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ncyclopedia of E VIROLOGY THIRD EDITION ncyclopedia of E VIROLOGY THIRD EDITION EDITORS-IN-CHIEF Dr BRIAN W J MAHY and Dr MARC H V VAN REGENMORTEL AcademicPressisanimprintofElsevier LinacreHouse,JordanHill,Oxford,OX28DP,UK 525BStreet,Suite1900,SanDiego,CA92101-4495,USA Copyrightã2008ElsevierInc.Allrightsreserved ThefollowingarticlesareUSgovernmentworksinthepublicdomainandarenotsubjecttocopyright: BovineViralDiarrheaVirus,Coxsackieviruses,PrionsofYeastandFungi,HumanRespiratorySyncytialVirus, FishRhabdoviruses,Varicella-ZosterVirus:GeneralFeatures,VirusesandBioterrorism,BeanCommonMosaic VirusandBeanCommonMosaicNecrosisVirus,Metaviruses,Crimean-CongoHemorrhagicFeverVirusandOther Nairoviruses,AIDS:GlobalEpidemiology,PapayaRingspotVirus,TranscriptionalRegulationinBacteriophage. Nepovirus,CanadianCrownCopyright2008 Nopartofthispublicationmaybereproduced,storedinaretrievalsystemortransmittedinanyformorby anymeanselectronic,mechanical,photocopying,recordingorotherwisewithoutthepriorwritten permissionofthepublisher PermissionsmaybesoughtdirectlyfromElsevier’sScience&TechnologyRightsDepartmentinOxford, UK:phone(+44)(0)1865843830;fax(+44)(0)1865853333;email:[email protected] youcansubmityourrequestonlinebyvisitingtheElsevierwebsiteat(http://elsevier.com/locate/permission), andselectingObtainingpermissiontouseElsevier material Notice Noresponsibilityisassumedbythepublisherforanyinjuryand/ordamagetopersonsorpropertyasa matterofproductsliability,negligenceorotherwise,orfromanyuseoroperationofanymethods,products, instructionsorideascontainedinthematerialherein.Becauseofrapidadvancesinthemedicalsciences, inparticular,independentverificationofdiagnosesanddrugdosagesshouldbemade BritishLibraryCataloguinginPublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary LibraryofCongressCatalogNumber:200892260 ISBN:978-0-12-373935-3 ForinformationonallElsevierpublications visitourwebsiteatbooks.elsevier.com PRINTEDANDBOUNDINSLOVENIA 08 09 10 11 10 9 8 7 6 5 4 3 2 1 EDITORS-IN-CHIEF BrianWJMahyMAPhDScDDSc SeniorScientificAdvisor, DivisionofEmergingInfectionsandSurveillanceServices, CentersforDiseaseControlandPrevention, AtlantaGA,USA MarcHVVanRegenmortelPhD EmeritusDirectorattheCNRS, FrenchNationalCenterforScientificResearch, BiotechnologySchooloftheUniversityofStrasbourg, Illkirch,France v ASSOCIATE EDITORS DennisHBamford,Ph.D. RobertA.Lamb,Ph.D.,Sc.D. DepartmentofBiologicalandEnvironmentalSciences DepartmentofBiochemistry, andInstituteofBiotechnology,Biocenter2, MolecularBiologyandCellBiology P.O.Box56(Viikinkaari5), HowardHughesMedicalInstitute 00014UniversityofHelsinki, NorthwesternUniversity Finland 2205TechDr. Evanston CharlesCalisher,B.S.,M.S.,Ph.D. IL60208-3500 Arthropod-borneandInfectiousDiseasesLaboratory USA DepartmentofMicrobiology,ImmunologyandPathology CollegeofVeterinaryMedicineandBiomedicalSciences OlivierLeGall ColoradoStateUniversity IPV,UMRGDPP,IBVM, FortCollins INRABordeaux-Aquitaine,BP81, CO80523 F-33883Villenaved’OrnonCedex USA FRANCE AndrewJDavison,M.A.,Ph.D. VincentRacaniello,Ph.D. MRCVirologyUnit DepartmentofMicrobiology InstituteofVirology ColumbiaUniversity UniversityofGlasgow NewYork,NY10032 ChurchStreet USA GlasgowG115JR UK DavidA.Theilmann,Ph.D.,B.Sc.,M.Sc PacificAgri-FoodResearchCentre ClaudeFauquet AgricultureandAgri-FoodCanada ILTAB/DonaldDanforthPlantScienceCenter Box5000,4200Highway97 975NorthWarsonRoad Summerland St.Louis,MO63132 BCV0H1Z0 SaidGhabrial,B.S.,M.S.,Ph.D. Canada PlantPathologyDepartment UniversityofKentucky H.JosefVetten,Ph.D. 201FPlantScienceBuilding JuliusKuehnInstitute,FederalResearchCentrefor 1405VeteransDrive CultivatedPlants(JKI) Lexington Messeweg11-12 KY4050546-0312 38104Braunschweig USA Germany EricHunter,B.Sc.,Ph.D. PeterJWalker,B.Sc.,Ph.D. DepartmentofPathologyandLaboratoryMedicine,and CSIROLivestockIndustries EmoryVaccineCenter AustralianAnimalHealthLaboratory(AAHL) EmoryUniversity PrivateBag24 954GatewoodRoadNE Geelong AtlantaGeorgia30329 VIC3220 USA Australia vii PREFACE ThisthirdeditionoftheEncyclopediaofVirologyisbeingpublishednineyearsafterthesecondedition,aperiodwhichhas seenenormousgrowthbothinourunderstandingofvirologyandinourrecognitionofthevirusesthemselves,manyof which were unknown when the second edition was prepared. Considering viruses affecting human hosts alone, the worldwideepidemicofsevereacuterespiratorysyndrome(SARS),causedbyapreviouslyunknowncoronavirus,ledto the discoveryof other human coronaviruses such as HKU1 and NL63. As manyas seven chapters are devoted to the AIDSepidemicandtohumanimmunodeficiencyviruses.Inaddition,thedevelopmentofnewmoleculartechnologies ledtothediscoveryofviruseswithnoobviousdiseaseassociations,suchastorque-tenovirus(oneofthemostubiquitous virusesinthehumanpopulation),humanbocavirus,humanmetapneumovirus,andthreenewhumanpolyomaviruses. OthernewdevelopmentsofimportancetohumanvirologyhaveincludedtheintroductionofavirulentstrainofWest NilevirusfromIsraeltoNorthAmericain1999.Sincethattimethevirushasbecomeestablishedinmosquito,birdand horsepopulationsthroughouttheUSA,theCaribbeanandMexicoaswellasthesouthernregionsofCanada. As in the two previous editions, we have tried to include information about all known species of virus infecting bacteria,fungi,invertebrates,plantsandvertebrates,aswellasdescriptionsofrelatedtopicsinvirologysuchasantiviral drug development, cell- and antibody-mediated immunity, vaccine development, electron microscopyand molecular methods for virus characterization and identification. Many chapters are devoted to the considerable economic importance of virus diseases of cereals, legumes, vegetable crops, fruit trees and ornamentals, and newapproaches to controlthesediseasesarereviewed. Generalissuessuchastheorigin,evolutionandphylogenyofvirusesarealsodiscussedaswellasthehistoryofthe differentgroupsofviruses. Tocoverallthesesubjectsandnewdevelopments,wehavehadtoincreasethesizeoftheEncyclopediafromthreetofive volumes. Throughoutthisworkwehaverelieduponthe8thReportoftheInternationalCommitteeonTaxonomyofViruses publishedin 2005, which lists morethan 6000 viruses classified into some 2000 virus species distributed among more than390differentgeneraandfamilies.Inrecentyearsthecriteriaforplacingvirusesindifferenttaxahaveshiftedaway from traditional serological methods and increasingly rely upon molecular techniques, particularly the nucleotide sequence of the virus genome. This has changed many of the previous groupings of viruses, and is reflected in this thirdedition. Needlesstosay,aworkofthismagnitudehasinvolvedmanyexpertscientists,whohavegivengenerouslyoftheirtime to bring it to fruition. We extend our grateful thanks to all contributors and associate editors for their excellent and timelycontributions. BrianWJMahy MarcHVvanRegenmortel ix HOW TO USE THE ENCYCLOPEDIA StructureoftheEncyclopedia Themajortopicsdiscussedindetailinthetextarepresentedinalphabeticalorder(seetheAlphabeticalContentslist whichappearsinallfivevolumes). FindingSpecificInformation Informationonspecificviruses,virusdiseasesandothermatterscanbelocatedbyconsultingtheGeneralIndexatthe endofVolume5. TaxonomicGroupsofViruses Forlocatingdetailedinformationonthemajortaxonomicgroupsofviruses,namelyvirusgenera,familiesandorders,the TaxonomicIndexinVolume5(page...)shouldbeconsulted. FurtherReadingsections Thearticlesdonotfeaturebibliographiccitationswithinthebodyofthearticletextitself.Thearticlesareintendedtobe afirstintroductiontothetopic,ora‘refresher’,readablefrombeginningtoendwithoutreferringthereaderoutsideof theencyclopediaitself.BibliographicreferencestoexternalliteraturearegroupedattheendofeacharticleinaFurther Readingsection,containingreviewarticles,‘seminal’primaryarticlesandbookchapters.Thesepointuserstothenext levelofinformationforanygiventopic. Crossreferencingbetweenarticles The‘‘Seealso’’sectionattheendofeacharticledirectsthereadertootherentriesonrelatedtopics.Forexample.The entryLassa,Junin,MachupoandGuanaritoVirusesincludesthefollowingcross-references: Seealso:LymphocyticChoriomeningitisVirus:GeneralFeatures. xi CONTRIBUTORS STAbedon BMArif TheOhioStateUniversity,Mansfield,OH,USA GreatLakesForestryCentre,SaultSte.Marie,ON, Canada GPAccotto IstitutodiVirologiaVegetaleCNR,Torino,Italy HAttoui Faculte´ deMe´decinedeMarseilles, H-WAckermann EtablissementFrançaisDuSang,Marseilles,France LavalUniversity,Quebec,QC,Canada HAttoui GAdam Universite´ delaMe´diterraneé,Marseille,France Universita¨tHamburg,Hamburg,Germany HAttoui MJAdams InstituteforAnimalHealth,Pirbright,UK RothamstedResearch,Harpenden,UK LAurelian CAdams UniversityofMarylandSchoolofMedicine,Baltimore, UniversityofDuisburg–Essen,Essen,Germany MD,USA EAdderson LABabiuk St.JudeChildren’sResearchHospital,Memphis,TN, UniversityofAlberta,Edmonton,AB,Canada USA SBabiuk SAdhya NationalCentreforForeignAnimalDisease,Winnipeg, NationalInstitutesofHealth,Bethesda,MD,USA MB,Canada CLAfonso AGBader SoutheastPoultryResearchLaboratory,Athens,GA,USA TheScrippsResearchInstitute,LaJolla,CA,USA PAhlquist SCBaker UniversityofWisconsin–Madison,Madison,WI,USA LoyolaUniversityofChicago,Maywood,IL,USA GMAir TSBaker UniversityofOklahomaHealthSciencesCenter, UniversityofCalifornia,SanDiego,LaJolla,CA,USA OklahomaCity,OK,USA JKHBamford DJAlcendor UniversityofJyva¨skyla¨,Jyva¨skyla¨,Finland JohnsHopkinsSchoolofMedicine,Baltimore,MD,USA YBao JWAlmond NationalInstitutesofHealth,Bethesda,MD,USA sanofipasteur,Lyon,France MBar-Joseph IAmin TheVolcaniCenter,BetDagan,Israel NationalInstituteforBiotechnologyandGenetic Engineering,Faisalabad,Pakistan HBarker ScottishCropResearchInstitute,Dundee,UK JAngel PontificiaUniversidadJaveriana,Bogota,Republicof ADTBarrett Colombia UniversityofTexasMedicalBranch,Galveston,TX,USA CApetrei JWBarrett TulaneNationalPrimateResearchCenter,Covington, TheUniversityofWesternOntario,London,ON, LA,USA Canada xiii xiv Contributors TBarrett RFBishop InstituteforAnimalHealth,Pirbright,UK MurdochChildrensResearchInstituteRoyalChildren’s Hospital,Melbourne,VIC,Australia RBartenschlager UniversityofHeidelberg,Heidelberg,Germany BABlacklaws UniversityofCambridge,Cambridge,UK NWBartlett ImperialCollegeLondon,London,UK CDBlair ColoradoStateUniversity,FortCollins,CO,USA SBasak UniversityofCalifornia,SanDiego,CA,USA SBlanc INRA–CIRAD–AgroM,Montpellier,France CFBasler MountSinaiSchoolofMedicine,NewYork, RBlawid NY,USA InstituteofPlantDiseasesandPlantProtection, Hannover,Germany TBasta InstitutPasteur,Paris,France GWBlissard BoyceThompsonInstituteatCornellUniversity,Ithaca, DBaxby NY,USA UniversityofLiverpool,Liverpool,UK SBlomqvist PBeard NationalPublicHealthInstitute(KTL),Helsinki,Finland ImperialCollegeLondon,London,UK JFBol MNBecker LeidenUniversity,Leiden,TheNetherlands UniversityofFlorida,Gainesville,FL,USA J-RBonami JJBecnel CNRS,Montpellier,France AgricultureResearchService,Gainesville,FL,USA LBos KLBeemon WageningenUniversityandResearchCentre(WUR), JohnsHopkinsUniversity,Baltimore,MD,USA Wageningen,TheNetherlands EDBelay HRBoseJr. CentersforDiseaseControlandPrevention,Atlanta,GA, UniversityofTexasatAustin,Austin,TX,USA USA HBourhy MBenko˝ InstitutPasteur,Paris,France VeterinaryMedicalResearchInstitute,Hungarian AcademyofSciences,Budapest,Hungary PRBowser CornellUniversity,Ithaca,NY,USA MBennett UniversityofLiverpool,Liverpool,UK DBBoyle CSIROLivestockIndustries,Geelong,VIC, MBergoin Australia Universite´ MontpellierII,Montpellier,France CBragard HUBernard Universite´ CatholiquedeLouvain,Leuven,Belgium UniversityofCalifornia,Irvine,Irvine,CA,USA JNBragg KIBerns UniversityofCalifornia,Berkeley,Berkeley,CA,USA UniversityofFloridaCollegeofMedicine,Gainesville,FL, USA RWBriddon NationalInstituteforBiotechnologyandGenetic PBiagini Engineering,Faisalabad,Pakistan EtablissementFrançaisduSangAlpes-Me´diterraneé, Marseilles,France MABrinton GeorgiaStateUniversity,Atlanta,GA,USA PDBieniasz AaronDiamondAIDSResearchCenter,TheRockefeller PBritton University,NewYork,NY,USA InstituteforAnimalHealth,Compton,UK YBigot JKBrown UniversityofTours,Tours,France TheUniversityofArizona,Tucson,AZ,USA CBillinis KSBrown UniversityofThessaly,Karditsa,Greece UniversityofManitoba,Winnipeg,MB,Canada