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

Abstract

The extreme 5-terminal sequences of the GB virus C͞hepatitis G virus (GBV-C͞HGV), containing elements essential for regulation of viral gene expression and replication, have not been determined. By using a RNA-ligasemediated 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-C͞HGV 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-C͞HGV virus by PCR assays.

Association of GB virus C (GBV-C)/hepatitis G virus (HGV) with haematological diseases of different malignant potential

“…Thus, among our patients, the NS3 sequence was highly conserved. Consequently, primers from this region appeared to be more efficient in the identification of different GBV-C/HGV genotypes than those derived from the 5Ј UTR region (exhibiting high sequence divergence between different isolates) [Hsieh et al, 1997]. No clear pattern emerged, and GBV-C/HGV infection was found in heterogeneous groups of hematological diseases with possibly different aetiologies.…”

Sequence variation and phylogenetic analysis of envelope glycoprotein of hepatitis G virus.

“…Furthermore, analysis of these isolates using the 400 bp envelope region sequence suggests that the definition of three HGV genotypes based on the entire genome might be similar to our grouping. Other groups have also suggested similar classification of HGV into two to five genotypes, subtypes or groups based on their analyses of 5h UTR region (Muerhoff et al, 1996 ;Fukushi et al, 1996 ;Ding et al, 1997 ;Hsieh et al, 1997 ;Mukaide et al, 1997) or NS3 helicase region sequences (Kao et al,1996). Furthermore, Mukaide et al (1997) also identified ' genotype '-specific restriction sites, ScrFI and BsmFI, and developed restriction polymorphism analysis.…”

GB virus C quasispecies detected in plasma and lymphocyte subsets in a natural human infection

“…1a). When analysing all sequenced clones, it was observed that most of the substitutions occurred within the three regions associated with specific polymorphisms in the 59 UTR, strongly correlated with phylogenetic clustering of variants (Hsieh et al, 1997;Smith et al, 1997), herein named V-1, V-2 and V-3 (Fig. 1a).…”