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A study of genotypes, mutants and nucleotide sequence of hepatitis B virus in Pakistan: HBV genotypes in pakistan.

ABSTRACT: BACKGROUND:Hepatitis B virus (HBV) genotypes and mutations are gaining importance in determining the clinical course of chronic liver disease. OBJECTIVES:To determine and compare the distribution of HBV genotypes and genomic variations in Pakistan to other parts of the world. PATIENTS AND METHODS:We conducted a prospective study at Aga Khan University Hospital from December 2006 to December 2008. HBV genotype was determined in 257 HBV DNA-positive patients. Patients were divided into two groups according to HBeAg positivity. Mutations in the pre-core and core promoter regions of HBV were determined in HBeAg-negative patients by line probe INNOLIPA assay. RESULTS:The mean±SD age of patients was 28±5 years; there were 201 (78%) men. HBeAg was positive in 219 (85%) patients and negative in 38 (15%). HBeAg-positive patients were younger than HBeAg-negative patients (95% vs 21% in ?30 years, p<0.001). HBV genotype D found in 247 (96.2 %) patients followed by a combined infection with HBV genotype B+D in 9 (3.3%) and 1 (0.5%) with genotype A. The mutations identified in 38 HBeAg-negative patients were T1762/A1764 in 21 (55.2%), PC mutant in 7 (18.4%), T1762/A1764/PC mutant in 2 (5%) and T1762/A1764/PC wild mutation in 1 (2%); no mutation identified in 7 (18.4%). Phylogenetic analysis did not show any significant differences between HBV genotype D isolated from Pakistan and those isolated from other parts of the world. CONCLUSIONS:HBV genotype D is predominant in Pakistan, irrespective of HBeAg status. PC and BCP mutations were found in significant numbers of patients infected with genotype D. The HBV genotype D isolates from Pakistan are identical to the sequences isolated from other parts of the world.

SUBMITTER: Mumtaz K

PROVIDER: S-EPMC3206661 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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A study of genotypes, mutants and nucleotide sequence of hepatitis B virus in Pakistan: HBV genotypes in pakistan.

Mumtaz Khalid K Hamid Saeed S Ahmed Shahid S Moatter Tariq T Mushtaq Shamim S Khan Anis A Mizokami Masashi M Jafri Wasim W

Hepatitis monthly 20110101 1

<h4>Background</h4>Hepatitis B virus (HBV) genotypes and mutations are gaining importance in determining the clinical course of chronic liver disease.<h4>Objectives</h4>To determine and compare the distribution of HBV genotypes and genomic variations in Pakistan to other parts of the world.<h4>Patients and methods</h4>We conducted a prospective study at Aga Khan University Hospital from December 2006 to December 2008. HBV genotype was determined in 257 HBV DNA-positive patients. Patients were di ...[more]

PMID: 22087110

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Project description:BackgroundKnowledge of the HBV genotype with which a patient is infected is crucial information for a physician to have when planning clinical treatment for that patient. Previous studies have suggested that there are possible differences in the pathogenicity and therapeutic response of different HBV genotypes. However, the prevalence of the various HBV genotypes and Precore and Core mutations is unknown in the UAE. Therefore, we sought to determine the prevalence of the different HBV genotypes in the UAE population.Methodology/principal findingsA total of 88 HBsAg-positive patients were included in the study. A method for genotyping and subtyping HBV by partial HBsAg gene sequencing using primers that are complementary to all known genotypes was used. Precore and core region of these viruses were also sequenced in 88 patients.HBV genotype D was the most prevalent (79.5%) genotype identified in our study population, followed by genotypes A (18.2%) and C (2.3%). The following subtypes were isolated: ayw2 (80.7%), adw2 (14.8%), and adw (2.3%). The HBV-DNA viral load was higher in HBeAg-positive patients than it was in patients who were HBeAg-negative. Precore mutants were found in 51 (58.0%) of 88 patients. Mutations in the basal core promotor were found in 22 (25.3%) of 88 patients.Conclusion/significanceHBV infection is a major health problem in the UAE, and while genotypes B and C are the most prevalent HBV genotypes in the Asian population, our study reveals that genotype D is the predominant genotype that is present in the UAE. More patients were HBeAg-negative than were HBeAg-positive in our study sample, which could be due to the duration of infection of the included patients. Additionally, the viral loads of the HBeAg-positive patients were higher those of the HBeAg-negative patients. Analysis of nucleotide 1858 showed presence of thymine in all patients with genotypes C, and D and in a few patients with genotypes A. This nucleotide was closely related to the presence of precore mutants. Mutations in the basal core promoter were found in 22 of 88 (25.3%) samples. These mutations were more frequent in patients infected with genotype A (37.5%) and not found in patients infected with genotype C.

Project description:We previously sequenced the 5' noncoding region of 44 isolates of hepatitis C virus (HCV), as well as the envelope 1 (E1) gene of 51 HCV isolates, and provided evidence for the existence of at least 6 major genetic groups consisting of at least 12 minor genotypes of HCV (i.e., genotypes I/1a, II/1b, III/2a, IV/2b, 2c, V/3a, 4a-4d, 5a, and 6a). We now report the complete nucleotide sequence of the putative core (C) gene of 52 HCV isolates that represent all of these 12 genotypes as well as two additional genotypes provisionally designated 4e and 4f that we identified in this study. The phylogenetic analysis of the C gene sequences was in agreement with that of the E1 gene sequences. A major division in the genetic distance was observed between HCV isolates of genotype 2 and those of the other genotypes in analysis of both the E1 and C genes. The C gene sequences of 9 genotypes have not been reported previously (i.e., genotypes 2c, 4a-4f, 5a, and 6a). Our analysis indicates that the C gene-based methods currently used to determine the HCV genotype, such as PCR with genotype-specific primers, should be revised in light of these data. We found that the predicted C gene was exactly 573 nt long in all 52 HCV isolates, with an N-terminal start codon and no in-frame stop codons. The nucleotide and predicted amino acid identities of the C gene sequences were in the range of 79.4-99.0% and 85.3-100%, respectively. Furthermore, we mapped universally conserved, as well as genotype-specific, nucleotide and deduced amino acid sequences of the C gene. The predicted C proteins of the different HCV genotypes shared the following features: (i) high content of proline residues, (ii) high content of arginine and lysine residues located primarily in three domains with 10 such residues invariant at positions 39-62, (iii) a cluster of 5 conserved tryptophan residues, (iv) two nuclear localization signals and a DNA-binding motif, (v) a potential phosphorylation site with a serine-proline motif, and (vi) three conserved hydrophilic domains that have been shown by others to contain immunogenic epitopes. Thus, we have extended analysis of the predicted C protein of HCV to all of the recognized genotypes, confirmed the existence of highly conserved regions of this important structural protein, and demonstrated that the genetic relatedness of HCV isolates is equivalent when analyzing the most conserved (i.e., C) and the most variable (i.e., E1) genes of the HCV genome.

Project description:BACKGROUND: Knowledge of HBV genotype is very important for clinical treatment. Studies have suggested possible pathogenic and therapeutic differences among HBV genotypes. The aim of this study was to determine HBV subtypes and genotypes in HBV-infected patients in our region (southeast Brazil) and to correlate results with clinical and histopathological data. METHODS: One hundred and thirty-nine HBsAg-positive patients were included in the study. All patients were anti-HCV and anti-HIV negative (64% male; mean age 42 +/- 14.5 years; range 7-80 years; 84% Caucasian) and were followed up at the University Hospital. A method for genotyping and subtyping HBV by partial HBsAg gene sequencing with primers common to all known genotypes was used. The viral load was measured by Amplicor Monitor assay (Roche). RESULTS: HBV genotype A was the most prevalent (55%), while genotypes C, D and F were found in 3%, 38% and 4% of HBV-infected patients, respectively. Among the patients infected by genotype A, 18.3% (14/76) were African descendents and, among the patients infected by genotype D, 11.3% (6/53) were also African descendents. In the four patients infected with genotype C, 2 were Asian descendents and 2 were Caucasians. All (7) genotype F infected patients were Caucasians. Seventy percent of our HBsAg-positive patients were HBeAg negative (62% genotypes A; 26.2% D; 7.1% C and 4.7%F). The viral load of HBV-DNA was about 5 times higher in HBeAg-positive than in HBeAg-negative patients. About 40% of these patients had alanine aminotransferase of up to 1.5 times the normal level. The mean stage of fibrosis in genotype A patients (2.8) was significantly higher than the mean stage of fibrosis in genotype D patients (2.0) (P = 0.0179). CONCLUSION: The genotypes encountered in our HBV-infected patients were apparently a consequence of the types of immigration that occurred in our region, where European and African descendents predominate. The HBeAg-negative status predominated, possibly due to the length of time of infection. The viral load in HBeAg-positive patients was higher than in HBeAg-negative individuals. The fibrosis grade in genotype A-infected patients was more advanced than genotype D-infected patients.

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A study of genotypes, mutants and nucleotide sequence of hepatitis B virus in Pakistan: HBV genotypes in pakistan.

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A study of genotypes, mutants and nucleotide sequence of hepatitis B virus in Pakistan: HBV genotypes in pakistan.

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