Classification of Hepatitis C Viruses Based on Phylogenetic Analysis of the Envelope 1 and Nonstructural 5B Regions and Identification of Five Additional Subtypes

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1994 Oct 11

PMID 7524083

Citations 41

Authors

L Stuyver

W van Arnhem

A Wyseur

F Hernandez

E Delaporte

G Maertens

Affiliations

Soon will be listed here.

Abstract

Genotyping of hepatitis C virus-positive sera by means of a line probe assay indicated that < 3% of European samples, but up to 30% of Gabonese sera, could not be classified as either 1a, 1b, 2a, 2b, 3a, 3b, 4c, 5a, or 6a. Such samples were analyzed in the 5' untranslated region and in the nonstructural 5 (NS5) region. Classification based on phylogenetic analysis of the commonly used 222-bp-long NS5B region was possible for most but not all of the selected sera. Therefore, the core/envelope 1 region (579 bp) and a larger NS5B (340 bp) region were also analyzed. Only the phylogenetic analysis of the 340-bp NS5B region of these newly identified and published isolates provided unambiguous classification into types and subtypes. Furthermore, unequivocal evidence for four subtypes in type 2 and eight subtypes in type 4 was provided. A specific recognition sequence in the 5' untranslated region was observed for every newly identified subtype. Based on 1830 pair-wise comparisons in NS5B, isolates belonging to the same subtype showed evolutionary distances of < 0.127 and isolates of the same type exhibited evolutionary distances of < 0.328. These phylogenetic border distances can be conveniently used for classification of hepatitis C virus isolates into types and subtypes.

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References

Choo Q, Richman K, Han J, Berger K, Lee C, Dong C . Genetic organization and diversity of the hepatitis C virus. Proc Natl Acad Sci U S A. 1991; 88(6):2451-5. PMC: 51250. DOI: 10.1073/pnas.88.6.2451. View

Takamizawa A, Mori C, FUKE I, Manabe S, Murakami S, Fujita J . Structure and organization of the hepatitis C virus genome isolated from human carriers. J Virol. 1991; 65(3):1105-13. PMC: 239876. DOI: 10.1128/JVI.65.3.1105-1113.1991. View

Okamoto H, Okada S, Sugiyama Y, Kurai K, Iizuka H, Machida A . Nucleotide sequence of the genomic RNA of hepatitis C virus isolated from a human carrier: comparison with reported isolates for conserved and divergent regions. J Gen Virol. 1991; 72 ( Pt 11):2697-704. DOI: 10.1099/0022-1317-72-11-2697. View

Inchauspe G, Zebedee S, Lee D, Sugitani M, Nasoff M, Prince A . Genomic structure of the human prototype strain H of hepatitis C virus: comparison with American and Japanese isolates. Proc Natl Acad Sci U S A. 1991; 88(22):10292-6. PMC: 52914. DOI: 10.1073/pnas.88.22.10292. View

Mori S, Kato N, Yagyu A, Tanaka T, Ikeda Y, Petchclai B . A new type of hepatitis C virus in patients in Thailand. Biochem Biophys Res Commun. 1992; 183(1):334-42. DOI: 10.1016/0006-291x(92)91648-a. View

Martell M, Esteban J, Quer J, Genesca J, Weiner A, Esteban R . Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution. J Virol. 1992; 66(5):3225-9. PMC: 241092. DOI: 10.1128/JVI.66.5.3225-3229.1992. View

Chen P, Lin M, Tai K, Liu P, Lin C, Chen D . The Taiwanese hepatitis C virus genome: sequence determination and mapping the 5' termini of viral genomic and antigenomic RNA. Virology. 1992; 188(1):102-13. DOI: 10.1016/0042-6822(92)90739-c. View

Okamoto H, Kurai K, Okada S, Yamamoto K, Lizuka H, Tanaka T . Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology. 1992; 188(1):331-41. DOI: 10.1016/0042-6822(92)90762-e. View

Chan S, McOmish F, Holmes E, Dow B, Peutherer J, Follett E . Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants. J Gen Virol. 1992; 73 ( Pt 5):1131-41. DOI: 10.1099/0022-1317-73-5-1131. View

10.

Bukh J, Purcell R, Miller R . Sequence analysis of the 5' noncoding region of hepatitis C virus. Proc Natl Acad Sci U S A. 1992; 89(11):4942-6. PMC: 49204. DOI: 10.1073/pnas.89.11.4942. View

11.

Tanaka T, Kato N, Nakagawa M, Ootsuyama Y, Cho M, Nakazawa T . Molecular cloning of hepatitis C virus genome from a single Japanese carrier: sequence variation within the same individual and among infected individuals. Virus Res. 1992; 23(1-2):39-53. DOI: 10.1016/0168-1702(92)90066-i. View

12.

Cha T, Beall E, Irvine B, Kolberg J, Chien D, Kuo G . At least five related, but distinct, hepatitis C viral genotypes exist. Proc Natl Acad Sci U S A. 1992; 89(15):7144-8. PMC: 49662. DOI: 10.1073/pnas.89.15.7144. View

13.

Okamoto H, Kojima M, Okada S, Yoshizawa H, Iizuka H, Tanaka T . Genetic drift of hepatitis C virus during an 8.2-year infection in a chimpanzee: variability and stability. Virology. 1992; 190(2):894-9. DOI: 10.1016/0042-6822(92)90933-g. View

14.

Machida A, Ohnuma H, Tsuda F, Munekata E, Tanaka T, Akahane Y . Two distinct subtypes of hepatitis C virus defined by antibodies directed to the putative core protein. Hepatology. 1992; 16(4):886-91. DOI: 10.1002/hep.1840160406. View

15.

Okamoto H, Kanai N, Mishiro S . Full-length nucleotide sequence of a Japanese hepatitis C virus isolate (HC-J1) with high homology to USA isolates. Nucleic Acids Res. 1992; 20(23):6410. PMC: 334535. DOI: 10.1093/nar/20.23.6410. View

16.

Simmonds P, McOmish F, Yap P, Chan S, Lin C, Dusheiko G . Sequence variability in the 5' non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity. J Gen Virol. 1993; 74 ( Pt 4):661-8. DOI: 10.1099/0022-1317-74-4-661. View

17.

Chayama K, Tsubota A, Arase Y, Saitoh S, Koida I, Ikeda K . Genotypic subtyping of hepatitis C virus. J Gastroenterol Hepatol. 1993; 8(2):150-6. DOI: 10.1111/j.1440-1746.1993.tb01507.x. View

18.

Stuyver L, van Arnhem W, Wyseur A, DeLeys R, Maertens G . Analysis of the putative E1 envelope and NS4a epitope regions of HCV type 3. Biochem Biophys Res Commun. 1993; 192(2):635-41. DOI: 10.1006/bbrc.1993.1462. View

19.

Stuyver L, Rossau R, Wyseur A, Duhamel M, Vanderborght B, Van Heuverswyn H . Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. J Gen Virol. 1993; 74 ( Pt 6):1093-102. DOI: 10.1099/0022-1317-74-6-1093. View

20.

Simmonds P, Rose K, Graham S, Chan S, McOmish F, Dow B . Mapping of serotype-specific, immunodominant epitopes in the NS-4 region of hepatitis C virus (HCV): use of type-specific peptides to serologically differentiate infections with HCV types 1, 2, and 3. J Clin Microbiol. 1993; 31(6):1493-503. PMC: 265567. DOI: 10.1128/jcm.31.6.1493-1503.1993. View