to the understanding of protective humoral and B cell responses in the light of emerging antigenically distinct VOCs, and highlights the need to study the immune system beyond serum neutralization <span>to gain a better understanding of the protection against emerging variants. </span></span></p>
Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
<p>Supplementary Figure S4. SNP alignment of multiple high-quality genomes from Cameroon, available genomes of lineage B.1.620 as well as earliest and latest genomes of lineages B.1.1.7, B.1.351, P.1, B.1.526.2, B.1.177.60, B.1.177.57, and B.1.1.280. Only polymorphic SNPs within the alignment that are shared by at least eight B.1.620 are shown and lineage B.1.620 is outlined with a dashed line. Sites identical to the reference (GenBank accession NC_045512) are shown in grey, changes from the reference are indicated and coloured by nucleotide (green for thymidine, red for adenosine, blue for cytosine, yellow for guanine, dark grey for ambiguities, black for gaps). The first 100 and the last 50 nucleotides are not included in the figure but were used to infer the phylogeny. If mutation results in an amino acid change, the column label indicates the gene, reference amino acid, amino acid site, and amino acid change in brackets. The maximum-likelihood phylogeny on the right shows the relationships between depicted genomes and was rooted on the reference sequence.</p>
RNA-Seq investigating the global landscape of the host molecular response to infection by SARS-CoV-2 variants of concern
GEO Series GSE213759. Homo sapiens. 340 samples. Type: Expression profiling by high throughput sequencing.
Data Deposit for "Ligation-based Assay for Variant-Typing without Sequencing: Application to SARS-CoV-2 Variants of Concern"
<p>No description provided.</p>
Ligation-based Assay for Variant-Typing without Sequencing: Application to SARS-CoV-2 Variants of Concern [Data Deposit]
<p>Data analyzed for the results of the original research article "<strong>Ligation-based Assay for Variant-Typing without Sequencing: Application to SARS-CoV-2 Variants of Concern</strong>".</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.