Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region.

Hepatitis C virus (HCV) showed 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 of nucleotide 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 two-tiered 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.

[1]  P. Simmonds,et al.  Analysis of viral sequence variation by PCR , 1993 .

[2]  P. Simmonds,et al.  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 , 1993, Journal of clinical microbiology.

[3]  E. Holmes,et al.  Sequence variability in the 5' non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity. , 1993, The Journal of general virology.

[4]  P. Simmonds,et al.  Detection of three types of hepatitis C virus in blood donors: investigation of type‐specific differences in serologic reactivity and rate of alanine aminotransferase abnormalities , 1993, Transfusion.

[5]  L. Ping,et al.  Secondary structure of the 5' nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. , 1992, Nucleic acids research.

[6]  Y. Ito,et al.  Genetic drift of hepatitis C virus during an 8.2-year infection in a chimpanzee: variability and stability. , 1992, Virology.

[7]  Motohiro Shibata,et al.  Detection of hepatitis C virus by polymerase chain reaction and response to interferon‐α therapy: Relationship to genotypes of hepatitis C virus , 1992, Hepatology.

[8]  B. Irvine,et al.  At least five related, but distinct, hepatitis C viral genotypes exist. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Koichi Kanai,et al.  HCV genotypes in chronic hepatitis C and response to interferon , 1992, The Lancet.

[10]  R. Purcell,et al.  Sequence analysis of the 5' noncoding region of hepatitis C virus. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[11]  C. Lee,et al.  Identification of hepatitis C viruses with a nonconserved sequence of the 5' untranslated region , 1992, Journal of clinical microbiology.

[12]  S. Mishiro,et al.  Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. , 1992, Virology.

[13]  Ding‐Shinn Chen,et al.  The Taiwanese hepatitis C virus genome: sequence determination and mapping the 5' termini of viral genomic and antigenomic RNA. , 1992, Virology.

[14]  E. Holmes,et al.  Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants. , 1992, The Journal of general virology.

[15]  S. Kunitada,et al.  Molecular cloning of hepatitis C virus genome from a single Japanese carrier: sequence variation within the same individual and among infected individuals. , 1992, Virus research.

[16]  T. Date,et al.  HCV genotypes in different countries , 1992, The Lancet.

[17]  N. Kato,et al.  A new type of hepatitis C virus in patients in Thailand. , 1992, Biochemical and biophysical research communications.

[18]  N. Enomoto,et al.  Clinical backgrounds of the patients having different types of hepatitis C virus genomes. , 1992, Journal of hepatology.

[19]  T. Ishikawa,et al.  Detection of hepatitis C virus by polymerase chain reaction and response to interferon-alpha therapy: relationship to genotypes of hepatitis C virus. , 1992, Hepatology.

[20]  R H Purcell,et al.  Importance of primer selection for the detection of hepatitis C virus RNA with the polymerase chain reaction assay. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[21]  N. Kato,et al.  Distribution of plural HCV types in Japan. , 1991, Biochemical and biophysical research communications.

[22]  S. Zebedee,et al.  Genomic structure of the human prototype strain H of hepatitis C virus: comparison with American and Japanese isolates. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[23]  B. Irvine,et al.  Use of a signature nucleotide sequence of hepatitis C virus for detection of viral RNA in human serum and plasma , 1991, Journal of clinical microbiology.

[24]  H. Okamoto,et al.  Nucleotide sequence of the genomic RNA of hepatitis C virus isolated from a human carrier: comparison with reported isolates for conserved and divergent regions. , 1991, The Journal of general virology.

[25]  C. Trépo,et al.  Two French genotypes of hepatitis C virus: homology of the predominant genotype with the prototype American strain. , 1991, Gene.

[26]  S. Kaneko,et al.  Severity of liver disease with different hepatitis C viral clones , 1991, The Lancet.

[27]  R. Purcell,et al.  Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[28]  P. Barr,et al.  Genetic organization and diversity of the hepatitis C virus. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Matthew J. Brauer,et al.  Characterization of the terminal regions of hepatitis C viral RNA: identification of conserved sequences in the 5' untranslated region and poly(A) tails at the 3' end. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[30]  H. Okayama,et al.  Structure and organization of the hepatitis C virus genome isolated from human carriers , 1991, Journal of virology.

[31]  N. Kato,et al.  Hypervariable regions in the putative glycoprotein of hepatitis C virus. , 1991, Biochemical and biophysical research communications.

[32]  Matthew J. Brauer,et al.  Variable and hypervariable domains are found in the regions of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins. , 1991, Virology.

[33]  T. Sugimura,et al.  Molecular cloning of the human hepatitis C virus genome from Japanese patients with non-A, non-B hepatitis. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[34]  P Balfe,et al.  Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1 , 1990 .

[35]  N. Enomoto,et al.  There are two major types of hepatitis C virus in Japan. , 1990, Biochemical and biophysical research communications.

[36]  H. Okamoto,et al.  The 5'-terminal sequence of the hepatitis C virus genome. , 1990, The Japanese journal of experimental medicine.

[37]  H J Alter,et al.  An assay for circulating antibodies to a major etiologic virus of human non-A, non-B hepatitis. , 1990, Science.

[38]  M. Houghton,et al.  A cDNA fragment of hepatitis C virus isolated from an implicated donor of post-transfusion non-A, non-B hepatitis in Japan. , 1989, Nucleic acids research.

[39]  Jules L. Dienstag,et al.  An assay for circulating antibodies to a major etiologic virus of human non-A, non-B hepatitis , 1989 .

[40]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[41]  C. Yanisch-Perron,et al.  Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. , 1985, Gene.