Cloning and characterization of the extreme 5′-terminal sequences of the RNA genomes of GB virus C/hepatitis G virus

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Abstract
The extreme 5′-terminal sequences of the GB virus C/hepatitis G virus (GBV-C/HGV), containing elements essential for regulation of viral gene expression and replication, have not been determined. By using a RNA-ligase-mediated RACE (rapid amplification of the cDNA ends) procedure, we have cloned the extreme 5′-terminal sequences of the viral genome from the serum of three Taiwanese patients. Sequence analysis of the 5′ noncoding region in alignment with one West African and two American isolates showed that (i) a consensus 5′-end sequence was cloned; (ii) about 97% of sequences were homologous among the three Taiwan isolates and also between the two American isolates, whereas about 90% of sequences were homologous among the isolates from the three different geographic areas; (iii) the sequence heterogeneity related to geographic separation is confined mainly to three domains; and (iv) a potential hairpin structure, resembling the hairpin structure found in the 5′ end of hepatitis C virus genome, was detected in the 5′ end of the noncoding region. Our data support the hypotheses that (i) the extreme 5′ end of the hepatitis GBV-C/HGV viral genome has been cloned, (ii) there are different genotypes correlated with geographic separation, and (iii) the viral translation and replication mechanisms may be similar to that of hepatitis C virus and pestiviruses. Our data have not only shed light on the viral replication mechanism but also offer information for selection of optimal primer sequences for the detection and genotyping of the hepatitis GBV-C/HGV virus by PCR assays.