Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A–I), and a putative 10th genotype (J), characterized thus far. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level. All of the generated data, including the alignments, phylogenies and chosen reference sequences, are available online (https://doi.org/10.6084/m9.figshare.8851946) as a simple open-access resource.
McNaughtonAL,
D’ArienzoV,
AnsariMA,
LumleySF,
LittlejohnM et al. Insights from deep sequencing of the HBV genome—unique, tiny, and misunderstood. Gastroenterology2019; 156:384–399 [View Article]
Torres-CornejoA,
LauerGM.
Hurdles to the development of effective HBV immunotherapies and HCV vaccines. Pathogens and Immunity2017; 2:102 [View Article]
PawlotskyJ-M,
NegroF,
AghemoA,
BerenguerM,
DalgardO et al. EASL recommendations on treatment of hepatitis C 2018. J Hepatol2018; 69:461–511 [View Article]
European Association for the Study of the Liver. Electronic address: easloffice@easloffice.euEuropean Association for the Study of the Liver EASL 2017 clinical practice guidelines on the management of hepatitis B virus infection. J Hepatol2017; 67:370–398 [View Article]
RajoriyaN,
CombetC,
ZoulimF,
JanssenHLA.
How viral genetic variants and genotypes influence disease and treatment outcome of chronic hepatitis B. time for an individualised approach?. J Hepatol2017; 67:1281–1297 [View Article]
PourkarimMR,
Amini-Bavil-OlyaeeS,
LemeyP,
MaesP,
Van RanstM.
Are hepatitis B virus "subgenotypes" defined accurately?. J Clin Virol2010; 47:356–360 [View Article]
JiaL,
HuF,
LiH,
LiL,
TangX et al. Characterization of small genomic regions of the hepatitis B virus should be performed with more caution. Virol J2018; 15:24–26 [View Article]
ShiW,
ZhangZ,
LingC,
ZhengW,
ZhuC et al. Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections. Infection, Genetics and Evolution2013; 16:355–361 [View Article]
SchaeferS,
MagniusL,
NorderH.
Under construction: classification of hepatitis B virus genotypes and subgenotypes. Intervirology2009; 52:323–325 [View Article]
AhnSH,
YuenL,
RevillP.
Clarification required for the definition of hepatitis B virus subgenotypes C1 and C2. Intervirology2009; 52:321–322 [View Article]
PanjaworayanN,
RoessnerSK,
FirthAE,
BrownCM.
HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences. Virol J2007; 4:136–10 [View Article]
BellTG,
YousifM,
KramvisA.
Bioinformatic curation and alignment of genotyped hepatitis B virus (HBV) sequence data from the GenBank public database. Springerplus2016; 5:1896 [View Article]
KramvisA,
ArakawaK,
YuMC,
NogueiraR,
StramDO et al. Relationship of serological subtype, basic core promoter and precore mutations to genotypes/subgenotypes of hepatitis B virus. J Med Virol2008; 80:27–46 [View Article]
KimH,
LeeS-A,
KimD-W,
LeeS-H,
KimB-J.
Naturally occurring mutations in large surface genes related to occult infection of hepatitis B virus genotype C. PLoS One2013; 8:e54486 [View Article]
SkeltonM,
KewMC,
KramvisA.
Distinct mutant hepatitis B virus genomes, with alterations in all four open reading frames, in a single South African hepatocellular carcinoma patient. Virus Res2012; 163:59–65 [View Article]
ValenzuelaP,
QuirogaM,
ZaldivarJ,
GrayP,
RutterWJ.
The nucleotide sequence of the hepatitis B viral genome and the identification of the major viral genes. Animal Virus Genetics198057–70
MühlemannB,
JonesTC,
DamgaardPdeB,
AllentoftME,
ShevninaI et al. Ancient hepatitis B viruses from the bronze age to the medieval period. Nature2018; 557:418–423 [View Article]
Patterson RossZ,
KlunkJ,
FornaciariG,
GiuffraV,
DuchêneS et al. The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathog2018; 14:e1006750 [View Article]
GalibertF,
MandartE,
FitoussiF,
TiollaisP,
CharnayP.
Nucleotide sequence of the hepatitis B virus genome (subtype ayw) cloned in E. coli. Nature1979; 281:646–650 [View Article]
HatakeyamaT,
NoguchiC,
HiragaN,
MoriN,
TsugeM et al. Serum HBV RNA is a predictor of early emergence of the YMDD mutant in patients treated with lamivudine. Hepatology2007; 45:1179–1186 [View Article]
MulyantoM,
DepamedeSN,
SurayahK,
TjahyonoAAH et al. Identification and characterization of novel hepatitis B virus subgenotype C10 in NusA Tenggara, Indonesia. Arch Virol2010; 155:705–715 [View Article]
MulyantoS,
DepamedeSN,
WahyonoA,
JirintaiN,
NagashimaS et al. Analysis of the full-length genomes of novel hepatitis B virus subgenotypes C11 and C12 in Papua, Indonesia. J Med Virol2011; 83:54–64 [View Article]
CavintaL,
SunJ,
MayA,
YinJ,
von MeltzerM et al. A new isolate of hepatitis B virus from the Philippines possibly representing a new subgenotype C6. J Med Virol2009; 81:983–987 [View Article]
MulyantoN,
PancawardaniP,
DepamedeSN,
WahyonoA,
JirintaiS et al. Identification of four novel subgenotypes (C13-C16) and two inter-genotypic recombinants (C12/G and C13/B3) of hepatitis B virus in Papua Province, Indonesia. Virus Res2012; 163:129–140 [View Article]
ParaskevisD,
MagiorkinisG,
MagiorkinisE,
HoSYW,
BelshawR et al. Dating the origin and dispersal of hepatitis B virus infection in humans and primates. Hepatology2013; 57:908–916 [View Article]
ZehenderG,
EbranatiE,
GabanelliE,
ShkjeziR,
LaiA et al. Spatial and temporal dynamics of hepatitis B virus D genotype in Europe and the mediterranean basin. PLoS One2012; 7:e37198–8 [View Article]
ParaskevisD,
AngelisK,
MagiorkinisG,
KostakiE,
HoSYW et al. Dating the origin of hepatitis B virus reveals higher substitution rate and adaptation on the branch leading to F/H genotypes. Mol Phylogenet Evol2015; 93:44–54 [View Article]
LivingstonSE,
SimonettiJP,
McMahonBJ,
BulkowLR,
HurlburtKJ et al. Hepatitis B virus genotypes in Alaska native people with hepatocellular carcinoma: preponderance of genotype F. J Infect Dis2007; 195:5–11 [View Article]
van der KuylAC,
ZorgdragerF,
HogemaB,
BakkerM,
JurriaansS et al. High prevalence of hepatitis B virus dual infection with genotypes A and G in HIV-1 infected men in Amsterdam, the Netherlands, during 2000-2011. BMC Infect Dis2013; 13:540 [View Article]
MühlemannB,
JonesTC,
DamgaardPdeB,
AllentoftME,
ShevninaI et al. Ancient hepatitis B viruses from the bronze age to the medieval period. Nature2018; 557:418–423 [View Article]
HraberPT,
FischerW,
BrunoWJ,
LeitnerT,
KuikenC.
Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5’ untranslated region (UTR) fails to classify subtypes. Virol J2006; 3:103 [View Article]
YinY,
HeK,
WuB,
XuM,
DuL et al. A systematic genotype and subgenotype re-ranking of hepatitis B virus under a novel classification standard. Heliyon2019; 5:e02556 [View Article]
NiebelM,
SingerJB,
NickbakhshS,
GiffordRJ,
ThomsonEC.
Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination?. Lancet Gastroenterol Hepatol2017; 2:700–701 [View Article]
TatematsuK,
TanakaY,
KurbanovF,
SugauchiF,
ManoS et al. A genetic variant of hepatitis B virus divergent from known human and ape genotypes isolated from a Japanese patient and provisionally assigned to new genotype J. J Virol2009; 83:10538–10547 [View Article]
ShiW,
ZhuC,
ZhengW,
ZhengW,
LingC et al. Subgenotyping of genotype C hepatitis B virus: correcting Misclassifications and identifying a novel subgenotype. PLoS One2012; 7:e47271 [View Article]
Del CampoJA,
Parra-SánchezM,
FigueruelaB,
García-ReyS,
QuerJ et al. Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: a real-life experience. Int J Infect Dis2018; 67:114–117 [View Article]
FokamJ,
BellocchiMC,
ArmeniaD,
NanfackAJ,
CariotiL et al. Next-Generation sequencing provides an added value in determining drug resistance and viral tropism in cameroonian HIV-1 vertically infected children. Medicine2018; 97:e0176 [View Article]
DavisC,
MgomellaGS,
da Silva FilipeA,
FrostEH,
GirouxG et al. Highly diverse hepatitis C strains detected in sub-Saharan Africa have unknown susceptibility to direct-acting antiviral treatments. Hepatology2019; 69:1426–1441 [View Article]
BorgiaSM,
HedskogC,
ParhyB,
HylandRH,
StammLM et al. Identification of a novel hepatitis C virus genotype from Punjab, India: expanding classification of hepatitis C virus into 8 genotypes. J Infect Dis2018; 218:1722–1729 [View Article]
ShiW,
ZhuC,
ZhengW,
CarrMJ,
HigginsDG et al. Subgenotype reclassification of genotype B hepatitis B virus. BMC Gastroenterol2012; 12:2–7 [View Article]
OchwotoM,
KimothoJH,
OyugiJ,
OkothF,
KiokoH et al. Hepatitis B infection is highly prevalent among patients presenting with jaundice in Kenya. BMC Infect Dis2016; 16:101
AndernachIE,
NolteC,
PapeJW,
MullerCP.
Slave trade and hepatitis B virus genotypes and subgenotypes in Haiti and Africa. Emerg Infect Dis2009; 15:1222–1228
TalloT,
NorderH,
TefanovaV,
KrispinT,
PriimägiL et al. Hepatitis B virus genotype D strains from Estonia share sequence similarity with strains from Siberia and may specify ayw4. J Med Virol2004; 74:221–227 [View Article]
AndernachIE,
NolteC,
PapeJW,
MullerCP.
Slave trade and hepatitis B virus genotypes and subgenotypes in Haiti and Africa. Emerg Infect Dis2009; 15:1222–1228
HorikitaM,
ItohS,
YamamotoK,
ShibayamaT,
TsudaF et al. Differences in the entire nucleotide sequence between hepatitis B virus genomes from carriers positive for antibody to hepatitis B e antigen with and without active disease. J Med Virol1994; 44:96–103
TangkijvanichP,
Sa-NguanmooP,
AvihingsanonA,
RuxrungthamK,
PoovorawanK et al. Characterization of hepatitis B virus mutations in untreated patients co-infected with HIV and HBV based on complete genome sequencing. J Med Virol2013; 85:16–25
WangH-Y,
ChienM-H,
HuangH-P,
ChangH-C,
WuC-C et al. Distinct hepatitis B virus dynamics in the immunotolerant and early immunoclearance phases. J Virol2010; 84:3454–3463 [View Article]
MulyantoM,
DepamedeSN,
SurayahK,
TsudaF,
IchiyamaK et al. A nationwide molecular epidemiological study on hepatitis B virus in Indonesia: identification of two novel subgenotypes, B8 and C7. Arch Virol2009; 154:1047–1059 [View Article]
SugauchiF,
OritoE,
IchidaT,
KatoH,
SakugawaH et al. Hepatitis B virus of genotype B with or without recombination with genotype C over the precore region plus the core gene. J Virol2002; 76:5985–5992
SakamotoT,
TanakaY,
SimonettiJ,
OsiowyC,
BorresenML et al. Classification of hepatitis B virus genotype B into 2 major types based on characterization of a novel subgenotype in Arctic Indigenous populations. J Infect Dis2007; 196:1487–1492
ChanHLY,
TsuiSKW,
TseC-H,
NgEYT,
AuTCC et al. Epidemiological and virological characteristics of 2 subgroups of hepatitis B virus genotype C. J Infect Dis2005; 191:2022–2032 [View Article]
ChenX,
GaoJ,
JiZ,
ZhangW,
ZhangL et al. A description of the hepatitis B virus genomic background in a high-prevalence area in China. Virol J2014; 11:101
MulyantoM,
DepamedeSN,
SurayahK,
TsudaF,
IchiyamaK et al. A nationwide molecular epidemiological study on hepatitis B virus in Indonesia: identification of two novel subgenotypes, B8 and C7. Arch Virol2009; 154:1047–1059 [View Article]
LittlejohnM,
DaviesJ,
YuenL,
EdwardsR,
SozziT et al. Molecular virology of hepatitis B virus, sub-genotype C4 in northern Australian Indigenous populations. J Med Virol2014; 86:695–706
LiZ,
XieZ,
NiH,
ZhangQ,
LuW et al. Mother-To-Child transmission of hepatitis B virus: evolution of hepatocellular carcinoma-related viral mutations in the post-immunization era. J Clin Virol2014; 61:47–54
AvazovaD,
KurbanovF,
TanakaY,
SugiyamaM,
RadchenkoI et al. Hepatitis B virus transmission pattern and vaccination efficiency in Uzbekistan. J Med Virol2008; 80:217–224
DattaS,
GhoshA,
DasguptaD,
GhoshA,
RoychoudhuryS et al. Novel point and combo-mutations in the genome of hepatitis B virus-genotype D: characterization and impact on liver disease progression to hepatocellular carcinoma. PLoS One2014; 9:e110012
MunshiSU,
TranTTT,
VoTNT,
TabassumS,
SultanaN et al. Molecular characterization of hepatitis B virus in Bangladesh reveals a highly recombinant population. PLoS One2017; 12:e0188944
GhoshS,
BanerjeeP,
RoyChoudhuryA,
SarkarS,
GhoshA et al. Unique hepatitis B virus subgenotype in a primitive tribal community in eastern India. J Clin Microbiol2010; 48:4063–4071
GarmiriP,
LouaA,
HabaN,
CandottiD,
AllainJ-P.
Deletions and recombinations in the core region of hepatitis B virus genotype E strains from asymptomatic blood donors in guinea, West Africa. J Gen Virol2009; 90:2442–2451
VenegasM,
Alvarado-MoraMV,
VillanuevaRA,
Rebello PinhoJR,
CarrilhoFJ et al. Phylogenetic analysis of hepatitis B virus genotype F complete genome sequences from Chilean patients with chronic infection. J Med Virol2011; 83:1530–1536
DevesaM,
LoureiroCL,
RivasY,
MonsalveF,
CardonaN et al. Subgenotype diversity of hepatitis B virus American genotype F in Amerindians from Venezuela and the general population of Colombia. J Med Virol2008; 80:20–26
BlancoRY,
LoureiroCL,
VillalbaJA,
SulbaránYF,
MaesM et al. Decreasing prevalence of hepatitis B and absence of hepatitis C virus infection in the Warao Indigenous population of Venezuela. PLoS One2018; 13:e0197662
González López LedesmaMM,
MojsiejczukLN,
RodrigoB,
SevicI,
MammanaL et al. Hepatitis B virus genotype distribution and genotype-specific BCP/preCore substitutions in acute and chronic infections in Argentina. PLoS One2015; 10:e0121436
KatoH,
OritoE,
SugauchiF,
UedaR,
GishRG et al. Determination of hepatitis B virus genotype G by polymerase chain reaction with hemi-nested primers. J Virol Methods2001; 98:153–159
FlichmanD,
GaldameO,
LivellaraB,
ViautM,
GadanoA et al. Full-Length genome characterization of hepatitis B virus genotype H strain isolated from serum samples collected from two chronically infected patients in Argentina. J Clin Microbiol2009; 47:4191–4193 [View Article]
NguyenCH,
IshizakiA,
ChungPTT,
HoangHT,
NguyenTV et al. Prevalence of HBV infection among different HIV-risk groups in HAI Phong, Vietnam. J Med Virol2011; 83:399–404
OlingerCM,
JutavijittumP,
HübschenJM,
YousukhA,
SamountryB et al. Possible new hepatitis B virus genotype, Southeast Asia. Emerg Infect Dis2008; 14:1777–1780