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1、ArchVirol(2004)149:621624DOI10.1007/s00705-003-0244-0ThephylogenyofSARScoronavirusBriefReportA.J.Gibbs,M.J.Gibbs,andJ.S.ArmstrongSchoolofBotanyandZoology,AustralianNationalUniversity,Canberra,AustraliaReceivedJuly10,2003;acceptedSeptember29,2003Publishedo
2、nlineJanuary5,2004cSpringer-Verlag2003Summary.Differenttree-buildingmethodsconsistentlyplacetheSARScorona-virus(SARS-CoV)asabasalGroup2coronavirusratherthanasanungroupedspeciesasconcludedbyothers.DetailedcomparisonsoftheSARS-CoVgenomicsequencewiththoseof
3、sixothercoronavirusesfailedtofindevidenceofrecombi-nationorgenomicrearrangementusingcomputationalmethodsdesignedforthatpurpose.∗IntheirreportoftheSARS-CoVgenomicsequence,Marraetal.[4]constructedunrootedphylogenetictreesbybootstrappeddistancemethodsusingthe
4、encodedmajorproteinsequencesofSARS-CoVandrepresentativesofthethreecorona-virusgroupsandreportedthatthoseencodedbySARS-CoVdonotclustermorecloselywithanyonegroup,andconcludedthatSARS-CoVshouldbeconsideredthefirstrepresentativeofGroup4coronaviruses.LikewiseRo
5、taetal.[5]usingthesamemethodsreportedthatSARS-CoVisapproximatelyequidistantfromallpreviouslycharacterizedcoronavirusesandformsadis-tinctgroupwithinthegenusCoronavirus.Howeverneitherofthosestudieshadoutgroupsequencesintheanalyses,andthereforeitwasnotpossib
6、letobesurewhetherSARS-CoVshowedconsistentrelationshipswithothercorona-viruses.ThelargestgeneoftheSARS-CoVgenomeisthatwhichencodesthemulti-functionalpolymeraseandcomprises70.7%ofthegenome,andthenextlargestisthespike(peplomer)gene,afurther12.7%.Wefoundthepo
7、lymerasegenesofthearterivirusestobeclearlyhomologoustothoseofcoronavirusesasGenBanksearchesusingBLASTXgaveEvaluesaround1×10−4−5betweenarterivirusandcoronavirussequences,andtheythereforeprovideanappropriateoutgroupto622A.J.Gibbsetal.coronaviruspolymerases,
8、howeversimilarsearchesusingBLASTN−Xand−Pfailedtofindoutgroupsequencesforthespikeproteingene.ThecompletepolymerasegenesofSARS-CoV,sixothercoronavirusesandtwoarteriviruseswerealigned[3,8]eitherasaminoacidsorasnucleotid
