Sequence and structural analysis of the 5′ noncoding region of hepatitis C virus in patients with chronic infection |
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| Authors: | Flávio Marcos Gomes Araújo Ariane Machado‐Lima Alan Mitchell Durham Rosangela Teixeira Guilherme Oliveira |
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| Affiliation: | 1. Instituto René Rachou/FIOCRUZ. Av. Augusto de Lima, Minas Gerais, Brazil;2. Instituto de Matemática e Estatística/Instituto de Psiquiatria, Universidade de S?o Paulo, S?o Paulo, Brazil;3. Instituto de Matemática e Estatística, Universidade de S?o Paulo, S?o Paulo, Brazil;4. Instituto Alfa de Gastroenterologia do Hospital das Clínicas da UFMG, Belo Horizonte, Minas Gerais, Brazil |
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| Abstract: | Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well conserved 5′ noncoding region (5′ NCR) among all genotypes. In this study, the structural features and translational efficiency of the HCV 5′ NCR sequences were analyzed using the programs RNAfold, RNAshapes and RNApdist and with a bicistronic dual luciferase expression system, respectively. RNA structure prediction software indicated that base substitutions will alter potentially the 5′ NCR structure. The heterogeneous sequence observed on 5′ NCR led to important changes in their translation efficiency in different cell culture lines. Interactions of the viral RNA with cellular transacting factors may vary according to the cell type and viral genome polymorphisms that may result in the translational efficiency observed. J. Med. Virol. 81:1212–1219, 2009. © 2009 Wiley‐Liss, Inc. |
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| Keywords: | HCV 5′ NCR RNA translation |
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