The entire nucleotide sequence of a hepatitis C virus (HCV) genome (NZL1) of genotype V/3a was determined from overlapping cDNA clones obtained from a human carrier in New Zealand. It comprised 9425 nucleotides (nt) including a 5-untranslated region of 339 nt, a single large open reading frame encoding a polyprotein of 3021 amino acids, a 3′-untranslated region of 23 nt, and 3 -terminal poly(U) stretches of variable lengths. The NZL1 genome was compared with 15 HCV isolates of other genotypes for which the full- length sequence has been determined. It differed from them by 31·1 to 34·3% in nucleotide sequence identity and by 24·5 to 29·1% in amino acid sequence identity, confirming the distinction of genotype V/3a from the other isolates.
The nucleotide sequence data reported in this paper are deposited in the DDBJ/GenBank/EMBL Data Libraries under the accession no. D17763.
BukhJ.,
PurcellR. H.,
MillerR. H.1992; Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proceedings of the National Academy of Sciences, U.S.A 89:4942–4946
BukhJ.,
PurcellR. H.,
MillerR. H.1993; At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative E1 gene of isolates collected worldwide. Proceedings of the National Academy of Sciences, U.S.A 90:8234–8238
ChaT. A.,
BeallE.,
IrvineB,
ChienD.,
KuoG.,
UrdeaM. S.1992; At least five related, but distinct, hepatitis C viral genotypes exist. Proceedings of the National Academy of Sciences, U.S.A 89:7144–7148
ChanS.-W.,
SimmondsP.,
McomishF.,
YapP.-L.,
MitchellR.,
DowB.,
FollettE.1991; Serological responses to infection with three different types of hepatitis C virus. Lancet 338:1391
ChanS.-W.,
McomishF.,
HolmesE. C.,
DowB.,
PeuthererJ. F.,
FollettE.,
YapP. L.,
SimmondsP.1992; Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants. Journal of General Virology 73:1131–1141
ChenP. J.,
LinM. H.,
TaiK. F.,
LiuP. C.,
LinC. J.,
ChenD. S.1992; The Taiwanese hepatitis C virus genome: sequence determination and mapping the 5′ termini of viral genomic and antigenomic RNA. Virology 188:102–113
ChooQ.-L.,
KuoG.,
WeinerA. J.,
OverbyL. R.,
BradleyD. W.,
HoughtonM.1989; Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244:359–362
ChooQ.-L.,
RichmanK. H.,
HanJ. H.,
BergerK.,
LeeC.,
DongC.,
GallegosC.,
CoitD.,
Medina-SelbyR.,
BarrP. J.,
WeinerA. J.,
BradleyD. W.,
KuoG.,
HoughtonM.1991; Genetic organization and diversity of the hepatitis C virus. Proceedings of the National Academy of Sciences, U.S.A 88:2451–2455
GrakouiA.,
MccourtD. W.,
WychowskiC.,
FeinstoneS. M.,
RiceC. M.1993; Characterization of the hepatitis C virus- encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites. Journal of Virology 67:2832–2843
HanJ. H.,
HoughtonM.1992; Group specific sequences and conserved secondary structures at the 3′ end of HCV genome and its implication for viral replication. Nucleic Acids Research 20:3520
HanJ. H.,
ShyamalaV.,
RichmanK. H.,
BrauerM. J.,
IrvineB.,
UrdeaM. S.,
Tekamp-OlsonP.,
KuoG.,
ChooQ.-L.,
HoughtonM.1991; 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. Proceedings of the National Academy of Sciences, U.S.A 88:1711–1715
HijikataM.,
KatoN.,
OotsuyamaY.,
NakagawaM.,
OhkoshiS.,
ShimotohnoK.1991a; Hypervariable regions in the putative glycoprotein of hepatitis C virus. Biochemical and Biophysical Research Communications 175:220–228
HijikataM.,
KatoN.,
OotsuyamaY.,
NakagawaM.,
ShimotohnoK.1991b; Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis. Proceedings of the National Academy of Sciences, U.S.A 88:5547–5551
HondaM.,
KanekoS.,
UnouraM.,
KobayashiK.,
MurakamiS.1992; Sequence comparisons for a hepatitis C virus genome RNA isolate from a patient with liver cirrhosis. Gene 120:317–318
HoughtonM.,
WeinerA.,
HanJ.,
KuoG.,
ChooQ.-L.1991; Molecular biology of the hepatitis C viruses: implications for diagnosis, development and control of viral disease. Hepatology 14:381–388
InchauspeG.,
ZebedeeS.,
LeeD. H.,
SugitaniM.,
NasoffM.,
PrinceA. M.1991; Genomic structure of the human prototype strain H of hepatitis C virus: comparison with American and Japanese isolates. Proceedings of the National Academy of Sciences, U.S.A 88:10292–10296
KatoN.,
HijikataM.,
OotsuyamaY.,
NakagawaM.,
OhkoshiS.,
SugimuraT.,
ShimotohnoK.1990; Molecular cloning of the human hepatitis C virus genome from Japanese patients with non-A, non-B hepatitis. Proceedings of the National Academy of Sciences, U.S.A 87:9524–9528
LeeC.-H.,
ChengC.,
WangJ.,
LumengL.1992; Identification of hepatitis C viruses with a nonconserved sequence of the 5′ untranslated region. Journal of Clinical Microbiology 30:1602–1604
McomishF.,
ChanS.-W.,
DowB. C.,
GillonJ.,
FrameW. D.,
CrawfordR. J.,
YapP.-L.,
FollettE. A.,
SimmondsP.1993; 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. Transfusion 33:7–13
MoriS.,
KatoN.,
YagyuA.,
TanakaT.,
IkedaY.,
PetchclaiB.,
ChiewsilpP.,
KurimuraT.,
ShimotohnoK.1992; A new type of hepatitis C virus in patients in Thailand. Biochemical and Biophysical Research Communications 183:334–342
NeiM.,
GojoboriT.1986; Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3:418–426
OkamotoH.,
OkadaS.,
SugiyamaY.,
YotsumotoS.,
TanakaT.,
YoshizawaH.,
TsudaF.,
MiyakawaY.,
MayumiM.1990; The 5′-terminal sequence of the hepatitis C virus genome. Japanese Journal of Experimental Medicine 60:167–177
OkamotoH.,
OkadaS.,
SugiyamaY.,
KuraiK.,
IizukaH.,
MachidaA.,
MiyakawaY.,
MayumiM.1991; Nucleotide sequence of the genomic RNA of hepatitis C virus isolated from a human carrier: comparison with reported isolates for conserved and divergent regions. Journal of General Virology 72:2697–2704
OkamotoH.,
KanaiN.,
MishiroS.1992a; Full-length nucleotide sequence of a Japanese hepatitis C virus isolate (HC-J1) with high homology to USA isolates. Nucleic Acids Research 20:6410
OkamotoH.,
KuraiK.,
OkadaS.,
YamamotoK.,
IizukaH.,
TanakaT.,
FukudaS.,
TsudaF.,
MishiroS.1992b; Full-length sequence of a hepatitis C vims genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology 188:331–341
OkamotoH.,
KojimaM.,
OkadaS.,
YoshizawaH.,
IizukaH.,
TanakaT.,
MuchmoreE. E.,
PetersonD. A.,
ItoY.,
MishiroS.1992c; Genetic drift of hepatitis C virus during an 8·2-year infection in a chimpanzee: variability and stability. Virology 190:894–899
OkamotoH.,
SugiyamaY.,
OkadaS.,
KuraiK.,
AkahaneY.,
SugaiY.,
TanakaT.,
SatoK.,
TsudaF.,
MiyakawaY.,
MayumiM.1992d; Typing hepatitis C virus by polymerase chain reaction with type-specific primers: application to clinical surveys and tracing infectious sources. Journal of General Virology 73:673–679
OkamotoH.,
TokitaH.,
SakamotoM.,
HorikitaM.,
KojimaM.,
IizukaH.,
MishiroS.1993; Characterization of the genomic sequence of type V (or 3a) hepatitis C virus isolates and PCR primers for specific detection. Journal of General Virology 74:2385–2390
OkamotoH.,
KojimaM.,
SakamotoM.,
IizukaH.,
HadiwandowoS.,
SuwignyoS.,
MiyakawaY.,
MayumiM.1994; The entire nucleotide sequence and classification of a hepatitis C virus isolate of a novel genotype from an Indonesian patient with chronic liver disease. Journal of General Virology 75:629–635
SimmondsP.,
McomishF.,
YapP. L.,
ChanS.-W.,
LinC. K.,
DusheikoG.,
SaeedA. A.,
HolmesE. C.1993; Sequence variability in the 5′ non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity. Journal of General Virology 14:661–668
StuyverL.,
van ArnhemW.,
WyseurA.,
DeleysR.,
MaertensG.1993a; Analysis of the putative El envelope and NS4a epitope regions of HCV type 3. Biochemical and Biophysical Research Communications 192:635–641
StuyverL.,
RossauR.,
WyseurA.,
DuhamelM.,
VanderborghtB.,
Van HeuverswynH.,
MaertensG.1993b; Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. Journal of General Virology 74:1093–1102
TakamizawaA.,
MoriC.,
FukeI.,
ManabeS.,
MurakamiS.,
FujitaJ.,
OnishiE.,
AndohT.,
YoshidaI.,
OkayamaH.1991; Structure and organization of the hepatitis C virus genome isolated from human carriers. Journal of Virology 65:1105–1113
TanakaT.,
KatoN.,
NakagawaM.,
OotsuyamaY.,
ChoM. J.,
NakazawaT.,
HijikataM.,
IshimuraY.,
ShimotohnoK.1992; Molecular cloning of hepatitis C virus genome from a single Japanese carrier: sequence variation within the same individual and among infected individuals. Virus Research 23:39–53
TokitaH.,
ShresthaS. M.,
OkamotoH.,
SakamotoM.,
HorikitaM.,
IizukaH.,
ShresthaS.,
MiyakawaY.,
MayumiM.1994; Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group. Journal of General Virology 75:931–936
WangY.,
OkamotoH.,
TsudaF.,
NagayamaR.,
TaoQ.-M.,
MishiroS.1993; Prevalence, genotypes, and an isolate (HC-C2) of hepatitis C virus in Chinese patients with liver disease. Journal of Medical Virology 40:254–260
YooB. J.,
SpaeteR. R.,
GeballeA. P.,
SelbyM.,
HoughtonM.,
HanJ. H.1992; 5′ End-dependent translation initiation of hepatitis C viral RNA and the presence of putative positive and negative translational control elements within the 5′untranslated region. Virology 191:889–899