We have identified four new hepatitis C virus (HCV) isolates whose genomic RNA could be amplified by PCR using primers from the 5′ untranslated region (UTR), but the RNA could not be detected with genotype I to IV (or types 1a, 1b, 2a and 2b respectively)-specific core region-derived primers. We compared the nucleotide sequences of the new isolates from positions 65 to 1850 (3′ end of 5′ UTR, C, E1 and 5′ end of E2/NS1) and 8276 to 9394 (3′ end of NS5 and 3′ UTR) with those for genotypes I to IV. The four isolates had the following characteristics: (i) the overall nucleotide sequence similarity between the four isolates was 95 to 96%, compared to 73 to 74%, 73%, 70% or 69 to 70% against genotypes I, II, III or IV, respectively; (ii) the sequence similarity to other reported ‘type V (3a)’ isolates was 88 to 100%; (iii) the hypervariable region 1 [(HVR)-1] was present but HVR-2 was absent within the E2/NS1 region; (iv) only one in-frame termination codon was present for the presumed polyprotein; (v) the 3′ UTR preceding a terminal poly(U) stretch was significantly shorter than in genotype I to IV isolates. We classified the four isolates as genotype V (3a), and searched for uniquely conserved nucleotide sequences that could be used for type-specific PCR. A core region-derived primer pair (no. 104V: 5′ CGTAAAACTTCT GAACGGTC, sense and no. 339: 5′ GCTGAGCCCA GGACCGGTCT, antisense) was identified and successfully used to diagnose genotype V (3a) HCV infection.
BukhJ.,
PurcellR.,
MillerR.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
ChaT.,
BeallE.,
IrvineB.,
KolbergJ.,
ChienD.,
KuoG.,
UrdeaM.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.,
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
HijikataM.,
KatoN.,
OotsuyamaY.,
NakagawaM.,
OhkoshiS.,
ShimotohnoK.1991; Hypervariable regions in the putative glycoprotein of hepatitis C virus. Biochemical and Biophysical Research Communications 175:220–228
LeeC.,
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.,
DowB.,
GillonJ.,
FrameW.,
CrawfordR.,
YapP.,
FollettE.,
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
OkadaS.,
AkahaneY.,
SuzukiH.,
OkamotoH.,
MishiroS.1992; The degree of variability in the amino–terminal region of E2/NS1 protein of hepatitis C virus correlates with responsiveness to interferon therapy in viremic patients. Hepatology 16:619–624
OkamotoH.,
OkadaS.,
SugiyamaY.,
TanakaT.,
SugaiY.,
AkahaneY.,
MachidaA.,
MishiroS.,
YoshizawaH.,
MiyakawaY.,
MayumiM.1990; Detection of hepatitis C virus RNA by a two-stage polymerase chain reaction with two pairs of primers deduced from the 5′-noncoding region. Japanese Journal of Experimental Medicine 60:215–222
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.,
KuraiK.,
OkadaS.,
YamamotoK.,
IizukaH.,
TanakaT.,
FukudaS.,
TsudaF.,
MishiroS.1992a; Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology 188:331–341
OkamotoH.,
SugiyamaY.,
OkadaS.,
KuraiK.,
AkahaneY.,
SugaiY.,
TanakaT.,
SatoK.,
TsudaF.,
MiyakawaY.,
MayumiM.1992b; 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.,
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.,
KanaiN.,
MishiroS.1992d; Full-length nucleotide sequence of a Japanese hepatitis C virus isolate (HC-J1) with high homology to USA isolates. Nucleic Acids Research 20:6410
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 vims: identification of a new virus type and restrictions on sequence diversity. Journal of General Virology 74:661–668
WeinerA. J.,
BrauerM. J.,
RosenblattJ.,
RichmanK. H.,
TungJ.,
CrawfordK.,
BoninoF.,
SaraccoG.,
ChooQ. L.,
HoughtonM.,
HanJ. H.1991; Variable and hypervariable domains are found in the regions of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins. Virology 180:841–848