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2,489 results for “Sars-CoV-2”
Detection of SARS-CoV-2 in conjunctival secretion and tears in patients with COVID-19 in a tertiary care centre, South India
<p><strong>Aims and objectives</strong>: The purpose of this study is to detect the presence of SAR-CoV-2 viral RNA in conjunctival secretions of COVID-19 patients and to compare the RT-PCR positivity rate for SARS-CoV-2 in conjunctival and nasopharyngeal swabs.</p> <p><strong>Materials and method</strong>: Eighty hospitalised COVID-19 patients whose nasopharyngeal swab tested positive for SARS-CoV-2 by RT-PCR were included in the study. Conjunctival swab was collected from the eyes of these patients and sent for detection of SARS-CoV-2 by RT-PCR method.</p> <p><strong>Results</strong>: <span>Among the eighty patients, 51 (63.7%) were males and 29 (36.3%) were females. The mean age of the patients was 55.93 ± 16.59. Six patients had ocular manifestations. Eleven (13.75%) patients tested positive on conjunctival swab for SARS-CoV-2 viral RNA, and only one of them had ocular manifestations out of the eleven.</span></p> <p><strong><span>Conclusion</span></strong><span>: In our study, the presence of SARS-CoV-2 in conjunctival secretions of COVID-19 patients was detected and this was not dependent on the presence of ocular manifestations or duration of disease. Though the conjunctival positivity is lower compared to the nasopharyngeal swab sampling, ocular surface and secretions can be a potential route of viral transmission.</span></p>
Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations
<p>The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. 7540 complete nucleotide genomes from 51 African nations were obtained and analysed from the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Influenza Data (GISAID) databases to examine genetic diversity and spread dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Utilising a variety of clade and lineage nomenclature schemes, we looked at their diversity, and used maximum parsimony inference methods to recreate their evolutionary divergence and history. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa after three years of the COVID-19 pandemic outbreak, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya, and Nigeria as key sources of viral transmissions between Sub-Saharan African nations. These findings provide insight into the viral strains that are circulating in Africa and their evolutionary patterns.</p>
Coronavirus Data Base (CoDaB-19): Banco de alvos moleculares contra o coronavírus da síndrome respiratória aguda grave 2 (SARS-CoV-2)
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Phase separation of SARS-CoV-2 nucleocapsid protein with TDP-43 is dependant on C-terminus domains
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SARS-CoV-2 in ferry wastewater
<p>Data for the journal paper "Use of wastewater from passenger ships to assess the movement of COVID-19 and other pathogenic viruses across maritime international boundaries" published in Frontiers in Public Health. doi: 10.3389/fpubh.2024.1377996</p>
Electron microscopy images and morphometric data of SARS-CoV-2 variants in ultrathin plastic sections - Dataset 05 (SARS-CoV-2 Delta B.1.617.2)
<p>Dataset 05 comprises 153 transmission electron microscopy images of extracellular SARS-CoV-2 (isolate Delta B.1.617.2) particles in ultrathin plastic sections (45 nm) through Vero cell cultures. The images were recorded with dimensions of 4112 x 3008 pixels at a pixel size of 0.1641 nm and stored in 16-bit TIF format. It is recommended that an image viewer capable of reading 16-bit images, such as IrfanView, be used to visualize the images. The image files have been size calibrated and can be opened with the correct size calibration using ImageJ or Fiji with the Bioformats importer. A PDF document is provided with the image files, which describes the methods used for the generation of the images. Additionally, an XLSX file is included, offering morphometric particle measurements and the calculated statistical values for their distribution. The dataset was produced as dataset 05 for a comparative morphometric analysis of evolving SARS-CoV-2 variants. Further datasets used for the analysis are available in this repository (see dataset description document).</p>
Electron microscopy images and morphometric data of SARS-CoV-2 variants in ultrathin plastic sections - Dataset 03 (SARS-CoV-2 Alpha B.1.1.7)
<p>Dataset 03 comprises 147 transmission electron microscopy images of extracellular SARS-CoV-2 (isolate Alpha B.1.1.7) particles in ultrathin plastic sections (45 nm) through Vero cell cultures. The images were recorded with dimensions of 4112 x 3008 pixels at a pixel size of 0.1641 nm and stored in 16-bit TIF format. It is recommended that an image viewer capable of reading 16-bit images, such as IrfanView, be used to visualize the images. The image files have been size calibrated and can be opened with the correct size calibration using ImageJ or Fiji with the Bioformats importer. A PDF document is provided with the image files, which describes the methods used for the generation of the images. Additionally, an XLSX file is included, offering morphometric particle measurements and the calculated statistical values for their distribution. The dataset was produced as dataset 03 for a comparative morphometric analysis of evolving SARS-CoV-2 variants. Further datasets used for the analysis are available in this repository (see dataset description document).</p>
Electron microscopy images and morphometric data of SARS-CoV-2 variants in ultrathin plastic sections - Dataset 01 (SARS-CoV-2 Munich929)
<p>Dataset 01 comprises 150 transmission electron microscopy images of extracellular SARS-CoV-2 (isolate Munich929) particles in ultrathin plastic sections (45 nm) through Vero cell cultures. The images were recorded with dimensions of 4112 x 3008 pixels at a pixel size of 0.1641 nm and stored in 16-bit TIF format. It is recommended that an image viewer capable of reading 16-bit images, such as IrfanView, be used to visualize the images. The image files have been size calibrated and can be opened with the correct size calibration using ImageJ or Fiji with the Bioformats importer. A PDF document is provided with the image files, which describes the methods used for the generation of the images. Additionally, an XLSX file is included, offering morphometric particle measurements and the calculated statistical values for their distribution. The dataset was produced as dataset 01 for a comparative morphometric analysis of evolving SARS-CoV-2 variants. Further datasets used for the analysis are available in this repository (see dataset description document).</p>
PanDDA analysis of ligand screen against the NSP3 macrodomain of SARS-CoV-2: ligands from FrankenROCS fragment-linking pipeline and subsequent optimization of AVI-313
<p>This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in Correy et al. 2024 (doi: https://doi.org/10.1101/2024.08.25.609621). Compounds were from fragment linking using FrankenROCS and subsequent optimization of AVI-313. </p> <p>frankenROCS_mac1.tar.gz contains structure factor intensities, PanDDA input/output and refined models/maps.</p> <p>frankenROCS_mac1_ligand-bound-states.tar.gz contains the ligand-bound states extracted from the multi-state PDB files.</p>
SARS-CoV-2 is Chinese bioweapon research
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Supplementary data for "Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2"
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Resources of "Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1"
<p>Resources of the article "Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1". See https://github.com/yunlongcaolab/SARS-CoV-2-JN.1-mAbs for future updates.</p>
Monte-Carlo simulations of aerosol-based exposure to SARS-CoV-2 in a shop/bar
<p>Data from new Monte-Carlo simulations of aerosol-based exposure to SARS-CoV-2 in shop and bar environments. For background and previous results see V. Vuorinen et al. Safety Science 130 (2020): 104866.</p> <p>The files are collected to a tar file that includes all data files used for analysis (binary files with NumPy data type .npy) and a readme.</p>
Sequences of different Coronavirus groups, including Receptor Binding Domains inferred from ancestors to SARS-CoV-2
<p>List of Coronavirus sequences used in 'Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2', by Juan Ángel Patiño-Galindo et al. Under review in Genome Medicine.</p>
Data from: Tradeoffs in moving citizen-based anuran call surveys online during the SARS-CoV-2 pandemic: lessons from rural Appalachia, USA
<p>Citizen science approaches provide adaptable methodologies for enhancing the natural history knowledge of understudied taxa and engaging underserved populations with biodiversity. However, transitions to remote, virtual training and participant recruitment in response to public health crises like the SARS-CoV-2 pandemic have the potential to disrupt citizen science projects. We present a comparison of outputs from a citizen science initiative built around call surveys for the Mountain Chorus Frog (<i>Pseudacris brachyphona</i>), an understudied anuran, in Appalachian Virginia, USA prior to and during the SARS-CoV-2 pandemic. A transition to virtual training in this initiative did not lead to a decrease in scientific output and led to unexpected natural history insight about our focal taxon; however, a reliance on virtual instruction did decrease overall participation by local residents, particularly for rural K-12 students. We discuss the tradeoffs exhibited by the adaptation of our initiative to a virtual format and provide recommendations for other citizen science initiatives facing similar restrictions in the face of current and future public health crises.</p>
Data and code underpinning: "The association of smoking status with SARS-CoV-2 infection, hospitalisation and mortality from COVID-19: A living rapid evidence review with Bayesian meta-analyses (version 12)"
<p>No description provided.</p>
Code related to article "The antibody response to SARS-CoV-2 infection persists over at least 8 months in symptomatic patients"
<p>This code is related to article "The antibody response to SARS-CoV-2 infection persists over at least 8 months in symptomatic patients"</p> <p>Abstract</p> <p>The factors involved in the persistence of antibodies to SARS-CoV-2 are unknown. We evaluated the antibody response to SARS-CoV-2 in personnel from 10 healthcare facilities and its association with individuals’ characteristics and COVID-19 symptoms in an observational study. We enrolled 4735 subjects (corresponding to 80% of all personnel) over a period of 5 months when the spreading of the virus was drastically reduced. For each participant, we determined the rate of antibody increase or decrease over time in relation to 93 features analyzed in univariate and multivariate analyses through a machine learning approach. In individuals positive for IgG ( ≥ 12 AU/mL) at the beginning of th study, we found an increase [p= 0.0002] in antibody response in symptomatic subjects, particularly with anosmia/dysgeusia (OR 2.75, 95% CI 1.753 – 4.301), in a multivariate logistic regression analysis. This may be linked to the persistence of SARS-CoV-2 in the olfactory bulb.</p>
Data for "Clinical and virological impact of single and dual infections with influenza A (H1N1) and SARS-CoV-2 in adult inpatients"
<p>The baseline enrolled 505 patients admitted to Guangzhou Eighth People's Hospital (Guangzhou, Guangdong) with a diagnosis of COVID-19 or H1N1. All the patients were tested by both viruses at admission. Demographic, clinical, treatment, and laboratory data were extracted from electronic medical records and compared among adults (≥18 years) hospitalized for H1N1 infection (<em>n</em> = 220), SARS-CoV-2 infection (<em>n</em> = 249) and co-infection with both viruses (<em>n</em> = 36). The prevalence rate of H1N1 co-infection was 12.6% (36/285) among patients hospitalized with COVID-19. Co-infection affected a predominantly older age group and was associated with poorer clinical outcome. We also described the viral load trajectory in patients with diverse types of infection. Lower initial Ct values (higher viral loads in nasopharyngeal swabs) of co-infected patients was found to be associated with a higher number of adverse events and clinical symptoms. Considering the COVID-19 pandemic and a simultaneous epidemic of seasonal influenza, the data in China may critically inform future therapeutic or prophylactic strategies, especially for other developing countries.</p>
Diagnostic accuracy of Panbio™ rapid antigen test for SARS-CoV-2 in paediatric population
<p>The aim was to evaluate the accuracy of the Panbio<sup>TM</sup> Rapid Antigen Test for SARS-CoV-2 in the setting of a primary health care centre (PHC) in paedriatic population, with use of the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) as gold standard.</p>
Structure prediction from SARS-CoV-2 accessory proteins ORF-6
<p>Structure prediction made with Collabfold for SARS-CoV-2 accessory protein ORF-6.</p> <p>The archive contains both the structure and</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.