Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region

Autores
Moratorio, Gonzalo; Martínez, Mariela; Gutiérrez, María F.; González, Katiuska; Colina, Rodney; López Tort, Fernando; López, Lilia; Recarey, Ricardo; Schijman, Alejandro Gabriel; Moreno, María P.; García Aguirre, Laura; Manascero, Aura R.; Cristina, Juan
Año de publicación
2007
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background. Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America. Methods. Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program. Results. Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region. Conclusion. Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The coexistence of distinct type 1 HCV subpopulations is consistent with quasispecies dynamics, and suggests that multiple coexisting subpopulations may allow the virus to adapt to its human host populations.
Fil: Moratorio, Gonzalo. Universidad de la República; Uruguay
Fil: Martínez, Mariela. Universidad de la República; Uruguay
Fil: Gutiérrez, María F.. Pontificia Universidad Javeriana; Colombia
Fil: González, Katiuska. Universidad Mayor de San Andrés; Bolivia
Fil: Colina, Rodney. McGill University; Canadá
Fil: López Tort, Fernando. Universidad de la República; Uruguay
Fil: López, Lilia. Universidad de la República; Uruguay
Fil: Recarey, Ricardo. Universidad de la República; Uruguay
Fil: Schijman, Alejandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Moreno, María P.. Universidad de la República; Uruguay
Fil: García Aguirre, Laura. Universidad de la República; Uruguay
Fil: Manascero, Aura R.. Pontificia Universidad Javeriana; Colombia
Fil: Cristina, Juan. Universidad de la República; Uruguay
Materia
Genotyping
Hepatitis C Virus
5' Non Coding Region
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/79636
Acceder
id CONICETDig_1ba3a46a7e73f3f094e520ce201f3eda
oai_identifier_str oai:ri.conicet.gov.ar:11336/79636
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American regionMoratorio, GonzaloMartínez, MarielaGutiérrez, María F.González, KatiuskaColina, RodneyLópez Tort, FernandoLópez, LiliaRecarey, RicardoSchijman, Alejandro GabrielMoreno, María P.García Aguirre, LauraManascero, Aura R.Cristina, JuanGenotypingHepatitis C Virus5' Non Coding Regionhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background. Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America. Methods. Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program. Results. Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region. Conclusion. Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The coexistence of distinct type 1 HCV subpopulations is consistent with quasispecies dynamics, and suggests that multiple coexisting subpopulations may allow the virus to adapt to its human host populations.Fil: Moratorio, Gonzalo. Universidad de la República; UruguayFil: Martínez, Mariela. Universidad de la República; UruguayFil: Gutiérrez, María F.. Pontificia Universidad Javeriana; ColombiaFil: González, Katiuska. Universidad Mayor de San Andrés; BoliviaFil: Colina, Rodney. McGill University; CanadáFil: López Tort, Fernando. Universidad de la República; UruguayFil: López, Lilia. Universidad de la República; UruguayFil: Recarey, Ricardo. Universidad de la República; UruguayFil: Schijman, Alejandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Moreno, María P.. Universidad de la República; UruguayFil: García Aguirre, Laura. Universidad de la República; UruguayFil: Manascero, Aura R.. Pontificia Universidad Javeriana; ColombiaFil: Cristina, Juan. Universidad de la República; UruguayBioMed Central2007-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/79636Moratorio, Gonzalo; Martínez, Mariela; Gutiérrez, María F.; González, Katiuska; Colina, Rodney; et al.; Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region; BioMed Central; Virology Journal; 4; 79; 12-2007; 1-121743-422XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://virologyj.biomedcentral.com/articles/10.1186/1743-422X-4-79info:eu-repo/semantics/altIdentifier/doi/10.1186/1743-422X-4-79info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:10:20Zoai:ri.conicet.gov.ar:11336/79636instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:10:21.205CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
title Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
spellingShingle Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
Moratorio, Gonzalo
Genotyping
Hepatitis C Virus
5' Non Coding Region
title_short Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
title_full Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
title_fullStr Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
title_full_unstemmed Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
title_sort Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
dc.creator.none.fl_str_mv Moratorio, Gonzalo
Martínez, Mariela
Gutiérrez, María F.
González, Katiuska
Colina, Rodney
López Tort, Fernando
López, Lilia
Recarey, Ricardo
Schijman, Alejandro Gabriel
Moreno, María P.
García Aguirre, Laura
Manascero, Aura R.
Cristina, Juan
author Moratorio, Gonzalo
author_facet Moratorio, Gonzalo
Martínez, Mariela
Gutiérrez, María F.
González, Katiuska
Colina, Rodney
López Tort, Fernando
López, Lilia
Recarey, Ricardo
Schijman, Alejandro Gabriel
Moreno, María P.
García Aguirre, Laura
Manascero, Aura R.
Cristina, Juan
author_role author
author2 Martínez, Mariela
Gutiérrez, María F.
González, Katiuska
Colina, Rodney
López Tort, Fernando
López, Lilia
Recarey, Ricardo
Schijman, Alejandro Gabriel
Moreno, María P.
García Aguirre, Laura
Manascero, Aura R.
Cristina, Juan
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genotyping
Hepatitis C Virus
5' Non Coding Region
topic Genotyping
Hepatitis C Virus
5' Non Coding Region
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background. Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America. Methods. Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program. Results. Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region. Conclusion. Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The coexistence of distinct type 1 HCV subpopulations is consistent with quasispecies dynamics, and suggests that multiple coexisting subpopulations may allow the virus to adapt to its human host populations.
Fil: Moratorio, Gonzalo. Universidad de la República; Uruguay
Fil: Martínez, Mariela. Universidad de la República; Uruguay
Fil: Gutiérrez, María F.. Pontificia Universidad Javeriana; Colombia
Fil: González, Katiuska. Universidad Mayor de San Andrés; Bolivia
Fil: Colina, Rodney. McGill University; Canadá
Fil: López Tort, Fernando. Universidad de la República; Uruguay
Fil: López, Lilia. Universidad de la República; Uruguay
Fil: Recarey, Ricardo. Universidad de la República; Uruguay
Fil: Schijman, Alejandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Moreno, María P.. Universidad de la República; Uruguay
Fil: García Aguirre, Laura. Universidad de la República; Uruguay
Fil: Manascero, Aura R.. Pontificia Universidad Javeriana; Colombia
Fil: Cristina, Juan. Universidad de la República; Uruguay
description Background. Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America. Methods. Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program. Results. Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region. Conclusion. Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The coexistence of distinct type 1 HCV subpopulations is consistent with quasispecies dynamics, and suggests that multiple coexisting subpopulations may allow the virus to adapt to its human host populations.
publishDate 2007
dc.date.none.fl_str_mv 2007-12
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/79636
Moratorio, Gonzalo; Martínez, Mariela; Gutiérrez, María F.; González, Katiuska; Colina, Rodney; et al.; Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region; BioMed Central; Virology Journal; 4; 79; 12-2007; 1-12
1743-422X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/79636
identifier_str_mv Moratorio, Gonzalo; Martínez, Mariela; Gutiérrez, María F.; González, Katiuska; Colina, Rodney; et al.; Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region; BioMed Central; Virology Journal; 4; 79; 12-2007; 1-12
1743-422X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://virologyj.biomedcentral.com/articles/10.1186/1743-422X-4-79
info:eu-repo/semantics/altIdentifier/doi/10.1186/1743-422X-4-79
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1842270115983261696
score 13.13397

Publicaciones similares