scholarly journals Genotype C of hepatitis B virus can be classified into at least two subgroups

2004 ◽  
Vol 85 (2) ◽  
pp. 283-292 ◽  
Author(s):  
Tran Thien-Tuan Huy ◽  
Hiroshi Ushijima ◽  
Vo Xuan Quang ◽  
Khin Maung Win ◽  
Pairoj Luengrojanakul ◽  
...  
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Far East ◽  
Full Length ◽  
Hbv Genotype ◽  
B Virus ◽  
Protein Amino Acids ◽  
Genotype C

A genomic characterization of hepatitis B virus (HBV) was done for 56 pre-S1/pre-S2 genes and 10 full-length HBV genotype C isolates from five Asian countries. Phylogenetic analysis of the pre-S1/pre-S2 genes revealed two major groups within genotype C: one for isolates from southeast Asia including Vietnam, Myanmar and Thailand (named HBV/C1) and the other for isolates from Far East Asia including Japan, Korea and China (named HBV/C2). This finding was confirmed by phylogenetic analysis based on the full-length sequence of 32 HBV genotype C isolates, including 22 from database entries. Two isolates from Okinawa, the island off the southern end of Japan, formed a different branch. Specific amino acid sequence changes were identified in the large S protein (amino acids 51, 54, 60, 62 and 73) and P protein (amino acids 231, 233, 236, 248, 252 and 304). Our results indicate that genotype C of HBV can be classified into at least two subgroups.

A case of hepatitis B virus infection in Eritrean Diciotti migrant: phylogenetic analysis and ‘mirror effect’

2019 ◽  
Vol 14 (8) ◽  
pp. 509-514
Author(s):  
Giancarlo Ceccarelli ◽  
Eleonora Cella ◽  
Serena Vita ◽  
Alessia Lai ◽  
Erika Ebranati ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Copy Number ◽  
Mirror Effect ◽  
Hepatitis B Virus Infection ◽  
Migrant Population ◽  
Hbv Genotype ◽  
B Virus ◽  
Epidemiological Approach

A case of hepatitis B virus (HBV) infection in an Eritrean migrant was described to provide an epidemiological approach based on phylogenetic analysis useful in developing countries with lacking information. Migrant, positive for HBsAg and HBeAg, carried HBV at high copy number. A sequence of HBV HBsAg region was used for phylogenetic relationships and genetic variability investigation. In the phylogenetic tree, the sequence corresponded to D2 HBV genotype and the cluster root dated 7 years ago. These data compared with the date of landing in Italy, suggest that he was infected at least 7 years before his arrival. This approach by ‘mirror effect’ allows the reconstruction of HBV epidemiology in the country of origin, analyzing the migrant population in the host country.

scholarly journals Genotype-Specific Genomic Markers Associated with Primary Hepatomas, Based on Complete Genomic Sequencing of Hepatitis B Virus

2008 ◽  
Vol 82 (7) ◽  
pp. 3604-3611 ◽  
Author(s):  
Joseph J. Y. Sung ◽  
Stephen K. W. Tsui ◽  
Chi-Hang Tse ◽  
Eddie Y. T. Ng ◽  
Kwong-Sak Leung ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Rule Learning ◽  
Hbv Infection ◽  
Control Group ◽  
Hbv Genotype ◽  
B Virus ◽  
Genomic Markers ◽  
Genotype C ◽  
Complete Genomic

ABSTRACT We aimed to identify genomic markers in hepatitis B virus (HBV) that are associated with hepatocellular carcinoma (HCC) development by comparing the complete genomic sequences of HBVs among patients with HCC and those without. One hundred patients with HBV-related HCC and 100 age-matched HBV-infected non-HCC patients (controls) were studied. HBV DNA from serum was directly sequenced to study the whole viral genome. Data mining and rule learning were employed to develop diagnostic algorithms. An independent cohort of 132 cases (43 HCC and 89 non-HCC) was used to validate the accuracy of these algorithms. Among the 100 cases of HCC, 37 had genotype B (all subgenotype Ba) and 63 had genotype C (16 subgenotype Ce and 47 subgenotype Cs) HBV infection. In the control group, 51 had genotype B and 49 had genotype C (10 subgenotype Ce and 39 subgenotype Cs) HBV infection. Genomic algorithms associated with HCC were derived based on genotype/subgenotype-specific mutations. In genotype B HBV, mutations C1165T, A1762T and G1764A, T2712C/A/G, and A/T2525C were associated with HCC. HCC-related mutations T31C, T53C, and A1499G were associated with HBV subgenotype Ce, and mutations G1613A, G1899A, T2170C/G, and T2441C were associated with HBV subgenotype Cs. Amino acid changes caused by these mutations were found in the X, envelope, and precore/core regions in association with HBV genotype B, Ce, and Cs, respectively. In conclusion, infections with different genotypes of HBV (B, Ce, and Cs) carry different genomic markers for HCC at different parts of the HBV genome. Different HBV genotypes may have different virologic mechanisms of hepatocarcinogenesis.

scholarly journals Genotyping Hepatitis B virus from whole- and sub-genomic fragments using position-specific scoring matrices in hbv star

2006 ◽  
Vol 87 (6) ◽  
pp. 1459-1464 ◽  
Author(s):  
Richard Myers ◽  
Caroline Clark ◽  
Arshad Khan ◽  
Paul Kellam ◽  
Richard Tedder
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Core Promoter ◽  
Full Length ◽  
Basal Core Promoter ◽  
Hbv Genotype ◽  
Promoter Sequences ◽  
Hbv Genotypes ◽  
Scoring Matrices ◽  
B Virus

Hepatitis B virus (HBV) genomes have been classified into eight genotypes based on phylogenetic analysis of sequence variation. Identifying and tracking the movement of HBV genotypes is important in terms of both monitoring infection rates and predicting disease and treatment. An HBV genotyping tool has been developed that compares query sequences with position-specific scoring matrices representing the eight HBV genotypes. This tool (hbv star) is rapid, robust and accurate and assigns genotype based on a statistically defined scoring model. hbv star confidently assigned 90 % of 590 full-length HBV genomes to an HBV genotype (Z score >2.0). Thirty-two of the residual 48 sequences were identified as non-human primate viruses and 16 sequences were identified as recombinant or putative recombinants. Receiver-Operated Characteristic (ROC) analysis was used to compare the accuracy of genotype prediction using basal core promoter sequences and surface and core genes with the accuracy achieved by using full-length sequences. A web interface to hbv star is available at http://www.vgb.ucl.ac.uk/starn.shtml.

Phylogenetic analysis of hepatitis B virus full-length genomes reveals evidence for a large nosocomial outbreak in Belgium

2009 ◽  
Vol 46 (1) ◽  
pp. 61-68 ◽  
Author(s):  
Mahmoud Reza Pourkarim ◽  
Jannick Verbeeck ◽  
Mustafizur Rahman ◽  
Samad Amini-Bavil-Olyaee ◽  
An-Marie Forier ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Full Length ◽  
Nosocomial Outbreak ◽  
B Virus

scholarly journals Hepatitis B virus pre-existing drug resistant mutation is related to the genotype and disease progression

2017 ◽  
Vol 11 (09) ◽  
pp. 727-732 ◽  
Author(s):  
Liping Wang ◽  
Fangzheng Han ◽  
Hualing Duan ◽  
Fang Ji ◽  
Xuebing Yan ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Hbv Infection ◽  
Drug Resistant ◽  
Resistance Mutations ◽  
Hbv Genotype ◽  
B Virus ◽  
Drug Resistant Mutation ◽  
Genotype C ◽  
Resistant Mutation

Introduction: Previous studies have indicated that the drug-resistant mutations of hepatitis B virus (HBV) are a major obstacle to antiviral therapy. However, it is still unclear whether there are pre-existent resistance mutations in patients with HBV infection and the relationship between drug-resistant mutation, genotypes, and progression of hepatitis B disease. Methodology: A total of 357 treatment-naïve patients with HBV infection were involved in this retrospective study. The drug-resistant mutations of HBV reverse transcriptase domain were screened by direct gene sequencing. Results: Lamivudine (LAM) resistance was detected in 8 patients (3.7%) with chronic hepatitis B (CHB), 13 (11.7%) patients with liver cirrhosis (LC), and 6 (21.4%) patients with hepatocellular carcinoma (HCC). Adefovir(ADV)-resistant mutations were detected in 10 (4.6%) patients with CHB, 15 (13.5%) patients with  LC and 4 (14.5%) patients with HCC. Both LAM and ADV resistant mutations were detected in 2 patients (0.9%) with CHB, 1 patient (0.9%) with LC and 1 patient (3.6%) with HCC. Significant differences (p <0.01) were observed in the drug-resistance rates among patients with CHB, LC and HCC. Meanwhile, all the drug-resistant mutations were found in patients with HBV genotype C. Conclusions: This study demonstrated higher risk of pre-existing drug-resistant mutations in patients with HBV genotype C comparing to patients with HBV genotype B. Likewise, increasing prevalence of pre-existing drug-resistant mutations was shown, alongside with the progression of the disease.

scholarly journals Discrepant Results of Hepatitis B Virus Genotype Determination by PCR and DNA Sequencing

2021 ◽  
Author(s):  
Yihan Xiao ◽  
Lan Ni ◽  
Zhigang Cui ◽  
Long Sun ◽  
Xiaojun Zhou ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Dna Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Full Length ◽  
Whole Genome ◽  
Hbv Genotype ◽  
Specific Primers ◽  
B Virus

Abstract Currently, multiplex-PCR with genotype-specific primers is widely used for preliminary screening of hepatitis B virus (HBV) genotyping, despite its relatively lower accuracy compared with whole genome sequencing. Here, we present the discrepant results of HBV genotyping by PCR and full-length sequencing. HBV DNA was isolated from chronic hepatitis B serum and the HBV genotype was detected by PCR using genotype-specific primers and full-length genome sequencing. As a result, the determination of genotype B by the PCR method was consistent with the DNA sequencing results; however, PCR revealed that genotype C exhibited a mixed genotype of B and C in the current study. In conclusion, the PCR-based genotyping method may not provide accurate information of the HBV genotype and whole genome sequencing remains the “gold standard” method for HBV genotyping.

Phylogenetic analysis of the hepatitis B virus (HBV) genotype F including Argentine isolates

2001 ◽  
Vol 146 (9) ◽  
pp. 1803-1810 ◽  
Author(s):  
V. A. Mbayed ◽  
L. Barbini ◽  
J. L. López ◽  
R. H. Campos
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Hbv Genotype ◽  
B Virus ◽  
Genotype F

High Viral Load and Hepatitis B Virus Subgenotype Ce Are Associated With Increased Risk of Hepatocellular Carcinoma

2008 ◽  
Vol 26 (2) ◽  
pp. 177-182 ◽  
Author(s):  
Henry Lik-Yuen Chan ◽  
Chi-Hang Tse ◽  
Frankie Mo ◽  
Jane Koh ◽  
Vincent Wai-Sun Wong ◽  
...  
Keyword(s):  
Risk Factors ◽  
Hepatocellular Carcinoma ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Hbv Dna ◽  
Hazard Ratio ◽  
Hbv Genotype ◽  
Hbv Genotypes ◽  
B Virus ◽  
Genotype C

Purpose We aimed to investigate the impact of hepatitis B virus (HBV) DNA and HBV genotypes/subgenotypes on the risk of hepatocellular carcinoma (HCC). Patients and Methods A prospective cohort of patients infected with chronic HBV in a surveillance program for HCC since 1997 was studied. Ultrasound and alpha-fetoprotein evaluation were regularly performed to detect HCC. Risk factors for HCC and the relationship between HBV DNA and HBV genotypes were determined. Results Among 1,006 patients with a median follow-up of 7.7 years, 86 patients (8.5%) developed HCC. With reference to the low HBV DNA stratum (log HBV DNA ≤ 4.5 copies/mL), the hazard ratio for HCC of the intermediate HBV DNA stratum (log HBV DNA > 4.5 to 6.5 copies/mL) was 1.62 (95% CI, 1.05 to 2.48; P = .027) and that of the high HBV DNA stratum (log HBV DNA > 6.5 copies/mL) was 2.73 (95% CI, 1.76 to 4.25; P < .001). Among patients with genotyping results, 330 patients had HBV genotype B and 439 patients had HBV genotype C (94 subgenotype Ce and 345 subgenotype Cs). With reference to HBV genotype B, HBV subgenotype Ce has the highest risk of HCC (hazard ratio = 2.75; 95% CI, 1.66 to 4.56; P < .0001) and HBV subgenotype Cs has intermediate risk (hazard ratio = 1.70; 95% CI, 1.09 to 2.64; P = .020). On multivariate analysis, HBV DNA, HBV genotypes, liver cirrhosis, male sex, older age, and lower serum albumin were independent risk factors of HCC. Conclusion High HBV DNA level and HBV genotype C, particularly subgenotype Ce, increased the risk of HCC in chronic hepatitis B.

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