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Dataset results
105 results for “Omicron”
Heterologous ChAdOx1-BNT162b2 vaccination in a Korean cohort induces a robust genetic immune and antibody response that includes Omicron [RNA_seq]
GEO Series GSE201533. Homo sapiens. 161 samples. Type: Expression profiling by high throughput sequencing.
Comparison of SARS-CoV-2 variants in primary human nasal cultures indicates Delta as most cytopathic and Omicron as fastest replicating
GEO Series GSE250155. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Heterologous immunization with inactivated vaccine followed by mRNA booster elicits strong humoral and cellular immune responses against the SARS-CoV-2 Omicron variant
<p>The recent emergence of the Omicron variant has raised concerns on vaccine efficacy and the urgent need to study more efficient vaccination strategies. Here we evaluated the effect of an mRNA vaccine booster on immunogenicity in individuals vaccinated with two doses of inactivated vaccine. We observed that an mRNA vaccine booster significantly increased the plasma level of specific antibodies that bind to the receptor-binding domain (RBD) or the spike (S) ectodomain (S1+S2) of both the G614 and the Omicron variants, compared to two doses of homologous inactivated vaccine. The level of RBD- and S-specific IgG antibodies and virus neutralization titers against variants of concern in the heterologous vaccination group were similar to that in individuals receiving three doses of homologous mRNA vaccine or a boost of mRNA vaccine after infection, but markedly higher than that in individuals receiving three doses of a homologous inactivated vaccine. Moreover, this heterologous vaccination regime significantly enhanced the RBD-specific memory B cell response and S1-specific T cell response compared to two or three doses of homologous inactivated vaccine. Our study demonstrates that an mRNA vaccine booster in individuals vaccinated with inactivated vaccines can be highly beneficial, as it markedly increases the humoral and cellular immune responses against the virus, including the Omicron variant</p>
Structural basis of Omicron immune evasion: A comparative computational study of Spike protein-Antibody interaction
<p>The COVID-19 pandemic has caused more than 424 million infections and 5.9 million deaths so far. The vaccines used against SARS-COV-2 by now have been able to develop some neutralising antibodies in the vaccinated human population and slow down the infection rate. The effectiveness of the vaccines has been challenged by the emergence of the new strains with numerous mutations in the spike (S) protein of SARS-CoV-2. Since S protein is the major immunogenic protein of the virus and also contains Receptor Binding Domain (RBD) that interacts with the human Angiotensin-Converting Enzyme 2 (ACE2) receptors, any mutations in this region should affect the neutralisation potential of the antibodies leading to the immune evasion. Several variants of concern (VOC) of the virus have emerged so far. Among them, the most critical are Delta (B.1.617.2), and recently reported Omicron (B. 1.1.529) which have acquired a lot of mutations in the spike protein. We have mapped those mutations on the modelled RBD and evaluated the binding affinities of various human antibodies with it. Docking and molecular dynamics simulation studies have been used to explore the effect of the mutations on the structure of the RBD and the RBD-antibody interaction. The analysis shows that the mutations mostly at the interface of a nearby region lower the binding affinity of the antibody by ten to forty per cent, with a downfall in the number of interactions formed as a whole and therefore, it implies the generation of immune escape variants. Notable mutations and their effect was characterised by performing various analyses that explain the structural basis of antibody efficacy in Delta and a compromised neutralisation effect for the Omicron variant. Our results pave the way for robust vaccine design that can be effective for many variants.</p>
Adaptive immune responses to Omicron BA.4/BA.5-containing bivalent mRNA booster vaccination
<p>This repository contains the immunoSEQ T-cell receptor (TCR) and B-cell receptor (BCR) repertoire data used in the manuscript titled "Adaptive immune responses to Omicron BA.4/BA.5-containing bivalent mRNA booster vaccination". This data set is composed of the TCR/BCR repertoire clonotype sequences and abundances derived from human peripheral blood mononuclear cell (PBMC) samples sorted for CD4, CD8 and CD19 before and after bivalent COVID mRNA booster vaccination. In total, 84 TCR samples (CD4+/CD8+ T cell populations at pre-/post-vaccination from 21 subjects) and 42 BCR samples (CD19+ populations at at pre-/post-vaccination from 21 subjects) are present in the data set.</p> <ul> <li><em><strong>Delmonte_TCR_data_84samples.rds</strong></em><br>R object with the amino acid and nucleotide sequences, VDJ gene calls, and abundances of the TCR clonotypes.</li> <li><strong><em>Delmonte_BCR_data_42samples.rds </em></strong> <br>R object with the amino acid and nucleotide sequences, VDJ gene calls, and abundances of the BCR clonotypes.</li> <li><em><strong>Delmonte_TCR_data_compact_84samples.rds</strong></em><br>R object with the amino acid sequences, VDJ gene calls, and abundances of the TCR clonotypes.</li> <li><em><strong>Delmonte_BCR_data_compact_42samples.rds </strong></em><br>R object with the amino acid sequences, VDJ gene calls, and abundances of the BCR clonotypes.</li> <li><em><strong>sampleExport_TCR.zip</strong></em><br>Compressed folder that includes the individual sample level TCR repertoire files in .tsv format.</li> <li><em><strong>sampleExport_BCR.zip</strong></em><br>Compressed folder that includes the individual sample level BCR repertoire files in .tsv format.</li> </ul> <p><br><em>Funding statement: This work was supported by the Division of Intramural Research Programs of the National Institute of Allergy and Infectious Diseases and of the National Institute of Dental and Craniofacial Research, National Institutes of Health (grant AI001270).</em><br><br></p> <p> </p>
Data and code for "Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa"
<p>Data and code for "Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa"</p>
Recombinant Omicron-Delta COVID-19 Vaccine (CHO Cell)
ClinicalTrials.gov study NCT05574985. IPD Sharing: NO. Countries: 1. Publications: 0.
Efficacy and Safety of Nirmatrelvir/Ritonavir for Treating Omicron Variant of COVID-19
ClinicalTrials.gov study NCT05813600. IPD Sharing: Not stated. Countries: 1. Publications: 0.
COVID-19 Omicron BA.5 Subvariant Dose Finding Infection Study
ClinicalTrials.gov study NCT06478420. IPD Sharing: NO. Countries: 1. Publications: 0.
An Observational Study of Moderna COVID-19 Bivalent Vaccines (Original and Omicron BA.4/BA.5) and 2023 Updated mRNA COVID-19 Vaccines (XBB.1.5)
ClinicalTrials.gov study NCT05765578. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Preliminary Exploratory Cohort Study of SARS-CoV-2 Variant (Omicron BA.5) mRNA Vaccine in Participants Aged 18 Years and Over in China
ClinicalTrials.gov study NCT05550142. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Preliminary Exploratory Study to Evaluate the Safety and Immunogenicity of Omicron Variant Bivalent Vaccine V-01-B5
ClinicalTrials.gov study NCT05585567. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Study to Evaluate the Safety and Immunogenicity of Omicron COVID-19 Vaccine (Vero Cell), Inactivated in Population 18 Years Old of Age and Above
ClinicalTrials.gov study NCT05365724. IPD Sharing: NO. Countries: 1. Publications: 0.
Symptom Spectrum and Risk Factors for Fever in Pediatric and Adult Patients With Omicron Infection
ClinicalTrials.gov study NCT06463821. IPD Sharing: NO. Countries: 1. Publications: 0.
Lianhua Qingke for the Rehabilitation of Patient With Omicron Infection
ClinicalTrials.gov study NCT05625022. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Study to Evaluate the Safety, Tolerability, and Immunogenicity of SARS-CoV-2 Variant (COVID-19 Omicron) mRNA Vaccine (Phase 1)
ClinicalTrials.gov study NCT05433194. IPD Sharing: NO. Countries: 1. Publications: 0.
Efficacy of Lianhua Qingwen in Treating Patients Infected With the Omicron Variant of the COVID-19
ClinicalTrials.gov study NCT05778318. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Sequential Immunization of Two Doses of Inactivated COVID-19 Vaccine (Omicron) in Vaccinated Population Aged 18 Years and Above
ClinicalTrials.gov study NCT05382871. IPD Sharing: NO. Countries: 1. Publications: 0.
Viral Excretion Among COVID-19 Omicron Recurrence Patients
ClinicalTrials.gov study NCT05470426. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Immunogenicity and Safety Study of Booster Vaccine With the COVID-19 Vaccine (Vero Cell), Inactivated, Omicron Strain
ClinicalTrials.gov study NCT05411471. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
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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)
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.