Discovering the Phylodynamics of RNA Viruses 英文参考文献.docVIP

Perspective DiscoveringthePhylodynamicsofRNAViruses EdwardC.Holmes1,2*,BryanT.Grenfell2,3 1CenterforInfectiousDiseaseDynamics,DepartmentofBiology,ThePennsylvaniaStateUniversity,MuellerLaboratory,UniversityPark,Pennsylvania,UnitedStatesof America,2FogartyInternationalCenter,NationalInstitutesofHealth,Bethesda,Maryland,UnitedStatesofAmerica,3DepartmentofEcologyandEvolutionaryBiology andWoodrowWilsonSchool,PrincetonUniversity,Princeton,NewJersey,UnitedStatesofAmerica Phylodynamics:TheDiscovery Phase select few human viruses for which large genome sequence datasets have been acquired, such as HIV and influenza A virus,andevenherefundamentalgapsin ourknowledgeremain(seebelow).Indeed, itisstrikingthatsofewcompletegenome andthatasmuchofthesedataarepublicly accessible as possible. A phylodynamic analysis has little value unless viral ge- nomes are sampled on the same scale as theepidemiologicalprocessesunderinves- tigation. Theadventofextremelyhighthrough- putDNAsequencingensuresthatgenomic data from microbial organisms can be acquired inunprecedented quantitiesand with remarkable rapidity. Although this genomicrevolutionwillaffectallmicrobes alike,ourfocushereisonRNAviruses,as the rapidity of their evolution, which is observable over the time scale of human observation, allows phylodynamic infer- encestobemadewithgreatprecision.In the foreseeable future it is likely that completegenomesequencingwillbecome thestandardmethodofviralcharacteriza- tion, providing the highest possible reso- lutionforphylogeneticstudies.Therapid- itywithwhichgenomesequencedatawere generated from the ongoing epidemic of swine-originH1N1influenzaAvirus[1]is testamenttothepowerofthistechnology. Understandably, pathogen discovery is a major focus of this new-scale genome sequencing [2]. It is now possible to sequence the entire assemblage of viruses in a particular tissue type or host species [3–5], as wellas allthose virusesthat are associatedwithspecificdiseasesyndromes [6,7]. Inessence, this