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Sequence and structural analysis of the 5′ noncoding region of hepatitis C virus in patients with chronic infection
Author(s) -
Araújo Flávio Marcos Gomes,
MachadoLima Ariane,
Durham Alan Mitchell,
Teixeira Rosangela,
Oliveira Guilherme
Publication year - 2009
Publication title -
journal of medical virology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.782
H-Index - 121
eISSN - 1096-9071
pISSN - 0146-6615
DOI - 10.1002/jmv.21507
Subject(s) - virology , virus , sequence (biology) , biology , hepatitis a virus , sequence analysis , chronic hepatitis , medicine , genetics , gene
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 RNA fold , RNA shapes and RNA pdist 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.