RNA病毒的变异与消失.docx

RNA病毒的变异与消失.docx

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RNA病毒的变异与消失

VirusResearch107（2005）129–139

QuasispeciesdynamicsandRNAvirusextinction

EstebanDomingoa,b,c,∗,CristinaEscarm´sa,EsterL´zarob,SusannaC.Manrubiabıa

a

CentrodeBiolog´aMolecular“SeveroOchoa”（CSIC-UAM）,ConsejoSuperiordeInvestigacionesCientificas,ı

UniversidadAut´nomadeMadrid,Cantoblanco,28049Madrid,Spaino

bCentrodeAstrobiolog´a（CSIC-INTA）,CarreteradeAjalvir,km4,28850Torrej´ndeArdoz,Madrid,Spainıo

cCentrodeInvestigaci´nenSanidadAnimal（INIA）,Valdeolmos,28130Madrid,Spaino

Availableonline8December2004

Abstract

Theextinctionoffoot-and-mouthdiseasevirus（FMDV）isstronglyinfluencedbymutationrates,typesofmutations,relativeviralfitness

andviruspopulationregimensduringinfection.Herewereviewexperimentalresultsandtheoreticalmodelsthatdescribeacontrastbetween

theeffectiveextinctionofFMDVsubjectedtoincreasedmutagenesis,andtheremarkableresistancetoextinctionofthesameandrelated

FMDVclonessubjectedtoserialbottleneckevents.Theresultssuggestprocedurestomasterkeyparameterstodevelopeffectiveantiviral

strategiesbasedonvirusentryintoerrorcatastrophe.

©2004ElsevierB.V.Allrightsreserved.

Keywords:

Foot-and-mouthdiseasevirus;5-Fluorouracil;5-Azacytidine;Mutation

1.Introduction

Criticalforatherapeuticapplicationoferrorcatastrophe

asanantiviralstrategyistounderstandthemainfactors（in-

trinsictothevirusaswellasthoserelatedtopopulationdy-

namics）thatmaycontributetolossofinfectivity.Thishas

provenacomplexissueandtheexperimentscarriedoutsofar

haveraisedmorequestionsthanprovidedanswers.Herewe

reviewstudiescarriedoutoverthelastdecadewiththeimpor-

tantanimalpathogenfoot-and-mouthdiseasevirus（FMDV）

aimedatunderstandinghowhighmutationratesandqua-

sispeciesdynamics（asopposedtolowmutationratesand

anon-quasispeciesdynamics）affectedtheaccumulationof

mutations,fitnessvariations,andvirussurvival.Themain

pointofthisarticleistocomparetheremarkablecapacity

todriveFMDVintoerrorcatastrophewhentheeffectsof

threecriticalparameters（mutationrates,viralfitness,andvi-

ralload）areunderstoodandcontrolled,withtheresistance

toextinctiondespiteaccumulationofmutationsuponsub-

jectingFMDVtorepeatedbottleneckevents（experimentally

realizedasplaque-to-plaquetransfers）.Theseverydiffer-

entresponsesregardingsurvivalmayshedlightonstrate-

gieswhosegoalistheeliminationofvirusduringinfectious

processesinvivo.

AsrecentintroductionstoFMDVthereaderisreferredto

thevolumesbyRowlands（2003）andSobrinoandDomingo

（2004）.Forclarity,Table1includesaglossaryofconcepts

andtermsusedinthisarticleandintheliteratureonquasis-

peciesanderrorcatastrophe.

2.ExtinctionofFMDVbyenhancedmutagenesis

Followingpioneerworkontheadverseeffectsofchemical

mutagenesisontheinfectivityofpoliovirusandvesicular

stomatitisvirus（VSV）byHollandetal.（1990）andLeeet

al.（1997）,ourgroupsettostudytheeffectofthemutagenic

baseanalog5-fluorouracil（FU）andthenucleosideanalog

5-azacytidine（AZT）ontheinfectivityandmutantspectrum

complexityofFMDV（Parienteetal.,2001,2003;Sierraet

al.,2000）.Theseexperiments,andtheeffectofribavirinon

persistentFMDVinfections（Airaksinenetal.,2003;dela

Torreetal.,1987）,arereviewedindetailby（Parienteetal.,

2005）.Hereweextractthemainconclusionsonlytoserve

∗

Correspondingauthor.Tel.:

+34914978485;fax:

+34914974799.

E-mailaddress:

edomingo@cbm.uam.es（E.Domingo）.

0168-1702/$–seefrontmatter©2004ElsevierB.V.Allrightsreserved.

doi:

10.1016/j.virusres.2004.11.003

130

E.Domingoetal./VirusResearch107（2005）129–139

Table1

Glossaryofsometermsfrequentlyusedintheliteratureofquasispeciesanderrorcatastrophe

Complexityofthemutantspectrum

Ameasureofthenucleotidesequencedifferencesamongcomponentsofamutantspectrum:

itisgenerallygiven

bythemutationfrequencyandShannonentropy.Complexityhasothermeaningsinscience,includingsizeof

genomes,usedalsointhetext

Thesequenceresultingfromtakingforeachpositionthemostfrequentresidue（nucleotideoraminoacid）foundat

thecorrespondingpositioninthehomologoussetofalignedsequences:

theconsensussequencemaynotexist

physicallyinthemutantspectrum

Acriticalerrorrateabovewhichtheinformationencodedbyageneticsystemcannotbemaintained:

violationof

theerrorthresholdresultsinthesystementeringerrorcatastrophe.Theerrorthresholdrelationshipisgivenby

νmax

¯maintainedduringreplication,σoisthesuperiorityofthemastersequencerelativetothemutantspectrum,andqis

theaveragecopyingfidelity（theaverageerrorrateis（1−q））¯

Aparameterthatquantifiestheadaptationofanorganismoravirustoagivenenvironment:

itisnecessarilya

relativevalue.Foravirus,relativefitnessmeasuresitsabilitytoproduceinfectiousprogenyrelativetoareference

viralclone,inadefinedenvironment.Epidemiologicalfitnessdescribesinsemi-quantitativeways（samplingof

definitorygenomicsequencesversusthoseofcompetitors）therelativecapacityofavirustobecomedominantin

thefieldduring（orasaresultof）epidemicoutbreaks

Thedominantgenomicnucleotidesequenceinaquasispecies:

itgenerallydepictsaselectiveadvantageoverthe

othercomponentsofthequasispecies.Itmayormaynotcoincidewiththeconsensussequence.Themaster

sequencemaychangeastheenvironmentismodified

Theensembleofmutantgenomesthatcomposeaquasispecies

Theproportionofmutantsinapopulationofgenomes:

itmaybecalculatedforanentiresequenceofforaspecific

siteofagenome（suchasinthefrequencyofmonoclonalantibody-escapemutants）

Thefrequencyofoccurrenceofamutationaleventduringgenomereplication:

intheliteratureofpopulation

genetics,mutationrateisoftenusedtomeantherateoffixation（oraccumulation）ofmutations,orrateofevolution

Thenumberofindividualsinapopulation:

forviruses,thetermreferstothenumberofinfectiousgenomespresent

inacell,tissue,organororganismthatatanygiventimeareeitherreplicatingorcanpotentiallyreplicate.The

numberofgenomesquantifiedinaninfectedhostisalsotermedtheviralload.Notallviralgenomesareinfectious

（seeSpecificinfectivity）

Amutagenizedviralpopulationthatprecedestheonefromwhichnoinfectivitycanberescued:

Preextinction

RNAistheRNAextractedformapreextinctionpopulation

Aweighteddistributionofmutantscenteredaroundonemastersequence:

initsinitialmathematicalformulation,a

quasispecieswasasteadystatedistributionofinfinitesizeinequilibrium.Mathematicalextensionstofinite

populationundernon-equilibriumconditionshavebeendeveloped.Virologistsuseanextendeddefinitionof

quasispeciesmeaning“dynamicdistributionsofnon-identicalbutcloselyrelatedmutantandrecombinantviral

genomessubjectedtoacontinuousprocessofgeneticvariation,competitionandselection,andwhichactasaunit

ofselection”

Thefrequencyofmutationsthatbecomedominantinagenomeperunittime:

foravirusitmaybecalculatedfor

sequentialgenomesinaninfectedhostofforviralgenomessampledatdifferenttimesfromdifferentinfected

hosts.Forvirusesthisrateisgenerallynotconstant.Theassumptionofa“molecularclock”isnotrealisticfor

RNAviruses

Atheoreticalrepresentationofallpossiblevariantsofagenomicsequence:

forasinglestrandedRNAvirusof

10,000residues（usingfourtypesofnucleotides）thetotalsequencespaceis410,000!

Viralgenomesoccupytiny

portionsoftheirtheoreticalsequencespace

Theproportionofdifferentnucleotidesequencesinamutantspectrum（avalueof1meanseachsequenceis

uniqueinthedistribution;avalueof0meansthatallsequencesareidentical）

Theproportionofinfectiousparticles（orinfectiousviralnucleicacid）inaviral（orviralgenome）population:

the

transitionintoerrorcatastropheisgenerallyprecededbydecreasesinspecificinfectivity

Thenumberofinfectious（activelyreplicatingorpotentiallyreplicating）particlesinaviralpopulation

Consensus（oraverage）sequence

Errorthreshold

Fitness

Mastersequence

Mutantspectrum

Mutationfrequency

Mutationrate

Populationnumber

Pre-extinctionviralpopulation

Quasispecies

Rateoffixation（oraccumulation）

ofmutations

Sequencespace

Shannonentropy

Specificinfectivity

Viralload

BasedonDomingo（1999,2003）andEigen（1992）.

asthebasistocompareextinctionmutagenesiswithsurvival

despiteaccumulationofmutationsassociatedwithbottleneck

events.

Duringcytolyticinfectionsincellculture,lowviralload

andlowrelativefitnessfavoredextinctionofFMDVbyFU

andAZC.Mutagenizedpopulations,includingpreextinction

RNA,didnotshowmutationsintheconsensussequences

analyzed,butdisplayedanincreaseinthecomplexityofmu-

tantspectra.Themaximumincreasesincomplexityoccurred

inthepolymerase（3D）gene,whichisveryconservedin

FMDV.Severalaminoacidreplacementsfoundinthemu-

tantspectrumof3Dinmutagenizedpopulationshavenever

beenobservedinnaturalorlaboratorypopulationsofthevirus

（Sierraetal.,2000;Airaksinenetal.,unpublishedresults;re-

viewinParienteetal.,2005）,suggestingthatoccurrenceof

highlydeleteriousmutationsisassociatedwithproximityto

theerrorthreshold（Eigen,2002）.

Thesamemutagenicagentcan