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Comparative analysis of variation and selection in the HCV genome

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Comparative analysis of variation and selection in the HCV genome

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dc.contributor.author Patiño-Galindo, Juan Ángel
dc.contributor.author González Candelas, Fernando
dc.date.accessioned 2017-02-20T15:06:46Z
dc.date.available 2018-01-10T05:45:05Z
dc.date.issued 2017
dc.identifier.citation Patiño-Galindo, Juan Ángel González Candelas, Fernando 2017 Comparative analysis of variation and selection in the HCV genome Infection, Genetics and Evolution 49 104 110
dc.identifier.uri http://hdl.handle.net/10550/57258
dc.description.abstract Genotype 1 of the hepatitis C virus (HCV) is themost prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and CD8), and secondary protein structure. Less than 10% of the genome was found to be under positive selection, and purifying selection was the main evolutionary process acting in both subtypes. We found differences in the number of positively selected sites between subtypes in several genes (Core, HVR2 in E2, P7, helicase in NS3 and NS4a). Heterozygosity values in positively selected sites and the rate of non-synonymous substitutions were significantly higher in subtype HCV-1b. Logistic regression analyses revealed that similar selective forces act at the genome level in both subtypes: RNA secondary structure and CD4 T-cell epitopes are associated with conserved sites, while CD8 T-cell epitopes are associatedwith positive selection in both subtypes. These results indicate that similar selective constraints are acting along HCV-1a and HCV-1 b genomes, despite some differences in the distribution of positively selected sites at independent genes.
dc.language.iso eng
dc.relation.ispartof Infection, Genetics and Evolution, 2017, vol. 49, p. 104-110
dc.subject Genoma humà
dc.subject Virus
dc.title Comparative analysis of variation and selection in the HCV genome
dc.type journal article es_ES
dc.date.updated 2017-02-20T15:06:46Z
dc.identifier.doi 10.1016/j.meegid.2017.01.010
dc.identifier.idgrec 116216
dc.embargo.terms 1 year
dc.rights.accessRights open access es_ES

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