Inithisisummaryiarticle,iIiamigoingitoishareisomeiinformationiaboutibioinformaticsitoolsii.e.,ionlineiwebiapplicationsioripublicirepositoriesiforitheievaluationiofiSARS.CoV.2igenome,ibetteriandirapididetectioniofiSARS.CoV.2iinfection, theirobustiandi reliableimethodsiforisequenceidataianalysis,ievaluationioficontainmentimeasureianditrackingiofiCOVID19.iFurthermore.iDiscoveryiofipotentialidrugitoitreatiCOVID19iandiotheritherapeuticistrategies.iIitriedimyibestitoibeiconciseianditoitheipointibecauseithereiisiailotiofiinformationipresentionitheiinternet.ii
Background:iNeediofithisistudy
OniDecemberi31,i2019,ifirstifouricasesiofipneumoniailikeiillnessiwereireportediinilocalihospitalibasediiniWuhan,iHebei,iChina.iAllitheilaboratoryiconfirmedicasesiwereisupposeditoibeilinkediwithitheiHuananiSeafoodiWholesaleiMarketiiniSouthiChinaibyisurveillanceimechanismifori“pneumoniaiofiunknownicause”.iThisimechanismiwasidevisediforitheiearlyiidentificationiofideadlyipathogensiiniresponseitoiSARS.CoV.2ioutbreakiini2003.iOnitheisameiday,iChineseiCenteriforiDiseaseiControliandiPreventioni(ChinaiCDC)imadeiaiteamiandisentitoiWuhanicityitoiinvestigateibriefly.iTheiinvestigationiresultediinitheidiagnosisiofiallitheiaffectedipatientsiwithinCoV-19-infectedipneumoniai(NCIP).i
TheicoronavirusipatientsihaveibeeniincreasingidayibyidayisinceitheipandemiciexplodediiniChinaianditoidatei(Junei8,i2020)iapproximatelyi7.1imillionipeopleihaveibeenidiagnosediwithicoronavirusiandi406,353ideathsihaveibeenireportediworldwide.iToibetteridetect,idiagnose,ievaluateitheiSARS.CoV.2igenomeiandifindiandidevelopibetteridrugioritreatmentistrategiesiforiCOVID19;iresearchersifromiallioveritheiglobiareiworkingiinicollaborationiwithibioinformaticians.iAllibioinformaticsitools,idescribediorigiveniexclusivelyiforiCOVID-19ievaluationiareifreelyiavailable.
So,ilet’sistartiwithibioinformaticsitools.
1-Detectioniandiannotation
TheiworldwideiroutinelyiusedimethodiforitheidetectioniofiSARS.CoV.2iisiairealitimeiquantitativeireverseitranscriptaseipolymeraseichainireactioni(qRTiPRC).iThisitestiisibasedioniamplificationiofispecificiregioniofiviraligenomeibyiaisetiofismallisyntheticipieceiofiDNAibasedioniviraligenome.iTheigenesiwhichiareimostlyiamplifiediforitheidetectioniofiSARS.CoV.2iareii)itheivirusienvelopi(E)igeneiandiii)iRNAidependentiRNAipolymerasei(RdRp)igene.iTheispecificityi(exclusioniofifalseipositiveioutcome)iandisensitivityi(exclusioniofifalseinegative)iveryiimportantipoints;iifinotianalyzedibyibioinformaticsitoolsibeforeisynthesizingiprimers;iainewisetiofiprimeriwouldibeirequirediforisuccessfulianalysis.i
Here,iailotiofitoolsiforidetectioniandiannotationsiofiSARS-CoV-2iareipresentiinitablei1ibelow.
1.1 PriSeT:iPrimeriSearchiTooli
PriSeTiisiaitoolithatiidentifiesichemicallyisuitableiPCRiprimersisetiiniaigivenidataiset.iTheireferenceidataiseticanibeiaiFASTAifileioficompleteigenomesioriaisetiofishortiregions.iPriSeTicomputesifrequentik.mersithaticouldiserveiasiprimericandidates,icombinesithemitoipairs,iandiranksithemibyifrequencyianditaxonomicicoverage.iPriSeTicomputesiprimeripairsithatioccuriinialligenomesiandiareisuitableiforiRTiPCR.iTheseiprimeripairsicanithenibeifilteredifurtheriforithoseiproducingitranscriptsithatihaveinoimatchesioutsideitheiSARS-CoV-2itaxon.
1.2 CoVPipe:iAmplicon-basedigenomeireconstructioni
CoVPipeiisiaihighlyioptimizediandifullyiautomatediworkflowiforitheireference_basedireconstructioniofiSARS.CoV.2igenomesibasedioninextigenerationiampliconisequencingidataiusingiCleanPlexiSARSCoV.2ipanelsi(ParagoniGenomics,iHayward,iCA,iUSA)ifromiswabisamples.iTheipipelineiappliesireadiclassification,iclippingiofirawireadsitoiremoveiterminaliPCRiprimerisequencesioriprimerihybridsiasiwelliasiIlluminaiadaptersiandilow-qualityibases.
1.3 poreCov:iRapidisampleianalysisiforinanoporeisequencing
TheiworkflowiporeCoviisiimplementediininextflowiforifulliparallelizationiofitheiworkloadiandistableisampleiprocessing.iporeCovigeneratesiallinecessaryiresultsiandiinformationibeforeiscientistsicontinueitoianalyzeitheirigenomesiorimakeithemipublicion,ie.g.,iGISAIDioriENAi/iNCBI.iTheiworkflowicarriesioutiallinecessaryistepsifromibasecallingitoiassemblyidependingionitheiuseriinput,ifollowedibyilineageipredictioniofieachigenomeiusingiPangolin.iFurthermore,ireadicoverageiplotsiareiprovidediforieachigenomeitoiassessitheiamplificationiqualityiofitheimultiplexiPCR.iIniaddition,iporeCoviincludesiaiquickitimeitreeibasedianalysisiofitheiinputsiagainstireferenceisequencesiusingiaugurianditoytreei11iforivisualization.iporeCovisupportsiscientistsiinitheiriSARS.CoV.2iresearchibyireducingitheitimeiconsumingibioinformaticibottlenecksiiniprocessingidozensiofiSARS.CoV.2isequencingiruns.
1.4 VADR:iSARS-CoV-2igenomeiannotationiandivalidation
VADRivalidatesiandiannotatesiviralisequencesibasedionimodelsibuiltifromireferenceisequences.iCoronavirusimodels,iincludingioneiforiSARS.CoV.2i(NC_045512.2),iareiavailableiforianalyzingicoronavirusisequences.iVADRicomputesianialignmentiofieachiincomingisequenceiagainstitheiRefSeqiandiusesiititoimapitheiRefSeqifeatures,iwhichiincludeiproteinicodingisequencesi(CDS),igenes,imatureipeptidesi(mat_peptide),iandistructuraliRNAi(stem_loop)ifeatures.iTheiORF1abipolyproteiniCDSiinvolvesiaiprogrammediribosomaliframeshift,iwhichiVADRiisicapableiofiproperlyiannotating.iTheitooliidentifiesiandioutputsiinformationiaboutimoreithani40itypesiofiproblemsiwithisequences,isuchiasiearlyistopicodonsiiniCDS,iandihasibeeniiniuseibyiGenBankiforiscreeningiandiannotatingiincomingiSARS-CoV-2isequenceisubmissionsisinceiMarchi2020.
1.5 V-Pipe:iCallingisingle-nucleotideivariantsiandiviralihaplotypesi
V_pipeiisiaibioinformaticsipipelineithatiintegratesivariousicomputationalitoolsiforitheianalysisiofiviralihighithroughputisequencingidata.iItisupportsitheireproducibleiend-to-endianalysisiofiintra-hostiNGSidata,iincludingiqualityicontrol,ireadimappingiandialignment,iandiinferenceiofiviraligenomicidiversityionitheileveliofibothisingleinucleotideivariantsi(SNVs)iandilongirangeiviralihaplotypes.
1.6 Haploflow:iMulti-strainiawareideinovoiassembly
Haploflowiisiainovel,ideiBruijnigraphbasediassembleriforitheideinovo,istrain.resolvediassemblyiofivirusesithatiisiableitoirapidlyiresolveidifferencesiupitoiaibasepairilevelibetweenitwoiviralistrains.iHaploflowiwillihelpiadvanceiSARS.CoV.2iresearchibyienablingitheidetectioniandifull_lengthireconstructioniofiSARS-CoV-2imulti-strainiinfections.
1.7 VIRify:iAnnotationiofivirusesiinimeta-omicidata
VIRifyiisiairecentlyideveloped,igenericipipelineiforitheidetection,iannotation,ianditaxonomiciclassificationiofiviraliandiphageicontigsiinimetagenomiciandimetatranscriptomiciassemblies.iThisipipelineiisipartiofitheirepertoireiofianalysisiservicesiofferedibyiMGnify.iVIRify’sitaxonomiciclassificationireliesionitheidetectioniofitaxon_specificiprofileihiddeniMarkovimodelsi(HMMs),ibuiltiuponiaisetiofi22,014iorthologousiproteinidomainsiandireferreditoiasiViPhOGs.iIncludediinithisiprofileiHMMidatabaseiarei139imodelsithatiserveiasispecificimarkersiforitaxaiwithinitheiCoronaviridaeifamily.
VIRifyicanibeiusediforitheiidentificationioficoronavirusesiiniclinicaliandienvironmentalisamples.iDueitoitheiintrinsicidifferencesibetweenimetatranscriptomesiandimetagenomes,iadditionaliconsiderationsiregardingiqualityicontrol,iassembly,ipost_processingiandiclassificationihaveitoibeikeptiinimind.
1.8 GenomeianalysisitoolsibyiVBRC
TheiViraliBioinformaticsiResearchiCentrei(VBRC)iisiaimatureiresourceibuiltispecificallyiforivirologistsitoifacilitateitheicomparativeianalysisiofiviraligenomes.iWithiniVBRC,iaiMySQLidatabaseicreatedifromiGenBankifilesisupportsinumerousianalysisitools.iTheiVBRCiwasidevelopediforidsDNAivirusesibutihasibeeniadaptediforicoronaviruses.iSARS.CoV.2iandicloselyirelatedivirusesihaveibeeniaddeditoitheidatabase.iVBRCitoolsiwillihelpitoivisualizeidifferencesibetweenicoronavirusisequencesiatidifferentilevelsiofiresolution.
1.9 VIRULIGN:iCodon-correctimultipleisequenceialignments
VIRULIGNiwasidevelopediforifast,icodon_correctimultipleisequenceialignmentiandiannotationiofivirusigenomes,iguidedibyiaireferenceisequence.iVIRULIGNiisieasyitoiinstall,ienablingiscientistsitoiperformilarge_scaleianalysesionitheirilocalicomputationaliinfrastructure.iVIRULIGNiisiparticularlyiwellisuiteditoistudyitheirapidlyigrowinginumberiofiSARS.CoV.2igenomesimadeiavailable,idueitoiitsiefficientialignmentialgorithmithatihasilinearicomputationalicomplexityiwithirespectitoitheinumberiofisequencesistudied.iFurthermore,iVIRULIGN’siflexibleioutputiformatsi(e.g.,iCSVifileiwithiheadersicorrespondingitoitheigenomeiannotation)ifacilitateiitsiintegrationiintoianalysisiworkflows,iloweringitheithresholdiforiscientistsitoideliveriadvancedibioinformaticsipipelinesiandidatabases,ithatiareinecessaryitoitrackitheiCOVID-19ipandemic.
1.10 RfamiCOVID-19iResources:iCoronavirusispecificiRNAifamilies
RfamiisiaidatabaseiofiRNAifamiliesithatihostsicuratedimultipleisequenceialignmentsiandicovarianceimodels.iToifacilitateitheianalysisiofiCoronavirusisequences,iRfamiproducediaispecialireleasei14.2iwithiteninewifamiliesirepresentingitheientirei5’iandi3’iuntranslatediregionsi(UTRs)ifromiAlpha-,iBeta-,iGamma-,iandiDelta_coronaviruses.iIniaddition,itheionlineiRfamisequenceisearchienablesiusersitoiscanigenomicisequencesiandifinditheiRNAielements.
1.11 UniProtiCOVID-19iproteiniportal:irapidiaccessitoiproteiniinformation
UniProtihasirecognizeditheiurgencyiofiannotatingiandiprovidingiaccessitoitheilatestiinformationioniproteinsirelevantitoitheidiseaseiforibothitheivirusiandihumanihost.iIniresponse,itheiCOVID19iUniProtiportaliprovidesiearlyipre_releaseiaccessitoi(i)iSARS.CoV.2iannotatediproteinisequences,i(ii)iclosestiSARSiproteinsifromiSARSi2003,i(iii)ihumaniproteinsirelevantitoitheibiologyiofiviraliinfection,ilikeireceptorsiandienzymes,i(iv)iProtVistai[51]ivisualizationiofisequenceifeaturesiforieachiprotein,i(v)ilinksitoisequenceianalysisitools,i(vi)iaccessitoicollatedicommunityicontributedipublicationsirelevantitoiCOVID19,iasiwelliasi(vii)ilinksitoirelevantiresources.
1.12 Pfamiproteinifamiliesidatabase
TheiPfamiproteinifamiliesidatabaseiisiwidelyiusediinitheifieldiofimolecularibiologyiforilarge_scaleifunctionaliannotationiofiproteins.iPfam,iversioni33.1,icontainsianiupdatedisetiofimodelsithaticomprehensivelyicoveritheiproteinsiencodedibyiSARS.CoV.2.iTheionlyiSARS.CoV.2iproteinithatilacksiaimatchiisiOrf10,iaismalliputativeiproteinifoundiatithei3’_endiofitheiSARS.CoV.2igenome,iwhichiappearsitoilackisimilarityitoianyiotherisequenceiiniUniProtKBi18i.iTheiPfamiprofileihiddeniMarkovimodeli(HMM)ilibraryiinicombinationiwithitheiHMMERisoftwareifacilitatesirapidisearchiandiannotationioficoronavirusesiandicanibeiuseditoigenerateimultipleisequenceialignmentsithatiallowitheiidentificationiofimutationsiandiclustersiofirelatedisequences,iparticularlyiusefuliforioutbreakitrackingiandistudyingitheievolutionioficoronaviruses.
2 Tracking,iepidemiologyiandievolutioni
Asithereiisinoiuniversaliapproachiforiclassifyingiaivirusispecies’igeneticidiversity,itheiphylogeneticicladesiareireferreditoibyidifferentiterms,isuchiasi‘subtypes’,i‘genotypes’,iori‘groups’.iHowever,iphylogeneticiassignmentiisiimportantiforistudiesionivirusiepidemiology,ievolution,iandipathogenesisi(seeiCovidex,iPangolin).iThus,iainomenclatureisystemiforinamingitheigrowinginumberiofiphylogeneticilineagesithatimakeiupitheipopulationidiversityiofiSARS-CoV-2iisineeded.
Foritracking,iepidemiologyiandievolutionilinks,itablei2iisidedicatedihereibelow.
2.1Covidex:iAlignment-freeisubtypingiusingimachineilearning
Viralisubtypesioricladesirepresenticlustersiamongiisolatesifromitheiglobalipopulationiofiaidefinedispecies.iSubtypificationiisirelevantiforistudiesionivirusiepidemiology,ievolutioniandipathogenesis.iMostisubtypeiclassificationimethodsirequireitheialignmentiofitheiinputidataiagainstiaisetiofipre_definedisubtypeireferenceisequences.iTheseimethodsicanibeicomputationallyiexpensive,iparticularlyiforilongisequencesisuchiasiSARS.CoV.2i(<30ikbiperigenome).iToitackleithisiproblem,imachineilearningitoolsimayibeiusediforivirusisubtyping.iCovidexiwasidevelopediasianiopen-sourceialignment-freeimachineilearningisubtypingitool.iItiisiaishinyiappithatiallowsifastiandiaccuratei(out_of_bagierroriratei<i1.5i%)iclassificationiofiviraligenomesiinipre_definediclusters.iForiSARS.CoV.2,itheidefaultiuploadedimodeliisibasedioniNextstrainiandiGISAIDidata.iAlternatively,iuser_uploadedimodelsicanibeiused.iCovidexiisibasedioniaifastiimplementationiofirandomiforestitrainedioveriaik_meridatabase.
2.2 Pangolin:iPhylogeneticiAssignmentiofiNamediGlobaliOutbreakiLINeages
PangoliniassignsiaiglobalilineageitoiqueryiSARS.CoV.2igenomesibyiestimatingitheimostilikelyiplacementiwithiniaiphylogeneticitreeiofirepresentativeisequencesifromiallicurrentlyidefinediglobaliSARS.CoV.2ilineagesibasedionitheilineageinomenclature.iItiisieasilyiscalableisoithatiiticanibeirunionieitherithousandsioriaihandfuliofisequences.iInternally,ipangolinirunsimafftiandiiqtree,iprovidingiaiguideitreeiandialignmentitoikeepianalysisioverheadirelativelyilightweight.iPangolinihasimanyiapplications,iincludingifrontlineihospitaliuseiandilocaliandiglobalisurveillance.iForiexample,iinihospitalsisequencingiSARS.CoV.2isamples,iiticouldibeiuseditoiruleioutiwithin_hospitalitransmission,iinformingiinfectionicontrolimeasures.iIticanialsoibeiusediforisurveillanceipurposes,isummarizingiwhichilineagesiareipresentiinianiareaiofiinterest. Pangolinimakesiitieasyitoigetiusefuliinformationioutiofiviraligenomeisequencingiinireal_timeiandicaniassistiiniidentifyinginewiintroductionsiandiinitrackingitheispreadiofiSARS.CoV.2.
2.3 BEAST2:iPhylodynamicsibasedioniBayesianiinference
BEASTi2iisianiadvancedicomputationalisoftwareiframeworkithatienablesisophisticatediBayesianianalysesiutilisingiairangeiofiphylodynamicipackages.iTheiphylogeneticihistoryi(theitree)icanibeiinferredisimultaneouslyiwithievolutionaryiandiepidemiologicaliparameters,isuchithatitheiuncertaintyifromialliaspectsiofitheijoinedimodeliisiaccountediforiandireflectediinitheiresults.i
2.4 Phylogeographicireconstructioniusingiairitransportationidata
Phylogeographicimethodsicombineigenomicidataiwithitheisamplingilocationsiofiviraliisolatesiandimodelsiofispread,ie.g.iusingiairitraveliorilocalidiffusion,itoireconstructitheiputativeispreadipathsiandioutbreakioriginsiofirapidlyievolvingipathogens.
PhylogeographicireconstructioniusingiairitransportationidataicanibeiuseditoistudyitheiglobalispreadiofitheiSARS.CoV.2ipandemic,iespeciallyiinitheiearlyiphasesiwheniairitravelistillisubstantiallyicontributeditoitheispreadiofitheivirus.iTheimethodiisicurrentlyiadapteditoiconsideribothiairitraveliandilocalimovementidataiwithinicountriesiduringiinferenceitoireflectitheichangingiworldwideimovementsiinidifferentiphasesiofitheipandemic.
2.5 COPASI:iModelingiSARS-CoV-2idynamicsiwithidifferentialiequations
COPASIiisiaidynamicsisimulator,ioriginallyifocusedionichemicaliandibiochemicalireactioninetworks.iHowever,iitiisibyinowialsoiwidelyiapplieditoiotherifields,iincludingiepidemiology.iItiallowsisimulatingimodelsiwithitheitraditionalidifferentialiequationiapproachithatirepresentsipopulationsiasicontinua,iasiwelliasiwithiaistochasticikineticsiapproachiwhichiconsidersipopulationsiareicomposediofiindividuals.iCOPASIihasiaicommonimodelirepresentationiforibothitheseiapproaches,iwhichiallowsiswitchingibetweenithemiwithiease.iAdditionally,ioneicaniaddiarbitraryidiscreteieventsitoimodels.iThisisoftwareiisiequippediwithiseveralialgorithmsithatiprovideicomprehensiveianalysesiofimodels,iandiitihasisupportiforiparameteriestimationiusingiaiseriesiofioptimizationialgorithms.
COPASIihasibeeniuseditoimodelivariousiaspectsiofivirology,iincludingimechanismsiofiaction,ipharmaceuticaliinterventions,ivirusilife_cycle,ivaccineidesigniandidynamicsiofiepidemics.iCOPASIihasialsoibeeniapplieditoiCOVID19,iparticularlyitoimodelitheidynamicsiofitheiepidemiciandieffectiofiinterventions.
2.6 COVIDSIM:iEpidemiologicalimodelsiofiviralispread
ClassicaliepidemiologicalimodelsihaveiseenibroadireuseiinidescribingitheiCOVID19ioutbreak.iDeterministicioricompartmentalimathematicalimodelsiassigniindividualsiiniaipopulationitoidifferentisubgroupsiandidescribeitheiridynamicichangesiusingisystemsiofidifferentialiequations.iInibrief,iinitheiSEIRioriSEIRDiModel,iindividualsiiniaipopulationiareigroupediintoiSusceptiblei(S),iExposedi(E),iInfectedi(I),iRecoveredi(R)iandiDeceasedi(D)iindividuals.i
Initially,ialliindividualsiexceptiforiaismallinumberiwhoiareialreadyiinfectediareiconsideredisusceptibleitoiinfection.iTheimodelicanithenisimulateitheipopulationiinfectionidynamics,iusingiparametersisuchiasitheiincubationitimeioritheiaverageidiseaseidurationiforiparameterizationiofitheidifferentialiequations.iSuchiSEIRimodelsihaveibeeniuseditoipredictitheiCOVID-19idynamics.
2.7 CoV-GLUE:itrackinginucleotideichangesiinitheiSARS-CoV-2igenomei
SARS.CoV.2iisinaturallyiaccumulatinginucleotideimutationsiiniitsiRNAigenomeiasitheipandemiciprogresses.iPointimutations,ispecificallyinonsynonymousisubstitutions,iwilliresultiiniaminoiacidireplacementsiiniviraligenomeisequences,iwhileiotherimutationsiwilliresultiiniinsertionsiorideletionsi(indels).iOniaverageitheiobservedichangesiwouldibeiexpecteditoihaveinoioriminimaliconsequenceiforivirusibiology.
TheipurposeiofiCoV_GLUEiisitoitrackitheichangesiaccumulatingiinitheiSARS.CoV.2igenome.iUsersicanibrowseitheiaccumulatingivariationiorisubmitiaiFASTAifileiofiainoveligenomeitoiCoV_GLUEiforicomparisonitoitheiavailableidata.iAniaminoiacidireplacement,iindelsiandidiagnosticiprimeridesignireportiisigeneratedifromitheisubmittedidata.iTheiusericaniaccessitheidetectedivariantsiandiusingiaiphylogeneticiplacementimaximumilikelihoodimethodivisualizeitheirisequenceirelativeitoiaireferenceidataiset.
2.8 PoSeiDon:iPositiveiSelectioniDetectioniandiRecombinationiAnalysis
PoSeiDonisimplifiesitheidetectioniofipositiveiselectioniiniprotein_codingisequences.iFirstly,itheipipelineibuildsiaimultipleisequenceialignment,iestimatesiaibest_fittingisubstitutionimodel,iandiperformsiairecombinationianalysisifollowedibyitheiconstructioniofiallicorrespondingiphylogenies.iSecondly,ipositivelyiselectedisitesiunderivaryingimodelsiareidetected.iTheiresultsiareisummarizediiniaiuser_friendlyiwebipage,iprovidingialliintermediateiresultsiandigraphicallyidisplayingirecombinationieventsiandipositivelyiselectedisites.
TheirapididetectioniofipositiveiselectionihelpsitoimonitoriproteinichangesiofiSARS.CoV.2iduringitheipandemic.iItiprovidesipotentialitargetisitesiforidrugidevelopment,ihelpingitoicounteractitheivirusiduringiitsi"armsirace"iwithitheihumanispecies.
3 Drugidesign
Toilimititheipandemicithreat,iitiisiofiutmostiimportanceitoidevelopitherapyiandivaccinationistrategiesiagainstiCOVID19.iUnderstandingitheimolecularimechanismsiunderlyingitheidisease’sipathogenesisiisikeyitoiidentifyingipotentialidrugicandidatesiforiclinicalitrials.iViralihostiprotein_proteiniinteractionsi(PPIs)iplayiaicrucialiroleiduringiviraliinfectioniandiholdipromisingitherapeuticiprospects.
(Hufsky et al., 2020)
3.1 VirHostNetiSARS-CoV-2ireleasei
TheicompleteiunderstandingiofimoleculariinteractionsibetweeniSARS.CoV.2iandihosticellulariproteinsiisikeyitoihighlightifunctionsithatiareiessentialiforiviralireplicationiandipathogenesisiofiCOVID19ioutbreak.iTowardithisiend,iVirHostNetiwasiupgradediiniMarchi2020itoiincludeiaicomprehensiveicollectioniofiprotein_proteiniinteractionsimanuallyiannotatedifromitheiliteratureiinvolvingiORFeomesifromimultipleicoronaviruses,iincludingiMERS_CoV,iSARS.CoV.1iandiSARS.CoV.2.iHence,iiniaifewidays,imoreithani650ibinaryiprotein_proteiniinteractionsiwereimadeiavailableitoiscientistsiworkingioniCOVID19.
3.2 CORDITE:iCORonaiDrugiInTERactionsidatabasei
CORDITEicollectsidataionipotentialidrugs,itargets,ianditheiriinteractionsiforiSARS.CoV.2ifromipublishediarticlesiandipreprints.iCORDITEiintegratesimanyifunctionalitiesitoienableiusersitoiaccess,isort,iandidownloadirelevantidataitoiconductimeta_analyses,itoidesigninewiclinicalitrials,iorievenitoiconductiaicuratediliteratureisearch.iCORDITEiautomaticallyiincorporatesipublicationsifromiPubMed,ibioRxiv,ichemRxiv,iandimedRxivithatireportiinformationionicomputational,iinivitro,ioricaseistudiesionipotentialidrugsiforiCOVID19.iBesidesioriginaliresearch,ireviewsiandicommentsiareialsoiincludediinitheidatabase.iTheiinformationifromitheiarticlesiandipreprintsiareimanuallyicuratedibyimoderatorsiandicanibeiaccessediviaitheiwebiserverioritheiopeniAPI.
TheiCORDITEidatabaseiisiupdatediweeklyiand,iatitheidateiofisubmission,iprovidesidataiforimoreithani700iinteractionsiofi23itargetsiforimoreithani530idrugsifromialmosti300ipublicationsiandimoreithani240iclinicalitrialsi(asiofiMayi19,i2020).iItiisithusitheilargest,icuratedidatabaseiavailableiforidrugiinteractionsiforiSARS.CoV.2.iItiallowsiresearchersitoicarryioutimeta_analysesionipotentialidrugsisystematicallyianditoiidentifyipotentialidrugicandidatesiforiclinicalitrials.
3.3 CoVex:iCoronaVirusiExplorer
CoVexiisiainetworkiandisystemsimedicineiwebiplatformithatiintegratesiexperimentalivirus_humaniproteiniinteractionsiforiSARS.CoV.2iandiSARS.CoV.1,ihumaniprotein_proteiniinteractionsiandidrug_proteiniinteractionsiintoiailarge_scaleiinteractome.iItiallowsibiomedicaliandiclinicaliresearchersitoipredictinovelidrugitargetsiasiwelliasidrugirepurposingicandidatesiusingiseveralistate_of_the_artigraphianalysisimethodsispecificallyitailoreditoitheinetworkimedicineicontext.
3.4 P-HIPSTer:iaivirus-hostiprotein-proteiniinteractioniresource
Viral_hostiprotein_proteiniinteractionsi(PPIs)iplayiaicrucialiroleiduringiviraliinfectionibyico_optingihosticellulariprocessesiandiholdipromisingitherapeuticiprospects.iAlongitheseilines,itheiP_HIPSTeridatabaseicanisignificantlyicontributeitoiSARS.CoV.2iresearchibyiproviding:i(1)itestableihypothesesionimoleculariinteractionsiunderlyingiviraliinfectioniandipathogenesisiand;i(2)ihighlightingihostifactorsiandipathwaysithatiserveiasipotentialidrugitargetsitoitreatiinfectionicausedibyidifferenticoronaviruses.
Conclusions
BioinformaticiansiarounditheiworldihaveireactediquicklyitoitheiCOVID19ipandemiciupgradedioridevelopedinewicoronavirus_specificitoolsitoiadvanceiSARS.CoV.2iresearchiandiboostitheidetection,iunderstanding,ianditreatmentiofiCOVID19.iThisilistiisinoticompleteisetiofibioinformaticsitoolsiforiSARS.CoV.2iresearch.iItiisipossibleithatiaccordingitoitheisituationiofiCOVID19ipandemiciresearchersimightidevelopinewibioinformaticsitoolsiforiresearchiinifuture.i
Toireadioriginaliarticleipleaseiclickihere.
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