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Inferred protein interactions between coronavirus and human proteins
<p>This repository contains the protein-protein interactions inferred by mimicINT (<a href="https://github.com/TAGC-NetworkBiology/mimicINT" target="_blank" rel="noopener">https://github.com/TAGC-NetworkBiology/mimicINT</a>) between the proteins of seven human coronaviruses (HCoV-229E, HCoV-HKU1, HCoV-NL63, HCoV-OC43, MERS-CoV, SARS-CoV and SARS-CoV-2) and substantial fraction of the human proteome. This dataset was generated in the context of the RiPCoN project (H2020-SC1-PHE-CORONAVIRUS-2020, <a href="https://cordis.europa.eu/project/id/101003633" target="_blank" rel="noopener">https://cordis.europa.eu/project/id/101003633</a>).</p>
Extended Data Fig. 7 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 7 | Analysis of the inter-subunitshydrogen bondsat the interfaceof RBDandhACE2. Frequencyofformationofhydrogenbondsat theinterface of RBDandhACE2 intheknob (A), base (B), andtipregions (C). 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. 3 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 3 | Nucleotideandamino-acidalignmentsof thefurin cleavagesiteregion. Completenucleotideandamino-acidspikesequencesof representativebat SARS-CoV-2-likecoronavirusesweredownloadedfrom GenBankand GISAIDandaligned with MAFFT (G-INS-I parameter) (A & C). Alignmentsweremanuallyeditedas proposedby Zhou2 andLytras47 with CLC Main Workbench (Qiagen) (B & D). Alignmentsof thefurincleavageregionare presentedatthenucleotide (A & B) andtheamino-acid (C & D) level, respectively.
Extended Data Fig. 1 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 1 | Spike identity matricesatthe genus level of representativesarbecoviruses. Amino-acid (lower) andnucleotide (upper) identitymatricesof Laotianandrepresentativehuman,bat, andpangolin sarbecoviruses.Spike N-terminal (NTD), Receptor-binding (RBD) and S2 nucleotideandamino-acidsequenceswerealigned with MAFFT, andidentity matriceswereconstructedusing CLCMain Workbench 21.0.4 (Qiagen). Matriceswerecoloredaccordingtotheidentityscale,from 25% (red) to 100% (green) of nucleotideoramino-acididentity.
Extended Data Fig. 2 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 2 | Alignmentofthespike RBDdomain. Protein alignmentof the Receptor Binding Domain (RBD) of Laotianandrepresentative human, batandpangolinsarbecoviruses.Sequenceswerealignedwith MAFFT in G-iNS-Imode. Residuesinteractingwithhuman ACE2 receptorare highlighted ingrey.Thedomainusedforinteractionsmodeling,basedonthe X-raystructure 6M0J (residues T333 to G526), ishighlightedbyablackline.
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.
Coronavirus Spike Protein Sequences from NCBI Virus
<p>For the study of taxonomic classification of coronaviruses across all genera (Alpha-, Beta-, Gamma-, and Deltacoronavirus), we can use spike protein sequences downloaded from the NCBI Virus website, \url{https://www.ncbi.nlm.nih.gov/labs/virus/vssi/}. The spike protein sequences used in this study were downloaded on November 21 and 27, 2021 using search terms such as ``spike'', ``S1 protein'', ``S2 protein'', and ``S protein'', in order to download as many spike protein sequences as possible.</p>
Ir and NMR for article Synthesis and Biological Activity Evaluation of New Isatin-Gallate Hybrids as Antioxidant and Anticancer Agents (in vitro) and In-silico Study as Anticancer Agents and Coronavirus Inhibitors
<p>this is IR and NMR data for article titled <strong>Synthesis and Biological Activity Evaluation of New Isatin-Gallate Hybrids as Antioxidant and Anticancer Agents (<em>in vitro</em>) and In-silico Study as Anticancer Agents and Coronavirus Inhibitors </strong></p> <p> </p>
Slovenian Coronavirus News Comments Corpus News-CommSLO
<p>A corpus of readers' news comments posted below news articles on the topic of the covid-19 pandemic, published in major Slovenian daily newspapers and news portals in the six-month early pandemic period (March 2020 to September 2020).</p> <div>The corpus is designed to facilitate research on crisis discourses, crisis communication, as well as pandemic-time linguistic innovation. It is available in plain text version and XML with full metadata. The corpus complements a separate corpus of news articles Slovenian Coronavirus Corpus NewsSLO. Parallel versions from Croatia and Serbia are also available.</div> <div> </div> <div>The project leading to this publication has received funding from the European Union’s Horizon 2020 research and innovation programme under the <a href="https://cordis.europa.eu/programme/id/H2020-EU.4./en">H2020-EU.4. - SPREADING EXCELLENCE AND WIDENING PARTICIPATION </a>programme Widening fellowships grant agreement No 101038047.</div>
Serbian Coronavirus News Comments Corpus News-CommSR
<p>A corpus of readers' news comments posted below news articles on the topic of the covid-19 pandemic, published in major Serbian daily newspapers and news portals in the six-month early pandemic period (March 2020 to September 2020).</p> <div>The corpus is designed to facilitate research on crisis discourses, crisis communication, as well as pandemic-time linguistic innovation. It is available in plain text version and XML with full metadata. The corpus complements a separate corpus of news articles Serbian Coronavirus Corpus NewsSR. Parallel versions from Croatia and Slovenia are also available.</div> <div> </div> <div>The project leading to this publication has received funding from the European Union’s Horizon 2020 research and innovation programme under the <a href="https://cordis.europa.eu/programme/id/H2020-EU.4./en">H2020-EU.4. - SPREADING EXCELLENCE AND WIDENING PARTICIPATION </a>programme Widening fellowships grant agreement No 101038047.</div>
Serbian Coronavirus Corpus NewsSR
<p>A corpus of news articles on the topic of the covid-19 pandemic, published in major Serbian daily newspapers and news portals in the six-month early pandemic period (March 2020 to September 2020).<br>The corpus is designed to facilitate research on crisis discourses, crisis communication, as well as pandemic-time linguistic innovation. It is available in plain text version and XML with full metadata. <br>Covid-NEWS-SR is complemented with a separate corpus of citizen metalanguage comments, i.e. online comments to the news articles, available as Covid-NEWS-Comm-SR. Parallel versions from Slovenia and Croatia are also available.</p> <p>The project leading to this publication has received funding from the European Union’s Horizon 2020 research and innovation programme under the <a href="https://cordis.europa.eu/programme/id/H2020-EU.4./en">H2020-EU.4. - SPREADING EXCELLENCE AND WIDENING PARTICIPATION </a>programme Widening fellowships grant agreement No 101038047.</p>
Seroprevalence of IgG antibodies against SARS coronavirus 2 in Belgium – a serial prospective cross-sectional nationwide study of residual samples (March – October 2020)
<p>This dataset contains information on seven prospective cross-sectional nationwide residual sera collection rounds. The samples were analyzed for IgG antibodies against S1 proteins of SARS-CoV-2 with a semi-quantitative commercial ELISA (EuroImmun, Luebeck, Germany).</p> <p>We provide a CSV file containing the following variables:</p> <ul> <li><strong>code</strong>: unique sample code</li> <li><strong>age_cat</strong>: age categories by 10-year age bands (0-10, 10-20, ..., 80-90, 90-Inf), the lower limit is included, e.g. 0-10 = [0,10)</li> <li><strong>sex</strong>: sex (f = female, m = male)</li> <li><strong>province</strong>: province of residence (11 categories)</li> <li><strong>region</strong>: region of residence (3 categories: Brussels, Flanders, Walloon)</li> <li><strong>collection_round</strong>: collection round (values 1 to 7)</li> <li><strong>collection_start</strong>: start date of the collection round</li> <li><strong>collection_end</strong>: end date of the collection round</li> <li><strong>igg_orig</strong>: measured IgG OD value as character (note, a semi-quantitative ELISA was used, i.e. this should not be interpreted continiously)</li> <li><strong>igg_cat</strong>: categorized IgG OD values <ul> <li><em>LoD</em>: IgG OD < 0.15</li> <li><em>negative</em>: 0.15 ≤ IgG OD < 0.8</li> <li><em>borderline</em>: 0.8 ≤ IgG OD < 1.1</li> <li><em>positive</em>: 1.1 ≤ IgG OD</li> </ul> </li> </ul> <p>Please see publication mentioned underneath for more details (<a href="https://doi.org/10.1101/2020.06.08.20125179">https://doi.org/10.1101/2020.06.08.20125179</a>).</p> <p><strong>Funding:</strong> This work received funding from the European Union's Horizon 2020 research and innovation program - project EpiPose (No 101003688), the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 682540 TransMID), the Flemish Research Fund (FWO 1150017N) and from The Antwerp University Fund; which is a community of donors who contribute to research and education with their personal commitment through a donation, gift, bequest or through academic chairs. The funders had no role in study design, data collection, data analysis, data interpretation, writing or submitting of the report. The corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication.</p>
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