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Jia JA, Zhang S, Bai X, Fang M, Chen S, Liang X, Zhu S, Wong DKH, Zhang A, Feng J, Sun F, Gao C. Sparse logistic regression revealed the associations between HBV PreS quasispecies and hepatocellular carcinoma. Virol J 2022; 19:114. [PMID: 35765099 PMCID: PMC9238101 DOI: 10.1186/s12985-022-01836-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chronic infection with hepatitis B virus (HBV) has been proved highly associated with the development of hepatocellular carcinoma (HCC). AIMS The purpose of the study is to investigate the association between HBV preS region quasispecies and HCC development, as well as to develop HCC diagnosis model using HBV preS region quasispecies. METHODS A total of 104 chronic hepatitis B (CHB) patients and 117 HBV-related HCC patients were enrolled. HBV preS region was sequenced using next generation sequencing (NGS) and the nucleotide entropy was calculated for quasispecies evaluation. Sparse logistic regression (SLR) was used to predict HCC development and prediction performances were evaluated using receiver operating characteristic curves. RESULTS Entropy of HBV preS1, preS2 regions and several nucleotide points showed significant divergence between CHB and HCC patients. Using SLR, the classification of HCC/CHB groups achieved a mean area under the receiver operating characteristic curve (AUC) of 0.883 in the training data and 0.795 in the test data. The prediction model was also validated by a completely independent dataset from Hong Kong. The 10 selected nucleotide positions showed significantly different entropy between CHB and HCC patients. The HBV quasispecies also classified three clinical parameters, including HBeAg, HBVDNA, and Alkaline phosphatase (ALP) with the AUC value greater than 0.6 in the test data. CONCLUSIONS Using NGS and SLR, the association between HBV preS region nucleotide entropy and HCC development was validated in our study and this could promote the understanding of HCC progression mechanism.
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Affiliation(s)
- Jian-an Jia
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438 China
- Department of Laboratory Medicine, The 901th Hospital of Joint Logistics Support Force of Chinese People’s Liberation Army, Hefei, 230031 China
| | - Shuqin Zhang
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, 200433 China
| | - Xin Bai
- Molecular and Computational Program, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, 90089 USA
| | - Meng Fang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438 China
| | - Shipeng Chen
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438 China
| | - Xiaotao Liang
- Department of Computer Science, Fudan University, Shanghai, 200433 China
| | - Shanfeng Zhu
- Department of Computer Science, Fudan University, Shanghai, 200433 China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China
| | - Danny Ka-Ho Wong
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR, China
| | - Anye Zhang
- Department of Medicine, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033 China
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL UK
| | - Fengzhu Sun
- Molecular and Computational Program, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, 90089 USA
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438 China
- Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437 China
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2
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Yin J, Chen X, Li N, Han X, Liu W, Pu R, Wu T, Ding Y, Zhang H, Zhao J, Han X, Wang H, Cheng S, Cao G. Compartmentalized evolution of hepatitis B virus contributes differently to the prognosis of hepatocellular carcinoma. Carcinogenesis 2021; 42:461-470. [PMID: 33247709 DOI: 10.1093/carcin/bgaa127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/26/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Serum hepatitis B virus (HBV) mutations can predict hepatocellular carcinoma (HCC) occurrence. We aimed to clarify if HBV evolves synchronously in the sera, adjacent liver and tumors and predict HCC prognosis equally. A total of 203 HBV-positive HCC patients with radical hepatectomy in Shanghai, China, during 2011-15 were enrolled in this prospective study. Quasispecies complexity (QC) in HBV core promoter region was assessed using clone-based sequencing. We performed RNA sequencing on tumors and paired adjacent tissues of another 15 HCC patients and analyzed it with three public data sets containing 127 samples. HBV QC was positively correlated to APOBEC3s' expression level (r = 0.28, P < 0.001), higher in the adjacent tissues than in the tumors (P = 6.50e-3), and higher in early tumors than in advanced tumors (P = 0.039). The evolutionary distance between the sera-derived HBV strains and the tumor-derived ones was significantly longer than that between the sera-derived ones and the adjacent tissue-derived ones (P < 0.001). Multivariate Cox regression analyses indicated that high HBV QC in the sera predicted an unfavorable overall survival (P = 0.002) and recurrence-free survival (RFS; P = 0.004) in HCC, whereas, in the tumors, it predicted a favorable RFS (P < 0.001). APOBECs-related HBV mutations, including G1764A, were more frequent in the sera than in the adjacent tissues. High-frequent A1762T/G1764A in the sera predicted an unfavorable RFS (P < 0.001), whereas, in the tumors, it predicted a favorable RFS (P = 0.035). In conclusion, HBV evolves more advanced in the sera than in the tumors. HBV QC and A1762T/G1764A in the sera and tumors have contrary prognostic effects in HCC.
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Affiliation(s)
- Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Xi Chen
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Nan Li
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Xuewen Han
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Wenbin Liu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Rui Pu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Ting Wu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Yibo Ding
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Hongwei Zhang
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Jun Zhao
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Xue Han
- Division of Chronic Diseases, Center for Disease Control and Prevention of Yangpu District, Shanghai, China
| | - Hongyang Wang
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, China
| | - Shuqun Cheng
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China.,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China.,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, China
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3
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Liu C, Lin J, Xun Z, Huang J, Huang E, Chen T, He Y, Lin N, Yang B, Ou Q. Establishment of Coamplification at Lower Denaturation Temperature PCR/Fluorescence Melting Curve Analysis for Quantitative Detection of Hepatitis B Virus DNA, Genotype, and Reverse Transcriptase Mutation and Its Application in Diagnosis of Chronic Hepatitis B. J Mol Diagn 2019; 21:1106-1116. [PMID: 31607557 DOI: 10.1016/j.jmoldx.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022] Open
Abstract
Dynamic and real-time hepatitis B virus (HBV) DNA, genotype, and reverse transcriptase mutation analysis plays an important role in diagnosing and monitoring chronic hepatitis B (CHB) and in assessing the therapeutic response. We established a highly sensitive coamplification at lower denaturation temperature PCR (COLD-PCR) coupled with probe-based fluorescence melting curve analysis (FMCA) for precision diagnosis of CHB patients. The imprecision with %CV and detection limit of HBV DNA detected by COLD-PCR/FMCA were 2.58% to 4.42% and 500 IU/mL, respectively. For mutation, the imprecision and detection limit were 3.35% to 6.49% and 1%, respectively. Compared with Sanger sequencing, the coincidence rates of genotype and mutation were 96.0% and 82.5%, respectively, whereas the inconsistent data resulted from a low proportion (<20%) of mixed genotypes or mixed mutations. The mutation ratio in HBV infection patients was as follows: hepatitis B e antigen (HBeAg)-positive infection (0/0.0%) < HBeAg-negative infection (16/4.5%) < HBeAg-positive hepatitis (30/5.5%) < HBeAg-negative hepatitis (36/6.5%). In patients with entecavir therapy, the proportion of mutation at baseline or week 4 in virologic response (VR) group was <4%, whereas in the partial VR group, it was mostly ≥4%. COLD-PCR/FMCA provides a novel tool with high sensitivity, convenience, and practicability for the simultaneous quantification of HBV DNA, genotype, and mutation. It might be used for distinguishing the different phases of HBV infection and predicting VR of CHB patients.
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Affiliation(s)
- Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Jinpiao Lin
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Zhen Xun
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Jinlan Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Er Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Yujue He
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Ni Lin
- School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, People's Republic of China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China.
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4
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Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC. PLoS Genet 2018; 14:e1007206. [PMID: 29474353 PMCID: PMC5841821 DOI: 10.1371/journal.pgen.1007206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 03/07/2018] [Accepted: 01/17/2018] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a common problem in the world, especially in China. More than 60–80% of hepatocellular carcinoma (HCC) cases can be attributed to HBV infection in high HBV prevalent regions. Although traditional Sanger sequencing has been extensively used to investigate HBV sequences, NGS is becoming more commonly used. Further, it is unknown whether word pattern frequencies of HBV reads by Next Generation Sequencing (NGS) can be used to investigate HBV genotypes and predict HCC status. In this study, we used NGS to sequence the pre-S region of the HBV sequence of 94 HCC patients and 45 chronic HBV (CHB) infected individuals. Word pattern frequencies among the sequence data of all individuals were calculated and compared using the Manhattan distance. The individuals were grouped using principal coordinate analysis (PCoA) and hierarchical clustering. Word pattern frequencies were also used to build prediction models for HCC status using both K-nearest neighbors (KNN) and support vector machine (SVM). We showed the extremely high power of analyzing HBV sequences using word patterns. Our key findings include that the first principal coordinate of the PCoA analysis was highly associated with the fraction of genotype B (or C) sequences and the second principal coordinate was significantly associated with the probability of having HCC. Hierarchical clustering first groups the individuals according to their major genotypes followed by their HCC status. Using cross-validation, high area under the receiver operational characteristic curve (AUC) of around 0.88 for KNN and 0.92 for SVM were obtained. In the independent data set of 46 HCC patients and 31 CHB individuals, a good AUC score of 0.77 was obtained using SVM. It was further shown that 3000 reads for each individual can yield stable prediction results for SVM. Thus, another key finding is that word patterns can be used to predict HCC status with high accuracy. Therefore, our study shows clearly that word pattern frequencies of HBV sequences contain much information about the composition of different HBV genotypes and the HCC status of an individual. HBV infection can lead to many liver complications including hepatocellular carcinoma (HCC), one of the most common liver cancers in China. High-throughput sequencing technologies have recently been used to study the genotype sequence compositions of HBV infected individuals and to distinguish chronic HBV (CHB) infection from HCC. We used NGS to sequence the pre-S region of a large number of CHB and HCC individuals and designed novel word pattern based approaches to analyze the data. We have several surprising key findings. First, most HBV infected individuals contained mixtures of genotypes B and C sequences. Second, multi-dimensional scaling (MDS) analysis of the data showed that the first principal coordinate was closely associated with the fraction of genotype B (or C) sequences and the second principal coordinate was highly associated with the probability of HCC. Third, we also designed K-nearest neighbors (KNN) and support vector machine (SVM) based classifiers for CHB and HCC with high prediction accuracy. The results were validated in an independent data set.
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5
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A comparative study on the characterization of hepatitis B virus quasispecies by clone-based sequencing and third-generation sequencing. Emerg Microbes Infect 2017; 6:e100. [PMID: 29116219 PMCID: PMC5717089 DOI: 10.1038/emi.2017.88] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/12/2017] [Accepted: 09/17/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) has a high mutation rate due to the extremely high replication rate and the proofreading deficiency during reverse transcription. The generated variants with genetic heterogeneity are described as viral quasispecies (QS). Clone-based sequencing (CBS) is thought to be the ‘gold standard’ for assessing QS complexity and diversity of HBV, but an important issue about CBS is cost-effectiveness and laborious. In this study, we investigated the utility of the third-generation sequencing (TGS) DNA sequencing to characterize genetic heterogeneity of HBV QS and assessed the possible contribution of TGS technology in HBV QS studies. Parallel experiments including 3 control samples, which consisted of HBV full gene genotype B and genotype C plasmids, and 10 patients samples were performed by using CBS and TGS to analyze HBV whole-genome QS. Characterization of QS heterogeneity was conducted by using comprehensive statistical analysis. The results showed that TGS had a high consistency with CBS when measuring the complexity and diversity of QS. In addition, to detect rare variants, there were strong advantages conferred by TGS. In summary, TGS was considered to be practicable in HBV QS studies and it might have a relevant role in the clinical management of HBV infection in the future.
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6
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Jia J, Liang X, Chen S, Wang H, Li H, Fang M, Bai X, Wang Z, Wang M, Zhu S, Sun F, Gao C. Next-generation sequencing revealed divergence in deletions of the preS region in the HBV genome between different HBV-related liver diseases. J Gen Virol 2017; 98:2748-2758. [PMID: 29022863 DOI: 10.1099/jgv.0.000942] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In order to investigate if deletion patterns of the preS region can predict liver disease advancement, the preS region of the hepatitis B virus (HBV) genome in 45 chronic hepatitis B (CHB) and 94 HBV-related hepatocellular carcinoma (HCC) patients was sequenced by next-generation sequencing (NGS) and the percentages of nucleotide deletion in the preS region were analysed. Hierarchical clustering and heatmaps based on deletion percentages of preS revealed different deletion patterns between CHB and HCC patients. Intergenotype comparison also indicated divergence in preS deletions between HBV genotype B and C. No significant difference was found in preS deletion patterns between sera and matched adjacent non-tumour tissues. Based on hierarchical clustering, HCC patients were classed into two groups with different preS deletion patterns and different clinical features. Finally, the support vector machine (SVM) model was trained on preS nucleotide deletion percentages and used to predict HCC versus CHB patients. The prediction performance was assessed with fivefold cross-validation and independent cohort validation. The median area under the curve (AUC) was 0.729 after repeating SVM 500 times with fivefold cross-validations. After parameter optimization, the SVM model was used to predict an independent cohort with 51 CHB patients and 72 HCC patients and the AUC was 0.727. In conclusion, the use of the NGS method revealed a prominent divergence in preS deletion patterns between disease groups and virus genotypes, but not between different tissue types. Quantitative NGS data combined with a machine learning method could be a powerful approach for prediction of the status of different diseases.
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Affiliation(s)
- Jian'an Jia
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China.,Department of Laboratory Medicine, The 105th Hospital of PLA, Hefei 230031, PR China
| | - Xiaotao Liang
- Shanghai Key Lab of Intelligent Information Processing and School of Computer Science, Fudan University, Shanghai, PR China.,Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, PR China
| | - Shipeng Chen
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
| | - Hui Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China.,Department of Clinical Laboratory, The First Affiliated Hospital of Chinese PLA's General Hospital, Beijing 100048, PR China
| | - Huiming Li
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
| | - Meng Fang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
| | - Xin Bai
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, PR China
| | - Ziyi Wang
- Shanghai Institute of Technology, Shanghai 201418, PR China
| | - Mengmeng Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
| | - Shanfeng Zhu
- Shanghai Key Lab of Intelligent Information Processing and School of Computer Science, Fudan University, Shanghai, PR China.,Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, PR China
| | - Fengzhu Sun
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, PR China.,Molecular and Computational Program Department of Biological Sciences, University of Southern California, LA 90089, USA
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
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7
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Liu Z, Liu F, Wang L, Liu Y, Zhang M, Li T. Clinical characteristics and outcomes of patients with recurrent chronic hepatitis B after nucleos(t)ide analog withdrawal with stringent cessation criteria: A prospective cohort study. Hepatol Res 2017; 47:1000-1007. [PMID: 27917568 DOI: 10.1111/hepr.12836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/02/2016] [Accepted: 10/30/2016] [Indexed: 12/28/2022]
Abstract
AIM The aim of this study was to explore the clinical characteristics and outcomes of patients with recurrent chronic hepatitis B meeting the cessation criteria outlined by the 2008 Asian Pacific Association for the Study of the Liver guidelines. METHODS In total, 223 chronic hepatitis B patients who met the cessation criteria and discontinued nucleos(t)ide analog therapy were prospectively included. They were monitored monthly during the first 4 months and every 3-6 months thereafter. Early relapse was defined as viral relapse (serum hepatitis B virus [HBV] DNA >104 copies/mL) confirmed within 3 months after cessation. RESULTS Of the 38 hepatitis B e antigen (HBeAg)-positive relapse cases, 44.7%, 65.8%, 76.3% and 89.5% occurred within 3 months, 6 months, 12 months, and 48 months, respectively; in the 49 HBeAg-negative relapse cases, 44.9%, 51.0%, 77.6% and 91.8% occurred within 3, 6, 12 and 36 months, respectively. Time to undetectable HBV DNA was a predictive factor of early relapse. Viral relapses were accompanied by elevated alanine aminotransferase in 70 (80.5%) patients. A peak alanine aminotransferase 10 times over the upper limit of normal after relapse was observed in 15.8% of the HBeAg-positive and 22.4% of the HBeAg-negative patients. Hepatic decompensation and liver failure were not observed. CONCLUSIONS For HBeAg-positive and HBeAg-negative patients meeting stringent cessation criteria, at least 4 years and 3 years of close follow-up are necessary. For those with a longer time to undetectable HBV DNA, more attention should be paid to the early stages after cessation. Nucleos(t)ide analog withdrawal in selected non-cirrhotic patients is generally safe, although close monitoring and timely intervention are needed.
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Affiliation(s)
- Zhirong Liu
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Jinan, China.,Jinan Infectious Disease Hospital, Shandong University School of Medicine, Jinan, China
| | - Feng Liu
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Jinan, China
| | - Lei Wang
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Jinan, China
| | - Youde Liu
- Yantai Infectious Disease Hospital, Yantai, China
| | - Meng Zhang
- Jinan Infectious Disease Hospital, Shandong University School of Medicine, Jinan, China
| | - Tao Li
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Jinan, China
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8
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Xu X, Xiang K, Su M, Li Y, Ji W, Li Y, Zhuang H, Li T. HBV Drug Resistance Substitutions Existed before the Clinical Approval of Nucleos(t)ide Analogues: A Bioinformatic Analysis by GenBank Data Mining. Viruses 2017; 9:v9080199. [PMID: 28749433 PMCID: PMC5580456 DOI: 10.3390/v9080199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
Naturally occurring nucleos(t)ide analogue resistance (NUCr) substitution frequencies in the reverse transcriptase (RT) of the hepatitis B virus (HBV) were studied extensively after the clinical approval of nucleos(t)ide analogues (NUCs; year of approval 1998). We aimed to study NUCr substitutions in HBV RT sequences obtained before 1998 and better understand the evolution of RT sequences without NUC pressures. Our strategy was to retrieve HBV sequences from GenBank deposited before 1998. The initial search used the keywords "hepatitis B virus" or "HBV" and 1139 sequences were found. Data analyses included information extraction: sequence quality control and amino acid substitution analysis on 8 primary NUCr and 3 secondary substitution codons. Three hundred and ninety-four RT-containing sequences of 8 genotypes from 25 countries in 4 continents were selected. Twenty-seven (6.9%) sequences were found to harbor substitutions at NUCr-related codons. Secondary substitutions (rtL80V and rtV173G/A/L) occurred more frequently than primary NUCr substitutions (rtI169L; rtA181G; T184A/S; rtS202T/R; rtM204L and rtM250K). Typical amino acid substitutions associated with NUCr were of rtL80V, rtV173L and rtT184A/S. We confirm the presence of naturally occurring typical HBV NUCr substitutions with very low frequencies, and secondary substitutions are more likely to occur than primary NUCr substitutions without the selective pressure of NUCs.
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Affiliation(s)
- Xizhan Xu
- Department of Microbiology and Center of Infectious Disease, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Kuanhui Xiang
- Department of Microbiology and Center of Infectious Disease, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Mingze Su
- Department of Microbiology and Center of Infectious Disease, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Yao Li
- Department of Microbiology and Center of Infectious Disease, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Wei Ji
- Department of Microbiology and Center of Infectious Disease, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Yutang Li
- Department of Microbiology and Center of Infectious Disease, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Hui Zhuang
- Department of Microbiology and Center of Infectious Disease, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Tong Li
- Department of Microbiology and Center of Infectious Disease, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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9
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Bell TG, Yousif M, Kramvis A. Bioinformatic curation and alignment of genotyped hepatitis B virus (HBV) sequence data from the GenBank public database. SPRINGERPLUS 2016; 5:1896. [PMID: 27843753 PMCID: PMC5084120 DOI: 10.1186/s40064-016-3312-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/13/2016] [Indexed: 12/18/2022]
Abstract
Background Hepatitis B virus (HBV) DNA sequence data from thousands of samples are present in the public sequence databases. No publicly available, up-to-date, multiple sequence alignments, containing full-length and subgenomic fragments per genotype, are available. Such alignments are useful in many analysis applications, including data-mining and phylogenetic analyses. Results By issuing a query, all HBV sequence data from the GenBank public database was downloaded (67,893 sequences). Full-length and subgenomic sequences, which were genotyped by the submitters (30,852 sequences), were placed into a multiple sequence alignment, for each genotype (genotype A: 5868 sequences, B: 4630, C: 7820, D: 8300, E: 2043, F: 985, G: 189, H: 108, I: 23), according to the results of offline BLAST searches against a custom reference library of full-length sequences. Further curation was performed to improve the alignment. Conclusions The algorithm described in this paper generates, for each of the nine HBV genotypes, multiple sequence alignments, which contain full-length and subgenomic fragments. The alignments can be updated as new sequences become available in the online public sequence databases. The alignments are available at http://hvdr.bioinf.wits.ac.za/alignments.
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Affiliation(s)
- Trevor G Bell
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, University of the Witwatersrand, 7 York Road, Parktown, South Africa
| | - Mukhlid Yousif
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, University of the Witwatersrand, 7 York Road, Parktown, South Africa
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, University of the Witwatersrand, 7 York Road, Parktown, South Africa
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10
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Xue Y, Wang MJ, Huang SY, Yang ZT, Yu DM, Han Y, Zhu MY, Huang D, Zhang DH, Gong QM, Zhang XX. Characteristics of CpG Islands and their quasispecies of full-length hepatitis B virus genomes from patients at different phases of infection. SPRINGERPLUS 2016; 5:1630. [PMID: 27722049 PMCID: PMC5031574 DOI: 10.1186/s40064-016-3192-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/01/2016] [Indexed: 12/23/2022]
Abstract
BACKGROUND CpG islands in hepatitis B virus (HBV) genome are potential targets for methylation mediated gene silencing, and may be involved in the pathogenesis of HBV infection. To date, their characteristics in HBV quasispecies (QS) remain largely unknown. The purpose of this study was to investigate the characteristics of CpG islands in HBV QS. METHODS Forty patients diagnosed as acute hepatitis B (AHB, n = 10), immune-tolerant HBV carriers (IT, n = 9), chronic hepatitis B (CHB, n = 11), or acute on chronic liver failure (ACLF, n = 10), were enrolled in this case-control study. A total of 599 clones were isolated, and full-length HBV genomes were sequenced. RESULTS CpG island II (CGII) in AHB group was shorter in length and its QS heterogeneity was lower than that in the chronic infection group. Among the chronic infection subgroups, CGII and CpG island III (CGIII) in IT group were longer and their heterogeneity was lower compared to CHB and ACLF groups. Length of CGII correlated with HBV DNA levels positively while the complexity and diversity of CGII correlated with HBV DNA levels negatively. Moreover, CGII and CGIII were shorter in genotype B than those in genotype C, while QS complexity and diversity of either CGII or CGIII had no significant difference between genotype B and C. CONCLUSIONS Overall, our results suggest that the distribution, length and QS heterogeneity of CpG islands in full-length HBV genome differ across clinical phases of infection, of which the mechanism warrants further study.
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Affiliation(s)
- Yuan Xue
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Ming-Jie Wang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Su-Yuan Huang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Zhi-Tao Yang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - De-Min Yu
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Yue Han
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Ming-Yu Zhu
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Dao Huang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Dong-Hua Zhang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Qi-Ming Gong
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Xin-Xin Zhang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
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11
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Wang XY, Harrison TJ, Chen QY, Li H, Li GJ, Liu MH, Hu LP, Tan C, Yang QL, Fang ZL. The incidence rate over 10 years of naturally occurring, cancer related mutations in the basal core promoter of hepatitis B virus. INFECTION GENETICS AND EVOLUTION 2015; 34:75-80. [PMID: 26192376 PMCID: PMC4666899 DOI: 10.1016/j.meegid.2015.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 07/10/2015] [Accepted: 07/17/2015] [Indexed: 02/07/2023]
Abstract
The annual incidence rate of the basal core promoter (BCP) double mutations is 3.8%. The incidence rate tends to decrease with age and the peak appeared early in the life. Nucleotide (nt) 1762 is the favoured site of the first mutation. Viruses with a single mutation at nt 1762 or 1764 are more prone to develop double mutations.
Cross-sectional analyses showed that the prevalence of basal core promoter (BCP) double mutations (nt 1762T, 1764A) of hepatitis B virus (HBV) gradually increases with age. We aimed to determine the incidence rate of the mutations over 10 years. Study subjects were selected from the Long An cohort established in 2004, including 59 with HBV with single mutations at nt 1762 or 1764 in the BCP and 342 with wild type BCP sequences at baseline. Their serum samples for analysis were obtained at the 3rd and 10th annual visits, respectively. The results showed that the annual incidence rate of BCP double mutations is 3.8% (95% confidence interval [CI]: 1.4–6.2) and tends to decrease with age. The peak incidence is in the 30–34 years age-group. The incidence rate in HBeAg positive individuals (5.5%) is significantly higher than in those without HBeAg (3.4%) (P < 0.05). The incidence rate is significantly higher in genotype C (4.8%) than in genotype B (2.8%) or I (3.1%). The incidence rate of the mutations (6.8%) developing from a single mutation at nt 1762 or 1764 is significantly higher than that (3.8%) from the wild type sequence (P < 0.005). The difference in incidence of single mutations between nt 1762 (0.7%) and 1764 (0.03%) is significant (P < 0.05). In conclusion, the incidence rate of BCP double mutations tends to decrease with age after the age of 35 years. Viruses with a single mutation at nt 1762 or 1764 are more prone to develop double mutations. Nt 1762 is the more common site of the first mutation.
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Affiliation(s)
- Xue-Yan Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | | | - Qin-Yan Chen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Hai Li
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Guo-Jian Li
- Department of Public Health of Guangxi Zhuang Autonomous Region, 35 TaoYuan Road, Nanning, Guangxi 530021, China
| | - Mo-Han Liu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China; School of Preclinical Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - Li-Ping Hu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China; School of Preclinical Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - Chao Tan
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Qing-Li Yang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Zhong-Liao Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China.
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12
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Characterization of Full-Length Genomes of Hepatitis B Virus Quasispecies in Sera of Patients at Different Phases of Infection. J Clin Microbiol 2015; 53:2203-14. [PMID: 25926495 DOI: 10.1128/jcm.00068-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/24/2015] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B virus (HBV) infection results in different clinical presentation due to different levels of immune response. Our study aimed to characterize HBV full-length genome quasispecies (QS) in patients with different phases of infection to better understand its pathogenesis. Forty treatment-naive HBV-infected patients were enrolled, including 10 cases of acute hepatitis B (AHB), 9 cases of immunotolerant (IT) HBV carriers, 11 cases of chronic hepatitis B (CHB), and 10 cases of acute-on-chronic liver failure (ACLF). The present study was conducted by clone-based sequencing. QS heterogeneity within each open reading frame was calculated. The mutation frequency index (MFI) and amino acid variations within the large HBsAg, HBcAg, and HBxAg regions were analyzed based on the different infection phases. In total, 606 HBV full-length sequences were obtained. HBV QS had higher heterogeneity in ACLF and CHB than that in IT among chronically infected individuals. AHB patients had the lower QS heterogeneity at onset than those with chronic infection. ACLF patients had the highest frequency of mutations in the core promoter and precore region. A triple mutation (A1762T/G1764A/G1896A) was observed more frequently in genotype C than in genotype B. The MFI indicated that specific peptides of the studied regions had more frequent mutations in ACLF. Furthermore, several amino acid variations, known as T- and B-cell epitopes, were potentially associated with the immunoactive phase of infection. More HBV genome mutations and deletions were observed in patients with more severe diseases, particularly in specific regions of the core and preS regions, the clinical significance and mechanism of which need to be further investigated.
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13
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Liu MH, Chen QY, Harrison TJ, Li GJ, Li H, Wang XY, Ju Y, Yang JY, Fang ZL. The correlation between serum HBsAg levels and viral loads depends upon wild-type and mutated HBV sequences rather than the HBeAg/anti-HBe status. J Med Virol 2015; 87:1351-60. [PMID: 25879734 PMCID: PMC4980755 DOI: 10.1002/jmv.24186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2015] [Indexed: 12/19/2022]
Abstract
Despite several studies regarding the correlation between serum HBsAg titers and viral loads, the association remains uncertain. Eighty‐nine individuals were selected randomly from a Chinese cohort of 2,258 subjects infected persistently with hepatitis B virus (HBV) for cross‐sectional and longitudinal analysis. Viral loads of mutant HBV are lower than those of wild type HBV. The serum HBsAg titers correlate positively with viral loads in both HBeAg positive and negative subjects (r = 0.449, P = 0.013; r = 0.300, P = 0.018, respectively). No correlation between serum HBsAg titer and viral loads was found in any of the four phases of chronic HBV infection. The serum HBsAg titers correlate positively with viral loads in the group with wild type sequences of the PreS/S, basal core promoter (BCP), and preC regions of HBV(r = 0.502, P = 0.040). However, the correlation was not seen in the group with mutations in these regions (r = 0.165, P = 0.257). The correlation between HBsAg titers and viral loads was seen in individuals with wild type PreS/S sequences but not in the subgroup with BCP double mutations or PreC stop mutation, although their sequences in the preS/S regions were wild type. All these findings were confirmed by the longitudinal analysis. In conclusion, the correlation between serum HBsAg levels and viral loads may not differ between HBeAg positive and negative individuals but may depend on wild‐type or mutated genomic sequences. Therefore, HBsAg quantitation may be used as a surrogate for viral loads in only wild‐type HBV infections. J. Med. Virol. 87:1351–1360, 2015. © 2015 The Authors. Journal of Medical Virology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Mo-Han Liu
- Department of Microbiology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, China.,Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi, China
| | - Qin-Yan Chen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, China.,Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi, China
| | | | - Guo-Jian Li
- Department of Public Health of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Hai Li
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, China.,Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi, China
| | - Xue-Yan Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, China.,Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi, China
| | - Yu Ju
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, China.,Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi, China
| | - Jin-Ye Yang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, China.,Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi, China
| | - Zhong-Liao Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, China.,Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi, China
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14
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Teufel A. Bioinformatics and database resources in hepatology. J Hepatol 2015; 62:712-9. [PMID: 25450718 DOI: 10.1016/j.jhep.2014.10.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/10/2014] [Accepted: 10/23/2014] [Indexed: 02/06/2023]
Abstract
Lately, advances in high-throughput technologies in biomedical research have led to a dramatic increase in the accessibility of molecular insights at multiple biological levels in hepatology. Much of this information is available in publications, but an increasing number of large-scale analyses are currently being stored in databases. Scopes of these databases are very divergent and may range from large, general databases collecting information on almost every known disease, to very specialized databases covering only a specific liver disease or aspect of hepatology. Over recent years, these bioinformatics data repositories have rapidly evolved into an essential aid for molecular hepatology. However, although publicly available through the internet, many of these databases are only known to a few experts. To facilitate access to these resources, the publicly available databases supporting research on liver diseases are summarized in this review.
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Affiliation(s)
- Andreas Teufel
- Department of Medicine I, University Medical Center, Regensburg, Germany.
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15
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Cai Y, Wu X, Shi Y, Liu W. Comparison of evolutionary patterns of different HBeAg status in HBV genotype B and C. Open Life Sci 2015. [DOI: 10.1515/biol-2015-0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractThe aim of this work was to investigate the different evolutionary patterns between HBeAg(+) and HBeAg(-) status of genotype B and genotype C of Hepatitis B virus (HBV). Complete HBV genome sequences were obtained from GenBank, and were classified as HBeAg(+) of genotype B, HBeAg(-) of genotype B, HBeAg(+) of genotype C, and HBeAg(-) of genotype C. The results showed that genotype B had lower diversity and a longer phylogenetic tree than genotype C. This means that genotype B was more conserved than genotype C. The genetic distance of HBeAg(+) was shorter than that of HBeAg(-) in genotype B. dN, dS, dN/dS of HBeAg(+) were lower than that of HBeAg(-). In addition, the Core and S genes had lower diversity, and were under lower selective pressure than other genes. We propose that by having different HBeAg HBV receives disparate immune selective pressures, however these different genotypes also receive disparate natural selective pressures. The evolutionary pattern of HBV could be one of the important factors that may affect viral replication in HBV infected patients and could therefore play an important role in the diseases progression.
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16
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Pourkarim MR, Amini-Bavil-Olyaee S, Kurbanov F, Van Ranst M, Tacke F. Molecular identification of hepatitis B virus genotypes/subgenotypes: revised classification hurdles and updated resolutions. World J Gastroenterol 2014; 20:7152-68. [PMID: 24966586 PMCID: PMC4064061 DOI: 10.3748/wjg.v20.i23.7152] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/28/2013] [Accepted: 01/02/2014] [Indexed: 02/06/2023] Open
Abstract
The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term "recombino-subgenotype". Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term "immigro-subgenotype" to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.
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17
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Clinical implications of evolutionary patterns of homologous, full-length hepatitis B virus quasispecies in different hosts after perinatal infection. J Clin Microbiol 2014; 52:1556-65. [PMID: 24574300 DOI: 10.1128/jcm.03338-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection via perinatal transmission is common in the Asia-Pacific region, but related quasispecies (QS) characteristics are not yet defined. To investigate the homologous, full-length HBV QS after perinatal infection and their clinical implications, five pairs of mother-daughter patients with chronic HBV infection (one patient with liver cirrhosis, one with immune tolerance, and eight with chronic hepatitis) were included. Full-length HBV were amplified by PCR from serum samples before antiviral treatment and cloned; an average of 17 clones per sample were sequenced, and the QS complexities, diversities, and evolution patterns were analyzed. Full-length HBV sequence similarities within mother-daughter pairs were 91.3 to 98.3%. The QS complexities of full-length HBV were similar between mothers and daughters (median of 0.9734 compared to 0.9688, P>0.05), as were the diversities (median of 3.396×10(-3) compared to 4.617×10(-3) substitutions/site, P>0.05). However, the distribution patterns of QS complexities and diversities within specific genes were different, and QS genetic distances of the mothers were higher than those of daughters, both more evident in pairs with different antiviral responses and different immune phases or stages. The nucleotide substitution rate of full-length HBV was 14.388×10(-5) substitutions/site/year, whereas the preC/C gene rate was the highest. Mutations and indels were more common in clones from the mothers, which decreased the affinity of epitopes by 6- to 89-fold. The various genes from homologous HBV genomes evolved in different patterns despite numerically comparable full-length QS complexities and diversities. The different patterns may correlate with the immune stages of chronic HBV infection, which warrants further study.
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18
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Chen QY, Harrison TJ, Sabin CA, Li GJ, Huang GM, Yang JY, Wang XY, Li H, Liu MH, Fang ZL. The Effect of HBV Genotype C on the Development of HCC Differs Between Wild-Type Viruses and Those With BCP Double Mutations (T(1762)A(1764)). HEPATITIS MONTHLY 2014; 14:e16214. [PMID: 24693312 PMCID: PMC3950570 DOI: 10.5812/hepatmon.16214] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 12/17/2013] [Accepted: 12/27/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Association of hepatitis B virus (HBV) genotype C with hepatocellular carcinoma (HCC) development remains controversial. HBV basal core promoter (BCP) double mutations (T(1762)A(1764)) are very strong confounding factors of genotypes B and C in HCC development. OBJECTIVES To investigate the association of HBV genotype C with HCC development after controlling for BCP double mutations. MATERIALS AND METHODS Four hundred and two serum samples from patients with HCC, liver cirrhosis (LC) and chronic hepatitis (CH) and also from asymptomatic HBsAg carriers were analyzed. RESULTS Genotypes B (31.1%), C (62.8%), and I (6.1%) were detected. With the severity of liver disease the prevalence of genotype B decreased, but genotype C increased. No trend was found for genotype I. The prevalence of BCP double mutations in genotypes C and I viruses was significantly higher than genotype B. BCP double mutations are risk factors for CH, LC and HCC. Genotype C was not identified as a particular risk factor for HCC prior to the stratification analysis but after that genotype C viruses with BCP double mutations were found to be a particular risk factor for HCC (P = 0.008, OR = 17.19 [95% CI: 2.10 - 140.41]), but those with the wild-type BCP were not. In the interaction analysis, genotype C and BCP double mutations were found to have a synergistic effect on HCC development (P < 0.0001, OR = 52.56 [95% CI: 11.49-240.52]). CONCLUSIONS The effect of HBV genotype C on the development of HCC differs between wild-type viruses and those with BCP double mutations, suggesting that not all individuals infected with genotype C HBV are at increased risk of HCC.
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Affiliation(s)
- Qin-Yan Chen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Tim J Harrison
- Division of Medicine, Faculty of Medical Sciences, University College London, London, UK
| | - Caroline A Sabin
- Research Department of Infection and Population Health, UCL Medical School, London, UK
| | - Guo-Jian Li
- Department of Public Health of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Gao-Ming Huang
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Jin-Ye Yang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Xue-Yan Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Hai Li
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Mo-Han Liu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
- School of Preclinical Medicine, Guangxi Medical University, Nanning, China
| | - Zhong-Liao Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
- School of Preclinical Medicine, Guangxi Medical University, Nanning, China
- Corresponding Author: Zhong-Liao Fang, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, 18 Jin Zhou Road, Nanning, Guangxi, China. Tel: +86-7712518306, Fax: +86-7712518678, E-mail:
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19
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Gong L, Han Y, Chen L, Liu F, Hao P, Sheng J, Li XH, Yu DM, Gong QM, Tian F, Guo XK, Zhang XX. Comparison of next-generation sequencing and clone-based sequencing in analysis of hepatitis B virus reverse transcriptase quasispecies heterogeneity. J Clin Microbiol 2013; 51:4087-4094. [PMID: 24088859 PMCID: PMC3838070 DOI: 10.1128/jcm.01723-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/26/2013] [Indexed: 02/06/2023] Open
Abstract
We previously reported that, based on clone-based sequencing (CBS), hepatitis B virus (HBV) heterogeneity within the reverse transcriptase (RT) region was a predictor of antiviral efficacy. Here, by comparing ultradeep pyrosequencing (UDPS), i.e., next-generation sequencing (NGS), with CBS in characterizing the genetic heterogeneity of HBV quasispecies within the RT region, we evaluated the performance of UDPS in the analysis of HBV viral populations. HBV genomic DNA was extracted from serum samples from 31 antiviral treatment-naive patients with chronic hepatitis B. The RT region quasispecies were analyzed in parallel using CBS and UDPS. Characterization of quasispecies heterogeneity was conducted using bioinformatics analysis. Quasispecies complexity values were calculated with the formula Sn = -Σi(pilnpi)/lnN. The number of qualified strains obtained by UDPS was much larger than that obtained by CBS (P < 0.001). Pearson analysis showed that there was a positive correlation of quasispecies complexity values at the nucleotide level for the two methods (P < 0.05), while the complexity value derived from UDPS data was higher than that derived from CBS data (P < 0.001). Study of the prevalences of variations within the RT region showed that CBS detected an average of 9.7 ± 1.1 amino acid substitutions/sample and UDPS detected an average of 16.2 ± 1.4 amino acid substitutions/sample. The phylogenetic analysis based on UDPS data showed more genetic entities than did that based on CBS data. Viral heterogeneity determination by the UDPS technique is more sensitive and efficient in terms of low-abundance variation detection and quasispecies simulation than that by the CBS method, although imperfect, and thus sheds light on the future clinical application of NGS in HBV quasispecies studies.
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Affiliation(s)
- Ling Gong
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yue Han
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Li Chen
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Feng Liu
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Pei Hao
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Jia Sheng
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Xin-Hua Li
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - De-Min Yu
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qi-Ming Gong
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fei Tian
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiao-kui Guo
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xin-Xin Zhang
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Li GJ, Hue S, Harrison TJ, Yang JY, Chen QY, Wang XY, Fang ZL. Hepatitis B virus candidate subgenotype I1 varies in distribution throughout Guangxi, China and may have originated in Long An county, Guangxi. J Med Virol 2013; 85:799-807. [PMID: 23508905 DOI: 10.1002/jmv.23533] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2013] [Indexed: 12/13/2022]
Abstract
Sequencing of the complete hepatitis B virus (HBV) genomes from Vietnam, China and Laos led to the identification of a complex recombinant, referred to initially as an aberrant genotype and later proposed to be a new genotype, I. However, epidemiological data regarding this new genotype are lacking. A cross-sectional study was carried out to investigate the epidemiology of HBV candidate genotype I in Guangxi, China using stratified, random cluster sampling. Four thousand five hundred thirteen subjects were recruited from five counties within Guangxi. Three genotypes, B, C, and I, were identified with a prevalence of 32.6% (114/350), 64% (224/350), and 3.4% (12/350), respectively. All the genotype I isolates belong to candidate subgenotype I1 and were found in Bing Yang (15.3%, 9/59) and Na Po (5.0%, 3/60) counties only. The prevalence of this subgenotype is significantly higher in males (5.1%, 10/195) than in females (1.3%, 2/155; X(2) = 3.959, P < 0.05) but does not differ significantly with age. It was found in the Han (4.5%, 9/201) and Zhuang (3.1%, 3/97) ethnic populations only. There is no significant difference from other genotypes in the prevalence of HBV serological markers. Phylogeographic analysis revealed that genotype I1 likely arose in Long An county, then spread later to Bing Yang, Na Po counties and elsewhere in southeast Asia. In conclusion, the distribution of candidate genotype I within Guangxi is not even and it is highly endemic in some counties. Its prevalence is associated with gender and ethnicity. Subgenotype I1 likely originated in Long An county.
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Affiliation(s)
- Guo-Jian Li
- Department of Public Health, Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
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21
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Tedder RS, Bissett SL, Myers R, Ijaz S. The 'Red Queen' dilemma--running to stay in the same place: reflections on the evolutionary vector of HBV in humans. Antivir Ther 2013; 18:489-96. [PMID: 23792884 DOI: 10.3851/imp2655] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2012] [Indexed: 01/28/2023]
Abstract
BACKGROUND Estimates for the evolutionary rate of HBV until now have been interpreted as showing that HBV is a relatively recent acquisition for mankind. The existence of defined HBV genotypes is thought to represent past founder effects. We have explored virus mutation in a group of 48 persistently infected blood donors sampled at two points in time and suggest otherwise. METHODS HBV-infected donors were detected by hepatitis B surface antigen (HBsAg) screening and staged by hepatitis B e markers. Serum DNA from those persistently infected with HBV was characterized by consensus sequencing and the amino acid sequences inferred. These were compared against consensus genotype sequences and divergence measured at two points in time. RESULTS Rates of viral mutation were higher across both HBsAg and hepatitis B core antigen in the group of donors seropositive for hepatitis B e antibody (1.36×10⁻³ and 1.54×10⁻³ changes per residue per year, respectively) than in those seropositive for hepatitis B e antigen (4.59×10⁻⁴ and 6.62×10⁻⁴ changes per residue per year, respectively). Codon mutations reverting to the genotype consensus were commonly seen. Codon changes were clustered close to the C-terminal region of HBsAg and were accommodated in overlapping polymerase by synonymous substitutions. CONCLUSIONS It is suggested that in vivo HBV behaves as a self-normalizing meme and mutational rates, although high, do not lead to significant change over time in a persistent infection. This would be compatible with co-evolution within its human host and introduction within humans being an ancient occurrence.
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Chen L, Zheng CX, Lin MH, Huang ZX, Chen RH, Li QG, Li Q, Chen P. Distinct quasispecies characteristics and positive selection within precore/core gene in hepatitis B virus HBV associated acute-on-chronic liver failure. J Gastroenterol Hepatol 2013; 28:1040-6. [PMID: 23278564 DOI: 10.1111/jgh.12109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/18/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIM The cause of hepatitis B virus associated acute-on-chronic liver failure (ACLF) remains unclear. Quasispecies can contribute to virus persistence and pathogenesis. We used a bioinformatics-based molecular evolution approach to compare quasispecies characteristics and positive selection sites within HBV precore/core gene between ACLF and chronic hepatitis B (CHB) patients. METHODS HBV precore/core gene were amplified from 11 ACLF and 10 CHB patients harboring HBV genotype B; following DNA cloning and sequencing quasispecies complexity, diversity, and positive selection sites within the precore/core gene were determined by bioinformatics analysis, and compared between the patient groups. RESULTS Both quasispecies complexity (P=0.022 at nucleotide level and 0.008 at amino acid level) and diversity (P<0.05) were found to be significantly greater in ACLF than in CHB. The frequency of G1896/A mutation in ACLF (175/298 clones, 58.7%) was also significantly higher than in CHB (100/230 clones, 43.5%) (P=0.0005). Moreover, analysis of positive selection revealed that significantly more patients with such sites were present in ACLF than in CHB (8/11 VS 2/10, P=0.03); the majority of these positive selection sites lay within HLA-restricted epitopes. CONCLUSIONS The ACLF patients showed distinct quasispecies characteristics with higher complexity and diversity within the HBV precore/core gene. The increased HBV quasispecies complexity and diversity, together with a distinct set of positive selection sites, is likely associated with the development of ACLF.
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Affiliation(s)
- Li Chen
- Department of Hepatology, Infectious Disease Hospital of Fujian Medical University, Fuzhou, China
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Chen P, Gan Y, Han N, Fang W, Li J, Zhao F, Hu K, Rayner S. Computational evolutionary analysis of the overlapped surface (S) and polymerase (P) region in hepatitis B virus indicates the spacer domain in P is crucial for survival. PLoS One 2013; 8:e60098. [PMID: 23577084 PMCID: PMC3618453 DOI: 10.1371/journal.pone.0060098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 02/23/2013] [Indexed: 12/21/2022] Open
Abstract
Introduction The Hepatitis B Virus (HBV) genome contains four ORFs, S (surface), P (polymerase), C (core) and X. S is completely overlapped by P and as a consequence the overlapping region is subject to distinctive evolutionary constraints compared to the remainder of the genome. Specifically, a non-synonymous substitution in one coding frame may produce a synonymous substitution in the alternative frame, suggesting a possible conflict between requirements for diversifying and purifying forces. To examine how these contrasting requirements are balanced within this region, we investigated the relationship amongst positive selection sites, conserved regions, epitopes and elements of protein structure to consider how HBV balances the contrasting evolutionary pressures. Methodology/Results 323 HBV genotype D genome sequences were collected and analyzed to identify sites under positive selection and highly conserved regions. Epitopes sequences were retrieved from previously published experimental studies stored in the Immune Epitope Database. Predicted secondary structures were used to investigate the association between structure and conservation. Entropy was used as a measure of conservation and bivariate logistic regression was used to investigate the relationship between positive selection/conserved sites and epitope/secondary structure regions. Our results indicate: (i) conservation in S is primarily dictated by α-helix elements in the protein structure, (ii) variable residues are mainly located in PreS, the major hydrophilic region (MHR) and the C-terminus, (iii) epitopes in S, which are directly targeted by the host immune system, are significantly associated with sites under positive selection. Conclusions The highly variable spacer domain in P, which corresponds to PreS in S, appears to act as a harbor for the accumulation of mutations that can provide flexibility for conformational changes and responding to immune pressure.
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Affiliation(s)
- Ping Chen
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yun Gan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Na Han
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Fang
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jiafu Li
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fei Zhao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Kanghong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Biomedical Center, Hubei University of Technology, Wuhan, China
- * E-mail: (SR); (KH)
| | - Simon Rayner
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (SR); (KH)
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24
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Beggel B, Neumann-Fraune M, Döring M, Lawyer G, Kaiser R, Verheyen J, Lengauer T. Genotyping hepatitis B virus dual infections using population-based sequence data. J Gen Virol 2012; 93:1899-1907. [PMID: 22694900 DOI: 10.1099/vir.0.043042-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The hepatitis B virus (HBV) is classified into distinct genotypes A-H that are characterized by different progression of hepatitis B and sensitivity to interferon treatment. Previous computational genotyping methods are not robust enough regarding HBV dual infections with different genotypes. The correct classification of HBV sequences into the present genotypes is impaired due to multiple ambiguous sequence positions. We present a computational model that is able to identify and genotype inter- and intragenotype dual infections using population-based sequencing data. Model verification on synthetic data showed 100 % accuracy for intergenotype dual infections and 36.4 % sensitivity in intragenotype dual infections. Screening patient sera (n = 241) revealed eight putative cases of intergenotype dual infection (one A-D, six A-G and one D-G) and four putative cases of intragenotype dual infection (one A-A, two D-D and one E-E). Clonal experiments from the original patient material confirmed three out of three of our predictions. The method has been integrated into geno2pheno([hbv]), an established web-service in clinical use for analysing HBV sequence data. It offers exact and detailed identification of HBV genotypes in patients with dual infections that helps to optimize antiviral therapy regimens. geno2pheno([hbv]) is available under http://www.genafor.org/g2p_hbv/index.php.
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Affiliation(s)
- Bastian Beggel
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | | | - Matthias Döring
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Glenn Lawyer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Jens Verheyen
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
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25
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Delwart E, Slikas E, Stramer SL, Kamel H, Kessler D, Krysztof D, Tobler LH, Carrick DM, Steele W, Todd D, Wright DJ, Kleinman SH, Busch MP. Genetic diversity of recently acquired and prevalent HIV, hepatitis B virus, and hepatitis C virus infections in US blood donors. J Infect Dis 2012; 205:875-85. [PMID: 22293432 DOI: 10.1093/infdis/jir862] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Genetic variations of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and hepatitis B virus (HBV) can affect diagnostic assays and therapeutic interventions. Recent changes in prevalence of subtypes/genotypes and drug/immune-escape variants were characterized by comparing recently infected vs more remotely infected blood donors. METHODS Infected donors were identified among approximately 34 million US blood donations, 2006-2009; incident infections were defined as having no or low antiviral antibody titers. Viral genomes were partially sequenced. RESULTS Of 321 HIV strains (50% incident), 2.5% were non-B HIV subtypes. Protease and reverse transcriptase (RT) inhibitor resistance mutations were found in 2% and 11% of infected donors, respectively. Subtypes in 278 HCV strains (31% incident) yielded 1a>1b>3a>2b>2a>4a>6d, 6e: higher frequencies of 3a in incident cases vs higher frequencies of 1b in prevalent cases were found (P = .04). Twenty subgenotypes among 193 HBV strains (26% incident) yielded higher frequencies of A2 in incident cases and higher frequencies of A1, B2, and B4 in prevalent cases (P = .007). No HBV drug resistance mutations were detected. Six percent of incident vs 26% of prevalent HBV contained antibody neutralization escape mutations (P = .01). CONCLUSIONS Viral genetic variant distribution in blood donors was similar to that seen in high-risk US populations. Blood-borne viruses detected through large-scale routine screening of blood donors can complement molecular surveillance studies of highly exposed populations.
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Affiliation(s)
- Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.
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26
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Zhong YW, Li J, Song HB, Duan ZP, Dong Y, Xing XY, Li XD, Gu ML, Han YK, Zhu SS, Zhang HF. Virologic and clinical characteristics of HBV genotypes/subgenotypes in 487 Chinese pediatric patients with CHB. BMC Infect Dis 2011; 11:262. [PMID: 21961963 PMCID: PMC3195169 DOI: 10.1186/1471-2334-11-262] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 09/30/2011] [Indexed: 12/11/2022] Open
Abstract
Background The association of hepatitis B virus (HBV) genotypes/subgenotypes with clinical characteristics is increasingly recognized. However, the virologic and clinical features of HBV genotypes/subgenotypes in pediatric patients remain largely unknown. Methods Four hundred and eighty-seven pediatric inpatients with CHB were investigated, including 217 nucleos(t)ide analog-experienced patients. HBV genotypes/subgenotypes and reverse transcriptase (RT) mutations were determined by direct sequencing. The stage of fibrosis and degree of inflammatory activity were evaluated by the Metavir score system. Results Among 487 enrolled pediatric patients, HBV genotype C2 and B2 were the most two prevalent (73.7% and 21.1%). Comparing with HBV/B2 infected patients, no significant difference was observed in the incidence rate and mutant patterns of lamivudine- or adefovir-resistant mutations in HBV/C2 infected patients (P > 0.05). Importantly, we found that the degree of hepatic inflammation degree, fibrosis stage and ALT level were significantly higher in HBV/C2-infected HBeAg positive patients than it was in HBV/B2-infected ones. Conclusions The pediatric patients with HBV/C2 infection might be more susceptible to develop severe liver pathogenesis.
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Affiliation(s)
- Yan-Wei Zhong
- Pediatric Liver Disease Therapy and Research Center, Beijing 302 Hospital, Beijing, China
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Liu F, Wang L, Li XY, Liu YD, Wang JB, Zhang ZH, Wang YZ. Poor durability of lamivudine effectiveness despite stringent cessation criteria: a prospective clinical study in hepatitis B e antigen-negative chronic hepatitis B patients. J Gastroenterol Hepatol 2011; 26:456-60. [PMID: 21332542 DOI: 10.1111/j.1440-1746.2010.06492.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Lamivudine, a nucleoside analog, is commonly used for treatment of chronic hepatitis B (CHB) but its durability of effectiveness after withdrawal is still uncertain. This study was designed to assess the durability of lamivudine treatment with stringent cessation criteria in hepatitis B e antigen (HBeAg)-negative patients and to explore potential predictive factors. METHODS Sixty one HBeAg-negative CHB patients who had received lamivudine for at least 24 months and had maintained undetectable serum hepatitis B virus (HBV) DNA plus normal alanine aminotransferase for ≥ 18 months before withdrawal were included. They were followed up monthly during the first 4 months and at 3-month or 6-month intervals thereafter. Relapse was defined as serum HBV DNA ≥ 10(4) copies/mL. RESULTS Thirty one of 61 patients relapsed during follow-up, over 90% occurred within 18 months after lamivudine withdrawal. Cumulative relapse rates at months 6, 12, 24, 36, 48 and 60 were 26.2%, 43.6%, 49.7%, 52.1%, 56.1% and 56.1%, respectively. Cox regression revealed that age was the only predictive factor for relapse, with lower relapse rates found in younger patients. Hepatitis B surface antigen (HBsAg) turned negative in eight patients, and none of them relapsed during follow-up. CONCLUSION Effectiveness of lamivudine treatment is not durable in HBeAg-negative CHB patients even when stringent cessation criteria are adopted, with the exception of patients aged ≤ 20 years. The ideal end point of lamivudine treatment is clearance of serum HBsAg.
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Affiliation(s)
- Feng Liu
- Department of Infectious Diseases and Hepatology, the Second Hospital of Shandong University, Shanghai, China
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Fang ZL, Hué S, Sabin CA, Li GJ, Yang JY, Chen QY, Fang KX, Huang J, Wang XY, Harrison TJ. A complex hepatitis B virus (X/C) recombinant is common in Long An county, Guangxi and may have originated in southern China. J Gen Virol 2010; 92:402-11. [PMID: 20965984 PMCID: PMC3081081 DOI: 10.1099/vir.0.026666-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recently, a complex (X/C) hepatitis B virus (HBV) recombinant, first reported in 2000, was proposed as a new genotype; although this was refuted immediately because the strains differ by less than 8 % in nucleotide distance from genotype C. Over 13.5 % (38/281) of HBV isolates from the Long An cohort in China were not assigned to a specific genotype, using current genotyping tools to analyse surface ORF sequences, and these have about 98 % similarity to the X/C recombinants. To determine whether this close identity extends to the full-length sequences and to investigate the evolutionary history of the Long An X/C recombinants, 17 complete genome sequences were determined. They are highly similar (96–99 %) to the Vietnamese strains and, although some reach or exceed 8 % nucleotide sequence difference from all known genotypes, they cluster together in the same clade, separating in a phylogenetic tree from the genotype C branch. Analysis of recombination reveals that all but one of the Long An isolates resembles the Vietnamese isolates in that they result from apparent recombination between genotype C and a parent of unknown genotype (X), which shows similarity in part to genotype G. The exception, isolate QL523, has a greater proportion of genotype C parent. Phylogeographic analysis reveals that these recombinants probably arose in southern China and spread later to Vietnam and Laos.
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Abstract
Hepatitis B is a DNA virus affecting hundreds of millions of individuals worldwide. As the clinical sequelae of cirrhosis and hepatocellular cancer are increasingly recognized to be related to viral levels, the impetus increases to offer treatment to those previously not treated. With the development of more robust antivirals with reasonable safety profiles, long-term treatment is becoming more common. The oral nucleos(t)ide analogs have become the preferred first-line therapies for most genotypes of hepatitis B. Five are now available, all with different potencies and resistance profiles. Long-term data spanning several years are now available for most compounds in this arena. This article focuses on the common natural variants and those secondary to nucleos(t)ide therapy, as well as diagnostic methods to detect resistance.
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Affiliation(s)
- Fred Poordad
- David Geffen School of Medicine at UCLA, Hepatology and Liver Transplantation, Cedars-Sinai Medical Center, Suite 1060, Los Angeles, CA 90048, USA.
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Wang L, Liu F, Liu YD, Li XY, Wang JB, Zhang ZH, Wang YZ. Stringent cessation criterion results in better durability of lamivudine treatment: a prospective clinical study in hepatitis B e antigen-positive chronic hepatitis B patients. J Viral Hepat 2010; 17:298-304. [PMID: 19758278 DOI: 10.1111/j.1365-2893.2009.01178.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The cessation criteria for lamivudine treatment vary in published articles and their results are contradictory, especially factors predicting relapse. To clarify these contradictions, this long-term follow-up study of 125 Chinese hepatitis B e antigen (HBeAg)-positive chronic hepatitis B patients was designed with stringent cessation criterion. All patients received lamivudine and achieved HBeAg seroconversion (group A, n = 82) or loss (group B, n = 43) with undetectable hepatitis B virus (HBV) DNA by PCR assay during the treatment. Lamivudine was withdrawn >or=6 months after HBeAg seroconversion/loss occurred. The median treatment durations were 24 (12-54) months and 36 (18-89) months in group A and group B, respectively. Patients were followed up for median 24 (2-84) months. The cumulative relapse (defined as serum HBV DNA >or=10(4) copies/mL) rates in the two groups at months 12, 24, 36 and 48 were 23.4%vs 35.0%, 25.0%vs 37.7%, 25.0%vs 41.1% and 29.4%vs 41.1%, respectively (log-rank test, P = 0.119). For patients whose total treatment duration >or=18 months in group A, the cumulative relapse rates at months 12, 24, 36 and 48 were 18.3%, 20.1%, 20.1% and 25.1%, which was significantly lower than those with a shorter duration (log-rank test, P = 0.002). The mean age and median total duration were statistically different between relapsers and nonrelapsers in group A (33.9 +/- 13.6 vs 23.1 +/- 11.0 years, P < 0.001 and 24 vs 26 months, P = 0.003). Cox regression revealed that age was the only predictive factor for relapse (RR, 1.069; 95% CI, 1.032-1.106, P < 0.001). Patients aged <30 years relapsed less frequently in 5 years (12.3%vs 53.5%, P = 0.001). In conclusion, for patients who maintained HBeAg seroconversion for >or=6 months and total duration for >or=18 months, lamivudine withdrawal is a reasonable option. Prolonged treatment may be required for patients aged greater than 30 years to reduce relapse.
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Affiliation(s)
- L Wang
- Department of Infectious Diseases and Hepatology, Second Hospital of Shandong University, Shandong University, Jinan, China.
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31
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Pujol FH, Navas MC, Hainaut P, Chemin I. Worldwide genetic diversity of HBV genotypes and risk of hepatocellular carcinoma. Cancer Lett 2009; 286:80-88. [PMID: 19683385 DOI: 10.1016/j.canlet.2009.07.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 07/17/2009] [Accepted: 07/18/2009] [Indexed: 12/21/2022]
Abstract
Hepatitis B viruses (HBV) are responsible for over 50% of the worldwide attributable risk of hepatocellular carcinoma (HCC) and this figure increases even further in regions of high endemicity. Systematic sequencing of HBV genomes has identified that this common virus existed as eight distinct genotypes (denoted A-H), each regrouping variants with less than 8% divergence in their DNA sequence. These genotypes differ by their geographic distribution in populations around the globe. There is evidence that HBV genotypes also differ by their pathogenic properties, including their risk of persistence as chronic infection and their capacity to induce precursor disease or cancer. On the other hand, HBV genes may undergo mutations that become selected during the course of chronic infection and progressive liver disease. The most significant of these mutations in the context of HCC are those occurring in the pre-core (Pre-C) and basal core promoter (BCP) regions. These mutations may upregulate HBV expression and increase its virulence. These mutations may occur in all HBV genotypes but are more common in genotypes associated with more severe disease and cancer, in particular genotype C. Understanding the molecular basis of pathological variations between HBV variants is critical for prediction of disease severity. It will also be important to determine whether differences among genotypes may have an impact on the long-term protective efficacy of universal HBV vaccination.
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Affiliation(s)
- Flor Helene Pujol
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020-A, Venezuela
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Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, Holmes SP, Babrzadeh F, Gharizadeh B, Hanczaruk B, Simen BB, Egholm M, Shafer RW. Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis 2009; 199:1275-85. [PMID: 19301976 PMCID: PMC3353721 DOI: 10.1086/597808] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The dynamics of emerging nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI) resistance in hepatitis B virus (HBV) are not well understood because standard dideoxynucleotide direct polymerase chain reaction (PCR) sequencing assays detect drug-resistance mutations only after they have become dominant. To obtain insight into NRTI resistance, we used a new sequencing technology to characterize the spectrum of low-prevalence NRTI-resistance mutations in HBV obtained from 20 plasma samples from 11 NRTI-treated patients and 17 plasma samples from 17 NRTI-naive patients, by using standard direct PCR sequencing and ultra-deep pyrosequencing (UDPS). UDPS detected drug-resistance mutations that were not detected by PCR in 10 samples from 5 NRTI-treated patients, including the lamivudine-resistance mutation V173L (in 5 samples), the entecavir-resistance mutations T184S (in 2 samples) and S202G (in 1 sample), the adefovir-resistance mutation N236T (in 1 sample), and the lamivudine and adefovir-resistance mutations V173L, L180M, A181T, and M204V (in 1 sample). G-to-A hypermutation mediated by the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like family of cytidine deaminases was estimated to be present in 0.6% of reverse-transcriptase genes. Genotype A coinfection was detected by UDPS in each of 3 patients in whom genotype G virus was detected by direct PCR sequencing. UDPS detected low-prevalence HBV variants with NRTI-resistance mutations, G-to-A hypermutation, and low-level dual genotype infection with a sensitivity not previously possible.
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Affiliation(s)
| | - Nancy S. Shulman
- Department of Medicine, Stanford University, Stanford, California
| | - Aijaz Ahmed
- Department of Medicine, Stanford University, Stanford, California
| | - Rajin Shahriar
- Department of Medicine, Stanford University, Stanford, California
| | - Tommy Liu
- Department of Medicine, Stanford University, Stanford, California
| | - Chunlin Wang
- Department of Medicine, Stanford University, Stanford, California
| | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, California
| | - Farbod Babrzadeh
- Department of Stanford Genome Technology Center, Stanford, California
| | - Baback Gharizadeh
- Department of Stanford Genome Technology Center, Stanford, California
| | | | | | - Michael Egholm
- 454 Life Sciences, a Roche Company, Branford, Connecticut
| | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, California
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Early changes of hepatitis B virus quasispecies during lamivudine treatment and the correlation with antiviral efficacy. J Hepatol 2009; 50:895-905. [PMID: 19304333 DOI: 10.1016/j.jhep.2008.12.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 12/13/2008] [Accepted: 12/15/2008] [Indexed: 12/14/2022]
Abstract
BACKGROUND/AIMS To investigate dynamic changes of hepatitis B virus (HBV) quasispecies within the reverse transcriptase (RT) region during the early stage of lamivudine treatment and the correlation with antiviral efficacy. METHODS Twenty-five chronic hepatitis B patients received lamivudine treatment for 48 weeks. Fourteen patients responded to lamivudine, while eleven patients were non-responders. HBV DNA was extracted from serum samples at baseline and week 4. The RT region of HBV was amplified, then cloned and sequenced. Quasispecies complexity and diversity within the RT region were analyzed at baseline and week 4, and viral nucleotide substitution rates during the first 4 weeks were calculated. RESULTS The quasispecies complexity and diversity were not different between responders and non-responders at baseline (p>0.05). However, the quasispecies complexity and diversity of responders were significantly lower than those of non-responders at week 4 (p<0.01). Furthermore, the viral nucleotide substitution rate of responders was significantly higher than that of non-responders (p<0.05). CONCLUSIONS The dynamic changes of HBV quasispecies within the RT region showed distinct patterns between responders and non-responders during early stage of lamivudine treatment. The dynamic changes of quasispecies complexity and diversity during the first 4 weeks were correlated with lamivudine antiviral efficacy and antiviral resistance.
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The association of HBV core promoter double mutations (A1762T and G1764A) with viral load differs between HBeAg positive and anti-HBe positive individuals: a longitudinal analysis. J Hepatol 2009; 50:273-80. [PMID: 19070921 PMCID: PMC2648871 DOI: 10.1016/j.jhep.2008.09.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 09/16/2008] [Accepted: 09/17/2008] [Indexed: 12/12/2022]
Abstract
BACKGROUND/AIMS Although there have been a few reports regarding the effect of basal core promoter (BCP) double mutations (A1762T and G1764A) on hepatitis B viral loads, the association remains uncertain. We aim to determine the association after controlling for HBeAg - a strong confounding factor. METHODS We selected randomly 190 individuals from a Chinese cohort of 2258 subjects for cross-sectional analysis and 56 of the 190 for longitudinal analysis of viral loads. RESULTS In multivariable analysis of the cross-sectional data, BCP double mutations are significantly associated with lower viral loads in HBeAg positive subjects but no difference was found in anti-HBe positive subjects. Triple mutations at nucleotide (nt) 1753, 1762 and 1764 and mutations between nt 1809 and 1817, precore stop mutation (nt 1896) and genotype are not associated with viral loads in either HBeAg or anti-HBe positive subjects. Analysis of the longitudinal data yielded similar results to the cross-sectional data. Viral loads differ significantly between individuals infected with wild-type and BCP double mutations prior to HBeAg seroconversion but this difference is lost after seroconversion. CONCLUSIONS BCP double mutations are associated with lower viral loads in HBeAg positive individuals but have no effect on the viral loads of anti-HBe positive individuals.
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Fang ZL, Sabin CA, Dong BQ, Wei SC, Chen QY, Fang KX, Yang JY, Huang J, Wang XY, Harrison TJ. Hepatitis B virus pre-S deletion mutations are a risk factor for hepatocellular carcinoma: a matched nested case-control study. J Gen Virol 2009; 89:2882-2890. [PMID: 18931087 PMCID: PMC2886956 DOI: 10.1099/vir.0.2008/002824-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A matched nested case-control study of 33 paired cases and controls was conducted, based on a study cohort in Long An county, Guangxi, China, to determine whether infection with hepatitis B virus (HBV) with pre-S deletions is independently associated with the development of hepatocellular carcinoma (HCC), without the confounding effects of basal core promoter (BCP) double mutations. The prevalence of pre-S deletions was significantly higher in HCC (45.5 %, 15 of 33) than the controls (18.2 %, 6 of 33) (P<0.01), under the control of the influence of BCP double mutations. Most of the pre-S deletions occurred in, or involved, the 5' half of the pre-S2 region and the difference between HCC (93.3 %, 14 of 15) and controls (66.7 %, four of six) was significant for this region (P=0.015). There was no significant difference in pre-S deletions between the BCP mutant group and BCP wild-type group (P>0.05), nor was the prevalence of pre-S deletions significantly different between genotypes B and C (P>0.1). These results suggest that pre-S deletions constitute an independent risk factor for HCC and their emergence and effect are independent of BCP mutations. The 5' terminus of pre-S2 is the favoured site for the deletion mutations, especially in HCC cases. Further prospective studies are required to confirm the role of these mutations in the development of HCC.
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Affiliation(s)
- Zhong-Liao Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Jin Zhou Road, Nanning, Guangxi 530028, PR China.,Department of Medicine, UCL Medical School, London W1T 4JF, UK
| | - Caroline A Sabin
- Research Department of Infection and Population Health, Division of Population Health, UCL Medical School, University College London, London NW3 2PF, UK
| | - Bai-Qing Dong
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Jin Zhou Road, Nanning, Guangxi 530028, PR China
| | - Shao-Chao Wei
- Sanitary and Antiepidemic Station of Long An, ChengXi Road, Cheng Xiang Town, Long An, Guangxi 532700, PR China
| | - Qin-Yan Chen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Jin Zhou Road, Nanning, Guangxi 530028, PR China
| | - Kong-Xiong Fang
- Sanitary and Antiepidemic Station of Long An, ChengXi Road, Cheng Xiang Town, Long An, Guangxi 532700, PR China
| | - Jin-Ye Yang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Jin Zhou Road, Nanning, Guangxi 530028, PR China
| | - Jian Huang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Jin Zhou Road, Nanning, Guangxi 530028, PR China
| | - Xue-Yan Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Jin Zhou Road, Nanning, Guangxi 530028, PR China
| | - Tim J Harrison
- Department of Medicine, UCL Medical School, London W1T 4JF, UK
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van Hemert FJ, Zaaijer HL, Berkhout B, Lukashov VV. Occult hepatitis B infection: an evolutionary scenario. Virol J 2008; 5:146. [PMID: 19077239 PMCID: PMC2637267 DOI: 10.1186/1743-422x-5-146] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 12/11/2008] [Indexed: 02/07/2023] Open
Abstract
Background Occult or latent hepatitis B virus (HBV) infection is defined as infection with detectable HBV DNA and undetectable surface antigen (HBsAg) in patients' blood. The cause of an overt HBV infection becoming an occult one is unknown. To gain insight into the mechanism of the development of occult infection, we compared the full-length HBV genome from a blood donor carrying an occult infection (d4) with global genotype D genomes. Results The phylogenetic analysis of polymerase, core and X protein sequences did not distinguish d4 from other genotype D strains. Yet, d4 surface protein formed the evolutionary outgroup relative to all other genotype D strains. Its evolutionary branch was the only one where accumulation of substitutions suggests positive selection (dN/dS = 1.3787). Many of these substitutiions accumulated specifically in regions encoding the core/surface protein interface, as revealed in a 3D-modeled protein complex. We identified a novel RNA splicing event (deleting nucleotides 2986-202) that abolishes surface protein gene expression without affecting polymerase, core and X-protein related functions. Genotype D strains differ in their ability to perform this 2986-202 splicing. Strains prone to 2986-202 splicing constitute a separate clade in a phylogenetic tree of genotype D HBVs. A single substitution (G173T) that is associated with clade membership alters the local RNA secondary structure and is proposed to affect splicing efficiency at the 202 acceptor site. Conclusion We propose an evolutionary scenario for occult HBV infection, in which 2986-202 splicing generates intracellular virus particles devoid of surface protein, which subsequently accumulates mutations due to relaxation of coding constraints. Such viruses are deficient of autonomous propagation and cannot leave the host cell until it is lysed.
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Affiliation(s)
- Formijn J van Hemert
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
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Kramvis A, Arakawa K, Yu MC, Nogueira R, Stram DO, Kew MC. Relationship of serological subtype, basic core promoter and precore mutations to genotypes/subgenotypes of hepatitis B virus. J Med Virol 2008; 80:27-46. [DOI: 10.1002/jmv.21049] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Chevrier MC, St-Louis M, Perreault J, Caron B, Castilloux C, Laroche J, Delage G. Detection and characterization of hepatitis B virus of anti-hepatitis B core antigen-reactive blood donors in Quebec with an in-house nucleic acid testing assay. Transfusion 2007; 47:1794-802. [PMID: 17880603 DOI: 10.1111/j.1537-2995.2007.01394.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) infection can be detected in blood donations by many serologic markers. Since the introduction of routine anti-hepatitis B core antigen (HBc) donor screening at Héma-Québec in April 2003, a large number of donors have been deferred on the basis of reactive anti-HBc test results. The objective of this study was to evaluate the correlation between the anti-HBc-reactive donations and the detection of HBV DNA with an in-house nucleic acid testing (NAT) assay. STUDY DESIGN AND METHODS The in-house HBV NAT assay is a conventional polymerase chain reaction amplifying part of the viral S gene. From October 2004 to November 2005, a total of 1169 anti-HBc-reactive donations were tested with this in-house assay. The results were correlated with hepatitis B surface antigen (HBsAg) and anti-HBs markers. HBV DNA-positive samples were further investigated by DNA sequencing. RESULTS All HBsAg-positive samples were detected by the NAT assay. Overall, 38 (3.25%) of anti-HBc-positive samples were found to be positive for the presence of HBV DNA. Of these 38, a total of 12 donations with a low level of HBV DNA were HBsAg-negative. The sequencing results clearly showed various genotypes and subtypes within a same genotype. CONCLUSION The 3.25 percent HBV DNA positivity rate among the anti-HBc-reactive donations and more particularly the low level of HBV DNA observed in occult donations underline the importance of the use of a sensitive assay to detect HBV DNA in conjunction with other markers. The HBV genetic diversity found in our donor population reflects the province demographics, particularly in the Montreal area where most of the positive donors were from.
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van Hemert FJ, Zaaijer HL, Berkhout B, Lukashov VV. Mosaic amino acid conservation in 3D-structures of surface protein and polymerase of hepatitis B virus. Virology 2007; 370:362-72. [PMID: 17935747 DOI: 10.1016/j.virol.2007.08.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 07/31/2007] [Accepted: 08/25/2007] [Indexed: 12/17/2022]
Abstract
Surface protein and polymerase of hepatitis B virus provide a striking example of gene overlap. Inclusion of more coding constraints in the phylogenetic analysis forces the tree toward accepted topology. Three-dimensional protein modeling demonstrates that participation in local protein function underlies the observed mosaic patterns of amino acid conservation and variability. Conserved amino acid residues of polymerase were typically clustered at the catalytic core marked by the YMDD motif. The proposed tertiary structure of surface protein displayed the expected transmembrane helices in a 2-domain constellation. Conserved amino acids like, for instance, cysteine residues are involved in the spatial orientation of the two domains, the exposed location of the a-determinant and the dimer formation of surface protein. By means of computational alanine replacement scanning, we demonstrated that the interfaces between domains in monomeric surface protein, between the monomers in dimeric surface protein and in a capsid-surface protein complex mainly consist of relatively well-conserved amino acid residues.
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Affiliation(s)
- Formijn J van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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Ferns RB, Naoumov NV, Gilson RJ, Tedder RS. Presence of hepatitis B virus core promoter mutations pre-seroconversion predict persistent viral replication after HBeAg loss. J Clin Virol 2007; 39:199-204. [PMID: 17526429 DOI: 10.1016/j.jcv.2007.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 03/15/2007] [Accepted: 04/13/2007] [Indexed: 01/30/2023]
Abstract
BACKGROUND In patients with chronic hepatitis B virus (HBV) infection DNA levels do not always fall after anti-hepatitis B e (anti-HBe) seroconversion. OBJECTIVES To follow longitudinally through HB e antigen (HBeAg) loss HBV DNA levels and core promoter/precore sequences in a cohort of 21 chronic HBV carriers. STUDY DESIGN Treatment-naïve HBeAg seropositive HBV carriers were monitored through HBeAg loss for between 2 and 22 years (mean 9.3). Core promoter/precore sequences, genotypes, HBV DNA levels and HBe status were determined. RESULTS Patients were grouped into those in whom serum/plasma HBV DNA remained high after HBeAg loss (group 1, n=11; HBV DNA>5log(10)IU/ml) and those in whom HBV DNA declined (group 2, n=10). Re-appearance of HBeAg was seen in seven group 1 patients. Pre-seroconversion mutations in the core promoter region including A1762T and/or G1764A were detected more frequently in group 1 (P=0.031). Overall sequence changes at sites other than 1762/1764 were more common post-seroconversion in group 1 than group 2 patients (P=0.037). CONCLUSIONS The presence of core promoter mutations prior to HBeAg loss identified those patients in whom HBV DNA persisted at high levels and was associated with temporary re-emergence of serum HBeAg. These patients may benefit from early anti-viral treatment.
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Affiliation(s)
- R Bridget Ferns
- Centre for Virology, Department of Infection, University College, Windeyer Building, 46 Cleveland Street, London W1T 4JF, United Kingdom.
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Abstract
Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclature is essential to describe gene segment reassortment. Specialized bioinformatic tools to analyze reassortment are not available, which hampers progress in understanding its role in host range, virulence and transmissibility of influenza viruses. To meet this need, we have developed a nomenclature to name influenza A genotypes and implemented a web server, FluGenome (http://www.flugenome.org/), for the assignment of lineages and genotypes. FluGenome provides functions for the user to interrogate the database in different modalities and get detailed reports on lineages and genotypes. These features make FluGenome unique in its ability to automatically detect genotype differences attributable to reassortment events in influenza A virus evolution.
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Affiliation(s)
- Guoqing Lu
- Department of Biology, Department of Computer Science, University of Nebraska at Omaha, Omaha, NE and Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - Thaine Rowley
- Department of Biology, Department of Computer Science, University of Nebraska at Omaha, Omaha, NE and Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - Rebecca Garten
- Department of Biology, Department of Computer Science, University of Nebraska at Omaha, Omaha, NE and Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - Ruben O. Donis
- Department of Biology, Department of Computer Science, University of Nebraska at Omaha, Omaha, NE and Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
- *To whom correspondence should be addressed. 404 639 4968404 639 2350
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Gnaneshan S, Ijaz S, Moran J, Ramsay M, Green J. HepSEQ: International Public Health Repository for Hepatitis B. Nucleic Acids Res 2006; 35:D367-70. [PMID: 17130143 PMCID: PMC1716715 DOI: 10.1093/nar/gkl874] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
HepSEQ is a repository for an extensive library of public health and molecular data relating to hepatitis B virus (HBV) infection collected from international sources. It is hosted by the Centre for Infections, Health Protection Agency (HPA), England, United Kingdom. This repository has been developed as a web-enabled, quality-controlled database to act as a tool for surveillance, HBV case management and for research. The web front-end for the database system can be accessed from . The format of the database system allows for comprehensive molecular, clinical and epidemiological data to be deposited into a functional database, to search and manipulate the stored data and to extract and visualize the information on epidemiological, virological, clinical, nucleotide sequence and mutational aspects of HBV infection through web front-end. Specific tools, built into the database, can be utilized to analyse deposited data and provide information on HBV genotype, identify mutations with known clinical significance (e.g. vaccine escape, precore and antiviral-resistant mutations) and carry out sequence homology searches against other deposited strains. Further mechanisms are also in place to allow specific tailored searches of the database to be undertaken.
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Affiliation(s)
- Saravanamuttu Gnaneshan
- Centre for Infections, Health Protection Agency, 61 Colindale Avenue, Colindale, London NW9 5EQ, UK.
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