Hepatitis C virus (HCV) shows substantial nucleotide sequence diversity distributed throughout the viral genome, with many variants showing only 68 to 79 % overall sequence similarity to one another. Phylogenetic analysis ofnucleofide sequences derived from part of the gene encoding a non-structural protein (NS-5) has provided evidence for six major genotypes of HCV amongst a worldwide collection of 76 samples from HCV-infected blood donors and patients with chronic hepatitis. Many of these HCV types comprised a number of more closely related subtypes, leading to a current total of 11 genetically distinct viral populations. Phylogenetic analysis of other regions of the viral genome produced relationships between published sequences equivalent to those found in NS-5, apart from the more highly conserved 5' non-coding region in which only the six major HCV types, but not subtypes, could be differentiated. A new nomenclature for HCV variants is proposed in this communication that reflects the twotiered nature of sequence differences between different viral isolates. The scheme classifies all known HCV variants to date, and describes criteria that would enable new variants to be assigned within the classification as they are discovered.

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Isolates of hepatitis C virus (HCV) show considerable nucleotide sequence variability throughout the genome. Comparisons of complete genome sequences have been used as the basis of classification of HCV into a number of genotypes that show 67 to 77 % sequence similarity. In order to investigate whether sequence relationships between genotypes are equivalent in different regions of the genome, we have carried out formal sequence analysis of variants in the 5' non-coding region (5'NCR) and in the genes encoding the core protein, an envelope protein (El) and a non-structural protein (NS-5). In the E1 region, variants grouped into a series of six major genotypes and a series of subtypes that could be matched to the phylogenetic groupings previously observed for the NS-5 region. Furthermore, core and E1 sequences showed three non-overlapping ranges of sequence similarity corresponding to those between different genotypes, subtypes and isolates previously described in NS-5. Each major genotype could also be reliably identified by sequence comparisons in the well conserved 5'NCR, although many subtypes, such as la/lb, 2a/2c and some of those of type 4, could not be reliably distinguished from each other in this region. These data indicate that subgenomic regions such as E1 and NS-5 contain sufficient phylogenetic information for the identification of each of the 11 or 12 known types and subtypes of HCV. No evidence was found for variants of HCV that had sequences of one genotype in the 5'NCR but of a different one in the E1 or NS-5 region. This suggests that recombination between different HCV types is rare or non-existent and does not currently pose a problem in the use of subgenomic regions in classification.

Hepatitis C virus, the major causative agent of blood-borne non-A, non-B hepatitis in the world, has been the subject of considerable nucleic acid sequence analysis. Although all reported hepatitis C sequences from the United States have been represented by the prototype hepatitis C virus type 1 sequence, two groups of variant sequences have been reported in Japan. However, we have noted five distinct, but related, genotypes (I-V) throughout the world, based on detailed sequence determination and analysis of the first 1700 nucleotides and part of the nonstructural region 5 at the C terminus of the open reading frme. The nucleotide sequence for a large number of hepaiis C virus islates sanning six continents was obtained by direct sequence analysis of PCR products after reverse transcription. Genotype was clafied by using several distinct sequence motifs. We observed that most genotypes coexist in several geographic regions, iuding the United States, Japan, Germany, and Italy. So far, genotype V has been found only in South Africa. Interestingly, each distinct genotype seems to be maintained throughout the genome in the segments tudied. These genotype dictions should be considered when d ing specific diagosic tests, developing potential vaccines, and studying viral transmio.Hepatitis C virus (HCV) was isolated from a chimpanzee chronically infected with a contaminated human factor VIII concentrate in 1989 (1). An immunoassay for circulating antibody to HCV was developed by using a yeast-derived recombinant antigen encoded by a segment of the cloned HCV genome (2). Results indicated HCV to be the major causative agent of the blood-borne non-A, non-B hepatitis (1-3).The genomic organization and characterization of HCV has been reported (4, 5). The HCV genome is a positivestrand RNA of -9.4 kilobases and contains a large open reading frame that encodes a polyprotein precursor of 3011 amino acids. Based on comparative sequence analysis of the genome and encoded polyprotein, HCV is thought to be distantly related to the flaviviruses and the pestiviruses. The large open reading frame appears to encode colinearly structural and nonstructural proteins, with the structural proteins located at the 5'-end portion of the genome. Putative boundaries are assigned that separate the 5'-untranslated region (5UT), the core protein (C), the glycoproteins envelope 1 (El) and nonstructural protein l/envelope 2 (NS1/E2), the nonstructural proteins 2-5 (NS2-NS5), and the 3'-untranslated region (3UT). The prototype HCV nucleotide sequence reported is termed HCV1 (refs. 4 and 5; see ref. 6 for review).Using pooled plasma samples from human non-A, non-B hepatitis patients and potential HCV carriers, Kato et al. (7), Takamizawa et al. (8), and Okamoto et al. (9) have reported entire genomic sequences of Japanese HCV strains. Some partial 5'-end HCV sequences from individual Japanese samples were reported by Takeuchi et al. (10,11) and Okamoto et al. (12). In addition, partial sequences in the NS3, NS4, and NS5 regions have been r...