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Gededzha MP, Sondlane TH, Malinga LA, Burnett RJ, Lebelo RL, Blackard JT, Mphahlele MJ, Selabe SG. Molecular characterization of hepatitis B virus X gene in HIV-positive South Africans. Virus Genes 2018; 54:190-198. [PMID: 29411271 DOI: 10.1007/s11262-018-1536-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 01/27/2018] [Indexed: 12/25/2022]
Abstract
Hepatitis B virus (HBV) infection is a major public health problem worldwide and the major cause of hepatocellular carcinoma (HCC) in South Africa. The role of HBV in HCC is not well understood, although the HBV X gene has been implicated as a critical factor. Data on the HBV X gene in HIV-positive South Africans are limited; thus, we investigated X gene variability in 24 HIV-infected treatment-naïve patients at Dr George Mukhari Academic Hospital. Quantitative and qualitative HBV DNA tests were conducted using real-time and in-house polymerase chain reaction (PCR) assays, respectively, targeting the complete HBV X gene. In-house PCR-positive samples were cloned using the P-Gem T-easy vector System II and sequenced. By phylogenetic analysis, X gene sequences were classified as subgenotype A1 (n = 15), A2 (n = 4), and D1 (n = 4), and one dual infection with subgenotypes as A1 and C. The basal core promoter mutations T1753C, A1762T, and G1764A were identified in the majority of sequences. Genotype D sequences had a 6-nucleotide insertion. In conclusion, subgenotype A1 was predominant, and a rare dual infection of HBV genotype A and C was detected. The 6-nucleotide insertion could represent a unique variant in the region and highlights the need for functional studies of HBV X gene variants, particularly from resource-limited settings.
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Affiliation(s)
- Maemu P Gededzha
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University and National Health Laboratory Service, P.O. Box 173, MEDUNSA, 0204, Pretoria, South Africa.,Department of Molecular Medicine and Haematology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Tsakani H Sondlane
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University and National Health Laboratory Service, P.O. Box 173, MEDUNSA, 0204, Pretoria, South Africa
| | - Lesibana A Malinga
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University and National Health Laboratory Service, P.O. Box 173, MEDUNSA, 0204, Pretoria, South Africa
| | - Rosemary J Burnett
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University and National Health Laboratory Service, P.O. Box 173, MEDUNSA, 0204, Pretoria, South Africa
| | - Ramokone L Lebelo
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University and National Health Laboratory Service, P.O. Box 173, MEDUNSA, 0204, Pretoria, South Africa
| | - Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - M Jeffrey Mphahlele
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University and National Health Laboratory Service, P.O. Box 173, MEDUNSA, 0204, Pretoria, South Africa.,South African Medical Research Council, Pretoria, South Africa
| | - Selokela G Selabe
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University and National Health Laboratory Service, P.O. Box 173, MEDUNSA, 0204, Pretoria, South Africa.
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Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing. Sci Rep 2017; 7:10168. [PMID: 28860476 PMCID: PMC5578979 DOI: 10.1038/s41598-017-10591-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 08/11/2017] [Indexed: 02/07/2023] Open
Abstract
Despite full immunoprophylaxis, mother-to-child transmission (MTCT) of Hepatitis B Virus still occurs in approximately 2–5% of HBsAg positive mothers. Little is known about the bottleneck of HBV transmission and the evolution of viral quasispecies in the context of MTCT. Here we adopted a newly developed tag linkage deep sequencing method and analyzed the quasispecies of four MTCT pairs that broke through immunoprophylaxis. By assigning unique tags to individual viral sequences, we accurately reconstructed HBV haplotypes in a region of 836 bp, which contains the major immune epitopes and drug resistance mutations. The detection limit of minor viral haplotypes reached 0.1% for individual patient sample. Dominance of “a determinant” polymorphisms were observed in two children, which pre-existed as minor quasispecies in maternal samples. In all four pairs of MTCT samples, we consistently observed a significant overlap of viral haplotypes shared between mother and child. We also demonstrate that the data can be potentially useful to estimate the bottleneck effect during HBV MTCT, which provides information to optimize treatment for reducing the frequency of MTCT.
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Lin YM, Chen BF. A putative hepatitis B virus splice variant associated with chronic hepatitis and liver cirrhosis. Virology 2017; 510:224-233. [PMID: 28750326 DOI: 10.1016/j.virol.2017.07.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) pre-S deletion was associated with chronic hepatitis (CH) and liver cirrhosis (LC); however, the type of pre-S deletion associated with these conditions and the mechanism of the generation of pre-S deletion remain unknown. Here, pre-S sequences from asymptomatic carriers (ASCs) and carriers with CH or LC were analyzed. The results indicated that deletion in the S promoter and the C-terminal half of the pre-S1 region was more frequent in CH and LC patients than in ASCs. RNA splicing analysis revealed that one type of pre-S1 deletion mutant, termed spPS1, was derived from splicing. This variant was associated with CH (12.7% vs. 1.8%, P = 0.06) and LC (14.5% vs. 1.8%, P = 0.032) when compared with ASC. In conclusion, spPS1, a putative splice variant; S promoter deletion mutant; and deletion in the C-terminal half of the pre-S1 region were closely associated with CH and LC development.
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Affiliation(s)
- Yu-Min Lin
- School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan; Division of Gastroenterology, Department of Internal Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Bing-Fang Chen
- School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan.
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Chen BF. Different pre-S deletion patterns and their association with hepatitis B virus genotypes. World J Gastroenterol 2017. [PMID: 27672298 DOI: 10.3748/wjg.v22.i35.8041.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/29/2022] Open
Abstract
AIM To investigate the associations of different types of pre-S deletions with hepatitis B virus (HBV) genotypes. METHODS The sequences of the pre-S region, basal core promoter (BCP) mutation, and precore (PC) mutation were examined through direct DNA sequencing or clonal analysis and sequencing in 273 HBV carriers, namely 55 asymptomatic carriers, 55 carriers with chronic hepatitis (CH), 55 with liver cirrhosis (LC), 53 with liver cirrhotic hepatocellular carcinoma (LC-HCC), and 55 with noncirrhotic HCC. A total of 126 HBV carriers (46.2%) harbored pre-S deletions. The DNA sequences of pre-S deletion mutants from 43 age-matched genotype B (HBV/B)-infected carriers and 43 age-matched genotype C (HBV/C)-infected carriers were further examined, aligned, and compared. RESULTS No significant difference was observed in the mean age distribution (P = 0.464), male sex (P = 0.805), viral load (P = 0.635), or BCP mutation (P = 0.117) between the HBV/B and HBV/C groups. However, the rate of PC mutation was significantly higher in the HBV/B-infected carriers than in the HBV/C-infected carriers (P = 0.003). Both genotypes exhibited a high rate of deletion in the C-terminal half of the pre-S1 region and N-terminus of the pre-S2 region (86.0% and 79.1% in the HBV/B group; 69.8% and 72.1% in the HBV/C group, respectively). Epitope mapping showed that deletion in several epitope sites was frequent in both genotypes, particularly pS1-BT and pS2-B2. Conversely, the rate of pS2-B1 deletion was significantly higher in the HBV/B group (72.1% vs 37.2%, P = 0.002), and the rate of pS2-T deletion was significantly higher in the HBV/C group (48.8% vs 25.6%, P = 0.044). Functional mapping showed that the rate of deletion in three functional sites (the nucleocapsid binding site, start codon of M, and site for viral secretion) located in the N-terminus of the pre-S2 region was significantly higher in the HBV/B group (P < 0.05). One type of N-terminus pre-S1 deletion mutant with deletion of the start codon of the L protein was frequently observed in the HBV/C group (20.9% vs 9.3%, P = 0.228), particularly in the LC patients (42.9% vs 12.5%). Different patterns of pre-S deletions were also found between the HBV/B and HBV/C groups according to different clinical outcomes. In CH patients, deletion in the site for polymerized human serum albumin was more frequent in the HBV/B group (88.9% vs 36.4%, P = 0.028). In the LC-HCC patients, the rate of deletion in the pre-S2 region was significantly higher in the HBV/B group than in the HBV/C group (P < 0.05). CONCLUSION HBV/B- and HBV/C-infected carriers exhibit different patterns of pre-S deletion, which may be associated with the progression of liver diseases.
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Affiliation(s)
- Bing-Fang Chen
- Bing-Fang Chen, School of Medicine, Fu Jen Catholic University, New Taipei City 24205, Taiwan
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Chen BF. Different pre-S deletion patterns and their association with hepatitis B virus genotypes. World J Gastroenterol 2016; 22:8041-8049. [PMID: 27672298 PMCID: PMC5028817 DOI: 10.3748/wjg.v22.i35.8041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/24/2016] [Accepted: 08/08/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the associations of different types of pre-S deletions with hepatitis B virus (HBV) genotypes.
METHODS The sequences of the pre-S region, basal core promoter (BCP) mutation, and precore (PC) mutation were examined through direct DNA sequencing or clonal analysis and sequencing in 273 HBV carriers, namely 55 asymptomatic carriers, 55 carriers with chronic hepatitis (CH), 55 with liver cirrhosis (LC), 53 with liver cirrhotic hepatocellular carcinoma (LC-HCC), and 55 with noncirrhotic HCC. A total of 126 HBV carriers (46.2%) harbored pre-S deletions. The DNA sequences of pre-S deletion mutants from 43 age-matched genotype B (HBV/B)-infected carriers and 43 age-matched genotype C (HBV/C)-infected carriers were further examined, aligned, and compared.
RESULTS No significant difference was observed in the mean age distribution (P = 0.464), male sex (P = 0.805), viral load (P = 0.635), or BCP mutation (P = 0.117) between the HBV/B and HBV/C groups. However, the rate of PC mutation was significantly higher in the HBV/B-infected carriers than in the HBV/C-infected carriers (P = 0.003). Both genotypes exhibited a high rate of deletion in the C-terminal half of the pre-S1 region and N-terminus of the pre-S2 region (86.0% and 79.1% in the HBV/B group; 69.8% and 72.1% in the HBV/C group, respectively). Epitope mapping showed that deletion in several epitope sites was frequent in both genotypes, particularly pS1-BT and pS2-B2. Conversely, the rate of pS2-B1 deletion was significantly higher in the HBV/B group (72.1% vs 37.2%, P = 0.002), and the rate of pS2-T deletion was significantly higher in the HBV/C group (48.8% vs 25.6%, P = 0.044). Functional mapping showed that the rate of deletion in three functional sites (the nucleocapsid binding site, start codon of M, and site for viral secretion) located in the N-terminus of the pre-S2 region was significantly higher in the HBV/B group (P < 0.05). One type of N-terminus pre-S1 deletion mutant with deletion of the start codon of the L protein was frequently observed in the HBV/C group (20.9% vs 9.3%, P = 0.228), particularly in the LC patients (42.9% vs 12.5%). Different patterns of pre-S deletions were also found between the HBV/B and HBV/C groups according to different clinical outcomes. In CH patients, deletion in the site for polymerized human serum albumin was more frequent in the HBV/B group (88.9% vs 36.4%, P = 0.028). In the LC-HCC patients, the rate of deletion in the pre-S2 region was significantly higher in the HBV/B group than in the HBV/C group (P < 0.05).
CONCLUSION HBV/B- and HBV/C-infected carriers exhibit different patterns of pre-S deletion, which may be associated with the progression of liver diseases.
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Zhang AY, Lai CL, Huang FY, Seto WK, Fung J, Wong DKH, Yuen MF. Evolutionary Changes of Hepatitis B Virus Pre-S Mutations Prior to Development of Hepatocellular Carcinoma. PLoS One 2015; 10:e0139478. [PMID: 26421619 PMCID: PMC4589234 DOI: 10.1371/journal.pone.0139478] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 09/14/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND AND AIMS Deletions/mutations in the hepatitis B virus (HBV) pre-S region have been associated with hepatocellular carcinoma (HCC). We aimed to study the evolutionary changes of pre-S mutations prior to HCC development. METHODS We studied the HBV pre-S sequences at 1 to 10 years preceding diagnosis of HCC in 74 patients with HBV-related HCC (HCC group). 148 chronic hepatitis B patients matched for sex and age in 2:1 ratio, who had been followed up for at least 3 years without HCC (HCC-free group) were recruited as controls. 56 and 47 patients of HCC and HCC-free groups respectively had serially stored sera for longitudinally examination at 1-3 years, 4-6 years, 7-9 years and ≥10 years prior to the recruitment of the study. RESULTS Compared to the HCC-free group, higher frequencies of pre-S deletions and point mutations (at 11 codons) were observed in the HCC group (p<0.05). Multiple logistic regression analysis showed that pre-S deletions, point mutations at codon 51 and 167 were independent factors associated with HCC. Longitudinal observation showed that pre-S deletions and most of the 11 HCC-associated pre-S point mutations existed at least 10 years before HCC development, and were more prevalent preceding HCC development in patients from HCC groups than HCC-free group. The number of HCC-associated pre-S point mutations increased over time preceding HCC development, and correlated positively with the time to HCC diagnosis (r = 0.220, p = 0.005). CONCLUSIONS High prevalence and cumulative evolution of pre-S mutations preceding HCC development suggested a possible carcinogenic role of pre-S mutations and their potential application in HCC risk prediction.
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Affiliation(s)
- An-Ye Zhang
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ching-Lung Lai
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR, China
| | - Fung-Yu Huang
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wai-Kay Seto
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR, China
| | - James Fung
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR, China
| | - Danny Ka-Ho Wong
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR, China
| | - Man-Fung Yuen
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR, China
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Evolutionary Changes of Hepatitis B Virus Pre-S Mutations Prior to Development of Hepatocellular Carcinoma. PLoS One 2015. [PMID: 26421619 DOI: 10.1371/journal.pone.0139478.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND AIMS Deletions/mutations in the hepatitis B virus (HBV) pre-S region have been associated with hepatocellular carcinoma (HCC). We aimed to study the evolutionary changes of pre-S mutations prior to HCC development. METHODS We studied the HBV pre-S sequences at 1 to 10 years preceding diagnosis of HCC in 74 patients with HBV-related HCC (HCC group). 148 chronic hepatitis B patients matched for sex and age in 2:1 ratio, who had been followed up for at least 3 years without HCC (HCC-free group) were recruited as controls. 56 and 47 patients of HCC and HCC-free groups respectively had serially stored sera for longitudinally examination at 1-3 years, 4-6 years, 7-9 years and ≥10 years prior to the recruitment of the study. RESULTS Compared to the HCC-free group, higher frequencies of pre-S deletions and point mutations (at 11 codons) were observed in the HCC group (p<0.05). Multiple logistic regression analysis showed that pre-S deletions, point mutations at codon 51 and 167 were independent factors associated with HCC. Longitudinal observation showed that pre-S deletions and most of the 11 HCC-associated pre-S point mutations existed at least 10 years before HCC development, and were more prevalent preceding HCC development in patients from HCC groups than HCC-free group. The number of HCC-associated pre-S point mutations increased over time preceding HCC development, and correlated positively with the time to HCC diagnosis (r = 0.220, p = 0.005). CONCLUSIONS High prevalence and cumulative evolution of pre-S mutations preceding HCC development suggested a possible carcinogenic role of pre-S mutations and their potential application in HCC risk prediction.
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Wang Y, Shan X, Liang Z, Shan Y, Huang W, Zhang D, Zen A, Zhou X, Zhao Y, Gong X, Xu G, Zhang X, Chen J, Huang A. Deep sequencing analysis of HBV genotype shift and correlation with antiviral efficiency during adefovir dipivoxil therapy. PLoS One 2015; 10:e0131337. [PMID: 26110616 PMCID: PMC4482366 DOI: 10.1371/journal.pone.0131337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 05/31/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Viral genotype shift in chronic hepatitis B (CHB) patients during antiviral therapy has been reported, but the underlying mechanism remains elusive. METHODS 38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method. RESULTS Sanger sequencing method found that 7.9% patients showed mixed genotype before ADV therapy. In contrast, all 38 patients showed mixed genotype before ADV treatment by deep sequencing. 95.5% mixed genotype rate was also obtained from additional 200 treatment-naïve CHB patients. Of the 13 patients with genotype shift, the fraction of the minor genotype in 5 patients (38%) increased gradually during the course of ADV treatment. Furthermore, responses to ADV and HBeAg seroconversion were associated with the high rate of genotype shift, suggesting drug and immune pressure may be key factors to induce genotype shift. Interestingly, patients with genotype C had a significantly higher rate of genotype shift than genotype B. In genotype shift group, ADV treatment induced a marked enhancement of genotype B ratio accompanied by a reduction of genotype C ratio, suggesting genotype C may be more sensitive to ADV than genotype B. Moreover, patients with dominant genotype C may have a better therapeutic effect. Finally, genotype shifts was correlated with clinical improvement in terms of ALT. CONCLUSIONS Our findings provided a rational explanation for genotype shift among ADV-treated CHB patients. The genotype and genotype shift might be associated with antiviral efficiency.
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Affiliation(s)
- Yuwei Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Xuefeng Shan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- Department of Pharmacy, the First Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Zhi Liang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Youlan Shan
- Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Wenxiang Huang
- Department of Infectious Diseases, the First Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Dazhi Zhang
- Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Aizhong Zen
- Department of Infectious Diseases, the First Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Xin Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yao Zhao
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuyang Gong
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ge Xu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xiuyu Zhang
- Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Juan Chen
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ailong Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
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Naturally occurring hepatitis B virus B-cell and T-cell epitope mutants in hepatitis B vaccinated children. ScientificWorldJournal 2013; 2013:571875. [PMID: 24379746 PMCID: PMC3860134 DOI: 10.1155/2013/571875] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 09/24/2013] [Indexed: 12/17/2022] Open
Abstract
To control hepatitis B virus (HBV) infection, a universal HBV vaccination program for infants was launched in Taiwan in 1984. The aim of this study was to investigate the role of B-cell and T-cell epitope variations of HBsAg and polymerase in HBV infection in vaccinated children. One hundred sixty-three sera from vaccinated children were enrolled randomly. HBV serum markers, including hepatitis B surface antigen (HBsAg) and antibodies to HBsAg (anti-HBs) and core antigen (anti-HBc), were detected by ELISA. Nucleotide sequences encoding the S and the pre-S regions of HBsAg were analyzed in all HBsAg positive sera. Five children were HBsAg positive. Sequence analysis of S, pre-S, and overlapped polymerase (P) genes showed that HBV isolates of HBsAg-positive vaccinees were variants; no G145R but G145A and other substitutions were found in the “a” determinant. Fifteen, six, and eight amino acid substitutions within B-cell and T-cell epitopes of S, pre-S, and P regions were detected, respectively. Several immune-epitope mutants, such as S45T/A, N131T, I194V, and S207N in S, were detected in all isolates. In conclusion, our results suggested that these naturally occurring immunoepitope mutants, which changed their immunogenicity leading to escape from immune response, might cause HBV infection.
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Coffin CS, Osiowy C, Myers RP, Gill MJ. Virology and clinical sequelae of long-term antiviral therapy in a North American cohort of hepatitis B virus (HBV)/human immunodeficiency virus type 1 (HIV-1) co-infected patients. J Clin Virol 2013; 57:103-8. [PMID: 23465393 DOI: 10.1016/j.jcv.2013.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/01/2013] [Accepted: 02/05/2013] [Indexed: 02/07/2023]
Abstract
UNLABELLED There are limited recent data worldwide on clinical and virological outcomes in hepatitis B virus (HBV) and human immunodeficiency virus (HIV) coinfected patients on dual active antiretroviral therapy (ART). METHODS We completed a retrospective review of 53 coinfected patients. HBV DNA in plasma was tested by PCR (sensitivity <20-<55 IU/ml or ∼100-300 copies/ml, Roche Diagnostics). Quantitative hepatitis B surface antigen (qHBsAg) was measured by an in-house assay (calibration range 0.24-62.5 IU/ml). HBV genotyping was done by line probe assay, and HBV variants determined by sequencing the HBV polymerase (P)/overlapping surface (S) gene. RESULTS There were 7% (4/53) non-liver related deaths, ∼11% (6/53) had >F2 fibrosis, including 3 with cirrhosis. The median CD4+ T cell count was 415 cells/mm(3) (range 60-1310). 54% (28/51) were HBeAg-positive, and 81% (43/53) on ART had undetectable HBV DNA but only 5% (3/51) lost HBeAg. In 11/53 with HBV sequencing, 90% (10/11) were found to have HBV genotype A (HBV-A) and/or 27% (3/11) had a mixed A/G infection. Anti-HBV drug resistant mutations were detected in 54% (6/11) (i.e., any combination of rtV173L, rtL180M, M204V) and 45% (5/11) had an immune escape mutation (sP120S). In 12 with qHBsAg testing, the majority (9/12) had low-level qHBsAg ∼1-3 log(10) IU/ml. SUMMARY Liver disease occurs in ∼10% of coinfected patients on ART and many have low-level HBV DNA and qHBsAg. In those sequenced most were HBV-A or mixed A/G genotype, and several carry P and S mutants highlighting the complex molecular virology of HBV during HIV coinfection.
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Affiliation(s)
- C S Coffin
- Liver Unit, Division of Gastroenterology and Hepatology, Department of Medicine, 3280 Hospital Drive NW, University of Calgary, Calgary, AB T2N 4Z6, Canada.
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Araujo NM, Araujo OC, Silva EM, Villela-Nogueira CA, Nabuco LC, Parana R, Bessone F, Gomes SA, Trepo C, Kay A. Identification of novel recombinants of hepatitis B virus genotypes F and G in human immunodeficiency virus-positive patients from Argentina and Brazil. J Gen Virol 2013; 94:150-158. [PMID: 23079380 DOI: 10.1099/vir.0.047324-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) genotype G (HBV/G) infection is almost always detected along with a co-infecting HBV strain that can supply HBeAg, typically HBV/A2. In this study we describe, in two human immunodeficiency virus (HIV)-positive patients from Argentina and Brazil, the first report of HBV/G infection in Argentina and co-circulation of HBV/G, HBV/F and G/F recombinants in the American continent. HBV isolates carrying the 36 bp insertion of HBV/G were the most prevalent in both patients, with >99 % of colonies hybridizing to a probe specific for this insertion. Phylogenetic analyses of full-length genomes and precore/core fragments revealed that F4 and F1b were the co-infecting subgenotypes in the Brazilian and Argentinian patients, respectively. Bootscanning analysis provided evidence of recombination in several clones from both patients, with recombination breakpoints located mainly at the precore/core region. These data should encourage further investigations on the clinical implications of HBV/G recombinants in HBV/HIV co-infected patients.
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Affiliation(s)
- Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Oscar C Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Edinete M Silva
- Centre de Recherche en Cancérologie de Lyon - INSERM U 1052/CNRS UMR 5286, 69424 Lyon Cedex 03, France
| | - Cristiane A Villela-Nogueira
- Hepatology Division, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-970, Brazil
| | - Letícia C Nabuco
- Hepatology Division, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-970, Brazil
| | - Raymundo Parana
- Department of Hepato-Gastroenterology, Prof. Edgard Santos University Hospital, Federal University of Bahia, Salvador 40110-060, Brazil
| | - Fernando Bessone
- Department of Gastroenterology and Hepatology, University of Rosario School of Medicine, Rosario 2000, Argentina
| | - Selma A Gomes
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Christian Trepo
- Centre de Recherche en Cancérologie de Lyon - INSERM U 1052/CNRS UMR 5286, 69424 Lyon Cedex 03, France
| | - Alan Kay
- Centre de Recherche en Cancérologie de Lyon - INSERM U 1052/CNRS UMR 5286, 69424 Lyon Cedex 03, France
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12
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Kao JH, Liu CJ, Jow GM, Chen PJ, Chen DS, Chen BF. Fine mapping of hepatitis B virus pre-S deletion and its association with hepatocellular carcinoma. Liver Int 2012; 32:1373-81. [PMID: 22676233 DOI: 10.1111/j.1478-3231.2012.02826.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/01/2012] [Indexed: 01/16/2023]
Abstract
BACKGROUND Naturally occurring pre-S deletion mutants have been identified in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). AIMS This study investigated whether specific deletions within the pre-S region were associated with HCC development. METHODS The virologic characteristics of 56 HBV chronic carriers and 112 age-matched patients with HBV-related HCC were examined. RESULTS The HCC patients had a significantly higher frequency of high viral load, basal core promoter mutation and pre-S deletion than chronic carriers. Sequencing analysis showed that the deleted regions were clustered mainly in the C terminus of pre-S1 (70.5%) and the N terminus of pre-S2 (72.7%) in HCC patients. Immuno-epitope mapping of these pre-S deletion sequences showed that all the deletion regions encompassed T- and B- cell epitopes and the B-cell epitope at amino acid 1-6 of pre-S2 was significantly deleted in HCC patients (60.0% vs. 0.0%; P = 0.036). Functional mapping of these deletion mutants showed that most of HCC patients lost one or more functional sites and the deletion of site for viral secretion (aa 1-5 of pre-S2 domain) was significantly detected in HCC patients than chronic carriers (62.5% vs. 0.0%; P = 0.029). Computational protein function prediction indicated that these mutants may have different molecular functions and participate in other biological processes compared with wild-type pre-S. CONCLUSIONS Deletion of B-cell epitope at amino acid 1-6 of pre-S2 region and the site for virion secretion are significantly associated with the development of HCC in HBV carriers.
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Affiliation(s)
- Jia-Horng Kao
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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13
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Functional analysis of hepatitis B virus pre-s deletion variants associated with hepatocellular carcinoma. J Biomed Sci 2012; 19:17. [PMID: 22313590 PMCID: PMC3323466 DOI: 10.1186/1423-0127-19-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 02/07/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Naturally occurring pre-S deletion mutants have been identified in hepatitis B carriers and shown to be associated with the development of hepatocellular carcinoma. The phenotypes of these pre-S deletion genomes remain unclear, and they were investigated in this study. METHODS The pre-S deletion genomes: (1) pre-S1 deletion, (2) deletion spanning pre-S1 and pre-S2, (3) pre-S2 N-terminal deletion, and (4) pre-S2 internal deletion were constructed and analyzed by transfection into Huh-7 cells. RESULTS Functional analyses reveal that these mutants were divided into two groups: S promoter deletion and non-S promoter deletion variants. Compared with the wild-type genome, S promoter deletion variants led to an inverse ratio of pre-S1 mRNA and pre-S2/S mRNA, and intracellular accumulation of surface proteins. An interesting finding is that a small amount of L proteins was detected in the medium from S promoter deletion variant-transfected cells. Non-S promoter deletion variants conversely displayed a wild-type like mRNA and protein pattern. The secretion of surface proteins from non-S promoter deletion variants was inhibited less than from S promoter deletion variant. Immunofluorescence analysis showed mutant surface proteins colocalized with ER and exhibited an atypical distribution: granular staining pattern in the S-promoter deletion variants and perinuclear staining pattern in the non-S promoter deletion variants. CONCLUSION This study shows that these pre-S deletion genomes exhibit two different phenotypes in mRNA transcription, surface protein expression and secretion. This diversity seems to result from the deletion of S promoter rather than result from the deletion of pre-S1 or pre-S2.
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Pondé RAA. The underlying mechanisms for the "simultaneous HBsAg and anti-HBs serological profile". Eur J Clin Microbiol Infect Dis 2011; 30:1325-40. [PMID: 21484253 DOI: 10.1007/s10096-011-1240-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 03/21/2011] [Indexed: 02/07/2023]
Abstract
The course of HBV infection is determined by the interplay between viral replication via HBV protein production and the host's immune response. Therefore, the diagnosis of infection in clinical practice is established by the serological detection of HBV protein products as well as antibodies produced by the host. Although the serological findings for assessing the clinical course of infection are already well established, the expression of viral proteins and the dynamics of antibody production may vary during the natural course of infection. This causes the HBV infection to be occasionally associated with the presence of unusual serologic profiles, which can lead to doubts in the interpretation of results and mistaken serological diagnosis. The simultaneous detection of HBsAg and anti-HBs in the blood stream comprises an atypical serological profile, somewhat incoherent, whose significance can be complicated to establish. Outlined in this article are some immunological and molecular mechanisms which could justify the existence of this profile in which there is a great laboratorial and clinical interest.
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Affiliation(s)
- R A A Pondé
- Laboratório de Virologia Humana, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia-Goiás, Brasil,
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15
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Mu SC, Wang GM, Jow GM, Chen BF. Impact of universal vaccination on intrafamilial transmission of hepatitis B virus. J Med Virol 2011; 83:783-90. [DOI: 10.1002/jmv.22055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2010] [Indexed: 12/12/2022]
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Chen XL, Sun DX, Zhang XL. Hepatitis B virus genotypes. Shijie Huaren Xiaohua Zazhi 2011; 19:389-393. [DOI: 10.11569/wcjd.v19.i4.389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) is a member of the hepadnavirus family and can lead to severe liver disease. HBV has a very high genetic variability. Currently, eight genotypes of HBV have been recognized, and most genotypes are now divided into subgenotypes with distinct virological and epidemiological properties. In addition, recombination among HBV genotypes increases the variability of HBV. This review summarizes current knowledge of the epidemiology of genetic variability in hepadnaviruses and, due to rapid progress in the field, updates several recent reviews on HBV genotypes and subgenotypes.
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Liu W, Zhai J, Liu J, Xie Y. Identification of natural recombination in duck hepatitis B virus. Virus Res 2010; 149:245-51. [PMID: 20144903 DOI: 10.1016/j.virusres.2010.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 02/01/2010] [Accepted: 02/01/2010] [Indexed: 12/29/2022]
Abstract
Due to its high similarity to human hepatitis B virus (HBV), duck HBV (DHBV) is often used as an important model for HBV research. While inter-genotypic recombination of HBV is common, it has not been reported with DHBV. In this study, 32 non-redundant DHBV complete genomes were analyzed using phylogenetic methods and classified into two clusters, corresponding to the 'Chinese' and 'Western country' branches previously reported based on geographical distribution. One 'Chinese' branch strain was isolated in Australia and three 'Western country' branch strains were isolated in China, suggesting cross-geographical distribution of both branches. Recombination analyses of the 32 DHBV genomes identified two possible inter-genotypic recombination events with high confidence value. These recombination events occurred between the lineages represented, respectively, by the Chinese isolate GD3 (AY536371, 'Chinese' branch) and the American isolate DHBV16 (K01834, 'Western country' branch), giving rise to two Chinese recombinant isolates CH4 (EU429324) and CH6 (EU429326). The identification of inter-genotypic recombination among circulating DHBV isolates suggests the usefulness of DHBV as a model for studying the mechanism of HBV recombination.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Medical Molecular Virology, Institute of Medical Microbiology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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18
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Huang HP, Hsu HY, Chen CL, Ni YH, Wang HY, Tsuei DJ, Chiang CL, Tsai YC, Chen HL, Chang MH. Pre-S2 deletions of hepatitis B virus and hepatocellular carcinoma in children. Pediatr Res 2010; 67:90-4. [PMID: 19816238 DOI: 10.1203/pdr.0b013e3181c1b0b7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The cause of early oncogenesis in hepatitis B virus (HBV)-related childhood hepatocellular carcinoma (HCC) remains unclear. This study investigated whether pre-S deletion of HBV is related to childhood HCC. By using nested polymerase chain reaction, we compared the pre-S sequence of HBV from sera of children with HCC against control children with similar chronic HBV infection. The HBV in sera of children with HCC had a significantly higher rate of pre-S deletion than that of children with chronic HBV infection (p = 0.008). All except one of the pre-S deletions from the HCC group involved the pre-S2 region, whereas no pre-S2 deletion was found in the chronic HBV group (p = 0.003). There was a trend whereby genotype-C sera had a higher rate of pre-S2 deletion than genotype-B sera (p = 0.11). A multivariate logistic regression model revealed that pre-S deletion was an independent risk factor for HCC in children (odds ratio: 36.69, p = 0.015). In conclusion, pre-S2 deletion does not need to take decades to occur; its presence in nearly half of children with HCC, in contrast to its absence in children with chronic HBV infection, suggests a link between pre-S2 deletion and HCC development in children.
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Affiliation(s)
- Hsiang-Po Huang
- Department of Medical Research, National Taiwan University Hospital, Taipei 100, Taiwan
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19
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Utama A, Octavia TI, Dhenni R, Miskad UA, Yusuf I, Tai S. Hepatitis B virus genotypes/subgenotypes in voluntary blood donors in Makassar, South Sulawesi, Indonesia. Virol J 2009; 6:128. [PMID: 19691824 PMCID: PMC2732614 DOI: 10.1186/1743-422x-6-128] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 08/19/2009] [Indexed: 12/14/2022] Open
Abstract
Background Hepatitis B virus (HBV) genotype appears to show varying geographic distribution. Molecular epidemiological study of HBV in particular areas in Indonesia is still limited. This study was aimed to identify the prevalence of HBV genotype/subgenotype and mutations in basal core promoter (BCP) region in voluntary blood donors in Makassar, one of the biggest cities in east part of Indonesia. A total of 214 hepatitis B surface antigen (HBsAg)-positive samples were enrolled in this study. HBV genotype/subgenotype was identified by genotype-specific PCR method or direct sequencing of pre-S region. Mutations in BCP were identified by direct sequencing of the corresponding region. Results HBV/B and HBV/C were detected in 61.21% and 25.23% of the samples, while mix of HBV/B and HBV/C was found in 12.62% of the samples. Based on pre-S region, among HBV/B and HBV/C, HBV/B3 (95.00%) and HBV/C1 (58.82%) were predominant. Interestingly, HBV/D was identified in two samples (22.165.07 and 22.252.07). Complete genome sequences of two HBV/D strains (22.165.07 and 22.252.07) demonstrated that both strains belong to HBV/D6, and the divergence between the two strains were 1.45%, while divergences of both 22.165.07 and 22.252.07 strains with reference strain (AM422939/France) were 2.67%. A1762T/G1764A mutation was observed in 1.96% and 5.36%, whereas T1753V mutation was found in 2.94% and 1.79% of HBV/B and HBV/C, respectively. Conclusion HBV/B and HBV/C are dominant in Makassar, similar to most areas in Indonesia. Mutations in BCP which might be associated with severity of liver disease are less common.
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Affiliation(s)
- Andi Utama
- Molecular Epidemiology Division, Mochtar Riady Institute for Nanotechnology, Lippo Karawaci, Tangerang, Banten 15810, Indonesia.
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Mu SC, Lin YM, Jow GM, Chen BF. Occult hepatitis B virus infection in hepatitis B vaccinated children in Taiwan. J Hepatol 2009; 50:264-72. [PMID: 19070923 DOI: 10.1016/j.jhep.2008.09.017] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 08/31/2008] [Accepted: 09/15/2008] [Indexed: 12/18/2022]
Abstract
BACKGROUND/AIMS Presence of occult HBV infection in HBV vaccinated children remains largely unknown. The aim of this study was to investigate the prevalence of occult HBV infection among HBV vaccinated children in Taiwan. METHODS Forty-six HBsAg negative sera from vaccinated children were enrolled randomly. HBV serum markers were detected by ELISA, and the titers of HBV DNA were determined by quantitative real-time PCR. Pre-S, S and pre-core/core genes were amplified by nested PCR and analyzed. RESULTS Anti-HBs was detected in 23 (50%) children, and the positivity decreased according to age. Five (10.9%) children were classified into occult HBV infection by positivity of nested PCR in at least two regions; they had a low titer (mean titer 1.60x10(4)copies/ml). Sequence analyses of S gene showed occult isolates were variants; no G145R but C139S vaccine escape mutant was found. Variation and deletion were found in pre-S region; pre-S deletion was more frequent in 3' terminus of pre-S1 which leads to loss of immune epitopes and function sites. CONCLUSIONS This pilot study indicates that the prevalence of occult HBV infection is 10.9% in HBV vaccinated children. Since this is a small study, a study of a large population is needed to confirm the findings herein.
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Affiliation(s)
- Shu-Chi Mu
- Department of Pediatrics, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
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Huang CF, Shi BB, Zhu Q, Wu L, Pei XH, Pu QH, Zhou Y. Relationship between therapeutic efficacy of interferon in treating chronic hepatitis B and HBV genotypes. Shijie Huaren Xiaohua Zazhi 2009; 17:329-332. [DOI: 10.11569/wcjd.v17.i3.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To study the effects of HBV genotypes on anti-virus-therapeutic efficacy of interferon in chronic HBV-infected patients.
METHODS: Thirty HBV-infected patients were treated with interferon for anti-virus. HBV genotypes were detected using PCR-RFLP and the response levels of interferon in different genotypes were observed.
RESULTS: For the 30 patients, the HBV genotypes were mainly type B (40.0%) and type C (56.67%). Level of HBV DNA was significantly higher in patients with type C than with type B (6.03 ± 1.35 vs 5.45 ± 1.21, P < 0.05), and the interferon response rate was higher in patients with type B than with type C. Among those with no response, 1 case with type B and another case with type C changed into type D.
CONCLUSION: It is suggested that HBV genotypes is correlated with the serum levels of HBV DNA and therapeutic efficacy of interferon. The genotype could be changed during the process of therapy.
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Abstract
Hepatitis B virus (HBV) infection is a global health issue. Effective and individualized treatment of chronic hepatitis B to prevent progression to end-stage liver diseases and hepatocellular carcinoma is needed. HBV can be classified into eight genotypes (A-H) on the basis of genome sequence divergence. In addition, several naturally occurring HBV mutants have also been identified. The epidemiology of HBV genotypes and their implications for response to antiviral therapy have become increasingly recognized. Recent studies suggested that responses to standard interferon treatment in patients with genotype A or B are better than those with genotype C or D; however, conflicting results exist regarding the response to pegylated interferon. The influence of dose and duration on interferon-based therapy remains to be clarified. In addition to genotype, naturally occurring mutations such as precore and core promoter mutations have also attracted much attention, because they have been shown to affect the disease progression of HBV-related chronic liver disease and possibly the response to antiviral therapy. Here, we review the differences in antiviral theraputic response among HBV genotypes and discuss the role of precore or core promoter mutations in response to antiviral therapy.
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Affiliation(s)
- Chun-Jen Liu
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, Taiwan
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23
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Baig S, Siddiqui AA, Ahmed W, Qureshi H, Arif A. The association of complex liver disorders with HBV genotypes prevalent in Pakistan. Virol J 2007; 4:128. [PMID: 18042293 PMCID: PMC2212638 DOI: 10.1186/1743-422x-4-128] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 11/27/2007] [Indexed: 02/06/2023] Open
Abstract
Background Genotyping of HBV is generally used for determining the epidemiological relationship between various virus strains and origin of infection mostly in research studies. The utility of genotyping for clinical applications is only beginning to gain importance. Whether HBV genotyping will constitute part of the clinical evaluation of Hepatitis B patients depends largely on the availability of the relevance of the evidence based information. Since Pakistan has a HBV genotype distribution which has been considered less virulent as investigated by earlier studies from south East Asian countries, a study on correlation between HBV genotypes and risk of progression to further complex hepatic infection was much needed Methods A total of 295 patients with HBsAg positive were selected from the Pakistan Medical Research Council's (PMRC) out patient clinics. Two hundred and twenty six (77%) were males, sixty nine (23%) were females (M to F ratio 3.3:1). Results Out of 295 patients, 156 (53.2%) had Acute(CAH), 71 (24.2%) were HBV Carriers, 54 (18.4%) had Chronic liver disease (CLD) Hepatitis. 14 (4.7%) were Cirrhosis and HCC patients. Genotype D was the most prevalent genotype in all categories of HBV patients, Acute (108), Chronic (39), and Carrier (53). Cirrhosis/HCC (7) were HBV/D positive. Genotype A was the second most prevalent with 28 (13%) in acute cases, 12 (22.2%) in chronics, 14 (19.7%) in carriers and 5 (41.7) in Cirrhosis/HCC patients. Mixed genotype (A/D) was found in 20 (12.8%) of Acute patients, 3 (5.6%) of Chronic and 4 (5.6%) of carriers, none in case of severe liver conditions. Conclusion Mixed HBV genotypes A, D and A/D combination were present in all categories of patients except that no A/D combination was detected in severe conditions. Genotype D was the dominant genotype. However, genotype A was found to be more strongly associated with severe liver disease. Mixed genotype (A/D) did not significantly appear to influence the clinical outcome.
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Affiliation(s)
- Saeeda Baig
- Department of Biochemistry, Ziauddin Medical College, Ziauddin University, Karachi, Pakistan.
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Zhang Q, Wu G, Richards E, Jia S, Zeng C. Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers. Virol J 2007; 4:92. [PMID: 17892576 PMCID: PMC2099425 DOI: 10.1186/1743-422x-4-92] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 09/24/2007] [Indexed: 01/05/2023] Open
Abstract
Background The highly heterogenic characteristic of viruses is the major obstacle to efficient DNA amplification. Taking advantage of the large number of virus DNA sequences in public databases to select conserved sites for primer design is an optimal way to tackle the difficulties in virus genome amplification. Results Here we use hepatitis B virus as an example to introduce a simple and efficient way for virus primer design. Based on the alignment of HBV sequences in public databases and a program BxB in Perl script, our method selected several optimal sites for HBV primer design. Polymerase chain reaction showed that compared with the success rate of the most popular primers for whole genome amplification of HBV, one set of primers for full length genome amplification and four sets of walking primers showed significant improvement. These newly designed primers are suitable for most subtypes of HBV. Conclusion Researchers can extend the method described here to design universal or subtype specific primers for various types of viruses. The BxB program based on multiple sequence alignment not only can be used as a separate tool but also can be integrated in any open source primer design software to select conserved regions for primer design.
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Affiliation(s)
- Qingrun Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China.
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Liu CJ, Chen PJ, Lai MY, Lin FY, Wang T, Kao JH, Chen DS. Viral factors correlate with hepatitis B e antigen seroconverson in patients with chronic hepatitis B. Liver Int 2006; 26:949-55. [PMID: 16953835 DOI: 10.1111/j.1478-3231.2006.01319.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND/AIMS Seroconversion (SC) from hepatitis B envelope antigen (HBeAg) to anti-HBe usually indicates lower viral loads, resolved hepatitis activity and improved long-term outcomes. However, the role of viral factors in the development of SC remains largely unknown. We thus comprehensively studied these factors in 25 patients with sustained HBeAg SC and seven control patients with sustained loss of HBeAg. METHODS We determined viral factors in serum samples obtained 1 year before, 6 months before, 3 months before, at the time of, 6 months after and 1 year after HBeAg SC or HBeAg loss. Precore A1896 and basal core promoter T1762/A1764 mutants were determined by polymerase chain reaction (PCR)-based assays. Serum HBV levels were determined by a real-time PCR assay. RESULTS We found that decline of serum viral load, frequently accompanied by hepatitis exacerbation, occurred within 1 year before HBeAg SC. The proportions of precore and BCP mutations also increased gradually throughout the process of HBeAg SC. The virologic features were similar between HBeAg SC group and HBeAg loss group. Before HBeAg SC or loss, genotype B patients had higher serum viral loads and lower proportions of BCP mutation compared with genotype C patients. CONCLUSION Our findings suggested that viral factors correlate with the development of sustained HBeAg SC or loss.
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Affiliation(s)
- Chun-Jen Liu
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, Taiwan
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Laperche S, Thibault V, Bouchardeau F, Alain S, Castelain S, Gassin M, Gueudin M, Halfon P, Larrat S, Lunel F, Martinot-Peignoux M, Mercier B, Pawlotsky JM, Pozzetto B, Roque-Afonso AM, Roudot-Thoraval F, Sauné K, Lefrère JJ. Expertise of laboratories in viral load quantification, genotyping, and precore mutant determination for hepatitis B virus in a multicenter study. J Clin Microbiol 2006; 44:3600-3607. [PMID: 17021089 PMCID: PMC1594785 DOI: 10.1128/jcm.00732-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 05/16/2006] [Accepted: 06/22/2006] [Indexed: 02/06/2023] Open
Abstract
A national evaluation study was performed in 14 specialized laboratories with the objective of assessing their capacities to provide (i) hepatitis B virus (HBV) viral loads (VL), (ii) HBV genotypes, and(iii) identification of precore/core mutants. The panel consisted of 12 HBV DNA-positive samples with VLs from 2.8 to 9.1 log(10) copies/ml, different HBV genotypes (A to F), and 3 mutant and 9 wild-type samples at nucleotide 1896. The coefficients of variation of the mean VLs ranged from 2.4% to 10.4% with the Cobas HBV Monitor assay, from 1.8% to 5.5% with the Cobas TaqMan 48, from 1.5 to 26.2% with RealArt HBV PCR, and from 0 to 7% with branched DNA (bDNA). The Cobas Monitor assay underestimated the VLs of genotype F samples, with differences ranging from 1.4 to 2.4 log(10) copies/ml. The accuracies of genotype determinations ranged from 33% to 100%, and those of precore mutant determinations ranged from 25 to 100%. This study showed some drawbacks of two widely used assays: (i) Cobas Monitor has a narrow dynamic range and underestimates genotype F sample VLs and (ii) bDNA shows poor sensitivity and may fail to identify patients with low VLs. With higher performance in terms of analytical sensitivity combined with a larger dynamic range and an ability to quantify the main genotypes equally, real-time PCR methods appear more appropriate for accurate monitoring of HBV DNA quantification. Furthermore, the clinical implications of HBV genotyping and the determination of precore/core mutants need to be clearly stated to justify the standardization of these methods.
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Affiliation(s)
- Syria Laperche
- Centre National de Référence pour les Hépatites B et C en Transfusion, Département des Agents Transmissibles par le Sang, Institut National de la Transfusion Sanguine, Paris, France.
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Yang J, Xing K, Deng R, Wang J, Wang X. Identification of Hepatitis B virus putative intergenotype recombinants by using fragment typing. J Gen Virol 2006; 87:2203-2215. [PMID: 16847116 DOI: 10.1099/vir.0.81752-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Eight hundred and thirty-seven human Hepatitis B virus (HBV) genomes were categorized into pure genotypes and potential intergenotypes, according to their fragment types which were determined based on similarity and phylogenetic analyses of 13 contrived fragments of 250 bp against the corresponding fragments of the consensus sequences of genotypes A-H. Twenty-five intergenotypes, including 171 genomes, were revealed from the potential intergenotype recombinants by phylogenetic analysis of the precisely derived mosaic fragments. Among these, four new intergenotypes were discovered. Many genomes were revealed as putative intergenotype recombinants for the first time. About 87 % of the putative recombinants were B/C (120) and A/D (29) hybrids. The other recombinants comprised A/B/C, A/C, A/E, A/G, C/D, C/F, C/G, C/U (U for unknown genotype) and B/C/U hybrids. Genotypes A and C showed a higher recombination tendency than did other genotypes. The results also demonstrated region priority and breakpoint hot spots in the intergenotype recombination. Recombination breakpoints were found to be concentrated mainly in the vicinity of the DR1 region (nt 1640-1900), the pre S1/S2 region (nt 3150-100), the 3'-end of the C gene (nt 2330-2450) and the 3'-end of the S gene (nt 650-830). These results support the suggestion that intergenotype recombinants may result from co-infection with different genotypes.
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Affiliation(s)
- Jie Yang
- Department of Infectious Diseases, Nanfang Hospital, Guangzhou 510515, People's Republic of China
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
| | - Ke Xing
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
| | - Riqiang Deng
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
| | - Jinwen Wang
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
| | - Xunzhang Wang
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
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