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Updated: Jun 22, 2026

A Protocol for Analyzing Hepatitis C Virus Replication
Published on: June 26, 2014
Sequence and structural analysis of the 5' noncoding region of hepatitis C virus in patients with chronic infection
Flávio Marcos Gomes Araújo1, Ariane Machado-Lima, Alan Mitchell Durham
1Instituto René Rachou/FIOCRUZ. Av. Augusto de Lima, Minas Gerais, Brazil. araujo@cpqrr.fiocruz.br
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.
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