Variants of hepatitis C virus (HCV) have been classified by nucleotide sequence comparisons in different regions of the genome. Many investigators have defined the ranges of sequence similarity values or evolutionary distances corresponding to divisions of HCV into types, subtypes and isolates. Using these criteria, novel variants of HCV from Vietnam, Thailand and Indonesia have been classified as types 7, 8, 9, 10 and 11, many of which can be further subdivided into between two to four subtypes. In this study, this distance-based method of virus classification was compared with phylogenetic analysis and statistical measures to establish the confidence of the groupings. Using bootstrap resampling of phylogenetic trees in several subgenomic regions (core, E1, NS5) and with complete genomic sequences, we found that one set of novel HCV variants (‘types 7, 8, 9 and 11’) consistently grouped together into a single clade that also contained type 6a, while ‘type 10a’ grouped with type 3. In contrast, no robust higher-order groupings were observed between any of the other five previously described HCV genotypes (types 1–5). In each subgenomic region, the distribution of pairwise distances between members of the type 6 clade were consistently bi-modal and therefore provided no justification for classification of these variants into the three proposed categories (type, subtype, isolate). Based on these results, we propose that a more useful classification would regard all these variants as subtypes of type 6 or type 3, even though the level of sequence diversity within the clade was greater than observed for other genotypes. Classification by phylogenetic relatedness rules out simple sequence similarity measurements as a method for assigning HCV genotypes, but provides a more appropriate description of the evolutionary and epidemiological history of a virus.
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
BhattacherjeeV.,
PrescottL. E.,
PikeI.,
RodgersB.,
BellH.,
ElzayadiA. R.,
KewM. C.,
ConradieJ.,
LinC. K.,
MarsdenH.,
SaeedA. A.,
ParkerD.,
YapP. L.,
SimmondsP.1995; Use of NS-4 peptides to identify type-specific antibody to hepatitis C virus genotypes 1, 2, 3, 4, 5 and 6. Journal of General Virology 76:1737–1748
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, 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
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, USA 88:2451–2455
DoiH.,
ApichartpiyakulC.,
OhbaK. I.,
MizokamiM.,
HottaH.1996; Hepatitis C virus (HCV) subtype prevalence in Chaing Mai, Thailand and identification of novel subtypes of HCV in major type 6. Journal of Clinical Microbiology 34:569–574
HillisD. M.,
BullJ. J.1993; An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42:182–192
HolmesE. C.,
NeeS.,
RambautA.,
GarnettG. P.,
HarveyP. H.1995; Revealing the history of infectious disease epidemics using phylogenetic trees. Philosophical Transactions of the Royal Society of London Series B Biological Sciences 349:33–40
HottaH.,
DoiH.,
HayashiT.,
PurwantaM.,
SoemartoW.,
MizokamiM.,
OhbaK.,
HommaM.1994a; Analysis of the core and e1 envelope region sequences of a novel variant of hepatitis C virus obtained in Indonesia. Archives of Virology 136:53–62
HottaH.,
HandajaniR.,
LusidaM. I.,
SoemartoW.,
DoiH.,
MiyajimaH.,
HommaM.1994b; Subtype analysis of hepatitis C virus in Indonesia on the basis of NS5b region sequences. Journal of Clinical Microbiology 32:3049–3051
LauJ. Y. N.,
DavisG. L.,
PrescottL. E.,
MaertensG.,
LindsayK. L.,
QianK. P.,
MizokamiM.,
SimmondsP.,
PerrilloR. P.,
SchiffE. R.,
BodenheimerH. C.,
BalartL. A.,
RegensteinF.,
DienstagJ. L.,
KatkovW. N.,
TamburroC. H.,
GoffJ. S.,
EversonG. T.,
GoodmanZ.,
AlbrechtJ.1996; Distribution of hepatitis C virus genotypes determined by line probe assay in patients with chronic hepatitis C seen at tertiary referral centers in the United States. Annals of Internal Medicine 124:868
MahaneyK.,
TedeschiV.,
MaertensG.,
DibisceglieA. M.,
VergallaJ.,
HoofnagleJ. H.,
SallieR.1994; Genotypic analysis of hepatitis C virus in American patients. Hepatology 20:1405–1411
McOmishF.,
ChanS.-W.,
DowB. C.,
GillonJ.,
FrameW. D.,
CrawfordR. J.,
YapP. L.,
FotlettE. A. C.,
SimmondsP.1993; Detection of three types of hepatitis C virus in blood donors: investigation of type-specific differences in serological reactivity and rate of alanine aminotransferase abnormalities. Transfusion 33:7–13
MellorJ.,
HolmesE. C.,
JarvisL. M.,
YapP.-L.,
SimmondsP.The International HCV Collaborative Study Group1995; Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: implications for virus classification. Journal of General Virology 76:2493–2507
MellorJ.,
WalshE. A.,
PrescottL. E.,
JarvisL. M.,
DavidsonF.,
YapP. L.,
SimmondsP.,
NowickiM. J.,
MosleyJ. W.,
LinC. K.,
LaiC. L.,
DeolimG.,
MartinsI. A.,
OngY. W.,
TeoD.,
LinM.,
NuchprayoonC.,
TanprasertS.1996; Survey of type 6 group variants of hepatitis C virus in southeast Asia by using a core-based genotyping assay. Journal of Clinical Microbiology 34:417–423
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.1993; 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.,
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.,
HatzakisE. C.,
HottaH.,
HoughtonM.,
IrvineB.,
KoharaM.,
KolbergJ. A.,
KuoG.,
LauJ. Y. N.,
DateT.,
Lelie P. N.,
MaertensG.,
McOmishF.,
MiyamuraT.,
MizokamiM.,
NomotoA.,
Prince, A. M.,
Reesink H. W.,
RiceC.,
RoggendorfM.,
SchalmS. W.,
ShikataT.1994a; A proposed system for the nomenclature of hepatitis C viral genotypes. Hepatology 19:1321–1324
SimmondsP.,
SmithD.B,
Comish F.,
Yap P. L.,
KolbergJ.,
UrdeaM.S.,
SchalmS. W.,
ShikataT.,
HolmesE. C.1994b; Identification of genotypes of hepatitis C virus by sequence comparisons in the core, E1 and NS-5 regions. Journal of General Virology 75:1053–1061
SmithD. B.,
MellorJ.,
JarvisL. M.,
DavidsonF.,
KolbergJ.,
UrdeaM.,
YapP.-L.,
SimmondsP.The International HCV Collaborative Study Group1995; Variation of the hepatitis C virus 5’ non-coding region: implications for secondary structure, virus detection and typing. Journal of General Virology 76:1749–1761
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
SugiyamaK.,
KatoN.,
NakazawaT.,
YonemuraY.,
PhornphutkulK.,
KunakornM.,
PetehdaiB.,
ShimotohnoK.1995; Novel genotypes of hepatitis C virus in Thailand. Journal of General Virology 76:2323–2327
TokitaH.,
OkamotoH.,
TsudaF.,
SongP.,
NakataS.,
ChosaT.,
LizukaH.,
MishiroS.,
MiyakawaY.,
MayumiM.1994; 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.,
OkamotoH.,
LuengrojanakulP.,
VareesangthipK.,
ChainuvatiT.,
LizukaH.,
TsudaF.,
MiyakawaY.,
MayumiM.1995; Hepatitis C virus variants from Thailand classifiable into five novel genotypes in the sixth (6b), seventh (7c, 7d) and ninth (9b, 9c) major genetic groups. Journal of General Virology 76:2329–2335
TokitaH.,
OkamotoH.,
LizukaH.,
KishimotoJ.,
TsudaF.,
LesmanaA.,
MiyakawaY.,
MayumiM.1996; Hepatitis C virus variants from Jakarta, Indonesia classifiable into novel genotypes in the second (2e and 2f), tenth (10a) and eleventh (11a) genetic groups. Journal of General Virology 77:293–301
Tsukiyama KoharaK.,
YamaguchiK.,
MakiN.,
OhtaY.,
MikiK.,
MizokamiM.,
OhbaK.,
TanakaS.,
HattoriN.,
NomotoA.,
KoharaM.1993; Antigenicities of group I and group II hepatitis C virus polypeptides-molecular basis of diagnosis. Virology 192:430–437