High prevalence of hepatitis B virus genotype C/C1 in the Minangkabau ethnic group in Indonesia
TL;DR: HBV/C with subgenotype C1 was the predominant HBV genotype among HBV carriers of Minangkabau ethnicity and the prevalence of pre-S, T1753V and A1762T/G1764A mutations was higher among the MinangKabau compared to IndonesianHBV carriers in general.
Abstract: The Minangkabau is one of the major ethnic groups in Indonesia. Previous studies with a limited number of samples have shown a different prevalence of HBV/C in the Minangkabau compared to the Indonesian population in general. The aim of this study was to assess the HBV genotype distribution pattern and the prevalence of pre-S, T1753V and A1762T/G1764A mutations among the Minangkabau HBV carriers. The samples were collected from Padang, West Sumatera and from western Java. Mixed primers for specific genotypes were used to determine the HBV genotype. Pre-S or S genes were amplified, sequenced and aligned with reference sequences from GenBank to derive a phylogenetic tree for subgenotyping. Pre-S genes were also analyzed for mutations. The basal core promoter (BCP) region was amplified and directly sequenced to analyze T1753V and A1762T/G1764A mutations. The predominant HBV genotype among the Minangkabau HBV carriers (n=117) was C (72.6%) followed by B (24.8%) and co-infection with B and C (2.6%). The prevalence of pre-S mutations, including both the pre-S deletion and pre-S2 start codon mutation, was 41.0%, and the T1753V and A1762T/G1764A mutations were found in 51.9% and 71.2% respectively. HBV/C1 was the predominant HBV subgenotype in the Minangkabau HBV carriers, and was found in 66.2%, followed by B3, B7, C8, B2, B9, C2, and C10 (18.3%, 7.0%, 2.8%, 1.4%, 1.4%, 1.4%, and 1.4% respectively). From samples that were found to be co-infected with HBV B and C, two samples were successfully cloned and subgenotyped, including one with mixed subgenotypes of B3 and C1, and another one with mixed subgenotypes of B7, C1, putative intergenotypic of B/A, and C/A. Furthermore, three samples from donors of non-Minangkabau ethnicity from Padang were found to be infected with an intragenotypic recombination form, including a putative recombinant of B8/B3 and B9/B7. HBV/C with subgenotype C1 was the predominant HBV genotype among HBV carriers of Minangkabau ethnicity. The prevalence of pre-S, A1762T/G1764A, and T1753V mutations was higher among the Minangkabau compared to Indonesian HBV carriers in general.
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TL;DR: Genotype determination in CHB infection is important in estimating disease progression and planning optimal antiviral treatment, as pathogenic differences between HBV genotypes explain disease intensity, progression to LC, and HCC.
Abstract: At least 600000 individuals worldwide annually die of hepatitis B virus (HBV)-related diseases, such as chronic hepatitis B (CHB), liver cirrhosis (LC), and hepatocellular carcinoma (HCC). Many viral factors, such as viral load, genotype, and specific viral mutations, are known to affect disease progression. HBV reverse transcriptase does not have a proofreading function, therefore, many HBV genotypes, sub-genotypes, mutants, and recombinants emerge. Differences between genotypes in response to antiviral treatment have been determined. To date, 10 HBV genotypes, scattered across different geographical regions, have been identified. For example, genotype A has a tendency for chronicity, whereas viral mutations are frequently encountered in genotype C. Both chronicity and mutation frequency are common in genotype D. LC and progression to HCC are more commonly encountered with genotypes C and D than the other genotypes. Pathogenic differences between HBV genotypes explain disease intensity, progression to LC, and HCC. In conclusion, genotype determination in CHB infection is important in estimating disease progression and planning optimal antiviral treatment.
313 citations
TL;DR: A previous study conducted in Indonesia revealed that hepatic steatosis was associated with disease progression and drug resistance to lamivudine, which is prominent in Indonesia, remains obscure.
Abstract: Approximately 240 million people are chronically infected with hepatitis B virus (HBV), 75% of whom reside in Asia. Approximately 600000 of infected patients die each year due to HBV-related diseases or hepatocellular carcinoma (HCC). The endemicity of hepatitis surface antigen in Indonesia is intermediate to high with a geographical difference. The risk of HBV infection is high in hemodialysis (HD) patients, men having sex with men, and health care workers. Occult HBV infection has been detected in various groups such as blood donors, HD patients, and HIV-infected individuals and children. The most common HBV subgenotype in Indonesia is B3 followed by C1. Various novel subgenotypes of HBV have been identified throughout Indonesia, with the novel HBV subgenotypes C6-C16 and D6 being successfully isolated. Although a number of HBV subgenotypes have been discovered in Indonesia, genotype-related pathogenicity has not yet been elucidated in detail. Therefore, genotype-related differences in the prognosis of liver disease and their effects on treatments need to be determined. A previous study conducted in Indonesia revealed that hepatic steatosis was associated with disease progression. Pre-S2 mutations and mutations at C1638T and T1753V in HBV/B3 have been associated with advanced liver diseases including HCC. However, drug resistance to lamivudine, which is prominent in Indonesia, remains obscure. Although the number of studies on HBV in Indonesia has been increasing, adequate databases on HBV infection are limited. We herein provided an overview of the epidemiology and clinical characteristics of HBV infection in Indonesia.
49 citations
TL;DR: Genetic variants of HLA-DP and the presence of anti-HBc are important predictors of OBI in Indonesian blood donors.
Abstract: Occult hepatitis B infection (OBI) is defined as the presence of hepatitis B virus (HBV) DNA in the serum and/or liver in HBsAg-negative individuals. OBI is associated with the risk of viral transmission, especially in developing countries, and with progressive liver disease and reactivation in immunosuppressive patients. The objective of this study was to evaluate the relation of OBI to HLA-DP single nucleotide polymorphisms (SNPs) encoding antigen-binding sites for the immune response to HBV infection. As HLA-DP variants affect the mRNA expression of HLA-DPA1 and HLA-DPB1 in the liver, we hypothesised that high levels of HLA-DPA1 and HLA-DPB1 expression favour OBI development. The study enrolled 456 Indonesian healthy blood donors (HBsAg negative). OBI was defined as the presence of HBV-DNA in at least two of four open reading frames (ORFs) of the HBV genome detected by nested PCR. SNPs in HLA-DPA1 (rs3077) and HLA-DPB1 (rs3135021, rs9277535, and rs2281388) were genotyped using real-time Taqman® genotyping assays. Of 122 samples positive for anti-HBs and/or anti-HBc, 17 were determined as OBI. The minor allele in rs3077 was significantly correlated with OBI [odds ratio (OR) = 3.87, 95% confidence interval (CI) = 1.58–9.49, p = 0.0015]. The prevalence of the minor allele (T) was significantly higher in subjects with OBI than in those without (59% and 33%, respectively). The combination of haplotype markers (TGA for rs3077–rs3135021–rs9277535) was associated with increased risk of OBI (OR = 4.90, 95%CI = 1.12–21.52 p = 0.038). The prevalence of OBI was highest in the isolated anti-HBc group among the three seropositive categories: anti-HBs <500 mIU/ml, anti-HBs ≥500 mIU/ml, and isolated anti-HBc (29.41%, p = 0.014). Genetic variants of HLA-DP and the presence of anti-HBc are important predictors of OBI in Indonesian blood donors. Ref: KE/FK/194/EC; registered 01 March 2013. Continuing approval Ref: KE/FK/536/EC; registered 12 May 2014.
11 citations
Cites result from "High prevalence of hepatitis B viru..."
...This is in accordance with previous studies showing that in Indonesia the most common HBV genotype is HBV B3 (HBV/B3), followed by HBV/C1, especially in Java island [21, 33]....
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Journal Article•
TL;DR: The development of multi-site mutations in the X gene may represent a strategy by which HBV can escape immune surveillance and thus contribute to hepatocarcinogenesis, even though the biological roles of some variants remain unclear.
Abstract: Multi-site mutations in the hepatitis B virus (HBV) X gene are often found in patients with advanced liver diseases such as liver cirrhosis and hepatocellular carcinoma. It has been reported that modifications in the X protein play crucial roles in the development of HBV-related severe liver disease. However, the prevalence of genetic variations in Indonesian strains has not been systematically assessed. In this study, we sought to investigate the profile of nonsynonymous mutations in the X gene. Overall, 114 Indonesian HBV strains, including 12 in-house samples, were retrieved from GenBank. The mutation frequency in the X gene was compared among strains obtained from patients with chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. The mutation frequencies of the domain and basal core promoter regions were significantly greater in advanced liver diseases compared with chronic hepatitis. In addition, the double mutation K130M/V131I and the triple mutation N88V/K130M/V131I were associated with a 2.5 times higher risk of advanced liver disease. However, the roles of two novel X gene mutations (A12S/T and L16F/P) on hepatocarcinogenesis are unclear relative to wild-type X gene. In conclusion, the development of multi-site mutations in the X gene may represent a strategy by which HBV can escape immune surveillance and thus contribute to hepatocarcinogenesis, even though the biological roles of some variants remain unclear.
4 citations
TL;DR: It is concluded that all the samples have nucleotide variation and the mutation implying that molecular progression between the virus and the host at chronically infected patients is implied.
Abstract: Background: Hepatitis B is a health issue that become major problem worldwide with high morbidity. Hepatitis B is a liver infection that caused by Hepatitis B Virus. Chronic hepatitis B is a liver inflammation that lasted more than 6 months and it has the potential to progress to liver cirrhosis and hepatocellular cancer. The disease is influenced by Gene X and viral genotype. Mutations in the Gene X are suspected to having a role in disease progression. The aim of this study was to detect Gene X polymorphism and the phylogeny of HBV from Padang local clinical samples of chronic hepatitis B (CHB), West Sumatera, Indonesia.Method: The entire chronically HBV-infected patients were enrolled in this study: 38 CHB. The research samples were the entire Hepatitis B serum from Indonesian Red Cross Blood Bank than Gene X was amplified using nested PCR, which produced two fragments and aligned with X sequence database continued with mutation analysis. Results: In this study we found all the samples were having nucleotide variation. Of various mutations, we observed the presence of known liver cirrhosis and HCC-related HBx protein mutant i.e double mutations (HBx130 and HBx131) and two triple mutations (HBx5/HBx130/HBx131) and (HBx127/HBx130/HBx131) were high. The analysis also showed that patients were infected mainly by genotype C at 72,2% and followed by B at 27,8%.Conclusion: We conclude that all the samples have nucleotide variation and the mutation implying that molecular progression between the virus and the host at chronically infected patients.
References
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TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
57,055 citations
"High prevalence of hepatitis B viru..." refers methods in this paper
...Reference sequences of all previously described HBV genotypes and subgenotypes were retrieved from GenBank database together with all samples obtained in this study to construct phylogenetic trees based on partial pre-S or S region by the neighbor-joining method [31] using the maximum composite likelihood method to calculate evolutionary distances [32]....
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TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Abstract: Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
39,110 citations
"High prevalence of hepatitis B viru..." refers methods in this paper
...All phylogenetic analyses were carried out using the MEGA5 software [33]....
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TL;DR: The simulation results show that the accuracy of NJ trees decline only by approximately 5% when the number of sequences used increases from 32 to 4,096 (128 times) even in the presence of extensive variation in the evolutionary rate among lineages or significant biases in the nucleotide composition and transition/transversion ratio.
Abstract: Current efforts to reconstruct the tree of life and histories of multigene families demand the inference of phylogenies consisting of thousands of gene sequences. However, for such large data sets even a moderate exploration of the tree space needed to identify the optimal tree is virtually impossible. For these cases the neighbor-joining (NJ) method is frequently used because of its demonstrated accuracy for smaller data sets and its computational speed. As data sets grow, however, the fraction of the tree space examined by the NJ algorithm becomes minuscule. Here, we report the results of our computer simulation for examining the accuracy of NJ trees for inferring very large phylogenies. First we present a likelihood method for the simultaneous estimation of all pairwise distances by using biologically realistic models of nucleotide substitution. Use of this method corrects up to 60% of NJ tree errors. Our simulation results show that the accuracy of NJ trees decline only by ≈5% when the number of sequences used increases from 32 to 4,096 (128 times) even in the presence of extensive variation in the evolutionary rate among lineages or significant biases in the nucleotide composition and transition/transversion ratio. Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies.
4,489 citations
"High prevalence of hepatitis B viru..." refers methods in this paper
...Reference sequences of all previously described HBV genotypes and subgenotypes were retrieved from GenBank database together with all samples obtained in this study to construct phylogenetic trees based on partial pre-S or S region by the neighbor-joining method [31] using the maximum composite likelihood method to calculate evolutionary distances [32]....
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TL;DR: There is a growing understanding of viral, host and environmental factors influencing disease progression, which ultimately could improve the management of chronic hepatitis B.
1,172 citations
"High prevalence of hepatitis B viru..." refers background in this paper
...The liver disease samples comprised of 16 samples from patients with chronic hepatitis (CH), 22 samples from those with liver cirrhosis (LC), and 4 samples from those with HCC. Chronic hepatitis patients were defined as those positive for HBsAg for more than 6 months, and have more than twice the normal ALT level....
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...The C1653T mutation in HBV subgenotype C2 and T1753V and A1762T/G1764A in HBV subgenotypes C1 and C2 were statistically significantly associated with an increased risk of HCC....
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...Among the Asian patients from Vietnam, significantly higher associations were found between mixed genotype infections and acute hepatitis B, liver cirrhosis, and HCC although the specific combination was impossible to identify due to the different mixtures reported [20]....
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...The frequencies of mutations at the pre-S2 promoters were significantly higher in the patients with HCC than in the patients without HCC (pre-S2 promoter mutation: 15.3% vs 8.9%, P=0.032) [10]....
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...Differences between the Asian genotypes B and C appears to be influenced by the subgroup of genotype B, because in Japan where the genotype B1 (Bj) is prevalent, no differences in the development of HCC between genotypes B and C was observed [24]....
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TL;DR: The hepatitis B virus (HBV) genotype was determined in a total of 121 plasma samples collected in France and the US from patients chronically infected with HBV as discussed by the authors, and subsequent phylogenetic analysis of the complete genome and the individual open reading frames, showed that the virus isolate from these samples was 3248 bp long and, phylogenetically, did not cluster with any of the known genotypes.
Abstract: The hepatitis B virus (HBV) genotype was determined in a total of 121 plasma samples collected in France and the US from patients chronically infected with HBV HBV genotype A was predominant in this collection, appearing in 66 samples (54%), while genotypes B, C, D, E and F occurred in 4 (3%), 14 (12%), 23 (19%), 1 (1%) and 0 (0%) of samples, respectively However, the genotype of a total of 13 (11%) samples (2 from France, 11 from the US) could not be determined with the methodology used Sequence analysis, and subsequent phylogenetic analysis of the complete genome and the individual open reading frames, showed that the virus isolate from these samples was 3248 bp long and, phylogenetically, did not cluster with any of the known genotypes This strain was provisionally called HBV genotype G Virus isolates that were obtained from geographically separated regions like France and the US were closely related to each other All virus strains analysed contained some characteristic differences when compared to genotype A: a translational stop codon at aa 2 and 28 of the preCore region; a 36 nt (12 aa) insert in the amino-terminal part of the Core antigen (HBcAg); a 2 aa deletion in the carboxy-terminal part of HBcAg; and a 1 aa deletion in the preS1 open reading frame The deduced amino acid sequence of HBsAg suggests that this newly discovered genotype G strain belongs to serological group adw2
922 citations
Additional excerpts
...nested PCR as previously described [15,30]....
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