Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
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 s...
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2007
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paper:paper_1743422X_v4_n_p_Moratorio2023-06-08T16:27:51Z Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region untranslated RNA article Bolivia Colombia controlled study genetic analysis genetic distance genetic line genotype Hepatitis C virus molecular evolution neighbor joining method nonhuman nucleotide sequence phylogeny RNA structure South America unindexed sequence Uruguay virus isolation virus strain 5' untranslated region adult aged chemistry child female gene frequency genetic variability genetics hepatitis C human male middle aged molecular evolution virology Hepatitis C virus 5' Untranslated Regions Adult Aged Child Colombia Evolution, Molecular Female Gene Frequency Hepacivirus Hepatitis C, Chronic Humans Male Middle Aged Phylogeny Uruguay Variation (Genetics) 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. © 2007 Moratorio et al; licensee BioMed Central Ltd. 2007 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_1743422X_v4_n_p_Moratorio http://hdl.handle.net/20.500.12110/paper_1743422X_v4_n_p_Moratorio |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
untranslated RNA article Bolivia Colombia controlled study genetic analysis genetic distance genetic line genotype Hepatitis C virus molecular evolution neighbor joining method nonhuman nucleotide sequence phylogeny RNA structure South America unindexed sequence Uruguay virus isolation virus strain 5' untranslated region adult aged chemistry child female gene frequency genetic variability genetics hepatitis C human male middle aged molecular evolution virology Hepatitis C virus 5' Untranslated Regions Adult Aged Child Colombia Evolution, Molecular Female Gene Frequency Hepacivirus Hepatitis C, Chronic Humans Male Middle Aged Phylogeny Uruguay Variation (Genetics) |
| spellingShingle |
untranslated RNA article Bolivia Colombia controlled study genetic analysis genetic distance genetic line genotype Hepatitis C virus molecular evolution neighbor joining method nonhuman nucleotide sequence phylogeny RNA structure South America unindexed sequence Uruguay virus isolation virus strain 5' untranslated region adult aged chemistry child female gene frequency genetic variability genetics hepatitis C human male middle aged molecular evolution virology Hepatitis C virus 5' Untranslated Regions Adult Aged Child Colombia Evolution, Molecular Female Gene Frequency Hepacivirus Hepatitis C, Chronic Humans Male Middle Aged Phylogeny Uruguay Variation (Genetics) Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region |
| topic_facet |
untranslated RNA article Bolivia Colombia controlled study genetic analysis genetic distance genetic line genotype Hepatitis C virus molecular evolution neighbor joining method nonhuman nucleotide sequence phylogeny RNA structure South America unindexed sequence Uruguay virus isolation virus strain 5' untranslated region adult aged chemistry child female gene frequency genetic variability genetics hepatitis C human male middle aged molecular evolution virology Hepatitis C virus 5' Untranslated Regions Adult Aged Child Colombia Evolution, Molecular Female Gene Frequency Hepacivirus Hepatitis C, Chronic Humans Male Middle Aged Phylogeny Uruguay Variation (Genetics) |
| 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. © 2007 Moratorio et al; licensee BioMed Central Ltd. |
| title |
Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American 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 |
| publishDate |
2007 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_1743422X_v4_n_p_Moratorio http://hdl.handle.net/20.500.12110/paper_1743422X_v4_n_p_Moratorio |
| _version_ |
1768543819797626880 |