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2,489 results for “Sars-CoV-2”
Impact of New Variants on SARS-CoV-2 Infectivity and Neutralization: A Molecular Assessment of the Alterations in the Spike-Host Protein Interactions
<p>MD simulation trajectories and structural models from the work which first appeared on bioRxiv (https://doi.org/10.1101/2021.01.10.426143), later ssrn (<a href="https://dx.doi.org/10.2139/ssrn.3907841">http://dx.doi.org/10.2139/ssrn.3907841</a>), and finally accepted for publication by Iscience.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run1_WT_RBD_ACE2.zip">Run1_WT_RBD_ACE2.zip</a></p> <p>Description: A compressed (zipped) folder contains three independent MD trajectories of WT RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run2_N501Y_RBD_ACE2.zip">Run2_N501Y_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Alpha RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run3_Beta_RBD_ACE2.zip">Run3_Beta_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Beta RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run4_Delta_RBD_ACE2.zip">Run4_Delta_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Delta RBD-ACE2 complex</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run5_UK2_E484K_N501Y_ACE2.zip">Run5_UK2_E484K_N501Y_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of UK2 RBD-ACE2 complex</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Structural_model_PDBs.zip">Structural_model_PDBs.zip</a></p> <p>Description: A compressed folder contains eight pdb files of those structural models plotted in Figs 1, 3, 5, 6, 7 and S1.</p>
Data from: Dispersion of SARS-CoV-2 in air surrounding COVID-19 infected individuals with mild symptoms
<p><span>Since the beginning of the pandemic, the transmission modes of SARS-CoV-2—particularly the role of aerosol transmission—has been much debated. Accumulating evidence suggests that SARS-CoV-2 can be transmitted by aerosols, and not only via larger respiratory droplets. In this study, we quantified SARS-CoV-2 in air surrounding 14 test subjects in a controlled setting. All subjects had SARS-CoV-2 infection confirmed by a recent positive PCR test and had mild symptoms when included in the study. RT-PCR and cell culture analyses were performed on air samples collected at distances of one, two, and four meters from test subjects. Oronasopharyngeal samples were taken from consenting test subjects and analyzed by RT-PCR. Additionally, total aerosol particles were quantified during air sampling trials. Air viral concentrations at one-meter distance were significantly correlated with both viral loads in the upper airways, mild coughing, and fever. One sample collected at four-meter distance was RT-PCR positive. No samples were successfully cultured. The results reported here have potential application for SARS-CoV-2 detection and monitoring schemes, and for increasing our understanding of SARS-CoV-2 transmission dynamics.</span></p>
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
<p>Scripts and metadata used in the analysis of the manuscript, <em>Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants.</em></p>
Dataset: Elisa cohort study on SARS-CoV-2 transmission
<p>The Elisa study is a population-based cohort study in Lübeck and the surrounding area (northern Germany) with the aim to determine the prevalence and influencing factors of infections with the Sars-CoV2 over a one-year period. The study collected data from April 2020 to February 2021. A cohort of 3000 randomly selected individuals were screened by swab (PCR) for active corona infection and blood draws were performed to determine antibodies at seven time points. In addition, continuous app-based questionnaires were administered to study participants regarding symptoms, behavior, and social factors.</p> <p>The data set consists of a file with baseline variables and examination results for the 3000 participants and another file with the continuous survey data (90,000 interviews).</p>
Figures S1–S10 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
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.
The translational landscape of SARS-CoV-2 and infected cells reveals suppression of innate immune genes
<p>SARS-CoV-2 utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2 infected model cell lines and primary airway cells grown at the air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We find that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy despite notable accumulation of ribosomes within the slippery sequence on the frameshifting element. In the highly permissive cell models, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokines, cytokines and interferon stimulated genes, many of these mRNAs were not translated efficiently. Impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development. The processed data presented here is derived from the relevant RNA-seq and ribo-seq libraries.</p>
Dataset for "Glycaemic control is associated with SARS-CoV-2 breakthrough infections in vaccinated patients with Type 2 diabetes"
<p>Dataset for "Glycaemic control is associated with SARS-CoV-2 breakthrough infections in vaccinated patients with Type 2 diabetes"</p>
Cleavage of SARS-CoV-2 spike protein mutants
<p class="MsoNormal"><span>Several SARS-CoV-2 variants emerged that harbor mutations in the surface unit of the viral spike (S) protein that enhance infectivity and transmissibility. Here, we analyzed whether ten naturally-occurring mutations found within the extended loop harboring the S1/S2 cleavage site of the S protein, a determinant of SARS-CoV-2 cell tropism and pathogenicity, impact S protein processing and function. None of the mutations increased but several decreased S protein cleavage at the S1/S2 site, including S686G and P681H, the latter of which is found in variants of concern B.1.1.7 (Alpha variant) and B.1.1.529 (Omicron variant). None of the mutations reduced ACE2 binding and cell-cell fusion although several modulated the efficiency of host cell entry. The effects of mutation S686G on viral entry were cell-type dependent and could be linked to the availability of cathepsin L for S protein activation. These results show that polymorphisms at the S1/S2 site can modulate S protein processing and host cell entry. </span></p>
Seroprevalence of SARS-CoV-2 infection in the general population in Togo in 2021
<p>Results of population-based age stratified seroepidemiological investigation in Togo</p> <p> </p>
Data for the manuscript 'Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework'.
<p>This zip file contains the data downloaded from external sources used to produce the results in the manuscript 'Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework'. Note that all of the data contained in this zip file was publicly available at the time of writing.</p> <p>The corresponding Github can be found here:<br> https://github.com/alan-turing-institute/jbc-turing-rss-testdebiasing</p> <p>The publication is available here:<br> https://doi.org/10.1038/s41564-021-01029-0</p>
SARS-CoV-2 nucleocapsid and RT-PCR results
<p><span>We collected blood samples from patients admitted to the hospital during a period with RT-PCR based-screening of patients for Severe Acute Respiratory Syndrome Cornavirus-2 (SARS-CoV-2). Retrospectively the SARS-CoV-2 nucleocapsid protein (NP) plasma concentrations were measured with an ELISA method and used for an initial time course study to find the optimal time-point for sampling blood. Next, we estimated the diagnostic accuracy i.e. the clinical sensitivity and specificity at different plasma NP cut-off concentrations.</span></p> <p><span>The time course study revealed profiles with rapid or more slow declines in NP titers after the RT-PCR result. Nevertheless, in the time interval 0 – 7 days after the RT-PCR result, the NP concentration was always above the level of detection at 1.66 pg/ml suggesting that the diagnosis could be established in the time interval of 0 - 7 days.</span></p> <p><span>The median time gap between the plasma NP and RT-PCR results was 0.0 days (n = 1957, interval: -26 to + 21 days). Reducing the time gap to seven days, the clinical sensitivity was 90.0% (n= 60, 95% CI, 82.4% to 97.6%) at a specificity of 95.9% (n=1876, 95% CI, 95.0% to 96.8%). Curve analysis by receiver operation characteristics identified a cut-off concentration of 1.87 pg/mL NP as optimal resulting in a positive predictive value of 41.2%, a negative predictive value of 99.7% and a prevalence of 3.1%.</span></p> <p><span>In conclusion, the NP method is acceptable for making the laboratory diagnosis of SARS-CoV-2, and an intended use of plasma NP as a prospective nosocomial screening method is considered feasible.</span></p>
Data and code for the manuscript titled "Persistence of SARS-CoV-2 immunity, Omicron's footprints, and projections of epidemic resurgences in South African population cohorts"
<p>Data and code for the manuscript titled “Persistence of SARS-CoV-2 immunity, Omicron’s footprints, and projections of epidemic resurgences in South African population cohorts”</p>
Nasopharyngeal swabs vs. saliva sampling for SARS-CoV-2 detection: A cross-sectional survey of acceptability for caregivers and children after experiencing both methods
<p><span>Background: </span><span>Saliva sampling is a promising alternative to nasopharyngeal swabs for SARS-CoV-2 testing, but acceptability data is lacking. We characterize the acceptability of saliva sampling and nasopharyngeal swabs for primary decision makers and their children after experiencing both testing modalities.</span></p> <p><span>Results: </span><span>48 participants and 48 primary decision makers completed the survey. Nasopharyngeal swab acceptability differed between scenarios, ranging 79% [95%CI: 66, 88] to 100% [95%CI: 95, 100]); saliva sampling acceptability was similar across scenarios, ranging 92% [95%CI: 82, 97]) to </span><span> </span><span>98% [95%CI: 89, 99]. 58% of youth described significant pain with nasopharyngeal swabbing, versus none with saliva sampling. 90% of children prefer saliva sampling. 66% of primary decision makers would prefer nasopharyngeal swabbing if it were 10% more sensitive.</span></p> <p><span>Conclusion: </span><span>Though youth prefer saliva sampling over nasopharyngeal swabs, primary decision makers present for testing remain highly accepting of both. Acceptance of nasopharyngeal swabs, however, varies with the testing indication and is influenced by perceived test accuracy. Understanding factors that influence sampling acceptance will inform more successful testing strategies.</span></p>
The Spike Protein of SARS-CoV-2 Impairs Lipid Metabolism and Increases Susceptibility to Lipotoxicity: Implication for a Role of Nrf2
<p>Original figures for the following publication: </p> <p>The Spike Protein of SARS-CoV-2 Impairs Lipid Metabolism and Increases Susceptibility to Lipotoxicity: Implication for a Role of Nrf2</p> <table align="left"> <tbody> <tr> <td> <p><em>Cells </em><strong>2022</strong>, <em>11</em>, x. https://doi.org/10.3390/xxxxx</p> </td> </tr> </tbody> </table>
Virtual screening on SARS-CoV-2 Nsp14_testing of 5474 hits in a Nsp14 biochemical assay and an A549-hACE2 SARS-CoV-2 infected cells
<p> </p> <p>This report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 Nsp14 and confirmation of potential hits in a SARS-CoV-2 Nsp10/Nsp14 biochemical exonuclease assay and in a A549-hACE2 cell-based anti-SARS-CoV-2 assay.</p>
Genomic epidemiology of SARS-CoV-2 in Mozambique
<p><strong>Abstract: </strong>Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020. Since then, the virus has spread to all provinces in the country. Here we set out to perform a retrospective molecular epidemiological analysis of the first 25 months of the epidemic in Mozambique. In total, 1 146 whole genome sequences from Mozambique were phylogenetically analyzed against a globally representative set of references to put the epidemic in the country into context. The domestic pandemic was marked by four successive waves of infection, with the first wave associated with B.1 ancestral lineages, while the Beta, Delta, and Omicron Variants of Concern (VOCs) were responsible for the majority of cases and death during the second, third, and fourth waves. Viral exchanges between Mozambique and the outside world mimicked pandemic waves, with most exchanges occurring during the second, third, and forth waves and most imports and exports being attributed to South Africa. Due to a health system already under constraint and paucity of data in Mozambique, there is a need to continue to strengthen and support genomic surveillance in the country as VOCs and Variants of interests (VOIs) are often reported from the southern African region.</p>
Removal of senescent cells reduces the viral load and attenuates pulmonary and systemic inflammation in SARS-CoV-2-infected, aged hamsters
<p>Older age is one of the strongest risk factors for coronavirus disease 2019 (COVID-19) morbidity and mortality. In an older adult, the chronic accumulation of senescent cells can interfere with the immune system and accentuate inflammation. Here, we sought to determine whether age-associated cellular senescence contributes to the severity of COVID-19 by studying the well-established golden hamster model of severe acute respiratory syndrome coronavirus (SARS-CoV-2)-driven lung disease. We found that aged hamsters (22 months of age) accumulate senescent cells in the lungs and that the senolytic drug ABT-263 (a Bcl-2-family inhibitor) depletes these cells at baseline and during a SARS-CoV-2 infection (when the senescent cell count is typically elevated). Relative to young hamsters (2 months of age), aged hamsters had a greater viral load during the acute phase of infection and displayed higher levels of fibrosis and worse body weight recovery during the post-acute phase. Interestingly, early treatment with ABT-263 was associated with a significantly lower pulmonary viral load and an amelioration of COVID-19-like lung disease in aged (but not young) animals. ABT-263 treatment of aged animals was also associated with lower pulmonary and systemic levels of senescence-associated secretory phenotype factors. We conclude that the removal of senescent cells via treatment with a senolytic reduces the pathologic severity of SARS-CoV-2 infection in aged hamsters. As several senolytics have recently moved into early-stage clinical trials, our present findings have clear clinical relevance.</p>
Seroprevalence of exposure to SARS-CoV-2 in domestic dogs and cats and its relationship with COVID-19 cases in the city of Villavicencio, Colombia
<p>Raw data from the article "Seroprevalence of exposure to SARS-CoV-2 in domestic dogs and cats and its relationship with COVID-19 cases in the city of Villavicencio, Colombia". It includes the consecutive number, name, sex, age, species, coordinates, commune, spectrophotometry results and Sample to Positive <em>Ratio</em> from the ELISA test performed in each dog and cat included in the study (435 tested animals). </p>
A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2
<p><span>The ongoing pandemic caused by SARS-CoV-2 has called for concerted efforts to generate new insights into the biology of betacoronaviruses to inform drug screening and development. Here, we establish a workflow to determine the RNA recognition and druggability of the nucleocapsid N-protein of SARS-CoV-2, a highly abundant protein crucial for the viral life cycle. We use a synergistic method that combines NMR spectroscopy and protein-RNA cross-linking coupled to mass spectrometry to quickly determine the RNA binding of two RNA recognition domains of the N-protein. Finally, we explore the druggability of these domains by performing an NMR fragment screening. This workflow identified small molecule chemotypes that bind to RNA binding interfaces and that have promising properties for further drug development.</span></p> <p><span>This deposition contains the NMR data acquired to determine the structural features of RBDs- RNA recognition as well as selected relevant data regarding the characterization of promising molecular fragments to disrupt protein-RNA interaction.</span></p> <p><span>Furthermore, we included the molecular docking files used to obtain the reported structural model.</span></p>
Dataset: Polystyrene and SARS-CoV-2 S protein MD simulations
<p>Coordinates (input files and equilibrated structures) corresponding to the MD simulations reported in Sahihi and Faraudo, J. Chem. Inf. Model. 2022, 62, 16, 3814–3824 <a href="https://doi.org/10.1021/acs.jcim.2c00562">https://doi.org/10.1021/acs.jcim.2c00562</a> . Please cite this publication and the dataset in any use of the data.</p> <p>The coordinate files in pdb format include fully glycosylated structures of the S1 subunit of SARS-CoV-2 spike protein (up and down confirmations) and a polystyrene slab.</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.