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1、ArchVirol(2005)150:22992311DOI10.1007/s00705-005-0573-2PhylogeneticandrecombinationanalysisofcoronavirusHKU1,anovelcoronavirusfrompatientswithpneumoniaP.C.Y.Woo1,2,3,?,S.K.P.Lau1,2,3,?,Y.Huang1,?,H.-W.Tsoi1,K.-H.Chan1,andK.-Y.Yuen1,2,31DepartmentofMicr

2、obiology,FacultyofMedicine,TheUniversityofHongKong,HongKong2ResearchCentreofInfectionandImmunology,FacultyofMedicine,TheUniversityofHongKong,HongKong3StateKeyLaboratoryofEmergingInfectiousDiseases,TheUniversityofHongKong,HongKongReceivedFebruary25,2005

3、;acceptedApril27,2005PublishedonlineJune28,2005cSpringer-Verlag2005Summary.PhylogenetictreesconstructedusingpredictedaminoacidsequencesofputativeproteinsofcoronavirusHKU1(CoV-HKU1)revealedthatCoV-HKU1formedadistinctbranchamonggroup2coronaviruses.Ofthe

4、14treesfromp65tonsp10,nineshowedthatCoV-HKU1wasclusteredwithmurinehepatitisvirus.Fromnsp11,thetopologiesofthetreeschangeddramatically.Fortheeighttreesfromnsp11toN,sevenshowedthattheCoV-HKU1branchwasthe?rstbranch.ThecodonusagepatternsofCoV-HKU1differeds

5、igni?cantlyfromthoseinothergroup2coronaviruses.SplitdecompositionanalysisrevealedthatrecombinationeventshadoccurredbetweenCoV-HKU1andothercoronaviruses.IntroductionIthasbeenestimatedthatcoronaviruses[humancoronaviruses229E(HCoV-229E)andOC43(HCoV-OC43)]

6、causeabout530%ofrespiratorytractinfec-tions.Inlate2002and2003,SevereAcuteRespiratorySyndrome(SARS),causedbySARScoronavirus(SARS-CoV),hasresultedinmorethan750deaths[12,15,16,17,2224].Inearly2004,anovelcoronavirusassociatedwithrespiratorytractinfections,

7、humancoronavirusNL63(HCoV-NL63),wasdiscovered[3,20].Asaresultofauniquemechanismofviralreplication,coronaviruseshaveahighfrequencyofrecombination[9,10,13,14].?Theseauthorscontributedequallytothemanuscript.2300P.C.Y.Wooetal.:CoronavirusHKU1phylogenyandre

8、combinationCoronavirusesweredividedintothreegroups,withHCoV-229EandHCoV-NL63beinggroup1coronavirusesandHCoV-OC43agroup2coronavirusrespec-tively[11].ForSARS-CoV,itwasinitiallyproposedthatSARS-CoVconstitutedadistinctgroupofcoronavirus[15,