Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection

Additional files: Additional file 1: Neighbour-joining, maximum likelihood and maximum parsimony analysis of populations RAp35 and RA0p35. Additional file 2: Maximum likelihood phylogenetic analysis of mutagenized populations of FMDV. Additional file 3: Standard errors.

Detalhes bibliográficos
Autores: Ojosnegros Martos, Samuel, Agudo, Rubén, Sierra García, Macarena, Briones, Carlos, Sierra, Saleta, González-López, Claudia, Domingo, Esteban, Cristina, Juan
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2008
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/8286
Acesso em linha:http://hdl.handle.net/10261/8286
Access Level:acceso abierto
Palavra-chave:Virus
Mutations
Partition Analysis of Quasispecies
PAQ
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spelling Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selectionOjosnegros Martos, SamuelAgudo, RubénSierra García, MacarenaBriones, CarlosSierra, SaletaGonzález-López, ClaudiaDomingo, EstebanCristina, JuanVirusMutationsPartition Analysis of QuasispeciesPAQAdditional files: Additional file 1: Neighbour-joining, maximum likelihood and maximum parsimony analysis of populations RAp35 and RA0p35. Additional file 2: Maximum likelihood phylogenetic analysis of mutagenized populations of FMDV. Additional file 3: Standard errors.Background The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. Results Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. Conclusion Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction.Work at Centro de Biología Molecular "Severo Ochoa" was supported by grants BFU2006-00863 from MEC, 36558/06 from FIPSE, and Fundación R.Areces. Work at Centro de Astrobiología was supported by INTA, MEC, CAM and UE. CIBERehd is funded by Instituto de Salud Carlos III. S.O. was supported by a predoctoral fellowship from the Ministerio de Educacion y Ciencia.Peer reviewedBioMed CentralMinisterio de Educación y Ciencia (España)Fundación para la Investigación y la Prevención del Sida en EspañaFundación Ramón ArecesInstituto Nacional de Técnica Aeroespacial (España)European CommissionInstituto de Salud Carlos III200820082008info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersion1725473 bytesapplication/pdfhttp://hdl.handle.net/10261/8286reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1186/1471-2148-8-207info:eu-repo/semantics/openAccessoai:digital.csic.es:10261/82862026-05-22T06:33:51Z
dc.title.none.fl_str_mv Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
title Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
spellingShingle Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
Ojosnegros Martos, Samuel
Virus
Mutations
Partition Analysis of Quasispecies
PAQ
title_short Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
title_full Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
title_fullStr Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
title_full_unstemmed Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
title_sort Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
dc.creator.none.fl_str_mv Ojosnegros Martos, Samuel
Agudo, Rubén
Sierra García, Macarena
Briones, Carlos
Sierra, Saleta
González-López, Claudia
Domingo, Esteban
Cristina, Juan
author Ojosnegros Martos, Samuel
author_facet Ojosnegros Martos, Samuel
Agudo, Rubén
Sierra García, Macarena
Briones, Carlos
Sierra, Saleta
González-López, Claudia
Domingo, Esteban
Cristina, Juan
author_role author
author2 Agudo, Rubén
Sierra García, Macarena
Briones, Carlos
Sierra, Saleta
González-López, Claudia
Domingo, Esteban
Cristina, Juan
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Educación y Ciencia (España)
Fundación para la Investigación y la Prevención del Sida en España
Fundación Ramón Areces
Instituto Nacional de Técnica Aeroespacial (España)
European Commission
Instituto de Salud Carlos III
dc.subject.none.fl_str_mv Virus
Mutations
Partition Analysis of Quasispecies
PAQ
topic Virus
Mutations
Partition Analysis of Quasispecies
PAQ
description Additional files: Additional file 1: Neighbour-joining, maximum likelihood and maximum parsimony analysis of populations RAp35 and RA0p35. Additional file 2: Maximum likelihood phylogenetic analysis of mutagenized populations of FMDV. Additional file 3: Standard errors.
publishDate 2008
dc.date.none.fl_str_mv 2008
2008
2008
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/8286
url http://hdl.handle.net/10261/8286
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1186/1471-2148-8-207
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 1725473 bytes
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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