Hepatitis C virus variants from Thailand classifiable into five novel genotypes in the sixth (6b), seventh (7c, 7d) and ninth (9b, 9c) major genetic groups

Abstract

Nine (10%) out of 90 hepatitis C virus (HCV) isolates from hepatitis patients and commercial blood donors inThailand were not classifiable into any of genotypes I/la, II/lb, III/2a, IV/2b, V/3a or VI/3b by RT-PCR with type-specific primers deduced from the HCV core gene. These isolates were sequenced over a 1-6 kb stretch of the 5'-terminal sequence and 1.1 kb of the 3'-terminal sequence covering 30 % of the entire genome. Based on two-by-two comparison and phylogenetic analyses of the nine Thailand isolates among themselves and with known full or partial sequences of previously reported HCV isolates, the Thailand isolates were classified into five genotypes not reported previously, viz. 6b, 7c, 7d, 9b and 9c. Along with HCV isolates reported already, they make at least nine major genetic groups of HCV which further break down into at least 28 genotypes with sequence similarity in the E1 gene (576 bp) of ~< 80%. As many more HCV isolates of distinct genotypes are expected to be found throughout the world, it will become increasingly difficult to classify them by comparison of any partial sequences of the genome. Complete sequence data will be required for the full characterization and classification of HCV genotypes.Hepatitis C virus (HCV) is a positive-stranded linear RNA virus of approximately 9500 nucleotides (nt), and is the major causative agent of blood-borne non-A, non-B hepatitis worldwide (for a review, see Houghton et al., 1991). It has a genomic structure and organization resembling those of pestiviruses and ftaviviruses (Miller & Purcell, 1990) with 5' and 3' untranslated regions (UTR) flanking the single open reading frame. The coding area of HCV is divided into nine regions-for core protein, envelope 1 (El) glycoprotein, envelope 2/nonstructural 1 (E2/NSl) glycoprotein, and six nonstructural proteins designated NS2, NS3, NS4a, NS4b, NS5a and NS5b (Houghton eta L, 1991 ;Grakoui et al., 1993).Based on sequence similarity across the entire genome, * Author for correspondence. Fax +81 285 44 1557.The sequences reported in this paper have been deposited in the DDBJ, GenBank and EMBL Nucleotide Sequence Databases (accession nos. D3783%D37841, D37843-D37846, D37848-D37850, D37853-D37855, D37857-D37860, D3786~D37864, D37867, D37869, D38078, D38079). five major HCV genotypes designated I, II, III, IV and V were proposed . Another classification scheme depends on the phylogenetic differences of two tiers, with major types designated 1, 2, 3 etc. which divide into subtypes such as a, b, c etc. (Simmonds et al., 1993). Genotype I corresponds to la, II to lb, III to 2a, IV to 2b and V to 3a. Within the past few years, many HCV variants with substantial sequence divergence have been found, resulting in at least nine major genetic groups/types and 28 genotypes/subtypes (Enomoto et al., 1990;Choo et al., 1991;Mori et al., 1992;Bukh et al., 1993Bukh et al., , 1994Simmonds et al., 1993;Stuyver et al., 1993Stuyver et al., , 1994Okamoto et al., 1990Okamoto et al., , 1992aOkamoto et al., , 1994 Tokita et al., 1994a, b)...

Hepatitis C virus variants from Jakarta, Indonesia classifiable into novel genotypes in the second (2e and 2f), tenth (10a) and eleventh (11a) genetic groups

“…First, they allow us to argue against the two-tiered classification of HCV genotypes presently advocated. We have reported group similarities (66.5-80.0%) which did not overlap with the genotype similarities (80.2-88.6 %) in a comparison of a 1093 bp NS5b sequence spanning nt 8279-9371 (Tokita et al, 1994b(Tokita et al, , 1995. The Jakarta HCV isolates of genotypes 10a and 1 la, however, were 77.4-82.9% and 78.7 81.0% similar, respectively, to genotypes in groups 3 and 7 within this sequence.…”

“…They were subjected to pair-wise comparison, along with 62 HCV isolates of 25 genotypes in nine genetic groups, within a 1093 bp (nt 8279 9371) sequence in the NS5b region (Table 1). We have reported that HCV isolates can be classified by the criteria of isolate similarity of 91.7 99.2%, genotype similarity of 80.2 88'6% and group similarity of 66.5-80-0% (Tokita et al, 1994b(Tokita et al, , 1995. The 22 Jakarta isolates of unknown genotype showed a sequence similarity of ~< 87.6 % to the reported isolates of 25 genotypes, indicating that they would belong to distinct genotypes.…”

“…Since the divergence in the entire genome and parts of the NS5b region distributes in two distinct tiers, HCV is classified into genetic groups or types named 1, 2, 3 etc. which divide further into genotypes Tokita et al, 1995) or subtypes called a, b, c etc. (Simmonds et at., 1993;Simmonds, 1995).…”

Genetic History of Hepatitis C Virus in East Asia

“…Indeed, the first HCV isolates from East Asia were so divergent that they were initially classified as separate genotypes, designated 7, 8, 9, and 11 (1,50,61,62,63). These strains have since been reclassified as individual subtypes within genotype 6 (52).…”

Genotypic analysis of hepatitis C virus in blood donors in Indonesia.

“…This initial molecular characterization led to the use of genomic sequence information from reverse transcription-polymerase chain reaction (RT-PCR)-assisted amplified partial and/or full length HCV RNA on viral isolates as a means to classify these isolates into genetic groups, genotypes, and subtypes, and to the definition of primers, probes and first-and second-round PCR techniques to identify, group, and classify known and unknown isolates of HCVs worldwide. [5][6][7][8][9][10][11][12][13][14][15][16] An accumulation of such sequence information has led to the definition of HCV types, subtypes, and genetic groups. So far, 6 major HCV types and more than 74 different subtypes have been catalogued, and the number continues to grow as new isolates are sequenced and more countries are included in the sampling of HCV.…”