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2,489 results for “SARS-CoV-2”
Fig. 2 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Fig. 2 | Recombinationevents in the evolutionaryhistoryof sarbecoviruses. Representationof the 15 recombinant fragmentsof relevant Sarbecovirus genomescomparedtothe SARS-CoV-2 humanprototypestrain (NC_045512). Thecoordinatesof thebreakpointsrefertothenucleotide positioninthealignment.Wherepossible,theclosestviralsequenceis indicatedforeachfragment.Inothercases,MULTindicatesagroupof multiple sequences.Theasteriskmarksunresolvedfragment phylogeny (fragment 13, from positions 27,344 to 27,800 inthealignment).Sequencesarecolouredas in Fig. 1. Thecomplete phylogeneticanalysesarepresentedin Supplementary Fig.2.
Fig. 1 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Fig. 1 | Genomicdescriptionofbat-bornesarbecovirusesidentifiedin Laos. a, Mapof samplingsites.All BANALisolateswerecollectedfromthesamesite (site 1). Themapwasdownloadedfrom DIVA-GIS (https://www.diva-gis.org/ gdata). b, Phylogeneticanalysisof theproteinsequenceof the RBDof Laotian andrepresentativehuman,bat,andpangolinsarbecoviruses.Sequenceswere alignedwith MAFFT (ref.49) inautomode, andmaximum-likelihood phylogeneticreconstructionwasperformedwith PhyMLimplemented throughthe NGPhylogenyportal50 withthe LG + Gsubstitutionmodel.Branch supportwasevaluatedwiththeaBayes parameter.Batspeciesarespecifiedin thename of thesequences.Sequencesarecolouredaccordingto Fig. 1c. c, Similarityplotanalysisof Laotianandrepresentativebatandpangolin sarbecovirusesbasedonthefull-lengthgenomesequenceof the SARS-CoV-2 humanprototypestrain (NC_045512, Wuhan-Hu-1) usedasareference. Theanalysiswasperformedwiththe SimPlotprogramversion 3.5.1 (ref.51) with the Kimuratwo-parametermodel, awindowsizeof 1,000 basepairs,astepsize of 100 basepairs,a transition/transversionrate (T/t) of 2.0, anda Gap/Strip parameter: on51. nsp,non-structural protein;RdRP, RNA-dependent RNA polymerase.d, Heatmapof identitiesattheproteinlevelof representative human,batandpangolinsarbecovirusescomparedtohuman SARS-CoV-2 lineage B (NC_045512). Spikeproteinhasbeendividedintofunctionaldomains, andthesequencesareorderedaccordingtopercentageof identityof the RBD domain.Theasteriskmarkstheabsenceof afunctional ORF10 in Thaibat RacCS203 (accessionnumber MW251308). Theheatmapwascreatedusingthe gplotspackagein R (version 3.6.3). AA, aminoacid.
Extended Data Fig. 5 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 5 | Additionalanalysisof the MDsimulationsof the BANAL-52/103 RBD–hACE2 complex. Comparisonof thetimeseriesof interface RMSDduringthecourseof two MDsimulationsof the BANAL-52/103 RBD–hACE2 complexwithshort (BANAL-52/103-CoV.1) andlong (BANAL- 52/103-CoV.1*) equilibrationphase.Thelargefluctuationsof theinterface RMSDareduetotheflexibilityof the RBDloopbetweenresidues S443 and Y449 (insets, inyellow).Whentheseresidueswerenotincludedinthe calculationof theinterface RMSD, thetimeseriesdisplayedamorestable behavior (BANAL-52/103-CoV.1-Land BANAL-52/103-CoV.1*-L).
Fig. 4 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Fig. 4 | BANAL-236 entryandpropagationinhumancells. a, Resultsof spike-pseudotyped BANAL-236 (squares) and SARS-CoV-2 (strain BetaCoV/ France/IDF0372/2020, GISAIDaccessionnumber EPI_ISL_406596,diamonds) pseudovirusentryassayin HEK-293T cellsexpressing (purple lines) ornot (grey lines) thehACE2 receptor,showninrelativeluminescenceunits (RLUs) producedbythefireflyluciferasepresentinthelentiviralbackbone andthe Bright-Gloluciferasesubstrate.Asingleexperimentperformedintriplicate representativeof twoexperiments isshown.Centrevaluesrepresentthe averageof thethreereplicatesanderrorbarsindicates.d. b, Resultsof spike-pseudotyped BANAL-236 (black) and SARS-CoV-2 (strain BetaCoV/ France/IDF0372/2020, grey) neutralizationassayexpressedas apercentageof neutralizationofluciferaseactivityintheabsenceof serum.Seraneutralizing SARS-CoV-2 werefrompatientswithconfirmedinfectionswhereas non-neutralizingserasampleswerecollectedbeforethespreadof SARS-CoV-2 Laos.Thedashedlinemarkstheneutralizationthreshold.Asingleexperiment representativeof threeindependentexperimentsisshown. c, Humancelllines expressingendogenous ACE2,Calu-3 (blue lines) and Caco-2 (green lines),were infectedatan MOIof 0.01 withthe BANAL-236 virus (squares) andthevirusfirst detectedin Wuhan (diamonds).VeroE6 cellswereinfectedatan MOI of 0.0001 with BANAL-236 virus (squares) and SARS-CoV-2 (strain BetaCoV/France/ IDF0372/2020, diamonds) pre-incubatedwith (grey lines) orwithout (pink lines) solublehACE2 (sACE2) at 25 Μgml−1 for 30 min. Genomecopynumberwas determinedbyquantitative RT-PCRinthesupernatantsrecovered 3 and 4 days post-infection. Asingleexperimentperformedintriplicateisshown.Centre valuesrepresenttheaverageof thethreereplicatesanderrorbarsindicates.d.
Fig. 3 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Fig. 3 | Dynamicsof thebindingof hACE2 to bat-sarbecovirus-borne RBDs andinsightintothestructureofthecomplex. a, Biolayerinterferometry (BLI) bindinganalysis of thehACE2 peptidasedomaintoimmobilized BANAL-52/103,BANAL-236 or SARS-CoV-2 RBDs.Black linescorrespondto aglobalfitof thedatausinga 1:1 bindingmodel.b, Frequencyofformationof saltbridgesclosetothe RBD–ACE2 interface (fromlefttoright:D30/K417, E35/ K493, D38/K493, K31/E35 and D38/K353) duringthecourseof the MD simulations.Theanalysiswasperformedforninedifferent MDsimulations (threereplicatesforeachcomplex) ofhACE2 incomplexwith RBDs from SARS-CoV-2 (SARS-CoV-2.1,SARS-CoV-2.2 and SARS-CoV-2.3, shadesof green), BANAL-236 (BANAL 236-CoV.1, BANAL 236-CoV.2 and BANAL 236-CoV.3,shadesof red) and BANAL-52/103 (BANAL 52/103-CoV.1, BANAL 52/103-CoV.2 and BANAL 52/103-CoV.3, shadesofblue). c, Ribbon representationsof thecrystalstructuresof thehACE2 peptidase domain (cyan) incomplexwith SARS-CoV-2 (PDB 6M0J) or BANAL-236 (this study,PDB 7PKI) RBDs (pink). Blackarrowsintheoverallstructuresindicatethestructural differencebetweenthetwocomplexesatthelevelofhelix H4. The magnificationsshowthemaininteractionsinthe ACE2–RBD interfaces. Residuesinthereceptor-bindingmotif alteredbetween SARS-CoV-2 and BANAL-236 arehighlighted withcolouredoutlines.Numbers 1, 2 and 3 indicate thethreemainclustersof interactionsbetweenhACE2 and RBDs.
Extended Data Fig. 4 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 4 | Analysisof thestability and conformational heterogeneityofRBD–hACE2 complexes. Timeseries (leftcolumn) and violinplots (rightcolumn) ofbackbone Root Mean Square Deviation (RMSD) fromtheinitial,energy-minimizedmodelcalculatedontheresiduesin RBD (A), hACE2 (B), attheinterface of RBDandhACE2 (C), andontheentirecomplex (D). Intheviolinplots,thewhitecirclecorrespondstothemedianvalue,the blackrectangleextendsfromthefirsttothethirdquantiles,andthethinblack linerepresentsthe 95% confidenceintervals.Populationof the 3 most significantclustersvisitedduringthecourseof the MDsimulations (E). Theanalysisisperformedfor 9 different MDsimulations:3 replicatesof the SARS-CoV-2 (shadesof green),BANAL-236 (shadesof red), and BANAL-52/103 (shadesofblue) RBD–hACE2 complexes.
Extended Data Fig. 8 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 8 | Stick representation. Stick representation of segments D364-S375 of BANAL-236 (left panel) and SARS-CoV-2 (right panel) RBDs.A 2Fo-Fc composite omit map (contoured at 3σ) is shown for this region in BANAL-236 RBD.
Extended Data Fig. 6 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 6 | Estimationof RBD–hACE2 bindingenergy. Time series (leftcolumn) andviolinplots (rightcolumn) of the RBD–hACE2 binding energyestimatedusing ROSETTA (A) and FoldX (B). Intheviolinplots,the whitecirclecorresponds tothemedianvalue,theblackrectangleextendsfrom thefirsttothethirdquantiles,andthethinblacklinerepresentsthe 95% confidenceintervals.Theanalysisisperformedfor 9 different MDsimulations: 3 replicatesof the SARS-CoV-2 (shadesof green), BANAL-236 (shadesof red), and BANAL-52/103 (shadesofblue) RBD–hACE2 complexes.
Extended Data Fig. 9 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 9 | Isolationof BANAL-236 on VeroE6 cells. (A) CPE observedon VeroE64 daysafterinoculationatan MOIof 10-4 fromthe C1. (B) Uninfected VeroE6 cellslayer.(C) Plaqueassayperformedfromthe C2 stock on VeroE6 cells.(D) Comparative CPEobservedon VeroE6 cellsinfectedwith SARS-CoV-2 ('Wuhan', toppanel) or BANAL-236 (bottom panel) inabsence (left) orinpresence (right) of soluble ACE2. Photosweretakenwitha EVOSXLCore microscopeatx10. Asingleexperimentperformedintriplicateisshownfor eachcellline.
Risk of bias assessments for the Cochrane review 'SARS-CoV-2-neutralising monoclonal antibodies to prevent COVID-19'
<p>Risk of bias assessments and support for judgement with ROB 2 tool for the Cochrane Review: SARS-CoV-2-neutralising monoclonal antibodies to prevent COVID-19.</p>
Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies.
<p>This repository contains the molecular dynamics trajectories of the SARS-CoV-2 Spike RBD bound to BD23 and B38 monoclonal antibodies. The simulations for the RBD only systems are also provided. The trajectories are available for the WT spike protein as well as for four different variants (alpha, beta, kappa and delta). The simulations of the RBD only system are propagated for 300 ns and for the RBD-Antibody complex for 500 ns. The trajectories are saved at 100 ps interval. The Steered MD simulation trajectories (WT_RBD_B38_SMD_1.dcd etc.) and collective variables files are also included (WT_RBD_B38_SMD_1.colvars.traj etc.). There are 5 SMD trajectories for each RBD antibody pair. The details of the simulation can be obtained from the preprint: https://doi.org/10.1101/2021.08.13.456317</p>
Supplementary Data: OpenCOVID model output underlaying Figures 1 and 2 of "Modelling the impact of Omicron and emerging variants on SARS-CoV-2 transmission and public health burden"
<p>Supplementary data files <strong>Figure_1.xlsx</strong> and <strong>Figure_2.xlsx</strong> contain the model simulation outcomes for Figures 1 and 2 of <a href="https://www.medrxiv.org/content/10.1101/2021.12.12.21267673v2">Le Rutte, Shattock <em>et al</em></a> "<strong>Modelling the impact of Omicron and emerging variants on SARS-CoV-2 transmission and public health burden</strong>" (2022)</p> <ul> <li><strong>Figure 1</strong>: Peak daily hospital occupancy (number of beds per 100,000 population over the six-month simulation period) for three variant properties; infectivity (relative to Delta), immune evading capacity (%), and severity (relative to Delta)<br> </li> <li><strong>Figure 2</strong>: Percentage of COVID-19 infections and deaths averted by third-dose vaccines for adults and vaccinating 5-11-year-olds with doses one and two.<br> </li> <li>Open access source-codes of the associated plotting functions are published <a href="http://zenodo.org/record/6532404#.Yqw7cezMKdb">here</a> on Zenodo.<br> </li> <li>Open access source-codes for the OpenCOVID model of all analyses as presented in <a href="https://www.medrxiv.org/content/10.1101/2021.12.12.21267673v2">Le Rutte, Shattock <em>et al.</em> (2022)</a> are publicly available at <a href="https://github.com/SwissTPH/OpenCOVID/tree/manuscript_december_2021/src">https://github.com/SwissTPH/OpenCOVID/tree/manuscript_december_2021/src</a>.<br> </li> <li>Detailed model descriptions and model equations of individual-based transmission model <strong>OpenCOVID</strong> are described in <a href="https://pubmed.ncbi.nlm.nih.gov/34923396/">Shattock <em>et al</em>. (2022)</a> and <a href="https://www.medrxiv.org/content/10.1101/2021.12.12.21267673v2">Le Rutte, Shattock <em>et al.</em> (2022).</a></li> </ul>
Screening of 2694 RdRP virtual screening hits in RdRP/Nsp7/Nsp8 biochemical assay and confirmation in cellular SARS-CoV-2 assay
<p>This report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 RNA polymerase and confirmation of potential hits in a biochemical SARS-CoV RTC assay and A549-hACE2 cell-based anti-SARS-CoV-2 assay.</p>
Alternative Covid-19 mitigation measures in school classrooms: Analysis using an agent-based model of SARS-CoV-2 transmission
<p>The SARS-CoV-2 epidemic continues to have major impacts on children's education, with schools required to implement infection control measures that have led to long periods of absence and classroom closures. We have developed an agent-based epidemiological model of SARS-CoV-2 transmission that allows us to quantify projected infection patterns within primary school classrooms, and related uncertainties; the basis of our approach is a contact model constructed using random networks, informed by structured expert judgment. The effectiveness of mitigation strategies is considered in terms of effectiveness at suppressing infection outbreaks and limiting pupil absence. Covid-19 infections in schools in the UK in Autumn 2020 are re-examined and the model used for forecasting infection levels in autumn 2021, as the more infectious Delta-variant was emerging and school transmission was thought likely to play a major role in an incipient new wave of the epidemic. Our results are in good agreement with available data and indicate that testing-based surveillance of infections in the classroom population with isolation of positive cases is a more effective mitigation measure than bubble quarantine both for reducing transmission in primary schools and for avoiding pupil absence, even accounting for the insensitivity of self-administered tests. Bubble quarantine entails large numbers of pupils being absent from school, with only a modest impact on classroom infection levels. However, maintaining a reduced contact rate within the classroom can have a major beneficial impact on managing Covid-19 in school settings.</p>
Dataset for: Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription-free exponential amplification reaction, RTF-EXPAR
<p>A dataset is reported for a rapid isothermal method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. The procedure uses an unprecedented reverse transcription–free (RTF) approach for converting genomic RNA into DNA. This involves the formation of an RNA/DNA heteroduplex whose selective cleavage generates a short DNA trigger strand, which is then rapidly amplified using the exponential amplification reaction (EXPAR). Deploying the RNA-to-DNA conversion and amplification stages of the RTF-EXPAR assay in a single step results in the detection, via a fluorescence read-out, of single figure copy numbers per microliter of SARS-CoV-2 RNA in under 10 min. In direct three-way comparison studies the assay has been found to be faster than both PCR and loop-mediated isothermal amplification (LAMP), while being just as sensitive. The assay protocol involves the use of standard laboratory equipment and is readily adaptable for the detection of other RNA-based agents.</p>
Data: Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection
<p>Contains data necessary to reproduce the quantitative results related to a SARS-CoV-2 outbreak in NSW, Australia in the associated paper.</p> <p><strong>icpmr_delta_gisaid.csv</strong><br> Tabular data containing the GISAID accession numbers, dates of collection and submission for all sequences used in the NSW outbreak analysis. The epi set is available on GISAID as EPI_SET_220919ef. The <code>wgs_cluster</code> column contains identifiers of genomic clusters defined at ICPMR, NSW Health Pathology. A value of "Other" means that the sequence either did not belong to a cluster or was part of a cluster that contained fewer than 30 sequences in the study period, and sequences with this value should not be considered to form a single cluster.</p> <p><strong>icpmr_delta_gisaid.dists.tsv.gz</strong><br> Compressed pairwise SNP distance matrix in the format output by snp-dists. The script that creates this file from sequence data is available in the linked code archive.</p>
The Huanan Market Origin of SARS-CoV-2 is unlikely: The ancestral lineage containing specimen appears to have arisen from laboratory contamination
<p>• There is universal agreement that the lineage B/L is not the ancestral SARS-CoV-2; lineage A/S is the most ancestral lineage<br> • Until the Gao paper, no lineage A/S virus was identified at the Huanan Market, making the market an unlikely origin for the pandemic<br> • The Gao paper found one specimen, A20, with both lineage A/S and B/L<br> • The lineage B/L reads in A20 and the specimen Ct matched the expected findings<br> • The lineage A/S reads were anomalously high compared to the Ct and meet the definition of a statistical outlier<br> • The SARS-CoV-2 reads from the A20 sample also had two SNVs not seen in GISAID sequences until at least 60-90 days after the specimen was collected from the market<br> • This analysis supports a finding that the ancestral lineage A/S virus sequences in sample A20 were not present on the glove on January 1, 2020 when the sample was collected but instead arose by inadvertent laboratory contamination later, probably during metagenomic sequencing</p> <p>The absence of an unimpeachable ancestral lineage specimen at the Hunan Market makes it unlikely the market was the origin of the pandemic.</p>
Synthetic single particle cryo-EM dataset of the SARS-CoV-2 spike protein
<p>PDBs were generated using molecular dynamics.<br> See DESRES_README.txt for more details on molecular dynamics simulation.<br> PDBs were converted to volumetric data using EMAN2.<br> The image stack contains 100 000 projection images each <br> of the 10 states (see PDBs), at an SNR of 1/10 in the following order:</p> <p>state00 (closed)<br> state01 (closed)<br> state02 (closed)<br> state10 (intermediate)<br> state11 (intermediate)<br> state12 (intermediate)<br> state13 (intermediate)<br> state20 (open)<br> state21 (open)<br> state22 (open)</p> <p>Projections were made using relion_project. <br> White gaussian noise with standard deviation 1.0<br> CTF multiplied signal<br> High signal-to-noise ratio<br> Image size 96x96x96<br> <br> MRC-files used for the projections not included, but can be generated using the PDB files.<br> Final RELION reconstruction resolution is 5.33334 Angstrom (Nyqvist is at 5.33334).</p> <p>Command line for RELION reconstruction:<br> relion_refine_mpi --o refine3d/run --auto_refine --split_random_halves --i rot_trans_ctf_noise/stack.star --ref pdb2mrc/state21.mrc --ini_high 20 --dont_combine_weights_via_disc --preread_images --pool 30 --pad 2 --ctf --particle_diameter 130 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --low_resol_join_halves 40 --norm --scale --j 2 --gpu --fristiter_cc --grad </p> <p>This dataset is generated as a testbed for cryo-EM heterogeneity analysis.</p>
A DNA biosensors-based microfluidic platform for attomolar real-time detection of unamplified SARS-CoV-2 virus
<p>Raw data associated to the study entitled:</p> <p><em>A DNA biosensors-based microfluidic platform for attomolar real-time detection of unamplified SARS-CoV-2 virus</em><strong> </strong></p> <p><em>- </em>Metadata file</p> <p>- Computational data</p> <p>- Extraction data</p> <p>- Fluorescence detection</p> <p>- Fluorescence imaging</p> <p>- Labbooks</p> <p>- Surface characterization</p>
Analysis of hMSC-derived chondrocytes in response to stimulation with SARS-CoV-2 spike proteins
<p>Previous studies have detected the presence of SARS-CoV-2 viral proteins in bronchial cartilage chondrocytes. We hypothesised that the leakage of viral proteins to local joint tissue was due to virus-induced endothelial dysfunction. Studies have also shown upregulation of endothelin-1 (ET-1), the most potent vasoconstrictor, in COVID patients. We are investigating the direct effect of SARS-CoV-2 spike protein (SP) and the host response to chondrocytes.</p> <p>Human mesenchymal stem cells (hMSCs)-differentiated chondrocytes were treated with either full-length SARS-CoV-2 spike protein (SP) only or a combination of spike protein, neutralising antibody to S1 and endothelin-1 (SAE) to mimic viral insult and host response respectively. RNA sequencing was performed to compared the change in transcriptome in control, SP, and SAE. All samples were processed in the same batch. Default quality control parameters were used.</p>
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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.