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1、ArchVirol(2003)148:22072235DOI10.1007/s00705-003-0162-1AcomparativesequenceanalysistorevisethecurrenttaxonomyofthefamilyCoronaviridaeJ.M.Gonz´alez1,P.Gomez-Puertas2,D.Cavanagh3,A.E.Gorbalenya4,andLuisEnjuanes11CentroNacionaldeBiotecnolog´ıa,CSIC,DepartmentofMolecularandCellBiology,CampusUnivers
2、idadAut´onoma,Cantoblanco,Madrid,Spain2BioinformaticsLab.CentrodeAstrobiolog´ıa(CSIC-INTA),Torrej´ondeArdoz,Madrid,Spain3InstituteforAnimalHealth,ComptonLaboratory,Compton,Newbury,U.K.4CenterofInfectiousDiseases,LeidenUniversityMedicalCenter,Leiden,TheNetherlandsReceivedApril2,2003;acceptedMay2
3、0,2003PublishedonlineAugust18,2003cSpringer-Verlag2003Summary.TheCoronaviridaefamily,comprisingtheCoronavirusandTorovirusgenera,ispartoftheNidoviralesorderthatalsoincludestwootherfamilies,ArteriviridaeandRoniviridae.Basedongeneticandserologicalrelationships,groups1,2and3werepreviouslyrecognize
4、dintheCoronavirusgenus.Inthisreportwepresentresultsofcomparativesequenceanalysisofthespike(S),envelope(E),membrane(M),andnucleoprotein(N)structuralproteins,andthetwomostconservedreplicasedomains,putativeRNA-dependentRNApolymerase(RdRp)andRNAhelicase(HEL),aimedatarevisionoftheCoro-naviridaetaxon
5、omy.TheresultsofpairwisecomparisonsinvolvingstructuralandreplicaseproteinsoftheCoronavirusgenuswereconsistentandproducedpercentagesofsequenceidentitiesthatweredistributedindiscontinuousclusters.Inter-grouppairwisescoresformedasingleclusterinthelowestpercentile.NohomologsoftheNandEproteinshavebe
6、enfoundoutsidecoronaviruses,andtheonly(very)distanthomologsofSandMproteinswereidentifiedintoroviruses.Intragroupsequenceconservationwashigher,althoughforsomepairs,especiallythosefromthemostdiversegroup1,scoreswerecloseorevenoverlappedwiththosefromtheintergroupcomparisons.Phylogeneticanalysisofsi
7、xproteinsusinganeighbor-joiningalgorithmconfirmedthreecoronavirusgroups.ComparativesequenceanalysisofRdRpandHELdomainswereextendedtoincludearterivirusandronivirushomologs.Thepairwisescoresbetweensequencesofthegenera2208J.M.Gonz´ale
