Genotypes of hepatitis C virus (HCV) present within 104 samples from HCV-infected individuals from Africa, the Middle East, the Indian subcontinent and South-East Asia were identified by sequence comparisons in the core and NS-5 regions. Relatively short sequences (such as the 222 bp fragment of NS-5) provided effective discrimination of types, subtypes and isolates, and produced equivalent relationships between genotypes as were found upon comparison of longer sequences of NS-5, of the core region, and by comparison of the limited number of complete genomic sequences currently available. Measurement of evolutionary distances in the core and NS-5 regions allowed 79 of the 104 samples to be identified as examples of known genotypes, while 17 of the remainder could be provisionally classified as new subtypes of types 1 (Nigeria), 2 (Gambia), 3 (India, Pakistan and Bangladesh) and 4 (Middle East) on the basis of sequence comparison in core and NS-5 (n = 9) or provisionally using core alone (n = 8). The remaining sequences from Thailand made up two groups showing no close similarity to any of the six major genotypes classified to date, although one corresponded to an as yet unclassified variant of HCV also found in Thailand. However, phylogenetic analysis of the core and NS-5 regions indicated a distant relationship between these sequences with variants found in Vietnam and with type 6a, and collectively they formed a diverse single phylogenetic group. The existence of great diversity within a single genotype was also found amongst type 3 sequences in the Indian subcontinent, amongst type 4 variants in Central Africa and the Middle East, and amongst type variants in Nigeria. These findings may provide clues for understanding the origins and mechanisms of transmission of HCV.
AbdelaalM.,
RowbottomD.,
ZawawiT.,
ScottT.,
GilpinC.1994; Epidemiology of hepatitis C virus-a study of male blood donors in Saudi Arabia. Transfusion 34:135–137
AbeK.,
InchauspeG.,
FujisawaK.1992; Genomic characterization and mutation rate of hepatitis C virus isolated from a patient who contracted hepatitis during an epidemic of non-A, non-B hepatitis in Japan. Journal of General Virology 73:2725–2729
ApichartpiyakulC.,
ChittivudikarnC.,
MiyajimaH.,
HommaM.,
HottaH.1994; Analysis of hepatitis C virus isolates among healthy blood donors and drug addicts in Chiang Mai, Thailand. Journal of Clinical Microbiology 32:2276–2279
BruceC.,
CleggC.,
FeatherstoneA.,
SmithJ.,
BiryahawahoB.,
DowningR.,
OramJ.1994; Presence of multiple genetic subtypes of human immunodeficiency virus type 1 proviruses in Uganda. AIDS Research and Human Retroviruses 10:1543–1550
BukhJ.,
PurcellR. H.,
MillerR. H.1993; At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative El gene of isolates collected worldwide. Proceedings of the National Academy of Sciences, USA 90:8234–8238
BukhJ.,
PurcellR. H.,
MillerR. H.1994; Sequence analysis of the core gene of 14 hepatitis c virus genotypes. Proceedings of the National Academy of Sciences, USA 91:8239–8243
ChaT. A.,
BeallE.,
IrvineB.,
KolbergJ.,
ChienD.,
KuoG.,
UrdeaM. S.1992; At least five related, but distinct, hepatitis C viral genotypes exist. Proceedings of the National Academy of Sciences, USA 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
ChooQ. L.,
WeinerA. J.,
OverbyL. R.,
KuoG.,
HoughtonM.,
BradleyD. W.1990; Hepatitis C virus: the major causative agent of viral non-A, non-B hepatitis. British Medical Bulletin 46:423–441
CuypersH. T. M.,
WinkelI. N.,
Van der PoelC. L.,
ReesinkH. W.,
LelieP. N.,
HoughtonM.,
WeinerA.1991; Analysis of genomic variability of hepatitis C virus. Journal of Hepatology 13:S15–S19
CuypersH. T. M.,
BrestersD.,
WinkelI. N.,
ReesinkH. W.,
WeinerA. J.,
HoughtonM.,
Van der PoelC. L.,
LeslieP. N.1992; Storage conditions of blood samples and primer selection affect the yield of cDNA polymerase chain reaction products of hepatitis C virus. Journal of Clinical Microbiology 30:3220–3224
DavidsonF.,
SimmondsP.,
FergusonJ. C.,
JarvisL. M.,
DowB. C.,
FollettE. A. C.,
KellerA. J.,
KrusiusT.,
LinC.,
MedgyesiG. A.,
KiyokawaH.,
OlimG.,
DuraisamyG.,
CuypersT.,
SaeedA. A.,
TeoD.,
ConradieJ.,
KewM. C.,
LinM.,
NuchaprayoonC.,
NdimbieO. K.,
YapP. L.1995; Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5′ non-coding region. Journal of General Virology 76:1197–1204
EnomotoN.,
TaKadaA.,
NakaoT.,
DateT.1990; There are two major types of hepatitis C virus in Japan. Biochemical and Biophysical Research Communications 170:1021–1025
HohneM.,
SchREIErE.,
RoggendorfM.1994; Sequence variability in the env-coding region of hepatitis C virus isolated from patients infected during a single source outbreak. Archives of Virology 137:25–34
HottaH.,
DoiH.,
HayashiT.,
PurwantaM.,
SoemartoW.,
MizokamiM.,
OhbaK.,
HommaM.1994a; Analysis of the core and e 1 envelope region sequences of a novel variant of hepatitis C virus obtained in Indonesia. Archives of Virology 136:53–62
HottaH.,
HandajanlR.,
LusidaM. I.,
SoemartoW.,
DotH.,
MiyajimaH.,
HommaM. F.1994b; Subtype analysis of hepatitis C virus in Indonesia on the basis of NS5b region sequences. Journal of Clinical Microbiology 32:3049–3051
KamelM. A.,
MillerF. D.,
ElmasryA. G.,
ZakariaS.,
KhattabM.,
EssmatG.,
GhaffarY. A.1994; The epidemiology of Schistosoma mansoni, hepatitis B and hepatitis C infection in Egypt. Annals of Tropical Medicine and Parasitology 88:501–509
KatoN.,
HijikataM.,
OotsuyamaY.,
NakagawaM.,
OhkoshiS.,
ShimotohnoK.1990; Sequence diversity of hepatitis C viral genomes. Molecular Biology and Medicine 7:495–501
KuoG.,
ChooQ. L.,
AlterH. J.,
GitnickG. L.,
RedekerA. G.,
PurcellR. H.,
MiyamuraT.,
DienstagJ. L.,
AlterM. J.,
StevensC. E.,
TegtmeierF.,
BoninoF.,
ColumboM.,
LeeW.-S.,
KuoC.,
BergerK.,
SchusterJ. R.,
OverbyL. R.,
BradleyD. W.,
HoughtonM.1989; An assay for circulating antibodies to a major etiologic virus of human non-A, non-B hepatitis. Science 244:362–364
LauJ. Y. N.,
MizokamiM.,
KolbergJ.,
DavisG. L.,
PrescottL. E.,
OhnoT.,
PerrilloR. P.,
LindsayK. L.,
GishR. G.,
KoharaM.,
SimmondsP.,
UrdeaM. S.1995; Application of hepatitis C virus genotyping systems in United States patients with chronic hepatitis C. Journal of Infectious Diseases 171:281–289
LouwagieL.,
McCutchanF. E.,
PeetersM.,
BrennanT. P.,
SandersbuellE.,
EddyG. A.,
VandergroenG.,
FransenK.,
GershydametG. M.,
DeleysR.,
BurkeD. S.1993; Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS 7:769–780
OgataN.,
AlterH. J.,
MillerR. H.,
PurcellR. H.1991; Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. Proceedings of the National Academy of Sciences, USA 88:3392–3396
OkamotoH.,
KojimaM.,
OkadaS.-L.,
YoshizawaH.,
IizukaH.,
TanakaT.,
MuchmoreE. E.,
ItoY.,
MishiroS.1992a; Genetic drift of hepatitis C virus during an 8-2 year infection in a chimpanzee: variability and stability. Virology 190:894–899
OkamotoH.,
KuraiK.,
OkadaS.,
YamamotoK.,
LizukaH.,
TanakaT.,
FukudaS.,
TsudaF.,
MishiroS.1992b; 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.,
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
OlsenG. J.,
MatsudaH.,
HagstromR.,
OverbeekR.1994; FastDNAML – a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. CABIOS 10:41–48
SaeedA. A.,
Al AdmawiA. M.,
Al RasheedA.,
FaircloughD.,
BacchusR.,
RingC.,
GarsonJ.1991; Hepatitis C virus infection in Egyptian volunteer blood donors in Riyadh. Lancet 338:459–460
SakamotoM.,
AkahaneY.,
TsudaF.,
TanakaT.,
WoodfieldD. G.,
OkamotoH.1994; Entire nucleotide sequence and characterization of a hepatitis C virus of genotype v/3a. Journal of General Virology 75:1761–1768
SimmondsP.,
HolmesE. C.,
ChaT. A.,
ChanS. W.,
McOmishF.,
IrvineB.,
BeallE.,
YapP. L.,
KolbergJ.,
UrdeaM. S.1993a; Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. Journal of General Virology 74:2391–2399
SimmondsP.,
RoseK. A.,
GrahamS.,
ChanS. W.,
McOmishF.,
DowB. C.,
FollettE. A. C.,
YapP. L.,
MarsdenH.1993b; 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 type 1, type 2, and type 3. Journal of Clinical Microbiology 31:1493–1503
SimmondsP.,
AlbertiA.,
AlterH. J.,
BoninoF.,
BradleyD. W.,
BrechotC.,
BrouwerJ. T.,
ChanS. W.,
ChayamaK.,
ChenD. S.,
ChooQ. L.,
ColomboM.,
CuypersH. T. M.,
DateT.,
DusheikoG. M.,
EstebanJ. I.,
FayO.,
HadziyannisS. J.,
HanJ.,
HatzakjsA.,
HolmesE. C.,
HottaH.,
HoughtonM.,
IrvineB.,
KoharaM.,
KolbergJ. A.,
KuoG.,
LauJ. Y. N.,
LelieP. N.,
MaertensG.,
McOmishF.,
MiyamuraT.,
MizokamiM.,
NomotoA.,
PrinceA. M.,
ReesinkH. W.,
RiceC.,
RoggendorfM.,
SchalmS. W.,
ShikataT.,
ShimotohnoK.,
StuyverL.,
TrepoC.,
WeinerA.,
YapP. L.,
UrdeaM. S.1994a; A proposed system for the nomenclature of hepatitis C viral genotypes. Hepatology 19:1321–1324
SimmondsP.,
SmithD. B.,
McOmishF.,
YapP. L.,
KolbergJ.,
UrdeaM. S.,
HolmesE. C.1994b; Identification of genotypes of hepatitis C virus by sequence comparisons in the core, El and NS-5 regions. Journal of General Virology 75:1053–1061
StuyverL.,
RossauR.,
WyseurA.,
DuhamelM.,
VanderborghtB.,
van HeuverswynH.,
MaertensG.1993; Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. Journal of General Virology 74:1093–1102
StuyverL.,
VanarnhemW.,
WyseurA.,
HernandezF.,
DelaporteE.,
MaertensG.1994; Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5b regions and identification of five additional subtypes. Proceedings of the National Academy of Sciences, USA 91:10134–10138
TokitaH.,
OkamotoH.,
TsudaF.,
SongP.,
NakataS.,
ChosaT.,
IizukaH.,
MishiroS.,
MiyakawaY.,
MayumiM.1994a; Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proceedings of the National Academy of Sciences, USA 91:11022–11026
TokitaH.,
ShresthaS. M.,
OkamotoH.,
SakamotoM.,
HirokitaM.,
IizukaH.,
ShresthaS.,
MiyakawaY.,
MayumiM.1994b; Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group. Journal of General Virology 75:931–936
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 proteins. Virology 180:842–848