Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
2,489
datasets available to search
ShareScore release 0.9.0
Dataset results
2,489 results for “Sars-CoV-2”
SARS-CoV-2 seroprevalence in Mongolia: Results from a national population survey
<p>Results of population-based age stratified seroepidemiological investigation in Mongolia</p>
SARS-CoV-2 Viral dynamics
<p><span><b>Background:</b><span> Cases of undiagnosed pneumonia have emerged, and sequencing of respiratory samples indicated the presence of SARS-CoV-2 causing COVID-19. Patients with higher viral load and lower Ct values tend to have progressive disease and severe lung injury.</span> The objective of this study is to describe the clinical manifestation and disease outcomes of COVID-19 patients in relation to their Ct values. </span></p> <p><strong>Methods:</strong> A retrospective, single-center observational study was performed, including patients admitted to King Faisal Specialist Hospital and Research Centre (KFSH&RC) Riyadh in one month in 2020 and have a confirmed diagnosis of COVID-19. The Ct value was identified to determine the viral load. All patients were treated according to KFSH&RC guidelines. <span>Patients were divided into HCQ/AZI and non HCQ/AZI treated groups. </span></p> <p><b><span>Results:</span></b><span> There were many days where Ct values were not available. An attempt at imputing information for missing Ct values was made using logic. The logic leads to an ordinal Ct score 1, 2, 3, or 4. As a result, complete Ct score profiles were available. There was no evidence of statistically significant difference between the two groups in regard to clinical severity, duration to negative test, or changes in Ct values. </span></p> <p><b><span>Conclusion:</span></b> There is little knowledge known to the time profile of Ct values and their relation to disease course of COVID-19. This study provides insight on how Ct values might be used to determine treatment efficacy. As it might be difficult to obtain Ct values at all times, this study provides an imputation method that may be used with conservative statistical assumptions for analyses of Ct profiles. </p>
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>
Figure 3 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 3 Structure of naturally occurring coumarins 13–37 reported possessing antiviral activity.
Figure 2 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 2 Structure of some coumarin drugs 4–13.
Figure 1 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 1 Structure of Aminocoumarin antibiotics Novobiocin, Clorobiocin, and Coumermycin.
Source data: Transmission of SARS-CoV-2 from humans to animals and potential host adaptation
<p>All source data required for reproducing the results of the associated manuscript. Contains data inputs for all associated custom code hosted on Zenodo (https://doi.org/10.5281/zenodo.6528187).</p>
Supplementary materials (s.m.) of "The first report on detecting SARS-CoV-2 inside bacteria of the human gut microbiome: A case series on asymptomatic family members and a child with COVID-19".
<p> These are Supplementary materials of the version 2 of the article published at the following link: https://f1000research.com/articles/11-135/v2. The article is: Brogna C, Cristoni S, Petrillo M <em>et al.</em> The first report on detecting SARS-CoV-2 inside bacteria of the human gut microbiome: A case series on asymptomatic family members and a child with COVID-19 [version 2; peer review]. <em>F1000Research</em> 2022, <strong>11</strong>:135 (<a href="https://doi.org/10.12688/f1000research.77421.2">https://doi.org/10.12688/f1000research.77421.2</a>) </p>
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>
Benchmark data derived from the antibodies for the spike receptor-binding domain of SARS-CoV-2
<p>enchmark data described in the publication:</p> <p>Improved deep learning prediction of antigen-antibody interactions</p> <p>Reference Authors: Mu Gao and Jeffrey Skolnick, PNAS, 2024</p> <p><br>Sequences.zip -- Lists and sequences of antibodies used in the study (Compressed in the zip format)<br>Dataset S1.xlsx -- Results of benchmark test 1 on the PDB36 set (MS Excel format)<br>Dataset S2.xlsx -- Results of benchmark test 2 on ~1000 antibodies (MS Excel format). <br>Dataset S3.xlsx -- Results of benchmark of RBD471 using reduced RBD-binder sequence libraries (MS Excel format). </p>
SARS-CoV-2 encephalitis presenting as a clinical cerebellar syndrome: a case report
<p>This report contributes to the rapidly expanding knowledgebase of COVID-19-associated neurological syndromes and highlights uncertainties regarding the pathogenesis of cerebellar dysfunction in, and optimal management of, patients with COVID-19-associated encephalitis.</p>
RNA-seq data for SARS-CoV-2 infected cells
<p>We performed our sequencing and analysis in CapitalBio Technology (Beijing, China). A549 cells were infected with SARS-CoV-2, panH1N1 and H7N9 at a MOI of 0.01 for 60 hr. Total RNAs from control and virus infected cells were extracted using the TRIzol reagent according to the manufacturer’s instructions (Invitrogen, USA). The genomic DNA was removed using DNase I (Takara, Japan). RNA samples were assessed for their quality using the RNA 6000 pico kit (Agilent, USA) and quantified using the ND-2000 (NanoDrop Technologies). Only the high quality RNA was selected to construct the sequencing library with the Illumina TruSeq Stranded mRNA Library Preparation kit (Illumina, USA). The NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) was used for RNA library preparation.</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>
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>
Humoral Effect of SARS-CoV-2 mRNA vaccination with booster dose in solid tumor patients with different anticancer treatments
<p>Cancer patients are at risk for serious complications in case of SARS-CoV-2 infection. In these patients SARS-CoV-2 vaccination is strongly recommended, with the preferential use of mRNA vaccines. The antibody response in cancer patients is variable, depending on the type of cancer and antitumoral treatments. In solid tumor patients an antibody response similar to healthy subjects has been confirmed after the second dose. Only few studies explored the duration of immunization after the two doses and the effect of the third dose. In our study we explored a cohort of 273 solid tumor patients at different stages and treated with different anticancer therapies. Our analysis demonstrated that the persistence of the neutralizing antibody and the humoral response after the booster dose of vaccine was not dependent on either the tumor type, the stage or type of anticancer treatment.</p>
Raw signals of nucleotides in the S gene of 12 SARS-COV-2 strains
<p>The surveillance of the SARS-CoV-2 genome has become one of the crucial techniques in the management of COVID-19, aiding the pandemic response and supporting effective public health interventions. Typically, whole genomic sequencing is used along with PCR-based target enrichment techniques to identify SARS-CoV-2 variants, which is a complicated and time-consuming process that requires central laboratory facilities. Thus, there is an urgent requirement for developing rapid and cost-effective tools that can precisely detect and identify SARS-CoV-2 strains on-site. In this study, we demonstrate the diagnosis of COVID-19 patients and rapid identification of SARS-CoV-2 variants by amplifying and sequencing the entire length of the SARS-CoV-2 S gene using an isothermal enzymatic recombinase amplification combined with the most advanced Oxford nanopore sequencing. The entire procedure, from sampling to sequencing, takes less than 8 hours and can be performed with limited resources. The newly developed method has noteworthy implications for examining the transmission dynamics of the virus, detecting novel genetic variants, and assessing how mutations affect the efficiency of diagnostic approaches, antiviral treatments, and vaccines.</p>
The panzootic potential of SARS-CoV-2
<p>Our dataset collection comprises files containing tree files and character matrices, serving as invaluable resources for researchers aiming to reproduce or extend the findings presented in our manuscript.</p> <ul> <li>panzootic_virus_metadata_lineage3.csv - metadata to make the trees (Figure 2)</li> <li>panzootic_virus.fa - the virus alignment file (Figure 2)</li> <li>panzootic_virus_rooted.treefile - the virus tree file (Figure 2)</li> <li>AA_gisaid_revANNA-ADR_05042022finalAL.xlsx - dataset for generation Figure 3</li> <li>COVID_ToL,csv - metadata for mammal tree and trait matrix</li> <li>COVID_ToL_Infection.csv - metadata for mammal tree and trait matrix</li> <li>COVID_ToL_ACE2.csv - metadata for mammal tree and trait matrix</li> <li>COVID_ToL_CAT.csv - metadata for cat tree and trait matrix</li> <li>TopoFree_ND_MCC_SpeciesTree.rdata - Species tree file</li> <li>TopoFree_ND_MCC_SpeciesTree_ace_ACE2_ARD.rdata - Figure S3</li> <li>TopoFree_ND_MCC_SpeciesTree_simmap_ACE2_ARD.rdata - Figure S2</li> <li>TopoFree_ND_MCC_Famtree_V2.rdata - Family tree file</li> <li>TopoFree_ND_MCC_FamTree_V2_ace_ACE2.rdata - Figure S4</li> <li>TopoFree_ND_MCC_Famtree_V2_simmap_ACE2.rdata - Figure 4</li> <li>TopoFree_ND_CatTree.rdata - Cat tree file</li> <li>TopoFree_ND_MCC_CatTree_ace_Infection_ARD.rdata - Figure S6</li> <li>TopoFree_ND_MCC_CatTree_simmap_Infection_ARD.rdata - Figure S5</li> </ul>
Unexpected single ligand occupancy and negative cooperativity in the SARS-CoV-2 Main protease
<p>This directory contains files for the project:<br> Unexpected single ligand occupancy and negative cooperativity in the SARS-CoV-2 Main protease<br> Authors: Simone Albani, Elisa Costanzi, Gia Linh Hoang, Maria Kuzikov, Marcus Frings, Narjes Ansari, Nicola Demitri, The Toan Nguyen, Valerio Rizzi, Jörg Bernhard Schulz, Carsten Bolm, Andrea Zaliani, Paolo Carloni, Paola Storici, Giulia Rossetti <br> Preprint DOI:10.26434/chemrxiv-2023-n1x1n</p> <p>Three sets of simulations were performed. This directory contains input files for simulations of three systems,<br> and link to scripts for water analysis.</p>
Niclosamide as a chemical probe for analyzing SARS-CoV-2 modulation of host cell lipid metabolism
<p>SARS-CoV-2 subverts host cell processes to facilitate rapid replication and dissemination, and this leads to pathological inflammation. We used niclosamide (NIC), a poorly soluble anti-helminth drug identified for repurposed treatment of COVID-19, which activates the cells' autophagic and lipophagic processes as a chemical probe to determine if it can modulate the host cell's total lipid profile that would otherwise be either amplified or reduced during SARS-CoV-2 infection. Through parallel lipidomic and transcriptomic analyses we observed massive reorganization of lipid profiles of SARS-CoV-2 infected Vero E6 cells, especially with triglycerides, which were elevated early during virus replication, but decreased thereafter, as well as plasmalogens, which were elevated at later timepoints during virus replication, but were also elevated under normal cell growth. These findings suggested a complex interplay of lipid profile reorganization involving plasmalogen metabolism. We also observed that NIC treatment of both low and high viral loads does not affect virus entry. Instead, NIC treatment reduced the abundance of plasmalogens, diacylglycerides, and ceramides, which we found elevated during virus infection in the absence of NIC, resulting in a significant reduction in the production of infectious virions. Unexpectedly, at higher viral loads, NIC treatment also resulted in elevated triglyceride levels, and induced significant changes in phospholipid metabolism. We posit that future screens of approved drugs should prioritize compounds that effectively counter SARS-CoV-2 subversion of lipid metabolism, thereby reducing virus replication, egress, and the subsequent regulation of key lipid mediators of pathological inflammation.</p>
Establishment of a Biological Biobank of Subjects Vaccinated Against SARS-CoV-2 Infection (COVID-19)
ClinicalTrials.gov study NCT05276388. IPD Sharing: NO. Countries: 1. Publications: 0.
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)
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.