Classification of hepatitis B virus genotype B into 2 major types based on characterization of a novel subgenotype in Arctic indigenous populations

Hepatitis B virus genotype B (HBV/B) has been classified into 5 subgenotypes. Except for Bj/B1 in Japan, the subgenotypes (Ba/B2-B5) have undergone recombination with HBV/C in the core promoter/precore/core genomic region. Phylogenetic analyses of complete sequences show that the Arctic strains belong to a novel subgenotype (HBV/B6) without the recombination, analogous to what is seen with Bj/B1. Comparison of 50 HBV/B6 carriers from the Arctic versus 50 Bj and 50 Ba age- and sex-matched carriers from Asia revealed that clinical characteristics of HBV/B6 carriers were similar to those of Bj/B1 carriers in Japan. The results suggest that HBV/B may be classified into nonrecombinant (Bj/B1 and B6) and recombinant (Ba/B2-B5) types.     

Distinct geographical and demographic distribution of hepatitis B virus genotypes in the Canadian Arctic as revealed through an extensive molecular epidemiological survey

Summary. Very little is known of hepatitis B virus (HBV) in Canadian Arctic indigenous populations, where HBV was considered endemic prior to the introduction of HBV vaccine. This study expands upon an HBV seroepidemiological survey conducted between 1983 and 1985 throughout the Canadian Arctic, to characterize HBV in this population. Archived hepatitis B surface antigen (HBsAg)‐positive sera (n = 401) were processed for HBV DNA, followed by sequencing and phylogenetic analysis of the HBsAg‐ and HBcAg‐coding regions. Sixty‐nine per cent of samples (277/401) were DNA positive, with most having low viral load (median 3.4 log 10 IU/mL). The predominant HBV genotype observed was genotype B (HBV/B, 75%), followed by HBV/D (24%) and HBV/A (1%). All HBV/B strains clustered within subgenotype B6, a newly recognized HBV genotype among western circumpolar Inuit and Alaska Native people. HBV/D strains included both D3 (88%) and D4 (12%) subgenotypes, while all HBV/A strains were subgenotype A2. An association of HBV genotype B with Inuit living in the eastern Arctic and an association of genotype D with First Nation (Dene) living in the western Arctic was observed. This study establishes the high prevalence of HBV/B6 and HBV/D genotypes in Arctic populations and reveals their marked distribution within the Canadian Arctic based on geographical and demographic attributes.     

中国广东地区乙型肝炎病毒基因亚型的分布

目的调查中国广东地区乙型肝炎病毒(HBV)基因型,主要是基因亚型的分布情况.方法应用聚合酶链反应-限制性片段长度多态性法以及序列测定法,对广东地区417例慢性HBV感染者血清进行研究.结果广东地区流行的HBV基因型主要为B型和C型,其中B型为Ba亚型,未发现Bj亚型的存在.C亚型有C1和C2两个亚型,其中C1占63%,C2占37%.结论广东地区流行的HBV基因型以Ba和C1亚型为主,C2亚型较少,Bj亚型极为罕见.     

A novel hepatitis B virus subgenotype D10 circulating in Ethiopia

Hepatitis B virus (HBV) is genetically highly divergent and classified in ten genotypes and forty subgenotypes in distinct ethno‐geographic populations worldwide. Ethiopia is a country with high HBV prevalence; however, little is known about the genetic variability of HBV strains that circulate. Here, we characterize the complete genome of 29 HBV strains originating from five Ethiopian regions, by 454 deep sequencing and Sanger sequencing. Phylogenetically, ten strains were classified as genotype A1 and nineteen as genotype D. Fifteen genotype D strains, provisionally named subgenotype D10, showed a novel distinct cluster supported by high bootstrap value and >4% nucleotide divergence from other known subgenotypes. In addition, the novel D10 strains harboured nine unique amino acid signatures in the surface, polymerase and X genes. Seventy‐two per cent of the genotype D strains had the precore premature stop codon G1896A. In addition, 63% genotype A and 33% genotype D strains had the basal core promoter mutations, A1762T/G1764A. Furthermore, four pre‐S deletion variants and two recombinants were identified in this study. In conclusion, we identified a novel HBV subgenotype D10 circulating in Ethiopia, underlining the high genetic variability of HBV strains in Africa.     

未经治疗的慢性乙型肝炎患者乙型肝炎病毒耐药变异、基因型和血清型研究

目的 研究未经核苷(酸)类似物(NA)治疗的慢性乙型肝炎患者HBV耐药变异、基因型、基因亚型和血清型特点.方法 从北京大学附属医院收集97例未经NA治疗的慢性乙型肝炎患者血清,用半巢式聚合酶链反应-直接测序法获得HBV全长逆转录酶区序列,用生物信息学技术筛查该区内11个经典耐药变异位点并鉴定基因型、基因亚型和血清型.用统计分析软件SPSS11.0进行t检验和χ~2检验. 结果 HBV在11个经典耐药变异位点上均为野生型氨基酸;B基因型和C基因型分别占36.1%(35/97)和63.9%(62/97),前者均属B2亚型,后者C2亚型占91.9%(57/62),C1亚型占6.5%(4/62),1例未能分出亚型.已知出生地的患者中,71.9%(23/32) B基因型感染者出生于我国南方地区,81.6%(40/49) C基因型感染者出生于北方地区,基因型地域分布特点明显,χ~2=23.19,P<0.01.血清型为adr者占60.8%(59/97),与C基因型相关;为adw者占38.1%(37/97),与B基因型相关,χ~2=87.83,P<0.01.结论 未经NA治疗的慢性乙型肝炎患者体内野毒株为优势株,其基因型、基因亚型和血清型与患者出生地有关.     

新疆维吾尔族慢性乙型肝炎病毒感染者病毒基因型及亚型分布特点

目的 了解新疆维吾尔自治区(简称新疆)维吾尔族慢性HBV感染者基因型、基因亚型分布情况及其与预后的关系.方法 采用聚合酶链反应限制性片段长度多态性分析方法,分析109例新疆维吾尔族慢性HBV感染者感染病毒的基因型及基因亚型.多标本均数比较采用单向方差分析.结果 109例新疆维吾尔族慢性HBV感染者,其中慢性乙型肝炎88例,乙型肝炎肝硬化17例,肝癌4例.13基因型HBV感染者9例,占8.3%,C基因型感染者50例,占45.9%,C/D基因型重组体32例,占29.4%,D基因型感染者18例,占16.5%,C基因型、C/D基因型重组体为主要基因型.经过聚合酶链反应限制性片段长度多态性分析及测序检测,鉴定9份B基因型HBV,均为Ba亚型.50例C基因型HBV感染者病毒基因亚型分布情况:Cl亚型27例,占54%,C2亚型23例,Cl亚型比C2亚型感染者多.在慢性乙型肝炎、乙型肝炎肝硬化、肝癌患者中,HBV Ba基因亚型感染者分别为8例(9.1%)、1例(5.8%)和0例;C2基因亚型感染者分别为17例(19.3%)、8例(47.5%)和2例(50%);C/D基因型感染者分别为29例(33.0%)、2例(11.9%)和1例(25%),随着病情加重,Ba基因亚型和C/D基因型感染者所占比例呈下降趋势,C2基因亚型感染者所占比例增加.结论 新疆地区维吾尔族慢性HBV感染者以Cl基因亚型为主,新疆维吾尔族慢性HBV感染者存在C/D基因型重组体.C2基因亚型HBV感染预示病情严重,预后差.     

山西省HBV基因型及亚型分布调查

目的了解山西省乙型肝炎病毒(HBV)的基因型及亚型分布情况。方法对136例乙型肝炎表面抗原(HBsAg)阳性者血清采用PCR-PFLP结合基因型特异性引物-PCR法进行HBV基因型及亚型检测。结果 136例HBV感染者的血清标本经PCR-PFLP分析,B基因型18例,均为Ba亚型,占13.2%;C基因型113例,占83.1%,除4例未分型外均为Ce亚型;D基因型5例,占3.7%。经型特异性引物-PCR分析,18例HBV B基因型中有4例为B/C基因型混合感染;5例经PCR-PFLP确定的D基因型病毒经型特异性引物法分析有2例扩增出E基因型条带。C、B基因型病毒感染者的平均年龄分别为(39.5±13.1)岁和(30.5±14.1)岁,差异有统计学意义(P<0.05);与B基因型相比,C基因型病毒感染者的HBeAg阴转率减慢。结论山西省HBV基因型主要为C(Ce),有少量的B(Ba)和D基因型,且存在B/C混合基因型,且可能存在D和E基因型病毒的重组体;与B基因型比较,感染C基因型病毒更难被机体清除,疾病更易慢性化。     

Hepatitis B virus subgenotypes and basal core promoter mutations in Indonesia

AIM： To identify the distribution of hepatitis B virus （HBV） subgenotype and basal core promoter （BCP） mutations among patients with HBV-associated liver disease in Indonesia.
METHODS： Patients with chronic hepatitis （CH, n =61）, liver cirrhosis （LC, n = 62）, and hepatocellular carcinoma （HCC, n = 48） were included in this study. HBV subgenotype was identified based on S or preS gene sequence, and mutations in the HBx gene including the overlapping BCP region were examined by direct sequencing.
RESULTS： HBV genotype B （subgenotypes B2, B3, B4, 85 and B7） the major genotype in the samples, accounted for 75.4%, 71.0% and 75.0% of CH, LC and HCC patients, respectively, while the genotype C （subgenotypes C1, C2 and C3） was detected in 24.6%, 29.0%, and 25.0% of CH, LC, and HCC patients, respectively. Subgenotypes B3 （84.9%） and C1 （82.2%） were the main subgenotype in HBV genotype B and C, respectively. Serotype adw2 （84.9%） and adrq＋ （89.4%） were the most prevalent in HBV genotype B and C, respectively. Double mutation （A1762T/G1764A） in the BCP was significantly higher in LC （59.7%） and HCC （54.2%） than in CH （19.7%）, suggesting that this mutation was associated with severity of liver disease. The T1753V was also higher in LC （46.8%）, but lower in HCC （22.9%） and CH （18.0%）, suggesting that this mutation may be an indicator of cirrhosis.
CONCLUSION： HBV genotype B/B3 and C/C1 are the major genotypes in Indonesia. Mutations in BCP, such as A1762T/G1764A and T1753V, might have an association with manifestations of liver disease.     

Hepatitis B virus genotypes and subgenotypes in China

Eight Hepatitis B virus (HBV) genotypes (A to H) have been identified based on an intergenotype divergence of 8% or more in the entire nucleotide sequence. Subgenotypes have also been identified in different HBV genotypes. As a highly endemic area for HBV infection, the prevalence of chronic HBV infection in China is between 8 and 20% of the general population. Genotypes B and C were identified as the most common HBV strains and account for approximately 95% of Chinese patients. Further study confirmed all genotype B strains belong to subgenotype Ba. Two of genotype C subgenotypes, C1 (Cs) and C2 (Ce), were found in China and they showed different geographic distributions. Genotype A was very rarely found, while genotypes E, F, G and H have not beenreported until now. Two types of HBV C/Drecombinant viruses have been identified in west China and distinct geographic and ethnic distributions were observed. Significant differences were observed ( P  < 0.001) in the prevalence of A1896 and T1762/A1764 mutations among HBV Ba, C1 and C2 subgenotypes in Chinese patients. Accumulating evidence showed the response rate to antiviral therapy in Chinese patients is higher in genotype B than genotype C patients on interferon treatment, but no difference was observed on nucleoside/nucleotide analog treatment.     

厦门市乙型肝炎病毒亚基因型分布的初步研究

目的探讨厦门地区乙型肝炎患者血清乙型肝炎病毒（HBV）基因型的分布情况。方法应用混合性型特异性引物聚合酶链反应法结合琼脂糖电泳，根据PCR产物片段大小直接判定HBV基因型；应用PCR扩增全S基因序列-DNA测序-生物信息学分析方法确定部分样本的亚基因型，并探讨前前S区编码的流行情况。结果在217例可以通过混合性型特异性引物聚合酶链反应法确定基因型的感染者中，B型83例（38．2％）、C型71例（32．7％），B／C混合型63例（29．0％）。HBeAg阳性患者中感染B基因型占50％，B／C型混合感染占22％；抗-HBe阳性患者中B／C型混合感染36％，B型38％；在慢性乙型肝炎患者中，以B基因型多见（46％），在肝硬化和肝癌患者中，以C（41％和42％）或B／C混合基因型（38％和33％）感染为主；20例患者血清经过DNA测序-生物信息学分析方法确定了亚基因型，其中B2亚型2例，C2亚型18例，其中混合性型特异性引物聚合酶链反应判断为B型的4例经过测序分析为C2亚型。B2亚型不编码前前S区，18例C2亚型均编码前前S区。结论本研究提示厦门地区乙型肝炎患者群的HBV基因型B、C型的感染率大致相同，亚基因型分析提示C2亚基因型占90％，可能是B／C基因型重组的结果。C2亚基因型病毒株均编码前前S区，提示前前S区的编码可能具有亚基因型特异性。     

Subgenotypes of hepatitis B virus genotype C do not correlate with disease progression of chronic hepatitis B in Taiwan.

BACKGROUND: Hepatitis B virus (HBV) genotype C (HBV/C) has two subgenotypes: HBV/Cs and Ce. The prevalence and clinical implications of subgenotype Cs and Ce in Taiwanese HBV carriers remain unknown. METHODS: Subgenotypes of HBV/C were determined in 242 Taiwanese HBV carriers with various stages of liver disease. The clinical as well as virologic features between patients with HBV/Cs and HBV/Ce infection were further compared. RESULTS: HBV/Ce was the predominant subgenotype in Taiwan. The prevalence of HBV/Ce was 93.6% in the inactive carriers group, 84.2% in chronic hepatitis patients, 81.2% in cirrhosis patients, 92.5% in hepatocellular carcinoma (HCC) patients without cirrhosis and 91.9% in HCC patients with cirrhosis. There was no significant difference in the distribution of the HBV/C subgenotypes among patients with different stages of liver disease. CONCLUSIONS: Subgenotypes of HBV/C may not have a clinical impact on the disease progression of chronic hepatitis B in Taiwan.     

New HBV subgenotype D9, a novel D/C recombinant,identified in patients with chronic HBeAg‐negative infection in Eastern India

Genome diversity is a hallmark of hepatitis B virus (HBV), which allowed its classification into 10 genotypes (A–J) and numerous subgenotypes. Among them, Genotype D is currently segregated into eight subgenotypes (D1–D8). Here, we report the identification and characterization of a novel subgenotype within genotype D of HBV from chronic hepatitis B e antigen (HBeAg)‐negative patients of Eastern India. Phylogenetic tree analysis based on complete genome sequences revealed that six of 39 HBV/D isolates formed a distinct cluster supported by high bootstrap value and had nucleotide divergence >4% relative to the known D subgenotypes (D1–D8), justifying their assignment into a new subgenotype (D9). By comparing the amino acid sequences of the four ORFs of HBV/D9 with D1–D8, 36 specific residues, including a unique one (E₁₁₂ in the core region), were identified that could be considered as a signature of D9. Further analysis by Simplot, BootScan and jpHMM demonstrated that D9 resulted from a discrete recombination with genotype C over the precore–core region. This type of recombination has not been described previously as all C/D recombinants reported so far possessed genotype C backbones with mosaic fragments derived from HBV/D. Interestingly, compared to other subgenotypes of HBV/D, D9 isolates had a higher frequency of mutations (A1762T and G1764A) in the basal core promoter region that had been implicated in the development of hepatocellular carcinoma. Further investigations are needed to determine the overall prevalence and clinical significance of these newly characterized D9 strains and to assess the impact of inter‐genotypic recombination on viral properties.     

A complete genomic analysis of hepatitis B virus genotypes and mutations in HBeAg-negative chronic hepatitis B in China

Summary.  We aimed to study the distribution of hepatitis B virus (HBV) genotypes/subgenotypes in different parts of China and their clinical impact on the severity of hepatitis B e antigen (HBeAg)-negative chronic hepatitis B. Residual serum samples from a cohort of HBeAg-negative chronic hepatitis B patients in Hong Kong, Shanghai and Beijing were studied. Complete HBV genomic sequencing was performed for phylogenetic tree analysis and determination of HBV mutations was carried out. Mutations associated with severe liver fibrosis (Ishak score 4 or more) were selected by computerized information gain criteria. Genotype B (all subgenotype Ba) HBV was present in 19 of 45 (42%), 12 of 31 (39%) and 5 of 25 (20%) patients in Hong Kong, Shanghai and Beijing, respectively ( P  = 0.16). Ninety-seven per cent of genotype C HBV in Shanghai and Beijing belonged to subgenotype Ce whereas 69% of genotype C patients in Hong Kong belonged to subgenotype Cs ( P  < 0.001). Patients infected by subgenotype Cs had the lowest serum albumin and highest alanine aminotransferase levels compared with subgenotype Ce and Ba. Patients infected by subgenotype Cs also had more severe histological necroinflammation than subgenotype Ce. Two HBV mutations were identified to associate with severe liver fibrosis (G2858C and C2289A) and one mutation was protective against severe liver fibrosis (T2201C). The T2201C mutation was found exclusively among patients (21 of 46 patients, 45%) infected by HBV subgenotype Ce. The clinical differences in HBeAg-negative chronic hepatitis B in China may be influenced by different distribution of subgenotype C HBV.     

Prevalence and genotype distribution of hepatitis B virus among migrant workers in Lombok Island,Indonesia

Objective: To examine the potential risk of hepatitis B virus(HBV) spread in Indonesia by migrant workers, based on the molecular characteristics of HBV strains.Methods: Sera collected from migrant workers traveling to their destination countries(pre-migrant workers) and those returning to Indonesia(post-migrant workers) were screened for HBsAg by ELISA, followed by HBV DNA detection by PCR and(sub)genotype/subtype determination according to surface region and whole genome sequencing. Results: Of 87 pre-migrant workers, 15(17.24%) were HBsAgpositive, whereas 15(12.10%) of 124 post-migrant workers were HBs Ag seropositive. HBV genotype analysis based on the S region showed that HBV-B3/adw2 was predominant(96.15%, 25/26) whereas 3.85%(1/26) of isolates were HBV-C3/adrq+. Whole genome sequencing of selected strains and phylogenetic tree analysis identified subgenotype B7 in three samples previously categorized as subgenotype B3 based on S region analysis, supporting a recent argument that subgenotypes B5/B7/B8/B9 could be considered as a quasi-subgenotype of B3. Conclusions: A high prevalence of HBsAg carriers was detected among migrant workers from Lombok Island, with no significant difference in prevalence between before and after returning to Indonesia. All strains were classified into genotypes common in Indonesia, and the results suggested that migrant workers are not a risk factor for HBV transmission into Indonesia.     

Genotype/subgenotype distribution of hepatitis B virus among hemodialysis patients with chronical hepatitis B

Introduction. Hepatitis B virus (HBV) infection in hemodialysis (HD) patients is a major concern, but limited information exists on the HBV genotyping in patients on maintenance HD in Turkey.Aim. To investigate the genotype and subgenotype distribution of HBV in Turkish HD patients with chronic hepatitis B.Material and methods. A total of 248 HBsAg positive patients undergoing long-term HD from all regions of Turkey were included in this study. HBV genotypes were determined by phylogenetic analysis and by genotyping tools.Results. HBV DNA was detected in 94/248 (38%) of the patients. Among the study patients, genotype D of HBV was predominant (99%) and one patient (1%) was infected with genotype G. The majority (82%) of HBV genotype D branched into subgenotype D1, and also in ayw2 HBsAg subtype clusters in the phylogenetic tree. However, 10% and 8% of the strains branched into subgenotype D2 (also in ayw3 HBsAg subtype cluster) and subgenotype D3 clusters, respectively.Conclusion. In conclusion, HBV genotyping should be routinely applied to HD patients to establish a baseline. Determination of genotypes/subgenotypes of HBV may provide robust epidemiological data related to their circulation as well as their transmissibility.     

Distribution and Epidemiologic Trends of HBV Genotypes and Subtypes in 14 Countries Neighboring China

Background:

The number of cases of HBV infection reported by the WHO for each district and country is positively correlated with the number of HBV sequences in the database isolated from the corresponding district and country.

Objectives:

This study determined distribution characteristics of HBV genotypes and subtypes in 14 countries neighboring China. The progress made in genomic research involving HBV was also reviewed.

Materials and Methods:

Nine hundred fifty-one complete genome sequences of HBV from 14 countries neighboring China were selected from NCBI. The sequence-related information was analyzed and recorded. One hundred seventy-two sequences of HBV genotype B were screened for alignment using DNA star and MEGA 5.1.

Results:

Dominant HBV genotypes in the countries neighboring China were genotypes B, C and D and dominant subtypes were adw2 and adrq+. The association between genotype and serotype of HBV in these countries was shown to differ from previous research results. As shown by sequence alignment, the sequence divergence between five subgenotypes (B3, B5, B7, B8 and B9) was below 4%. The B subgenotypes shared six common specific amino acid sites in the S region.

Conclusions:

The B3, B5, B7, B8 and B9 subgenotypes can be clustered into quasi-sub-genotype B3 and the open reading frame of HBV has a start codon preference; however, whether a mutation in the start codon in the pre-S2 region has an impact on survival and replication of HBV remains to be determined.     

福州市乙肝病毒基因型和基因亚型的分布及其与前C、C基因启动子变异的关系

目的 研究福州市乙肝病毒基因型和亚型分布及其与T1762/A1764、A1896变异的关系,为完善预防、诊断、治疗病毒感染的策略和方法提供科学依据. 方法 应用型特异性引物PCR法检测HBsAg阳性血清的基因型,应用PCR-RFLP方法检测基因亚型、T1762/A1764变异和A1896变异. 结果 282份HBsAg阳性血清样品中103份未能成功分型,其余179份样品中B基因型122份(68.2%),C基因型54份(30.2%),B C型3份(1.7%),未检测到其他基因型.随机选取的100份B基因型样品中,Ba亚型71份(71.0%),Bj亚型8份(8.0%),未能分亚型者21份(21.0%).54份C基因型样品中Ce亚型 31份(57.4%),Cs亚型 14份(25.9%),Ce Cs 1份(1.9%),未能分亚型者8份(14.8%).T1762/A1764变异标本9份(8.7%),Ce亚型变异率最高(29.2%),Ba亚型次之(3.3%),Cs和Bj亚型未检测到变异株,T1762/A1764变异在不同基因型和亚型间的分布差异有统计学意义(P＜0.05).A1896变异标本10份(10.0%),Ba亚型变异率最高(14.0%),Cs亚型次之(10.0%),Ce亚型最低(4.0%),不同基因型和亚型中的变异差异无统计学意义(P＞0.05).HBeAg阳性和阴性样品中的基因型和亚型分布差异无统计学意义(P＞0.05). 结论 福州市乙肝病毒以B、C基因型为主,Ba、Ce亚型占优势,HBV各基因型和亚型发生T1762/A1764、A1896变异的模式不同.     

Long‐term evolution of hepatitis B virus genotype F: Strong association between viral diversification and the prehistoric settlement of Central and South America

The genotype F (HBV‐F) is an autochthonous Native American strain of the hepatitis B virus. In this study, we reconstruct the HBV‐F long‐term evolution under a hypothesis of co‐divergence with humans in Central and South America, since their entry into the region 14.5‐16 thousand years ago. The Bayesian phylogeographic reconstruction supported a virus‐host co‐expansion; however, two evolutionary scenarios would have been present. Whereas subgenotype F1 spreads along a Pacific coastal route and would have evolved associated with Central American and Andean cultures from the west of the continent, subgenotypes F2‐F6 spread along the Atlantic coastline and inner pathways associated with communities inhabiting the tropical forest lowlands. Then, we propose a model for HBV‐F evolution in which the selection of differential biological characteristics in these two main groups would be related to their evolution in host populations with different genetic backgrounds and dissimilar demographic conditions.