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Seven nucleotide changes characteristic of the hepatitis C virus genotype 3 5' untranslated region: correlation with reduced in vitro replication

Cyril Masante^1,

Kathleen Mahias^1,

¹ UMR 5234 CNRS, IFR66, Université Victor Segalen Bordeaux 2, 146, rue Léo Saignat, 33076 Bordeaux cedex, France
² UPRES EA 23873, Laboratoire de Virologie, Université Pierre et Marie Curie, CERVI, Hôpital Pitié-Salpêtrière, 75651 Paris Cedex 13, France
³ Laboratoire de Virologie, IFR66, Université Victor Segalen Bordeaux 2, 146, rue Léo Saignat, 33076 Bordeaux cedex, France

Correspondence
Michel Ventura
michel.ventura{at}reger.u-bordeaux2.fr

Computer analysis of 158 hepatitis C virus (HCV) 5' untranslated region (5' UTR) sequences from the six genotypes showed that the 5' UTR from genotype 3 displays seven specific non-contiguous nucleotide changes, at positions 8, 13, 14, 70, 97, 203 and 224. The purpose of this study was to investigate the impact of these changes on translation and replication activities. Indeed, these modifications could alter both the internal ribosome entry site (IRES) present in the 5' UTR of the plus-strand RNA and the 3' end of the minus strand involved in the initiation of plus-strand RNA synthesis. We found that the genotype 3-specific nucleotide changes do not modify the in vitro or ex vivo translation activity of the corresponding IRES, in comparison with that of genotype 1. In contrast, in vitro replication from the minus-strand RNA is eight times less efficient for genotype 3 than for genotype 1 RNA, suggesting the involvement of some nucleotide changes in the reduction of RNA synthesis. Nucleotides 13, 14 and 224 were found to be responsible for this effect. Moreover, a reduced replicative activity was confirmed ex vivo for genotype 3, but to a lesser extent than that observed in vitro, using an RNA minigenome.

These authors contributed equally to this work.

Details of oligonucleotides and plasmids and a phylogenetic tree derived from complete 5' UTR sequences are available with the online version of this paper.