Sequence-motif analysis of 5 '-untranslated region of GB virus-C in Japanese patients

Background: GB Virus C (GBV-C) is considered to belong to the Flaviviridae; however, the structures of the N-terminal end of its putative polyprotein are not well known. The internal ribosomal entry site (IRES) at the 5'-untr anslated region of GBV-C and an initiating codon at nucleotides (nt) 552-55 4 have been proposed. We investigated the validity of this proposal. Methods: The 5'-untranslated region of GBV-C was amplified from serum sampl es of 17 Japanese patients. Polymerase chain reaction-amplified products we re directly sequenced and the obtained sequences were analysed by comparing them with the IRES structure of other viruses. Results: Fifteen of the 17 (88%) GBV-C strains in our patients were classif ied as being Asian type. The box-A-like sequence (UUUC) and box-B-like sequ ence (AUCAUGG) observed in the IRES of picornaviruses were highly conserved in all the strains. Based on pair-wise comparisons with the multiple align ment data, overall sequence divergence for the 5'-terminus was 2.9-12%. Whe n compared with the proposed secondary structure of the IRES model, the seq uence divergences of the Asian-type GBV-C were higher at the regions of loo p structures and lower at the regions of double-stranded RNA. The AUG codon s, except for the one located at nt 552-554, produced truncated polyprotein s or were not in-frame with the putative protein. Conclusions: Our examination of the sequence motif of GBV-C supports the pr oposal that the GBV-C has common structural motifs for IRES at its 5'-untra nslated region and the AUG codon at nt 552-554 may be an initiating codon. (C) 2000 Blackwell Science Asia Pty Ltd.