RNA病毒的变异与消失.docx

1、RNA病毒的变异与消失Virus Research 107 (2005) 129139Quasispecies dynamics and RNA virus extinctionEsteban Domingoa,b,c, , Cristina Escarmsa , Ester L zarob , Susanna C. ManrubiabaaCentro de Biologa Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Cienticas, Universidad Aut noma de Mad

2、rid, Cantoblanco, 28049 Madrid, Spainob Centro de Astrobiologa (CSIC-INTA), Carretera de Ajalvir, km 4, 28850 Torrej n de Ardoz, Madrid, Spaino c Centro de Investigaci n en Sanidad Animal (INIA), Valdeolmos, 28130 Madrid, SpainoAvailable online 8 December 2004Abstract The extinction of foot-and-mout

3、h disease virus (FMDV) is strongly inuenced by mutation rates, types of mutations, relative viral tnessand virus population regimens during infection. Here we review experimental results and theoretical models that describe a contrast betweenthe effective extinction of FMDV subjected to increased mu

4、tagenesis, and the remarkable resistance to extinction of the same and relatedFMDV clones subjected to serial bottleneck events. The results suggest procedures to master key parameters to develop effective antiviralstrategies based on virus entry into error catastrophe. 2004 Elsevier B.V. All rights

5、 reserved.Keywords: Foot-and-mouth disease virus; 5-Fluorouracil; 5-Azacytidine; Mutation1. Introduction Critical for a therapeutic application of error catastropheas an antiviral strategy is to understand the main factors (in-trinsic to the virus as well as those related to population dy-namics) th

6、at may contribute to loss of infectivity. This hasproven a complex issue and the experiments carried out so farhave raised more questions than provided answers. Here wereview studies carried out over the last decade with the impor-tant animal pathogen foot-and-mouth disease virus (FMDV)aimed at unde

7、rstanding how high mutation rates and qua-sispecies dynamics (as opposed to low mutation rates anda non-quasispecies dynamics) affected the accumulation ofmutations, tness variations, and virus survival. The mainpoint of this article is to compare the remarkable capacityto drive FMDV into error cata

8、strophe when the effects ofthree critical parameters (mutation rates, viral tness, and vi-ral load) are understood and controlled, with the resistanceto extinction despite accumulation of mutations upon sub-jecting FMDV to repeated bottleneck events (experimentallyrealized as plaque-to-plaque transf

9、ers). These very differ-ent responses regarding survival may shed light on strate-gies whose goal is the elimination of virus during infectiousprocesses in vivo. As recent introductions to FMDV the reader is referred tothe volumes by Rowlands (2003) and Sobrino and Domingo(2004). For clarity, Table

10、1 includes a glossary of conceptsand terms used in this article and in the literature on quasis-pecies and error catastrophe.2. Extinction of FMDV by enhanced mutagenesis Following pioneer work on the adverse effects of chemicalmutagenesis on the infectivity of poliovirus and vesicularstomatitis vir

11、us (VSV) by Holland et al. (1990) and Lee etal. (1997), our group set to study the effect of the mutagenicbase analog 5-uorouracil (FU) and the nucleoside analog5-azacytidine (AZT) on the infectivity and mutant spectrumcomplexity of FMDV (Pariente et al., 2001, 2003; Sierra etal., 2000). These exper

12、iments, and the effect of ribavirin onpersistent FMDV infections (Airaksinen et al., 2003; de laTorre et al., 1987), are reviewed in detail by (Pariente et al.,2005). Here we extract the main conclusions only to serveCorresponding author. Tel.: +34 91 4978485; fax: +34 91 4974799.E-mail address: edo

13、mingocbm.uam.es (E. Domingo).0168-1702/$ see front matter 2004 Elsevier B.V. All rights reserved.doi:10.1016/j.virusres.2004.11.003130E. Domingo et al. / Virus Research 107 (2005) 129139Table 1Glossary of some terms frequently used in the literature of quasispecies and error catastropheComplexity of

14、 the mutant spectrumA measure of the nucleotide sequence differences among components of a mutant spectrum: it is generally givenby the mutation frequency and Shannon entropy. Complexity has other meanings in science, including size ofgenomes, used also in the textThe sequence resulting from taking

15、for each position the most frequent residue (nucleotide or amino acid) found atthe corresponding position in the homologous set of aligned sequences: the consensus sequence may not existphysically in the mutant spectrumA critical error rate above which the information encoded by a genetic system can

16、not be maintained: violation ofthe error threshold results in the system entering error catastrophe. The error threshold relationship is given bymax ln o /(1 q) in which max is the maximum length of the sequence (genetic complexity) that can be maintained during replication, o is the superiority of

17、the master sequence relative to the mutant spectrum, and q isthe average copying delity (the average error rate is (1 q)A parameter that quanties the adaptation of an organism or a virus to a given environment: it is necessarily arelative value. For a virus, relative tness measures its ability to pr

18、oduce infectious progeny relative to a referenceviral clone, in a dened environment. Epidemiological tness describes in semi-quantitative ways (sampling ofdenitory genomic sequences versus those of competitors) the relative capacity of a virus to become dominant inthe eld during (or as a result of)

19、epidemic outbreaksThe dominant genomic nucleotide sequence in a quasispecies: it generally depicts a selective advantage over theother components of the quasispecies. It may or may not coincide with the consensus sequence. The mastersequence may change as the environment is modiedThe ensemble of mut

20、ant genomes that compose a quasispeciesThe proportion of mutants in a population of genomes: it may be calculated for an entire sequence of for a specicsite of a genome (such as in the frequency of monoclonal antibody-escape mutants)The frequency of occurrence of a mutational event during genome rep

21、lication: in the literature of populationgenetics, mutation rate is often used to mean the rate of xation (or accumulation) of mutations, or rate of evolutionThe number of individuals in a population: for viruses, the term refers to the number of infectious genomes presentin a cell, tissue, organ or

22、 organism that at any given time are either replicating or can potentially replicate. Thenumber of genomes quantied in an infected host is also termed the viral load. Not all viral genomes are infectious(see Specic infectivity)A mutagenized viral population that precedes the one from which no infect

23、ivity can be rescued: PreextinctionRNA is the RNA extracted form a preextinction populationA weighted distribution of mutants centered around one master sequence: in its initial mathematical formulation, aquasispecies was a steady state distribution of innite size in equilibrium. Mathematical extens

24、ions to nitepopulation under non-equilibrium conditions have been developed. Virologists use an extended denition ofquasispecies meaning “dynamic distributions of non-identical but closely related mutant and recombinant viralgenomes subjected to a continuous process of genetic variation, competition

25、 and selection, and which act as a unitof selection”The frequency of mutations that become dominant in a genome per unit time: for a virus it may be calculated forsequential genomes in an infected host of for viral genomes sampled at different times from different infectedhosts. For viruses this rat

26、e is generally not constant. The assumption of a “molecular clock” is not realistic forRNA virusesA theoretical representation of all possible variants of a genomic sequence: for a single stranded RNA virus of10,000 residues (using four types of nucleotides) the total sequence space is 410,000 ! Vir

27、al genomes occupy tinyportions of their theoretical sequence spaceThe proportion of different nucleotide sequences in a mutant spectrum (a value of 1 means each sequence isunique in the distribution; a value of 0 means that all sequences are identical)The proportion of infectious particles (or infec

28、tious viral nucleic acid) in a viral (or viral genome) population: thetransition into error catastrophe is generally preceded by decreases in specic infectivityThe number of infectious (actively replicating or potentially replicating) particles in a viral populationConsensus (or average) sequenceErr

29、or thresholdFitnessMaster sequenceMutant spectrumMutation frequencyMutation ratePopulation numberPre-extinction viral populationQuasispeciesRate of xation (or accumulation) of mutationsSequence spaceShannon entropySpecic infectivityViral loadBased on Domingo (1999, 2003) and Eigen (1992).as the basi

30、s to compare extinction mutagenesis with survivaldespite accumulation of mutations associated with bottleneckevents. During cytolytic infections in cell culture, low viral loadand low relative tness favored extinction of FMDV by FUand AZC. Mutagenized populations, including preextinctionRNA, did not

31、 show mutations in the consensus sequencesanalyzed, but displayed an increase in the complexity of mu-tant spectra. The maximum increases in complexity occurredin the polymerase (3D) gene, which is very conserved inFMDV. Several amino acid replacements found in the mu-tant spectrum of 3D in mutageni

32、zed populations have neverbeen observed in natural or laboratory populations of the virus(Sierra et al., 2000; Airaksinen et al., unpublished results; re-view in Pariente et al., 2005), suggesting that occurrence ofhighly deleterious mutations is associated with proximity tothe error threshold (Eigen, 2002). The same mutagenic agent can