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Wang LT, Chen YH, Cheng Y, Fan HL, Chen TW, Shih YL, Hsieh TY, Huang WY, Huang WC. Clinical implications of hepatitis B virus core antigen-mediated immunopathologic T cell responses in chronic hepatitis B. J Med Virol 2024; 96:e29515. [PMID: 38469923 DOI: 10.1002/jmv.29515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
Hepatitis B virus (HBV) infection significantly impacts Asian populations. The influences of continuous HBV antigen and inflammatory stimulation to T cells in chronic hepatitis B (CHB) remain unclear. In this study, we first conducted bioinformatics analysis to assess T-cell signaling pathways in CHB patients. In a Taiwanese cohort, we examined the phenotypic features of HBVcore -specific T cells and their correlation with clinical parameters. We used core protein overlapping peptides from the Taiwan prevalent genotype B HBV to investigate the antiviral response and the functional implication of HBV-specific T cells. In line with Taiwanese dominant HLA-alleles, we also evaluated ex vivo HBVcore -specific T cells by pMHC-tetramers targeting epitopes within HBV core protein. Compared to healthy subjects, we disclosed CD8 T cells from CHB patients had higher activation marker CD38 levels but showed an upregulation in the inhibitory receptor PD-1. Our parallel study showed HBV-specific CD8 T cells were more activated with greater PD-1 expression than CMV-specific subset and bulk CD8 T cells. Moreover, our longitudinal study demonstrated a correlation between the PD-1 fluctuation pattern of HBVcore -specific CD8 T cells and liver inflammation in CHB patients. Our research reveals the HBV core antigen-mediated immunopathologic profile of CD8 T cells in chronic HBV infection. Our findings suggest the PD-1 levels of HBVcore -specific CD8 T cells can be used as a valuable indicator of personal immune response for clinical application in hepatitis management.
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Affiliation(s)
- Li-Tzu Wang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yu-Hong Chen
- Department of Internal Medicine, Division of Gastroenterology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yang Cheng
- Division of Infectious Disease & Immunology, Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Lung Fan
- Department of Surgery, Division of Organ Transplantation Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Teng-Wei Chen
- Department of Surgery, Division of Organ Transplantation Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Lueng Shih
- Department of Internal Medicine, Division of Gastroenterology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Tsai-Yuan Hsieh
- Department of Internal Medicine, Division of Gastroenterology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wen-Yen Huang
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wei-Chen Huang
- Department of Internal Medicine, Division of Gastroenterology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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Wang Y, Pang B, Wang Z, Tian X, Xu X, Chong X, Liang H, Ma W, Kou Z, Wen H. Genomic diversity and evolution analysis of severe fever with thrombocytopenia syndrome in East Asia from 2010 to 2022. Front Microbiol 2023; 14:1233693. [PMID: 37670982 PMCID: PMC10476882 DOI: 10.3389/fmicb.2023.1233693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/08/2023] [Indexed: 09/07/2023] Open
Abstract
Background Conducting an up-to-date analysis on the genomic diversity and evolution patterns of severe fever with thrombocytopenia syndrome virus (SFTSV) is crucial for elucidating the underlying mechanisms of its emergency and pathogenicity, as well as assessing the extent of its threat to public health. Methods Complete genome sequences of SFTSV were obtained from GenBank until December 19, 2022. A thorough phylogenetic analysis was conducted using comprehensive bioinformatics methods to estimate the genomic diversity and evolution. Results The phylogenetic classification of SFTSV strains yielded seven lineages (A-G) for each genome segment. SFTSV displayed notable variations in evolutionary patterns among different regions and segments, without a linear accumulation of nucleotide substitutions within segments and regions. The comprehensive analysis revealed 54 recombination events and 17 reassortment strains, including the first discovery of recombination events involving sea-crossing and species-crossing. Selection analysis identified three positive sites (2, 671, 1353) in RNA-dependent RNA polymerase, three positive sites (22, 298, 404) in glycoprotein, and two positive sites (9, 289) in nonstructural protein. No positive selection sites were found in nucleoprotein. Conclusion Our study unveiled the existence of multiple evolutionary forces influencing SFTSV, contributing to its increasing genetic diversity, which had the potential to modify its antigenicity and pathogenicity. Furthermore, our study highlights the importance of tracking the spread of SFTSV across regions and species.
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Affiliation(s)
- Yao Wang
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bo Pang
- Infection Disease Control of Institute, Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Disease Prevention and Control, Jinan, China
| | - Zequn Wang
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xueying Tian
- Infection Disease Control of Institute, Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Disease Prevention and Control, Jinan, China
| | - Xiaoying Xu
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaowen Chong
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hao Liang
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wei Ma
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zengqiang Kou
- Infection Disease Control of Institute, Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Disease Prevention and Control, Jinan, China
| | - Hongling Wen
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
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Glebe D, Goldmann N, Lauber C, Seitz S. HBV evolution and genetic variability: Impact on prevention, treatment and development of antivirals. Antiviral Res 2020; 186:104973. [PMID: 33166575 DOI: 10.1016/j.antiviral.2020.104973] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Hepatitis B virus (HBV) poses a major global health burden with 260 million people being chronically infected and 890,000 dying annually from complications in the course of the infection. HBV is a small enveloped virus with a reverse-transcribed DNA genome that infects hepatocytes and can cause acute and chronic infections of the liver. HBV is endemic in humans and apes representing the prototype member of the viral family Hepadnaviridae and can be divided into 10 genotypes. Hepadnaviruses have been found in all vertebrate classes and constitute an ancient viral family that descended from non-enveloped progenitors more than 360 million years ago. The de novo emergence of the envelope protein gene was accompanied with the liver-tropism and resulted in a tight virus-host association. The oldest HBV genomes so far have been isolated from human remains of the Bronze Age and the Neolithic (~7000 years before present). Despite the remarkable stability of the hepadnaviral genome over geological eras, HBV is able to rapidly evolve within an infected individual under pressure of the immune response or during antiviral treatment. Treatment with currently available antivirals blocking intracellular replication of HBV allows controlling of high viremia and improving liver health during long-term therapy of patients with chronic hepatitis B (CHB), but they are not sufficient to cure the disease. New therapy options that cover all HBV genotypes and emerging viral variants will have to be developed soon. In addition to the antiviral treatment of chronically infected patients, continued efforts to expand the global coverage of the currently available HBV vaccine will be one of the key factors for controlling the rising global spread of HBV. Certain improvements of the vaccine (e.g. inclusion of PreS domains) could counteract known problems such as low or no responsiveness of certain risk groups and waning anti-HBs titers leading to occult infections, especially with HBV genotypes E or F. But even with an optimal vaccine and a cure for hepatitis B, global eradication of HBV would be difficult to achieve because of an existing viral reservoir in primates and bats carrying closely related hepadnaviruses with zoonotic potential.
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Affiliation(s)
- Dieter Glebe
- Institute of Medical Virology, Justus Liebig University of Giessen, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Schubertstr. 81, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner Sites Giessen, Heidelberg, Hannover, Germany.
| | - Nora Goldmann
- Institute of Medical Virology, Justus Liebig University of Giessen, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Schubertstr. 81, 35392, Giessen, Germany
| | - Chris Lauber
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany; Research Group Computational Virology, Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz Centre for Infection Research and the Hannover Medical School, Cluster of Excellence RESIST, Hannover Medical School, 30625, Hannover, Germany; German Center for Infection Research (DZIF), Partner Sites Giessen, Heidelberg, Hannover, Germany
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany; Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120, Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Sites Giessen, Heidelberg, Hannover, Germany.
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The evolution and clinical impact of hepatitis B virus genome diversity. Nat Rev Gastroenterol Hepatol 2020; 17:618-634. [PMID: 32467580 DOI: 10.1038/s41575-020-0296-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 02/06/2023]
Abstract
The global burden of hepatitis B virus (HBV) is enormous, with 257 million persons chronically infected, resulting in more than 880,000 deaths per year worldwide. HBV exists as nine different genotypes, which differ in disease progression, natural history and response to therapy. HBV is an ancient virus, with the latest reports greatly expanding the host range of the Hepadnaviridae (to include fish and reptiles) and casting new light on the origins and evolution of this viral family. Although there is an effective preventive vaccine, there is no cure for chronic hepatitis B, largely owing to the persistence of a viral minichromosome that is not targeted by current therapies. HBV persistence is also facilitated through aberrant host immune responses, possibly due to the diverse intra-host viral populations that can respond to host-mounted and therapeutic selection pressures. This Review summarizes current knowledge on the influence of HBV diversity on disease progression and treatment response and the potential effect on new HBV therapies in the pipeline. The mechanisms by which HBV diversity can occur both within the individual host and at a population level are also discussed.
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In silico Analysis of Genetic Diversity of Human Hepatitis B Virus in Southeast Asia, Australia and New Zealand. Viruses 2020; 12:v12040427. [PMID: 32283837 PMCID: PMC7232418 DOI: 10.3390/v12040427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 02/08/2023] Open
Abstract
The extent of whole genome diversity amongst hepatitis B virus (HBV) genotypes is not well described. This study aimed to update the current distribution of HBV types and to investigate mutation rates and nucleotide diversity between genotypes in Southeast Asia, Australia and New Zealand. We retrieved 930 human HBV complete genomes from these regions from the NCBI nucleotide database for genotyping, detection of potential recombination, serotype prediction, mutation identification and comparative genome analyses. Overall, HBV genotypes B (44.1%) and C (46.2%) together with predicted serotypes adr (36%), adw2 (29%) and ayw1 (19.9%) were the most commonly circulating HBV types in the studied region. The three HBV variants identified most frequently were p.V5L, c.1896G>A and double mutation c.1762A>T/c.1764G>A, while genotypes B and C had the widest range of mutation types. The study also highlighted the distinct nucleotide diversity of HBV genotypes for whole genome and along the genome length. Therefore, this study provided a robust update to HBV currently circulating in Southeast Asia, Australia and New Zealand as well as an insight into the association of HBV genetic hypervariability and prevalence of well reported mutations.
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Evidence for Internal Initiation of RNA Synthesis by the Hepatitis C Virus RNA-Dependent RNA Polymerase NS5B In Cellulo. J Virol 2019; 93:JVI.00525-19. [PMID: 31315989 DOI: 10.1128/jvi.00525-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/07/2019] [Indexed: 12/11/2022] Open
Abstract
Initiation of RNA synthesis by the hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) NS5B has been extensively studied in vitro and in cellulo Intracellular replication is thought to rely exclusively on terminal de novo initiation, as it conserves all genetic information of the genome. In vitro, however, additional modes of initiation have been observed. In this study, we aimed to clarify whether the intracellular environment allows for internal initiation of RNA replication by the HCV replicase. We used a dual luciferase replicon harboring a terminal and an internal copy of the viral genomic 5' untranslated region, which was anticipated to support noncanonical initiation. Indeed, a shorter RNA species was detected by Northern blotting with low frequency, depending on the length and sequence composition upstream of the internal initiation site. By introducing mutations at either site, we furthermore established that internal and terminal initiation shared identical sequence requirements. Importantly, lethal point mutations at the terminal site resulted exclusively in truncated replicons. In contrast, the same mutations at the internal site abrogated internal initiation, suggesting a competitive selection of initiation sites, rather than recombination or template-switching events. In conclusion, our data indicate that the HCV replicase is capable of internal initiation in its natural environment, although functional replication likely requires only terminal initiation. Since many other positive-strand RNA viruses generate subgenomic messenger RNAs during their replication cycle, we surmise that their capability for internal initiation is a common and conserved feature of viral RdRps.IMPORTANCE Many aspects of viral RNA replication of hepatitis C virus (HCV) are still poorly understood. The process of RNA synthesis is driven by the RNA-dependent RNA polymerase (RdRp) NS5B. Most mechanistic studies on NS5B so far were performed with in vitro systems using isolated recombinant polymerase. In this study, we present a replicon model, which allows the intracellular assessment of noncanonical modes of initiation by the full HCV replicase. Our results add to the understanding of the biochemical processes underlying initiation of RNA synthesis by NS5B by the discovery of internal initiation in cellulo Moreover, they validate observations made in vitro, showing that the viral polymerase acts very similarly in isolation and in complex with other viral and host proteins. Finally, these observations provide clues about the evolution of RdRps of positive-strand RNA viruses, which might contain the intrinsic ability to initiate internally.
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A novel hepatitis B virus recombinant genotype D4/E identified in a South African population. Heliyon 2019; 5:e01477. [PMID: 31008405 PMCID: PMC6453802 DOI: 10.1016/j.heliyon.2019.e01477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/08/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022] Open
Abstract
Background Genetic diversity is a characteristic trait of the hepatitis B virus (HBV) and has been associated with different clinical outcomes. In South Africa, HBV infection is a major public health concern. Most HBV infections are caused by genotype A strains. However rare cases of infection with HBV genotype D have been reported. The purpose of this study was to investigate the molecular characteristics of a rare HBV subgenotype D4 isolate. Methods The full-length genome of isolate ZADGM6964 was amplified in a one-step polymerase chain reaction. The amplified product was purified and cloned into a pGEM®-T Easy Vector System to investigate the genetic diversity of the viral quasi-populations. The primary isolate and clones were then directly sequenced and analysed using an array of bioinformatics software. Results Phylogenetic analysis showed that the primary isolate and cloned sequences formed a monophyletic cluster away from subgenotype D4 reference strains. Further recombination analysis revealed that isolate ZADGM6964 was in fact a D4/E recombinant strain with breakpoints identified within the X and overlapping pre-Core/Core open reading frames with a >70% bootstrap confidence level. The recombinant genotype D4/E was found to be unique from other D/E strains archived in the genetic database, GenBank. Conclusion This study represents the first ever report on the isolation and molecular characterization of an HBV D4/E recombinant strain in South Africa. The findings provide evidence of further HBV genetic diversity in South Africa than has been previously reported.
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Gourari S, Brichler S, Le Gal F, Abdou-Chekaraou M, Beloufa MA, Khelifa R, Djaballah H, Boufekane M, Nani A, Afredj N, Debzi N, Dény P, Gordien E, Tazir M. Hepatitis B virus and hepatitis delta virus subtypes circulating in Algeria and seroprevalence of HDV infection. J Med Virol 2018; 91:72-80. [PMID: 30168584 DOI: 10.1002/jmv.25301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 06/15/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Little is known about molecular characteristics of HBV strains circulating in Algeria and there are few data regarding HDV infection. OBJECTIVES The aim of this study is to describe the genetic diversity of HBV and HDV strains existing in Algeria and to determine the seroprevalence of HDV infection. STUDY DESIGN Plasma samples from 134 patients were analyzed by enzyme immunoassay method for HBV and HDV serological markers. Genotyping of HBV and HDV strains were performed using direct sequencing followed by phylogenetic analyses of the PreS1 and R0 region of the HBV and HDV genome respectively. RESULTS The PreS1 gene was successfully amplified in 119 patients (82 males and 37 females). Phylogenetic analysis of HBV strains revealed the presence of genotypes D (86.5%) and A2 (11.76%). The subgenotypes D are distributed as follows: HBV/D7 (43.5%), HBV/D3 (24.75%), HBV/D1 (16.8%) and HBV/D2 (14.85%). A recombinant between genotypes A, E and D was found. The seroprevalence of HDV infection among HBV carriers was less than 5.35%. Only one isolate of HDV genotype 1 was identified. CONCLUSIONS Our data indicate the predominance of HBV subgenotype D7 and a low prevalence of HDV infection.
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Affiliation(s)
- Samir Gourari
- Service de Microbiologie, CHU Mustapha, Algiers, Algeria
| | - Ségolène Brichler
- Service de Bactériologie, Virologie-Hygiène, Laboratoire associé au Centre National de Référence des Hépatites B, C et delta, Hôpital Avicenne, Bobigny, France
| | - Frédéric Le Gal
- Service de Bactériologie, Virologie-Hygiène, Laboratoire associé au Centre National de Référence des Hépatites B, C et delta, Hôpital Avicenne, Bobigny, France
| | - Mariama Abdou-Chekaraou
- Service de Bactériologie, Virologie-Hygiène, Laboratoire associé au Centre National de Référence des Hépatites B, C et delta, Hôpital Avicenne, Bobigny, France
| | | | - Rim Khelifa
- Service de Microbiologie, CHU Mustapha, Algiers, Algeria
| | | | | | | | - Nawel Afredj
- Service d'Hépatologie, CHU Mustapha, Algiers, Algeria
| | - Nabil Debzi
- Service d'Hépatologie, CHU Mustapha, Algiers, Algeria
| | - Paul Dény
- Service de Bactériologie, Virologie-Hygiène, Laboratoire associé au Centre National de Référence des Hépatites B, C et delta, Hôpital Avicenne, Bobigny, France
| | - Emmanuel Gordien
- Service de Bactériologie, Virologie-Hygiène, Laboratoire associé au Centre National de Référence des Hépatites B, C et delta, Hôpital Avicenne, Bobigny, France
| | - Mohamed Tazir
- Service de Microbiologie, CHU Mustapha, Algiers, Algeria
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Choi YM, Lee SY, Kim BJ. Naturally occurring hepatitis B virus reverse transcriptase mutations related to potential antiviral drug resistance and liver disease progression. World J Gastroenterol 2018; 24:1708-1724. [PMID: 29713126 PMCID: PMC5922991 DOI: 10.3748/wjg.v24.i16.1708] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/10/2018] [Accepted: 04/15/2018] [Indexed: 02/06/2023] Open
Abstract
The annual number of deaths caused by hepatitis B virus (HBV)-related disease, including cirrhosis and hepatocellular carcinoma (HCC), is estimated as 887000. The reported prevalence of HBV reverse transcriptase (RT) mutation prior to treatment is varied and the impact of preexisting mutations on the treatment of naïve patients remains controversial, and primarily depends on geographic factors, HBV genotypes, HBeAg serostatus, HBV viral loads, disease progression, intergenotypic recombination and co-infection with HIV. Different sensitivity of detection methodology used could also affect their prevalence results. Several genotype-dependent HBV RT positions that can affect the emergence of drug resistance have also been reported. Eight mutations in RT (rtL80I, rtD134N, rtN139K/T/H, rtY141F, rtM204I/V, rtF221Y, rtI224V, and rtM309K) are significantly associated with HCC progression. HBeAg-negative status, low viral load, and genotype C infection are significantly related to a higher frequency and prevalence of preexisting RT mutations. Preexisting mutations are most frequently found in the A-B interdomain of RT which overlaps with the HBsAg “a” determinant region, mutations of which can lead to simultaneous viral immune escape. In conclusion, the presence of baseline RT mutations can affect drug treatment outcomes and disease progression in HBV-infected populations via modulation of viral fitness and host-immune responses.
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Affiliation(s)
- Yu-Min Choi
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
| | - So-Young Lee
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
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Munshi SU, Tran TTT, Vo TNT, Tabassum S, Sultana N, Nguyen TH, Jahan M, Le CN, Baker S, Rahman M. Molecular characterization of hepatitis B virus in Bangladesh reveals a highly recombinant population. PLoS One 2017; 12:e0188944. [PMID: 29216251 PMCID: PMC5720799 DOI: 10.1371/journal.pone.0188944] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022] Open
Abstract
The natural history and treatment outcome of hepatitis B viruses (HBV) infection is largely dependent on genotype, subgenotype, and the presence or absence of virulence associated mutations. We have studied the prevalence of genotype and subgenotype as well as virulence and drug resistance associated mutations and prevalence of recombinant among HBV from Bangladesh. A prospective cross-sectional study was conducted among treatment naïve chronic HBV patients attending at Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh for HBV viral load assessment between June and August 2015. Systematical selected 50% of HBV DNA positive patients (every second patient) were enrolled. Biochemical and serological markers for HBV infection and whole genome sequencing (WGS) was performed on virus positive sample. Genotype, subgenotype, virulence, nucleos(t)ide analogue (NA) resistance (NAr) mutations, and the prevalence of recombinant isolates were determined. Among 114 HBV DNA positive patients, 57 were enrolled in the study and 53 HBV WGS were generated for downstream analysis. Overall, 38% (22/57) and 62% (35/57) of patients had acute and chronic HBV infections, respectively. The prevalence of genotypes A, C, and D was 18.9% (10/53), 45.3% (24/53), and 35.8% (19/53), respectively. Among genotype A, C and D isolates subgenotype A1 (90%; 9/10), C1 (87.5%; 21/24) and D2 (78.9%; 15/19) predominates. The acute infection, virulence associated mutations, and viral load was higher in the genotype D isolates. Evidence of recombination was identified in 22.6% (12/53) of the HBV isolates including 20.0% (2/10), and 16.7% (4/24) and 31.6% (6/19) of genotype A, C and D isolates, respectively. The prevalence of recombination was higher in chronic HVB patients (32.2%; 10/31 versus 9.1%; 2/22); p<0.05. NAr mutations were identified in 47.2% (25/53) of the isolates including 33.9% novel mutations (18/53). HBV genotype C and D predominated in this population in Bangladesh; a comparatively high prevalence of recombinant HBV are circulating in this setting.
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Affiliation(s)
- Saif Ullah Munshi
- Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - Thanh Thi Thanh Tran
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Truc Nhu Thanh Vo
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Shahina Tabassum
- Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - Nahida Sultana
- Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - Trang Hoa Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Munira Jahan
- Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - Chau Ngoc Le
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Motiur Rahman
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
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Liu B, Yang JX, Yan L, Zhuang H, Li T. Novel HBV recombinants between genotypes B and C in 3'-terminal reverse transcriptase (RT) sequences are associated with enhanced viral DNA load, higher RT point mutation rates and place of birth among Chinese patients. INFECTION GENETICS AND EVOLUTION 2017; 57:26-35. [PMID: 29111272 DOI: 10.1016/j.meegid.2017.10.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022]
Abstract
As one of the major global public health concerns, hepatitis B virus (HBV) can be divided into at least eight genotypes, which may be related to disease severity and treatment response. We previously demonstrated that genotypes B and C HBV, with distinct geographical distribution in China, had divergent genotype-dependent amino acid polymorphisms and variations in reverse transcriptase (RT) gene region, a target of antiviral therapy using nucleos(t)ide analogues. Recently recombination between HBV genotypes B and C was reported to occur in the RT region. However, their frequency and clinical significance is poorly understood. Here full-length HBV RT sequences from 201 Chinese chronic hepatitis B (CHB) patients were amplified and sequenced, among which 31.34% (63/201) were genotype B whereas 68.66% (138/201) genotype C. Although no intergenotypic recombination was detected among C-genotype HBV, 38.10% (24/63) of B-genotype HBV had recombination with genotype C in the 3'-terminal RT sequences. The patients with B/C intergenotypic recombinants had significantly (P<0.05) higher serum HBV DNA level than the "pure" B-genotype cohort did. Moreover, the B/C intergenotypic recombinants were prone to more substitutions at several specific residues in the RT region than genotype B or C. Besides, unlike their parental genotypes, the recombinant HBV appeared to display an altered geographic distribution feature in China. Our findings provide novel insight into the virological, clinical and epidemiological features of new HBV B/C intergenotypic recombinants at the 3' end of RT sequences among Chinese CHB patients. The highly complex genetic background of the novel recombinant HBV carrying new mutations affecting RT protein may contribute to an enhanced heterogeneity in treatment response or prognosis among CHB patients.
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Affiliation(s)
- Baoming Liu
- Department of Microbiology and Center of Infectious Diseases, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Jing-Xian Yang
- Department of Microbiology and Center of Infectious Diseases, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ling Yan
- Department of Microbiology and Center of Infectious Diseases, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hui Zhuang
- Department of Microbiology and Center of Infectious Diseases, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Tong Li
- Department of Microbiology and Center of Infectious Diseases, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
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12
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Castelhano N, Araujo NM, Arenas M. Heterogeneous recombination among Hepatitis B virus genotypes. INFECTION GENETICS AND EVOLUTION 2017; 54:486-490. [PMID: 28827173 DOI: 10.1016/j.meegid.2017.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/13/2017] [Accepted: 08/17/2017] [Indexed: 02/06/2023]
Abstract
The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic.
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Affiliation(s)
- Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Miguel Arenas
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
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13
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Matsuo J, Do SH, Yamamoto C, Nagashima S, Chuon C, Katayama K, Takahashi K, Tanaka J. Clustering infection of hepatitis B virus genotype B4 among residents in Vietnam, and its genomic characters both intra- and extra-family. PLoS One 2017; 12:e0177248. [PMID: 28753615 PMCID: PMC5533320 DOI: 10.1371/journal.pone.0177248] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/24/2017] [Indexed: 02/07/2023] Open
Abstract
Vietnam has a high rate of hepatitis B virus (HBV) infection and a high mortality rate from hepatocellular carcinoma. We performed a detailed genetic analysis of 48 residents and four families from Binh Thuan Province, a southern coastal area of Vietnam. The route of infection and genomic characteristics related to hepatocellular carcinoma (HCC) were studied in HBV spread among carriers that we detected in our previous hepatitis survey. The HBV genotype was B4 in 91.7% and C1 in 8.3% of the cases. The intra-family’s HBV sequence homology was high at 96.8–99.4%. However, it was also high at 99.4–99.8% among residents of the same age and sex as family members. In addition, full genome analysis was performed in 21 cases. The core region of all 20 isolates with genotype B4 was a recombinant of genotype C, and pre-S deletion was found in 20% of cases. The promoter mutation G1613A was found in 13.6% of cases, and a 24 bp insertion from nt1673 in the X region was found in 6.3% of cases. The phylogenetic tree and homology analysis of the HBV full genome suggested the probability and its possibility of horizontal transmission not only within families nor vertical transmission but within cohorts of the same generation in the population. Moreover, the HBV genotype B4 isolates were found not only to be recombinants of genotype C, which results in a high cancer risk, but also to have other risk of HCC, pre-S deletions, the G1613A mutation, and X region insertions corresponding to the promoter. These genomic characters were suggested to be one of the factors to explain the high HCC mortality rate in Vietnam.
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Affiliation(s)
- Junko Matsuo
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Son Huy Do
- Binh Thuan Medical College, Phan Thiet City, Binh Thuan Province, Vietnam
| | - Chikako Yamamoto
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shintaro Nagashima
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Channarena Chuon
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Keiko Katayama
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuaki Takahashi
- Department of Medical Sciences, Toshiba General Hospital, Tokyo, Japan
| | - Junko Tanaka
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- * E-mail:
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14
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Quer J, Rodríguez-Frias F, Gregori J, Tabernero D, Soria ME, García-Cehic D, Homs M, Bosch A, Pintó RM, Esteban JI, Domingo E, Perales C. Deep sequencing in the management of hepatitis virus infections. Virus Res 2017; 239:115-125. [PMID: 28040474 DOI: 10.1016/j.virusres.2016.12.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/10/2016] [Accepted: 12/22/2016] [Indexed: 02/07/2023]
Abstract
The hepatitis viruses represent a major public health problem worldwide. Procedures for characterization of the genomic composition of their populations, accurate diagnosis, identification of multiple infections, and information on inhibitor-escape mutants for treatment decisions are needed. Deep sequencing methodologies are extremely useful for these viruses since they replicate as complex and dynamic quasispecies swarms whose complexity and mutant composition are biologically relevant traits. Population complexity is a major challenge for disease prevention and control, but also an opportunity to distinguish among related but phenotypically distinct variants that might anticipate disease progression and treatment outcome. Detailed characterization of mutant spectra should permit choosing better treatment options, given the increasing number of new antiviral inhibitors available. In the present review we briefly summarize our experience on the use of deep sequencing for the management of hepatitis virus infections, particularly for hepatitis B and C viruses, and outline some possible new applications of deep sequencing for these important human pathogens.
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Affiliation(s)
- Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Francisco Rodríguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Roche Diagnostics, S.L., Sant Cugat del Vallés, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Maria Eugenia Soria
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain
| | - Damir García-Cehic
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Maria Homs
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Albert Bosch
- Department of Microbiology, Enteric Virus Laboratory, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Rosa María Pintó
- Department of Microbiology, Enteric Virus Laboratory, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Celia Perales
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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15
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Jia J, Li H, Wang H, Chen S, Wang M, Feng H, Gao Y, Wang Y, Fang M, Gao C. Hepatitis B virus core antigen mutations predict post-operative prognosis of patients with primary hepatocellular carcinoma. J Gen Virol 2017; 98:1399-1409. [PMID: 28640739 PMCID: PMC5656792 DOI: 10.1099/jgv.0.000790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/26/2017] [Indexed: 12/11/2022] Open
Abstract
The aim of this study was to explore the relationship between hepatitis B virus (HBV) core antigen (HBc) mutations and the post-operative prognosis of HBV-related hepatocellular carcinoma (HCC). In total, 98 patients suffering from HBV-related HCC and treated with surgery were enrolled, with a 48 month follow-up. The preCore/Core region of the HBV genome from tumour tissue (TT) and paired adjacent non-tumour tissue (ANTT) of these patients was sequenced, and a phylogenetic tree was reconstructed. The correlations between the viral features and evolutionary divergence of preCore/Core amino acid sequences from 67 paired TTs and ANTTs were analysed. Cox proportional hazard model analysis was applied for post-operative hazard risk evaluation. Phylogenetic analysis revealed that all of the sequences were ascribed to genotype C. The evolutionary divergence of amino acid sequences from matched TTs and ANTTs was significantly negatively correlated with serum and intrahepatic HBV DNA levels. Multivariate analysis showed that the HBc E77 mutation was associated with shorter overall survival, and HBc S87 and P156 mutations were independent risk factors for relapse. Furthermore, in contrast to with patients without the S87 mutation, no correlation was observed between serum HBV DNA and intrahepatic HBV DNA in HCC patients with the S87 mutation. Analysis of the intrahepatic sequence may advance our understanding of viral status; thus, it is useful for prognosis prediction for HBV-related HCC.
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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, 105th Hospital of PLA, Hefei 230031, PR China
| | - Huiming Li
- 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, First Affiliated Hospital of Chinese PLA’s General Hospital, Beijing 100048, PR China
| | - Shipeng Chen
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Mengmeng Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Huijuan Feng
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Yuzhen Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Yunjiu Wang
- 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
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
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16
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Li S, Wang Z, Li Y, Ding G. Adaptive evolution of proteins in hepatitis B virus during divergence of genotypes. Sci Rep 2017; 7:1990. [PMID: 28512348 PMCID: PMC5434055 DOI: 10.1038/s41598-017-02012-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/03/2017] [Indexed: 12/12/2022] Open
Abstract
Hepatitis B virus (HBV) is classified into several genotypes, correlated with different geographic distributions, clinical outcomes and susceptible human populations. It is crucial to investigate the evolutionary significance behind the diversification of HBV genotypes, because it improves our understanding of their pathological differences and pathogen-host interactions. Here, we performed comprehensive analysis of HBV genome sequences collected from public database. With a stringent criteria, we generated a dataset of 2992 HBV genomes from eight major genotypes. In particular, we applied a specified classification of non-synonymous and synonymous variants in overlapping regions, to distinguish joint and independent gene evolutions. We confirmed the presence of selective constraints over non-synonymous variants in consideration of overlapping regions. We then performed the McDonald-Kreitman test and revealed adaptive evolutions of non-synonymous variants during genotypic differentiation. Remarkably, we identified strong positive selection that drove the differentiation of PreS1 domain, which is an essential regulator involved in viral transmission. Our study presents novel evidences for the adaptive evolution of HBV genotypes, which suggests that these viruses evolve directionally for maintenance or improvement of successful infections.
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Affiliation(s)
- Shengdi Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Zhen Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, China
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, China.
- Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, 1278 Keyuan Road, 201203, Shanghai, China.
| | - Guohui Ding
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, China.
- Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, 1278 Keyuan Road, 201203, Shanghai, China.
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17
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Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I. Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep 2017; 7:40712. [PMID: 28102365 PMCID: PMC5244389 DOI: 10.1038/srep40712] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/08/2016] [Indexed: 11/25/2022] Open
Abstract
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. The resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.
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Affiliation(s)
- Qian Zhang
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA
| | - Se-Ran Jun
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Michael Leuze
- Joint Institute for Computational Sciences, University of Tennessee, Knoxville, TN 37831, USA
- Computational Biomolecular Modeling and Bioinformatics Group, Computer Science and Mathematics Division, Oak Ridge National Laboratories, Oak Ridge, TN 37831, USA
| | - David Ussery
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Intawat Nookaew
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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18
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Lv Q, Zhang H, Tian L, Zhang R, Zhang Z, Li J, Tong Y, Fan H, Carr MJ, Shi W. Novel sub-lineages, recombinants and reassortants of severe fever with thrombocytopenia syndrome virus. Ticks Tick Borne Dis 2017; 8:385-390. [PMID: 28117273 DOI: 10.1016/j.ttbdis.2016.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 11/30/2022]
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) has been continuously circulating in Eastern Asia in recent years, without the availability of effective vaccines or antiviral drugs, posing a serious threat to public health, particularly in the central-eastern provinces of China. In this study, we isolated and sequenced four new SFTSV strains from Shandong Province identified in 2015. Phylogenetic analysis, with all publicly available L, M and S gene segments, revealed that the four newly described SFTSV strains belonged to genotype C3. In addition, our phylogenetic analyses also identified two potentially novel sub-lineages of SFTSV, tentatively named C6 and J4. Our comprehensive analysis revealed twenty recombination events in fourteen SFTSV genomes and recombination events were found in the S gene segment for the first time. A total of twenty-six strains were probable SFTSV reassortants, including sixteen which were previously unidentified. We further characterised the genetic constellation of these putative reassortants and classified them into twelve different reassortment forms. Our study revealed multiple evolutionary forces acting on SFTSV, responsible for the increasing genetic diversity of this agent, which could potentially alter the antigenicity and pathogenicity of the virus. This calls for an urgent need for intensified surveillance and the development of vaccines and antiviral drugs against this high-consequence pathogen.
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Affiliation(s)
- Qiang Lv
- Institute of Pathogen Biology, Taishan Medical College, Taian, Shandong 271000, China
| | - Hong Zhang
- The Affiliated Hospital of Taishan Medical University, Taian, Shandong 271000, China
| | - Lei Tian
- The 88 Hospital of The Chinese People's Liberation Army, Taian, Shandong 271000, China
| | - Ruiling Zhang
- Institute of Pathogen Biology, Taishan Medical College, Taian, Shandong 271000, China
| | - Zhenjie Zhang
- Institute of Pathogen Biology, Taishan Medical College, Taian, Shandong 271000, China
| | - Juan Li
- Institute of Pathogen Biology, Taishan Medical College, Taian, Shandong 271000, China
| | - Yigang Tong
- Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Hang Fan
- Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Michael J Carr
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0020, Japan; National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Weifeng Shi
- Institute of Pathogen Biology, Taishan Medical College, Taian, Shandong 271000, China.
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19
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Liao H, Li X, Liu Y, Xu Z, Huang P, Nian X, Liu X, Xu D. Intergenotype recombinant analysis of full-length hepatitis B virus genomes from 516 Chinese patients with different illness categories. J Med Virol 2016; 89:139-145. [PMID: 27328656 DOI: 10.1002/jmv.24609] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 01/05/2023]
Abstract
This study aimed to reveal characteristics and clinical relevance of HBV intergenotypic recombinants. Serum samples of 516 patients from Northern China were collected, including 131 with acute hepatitis B (AHB), 239 with chronic hepatitis B (CHB), and 146 with acute-on-chronic liver failure (ACLF). Full-length HBV genomes were sequenced and HBV genotypes were analyzed. Genotypes C, B, D, and intergenotypic recombinants were detected in 71.12% (367/516), 19.96% (103/516), 0.78% (4/516), and 8.14% (42/516) of the patients. The latter comprised 21 with AHB, 10 with CHB, and 11 with ACLF; and the occupations of intergenotypic recombinants in AHB, CHB, and ACLF groups were 16.03%, 4.18%, and 7.53% (P < 0.01), respectively. HBV B/C and C/D hybrids accounted for 85.71% (36/42) and 14.29% (6/42) of the intergenotypic recombinants. In AHB and CHB groups, serum HBV DNA levels were significantly lower in patients with intergenotypic recombinants than those without intergenotypic recombinants. Difference in basal core promoter A1762T/G1764A mutations and precore G1896A mutation incidences was not significant between B/C recombinant and genotypes B or C virus, although the significance was there between genotypes B and C viruses. Clonal sequence analysis showed that intergenotypic recombinant viral strains existed in single or in concomitance with other genotype virus. Phenotypic analysis showed that viral replication capacity was similar between recombinant and non-recombinant strains in tested samples. Taken together, the occurrence of intergenotypic recombinant HBV is relatively low in HBV-infected patients in Northern China, and intergenotypic recombinant HBV infection is likely favorable to induce an acute course of disease. J. Med. Virol. 89:139-145, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hao Liao
- Research Center for Clinical and Translational Medicine, Beijing 302 Hospital, Beijing, China
| | - Xiaodong Li
- Research Center for Clinical and Translational Medicine, Beijing 302 Hospital, Beijing, China
| | - Yan Liu
- Research Center for Clinical and Translational Medicine, Beijing 302 Hospital, Beijing, China
| | - Zhihui Xu
- Research Center for Clinical and Translational Medicine, Beijing 302 Hospital, Beijing, China
| | - Pengyu Huang
- Institute of Biochemistry and Molecular Biology, Guangdong Medical College, Guangdong, China
| | - Xueyuan Nian
- Research Center for Clinical and Translational Medicine, Beijing 302 Hospital, Beijing, China
| | - Xinguang Liu
- Institute of Biochemistry and Molecular Biology, Guangdong Medical College, Guangdong, China. .,Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong, China.
| | - Dongping Xu
- Research Center for Clinical and Translational Medicine, Beijing 302 Hospital, Beijing, China. .,Institute of Biochemistry and Molecular Biology, Guangdong Medical College, Guangdong, China.
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Kramvis A. The clinical implications of hepatitis B virus genotypes and HBeAg in pediatrics. Rev Med Virol 2016; 26:285-303. [PMID: 27139263 PMCID: PMC5084815 DOI: 10.1002/rmv.1885] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/02/2016] [Accepted: 04/04/2016] [Indexed: 12/12/2022]
Abstract
Although a successful vaccine against HBV has been implemented in 184 countries, eradication of hepatitis B virus (HBV) is still not on the horizon. There are over 240 million chronic carriers of HBV globally. The risk of developing chronic hepatitis ranges from >90% in newborns of hepatitis Be antigen (HBeAg)‐positive mothers, 25%–35% in children under 5 years of age and <5% in adults. HBeAg, a non‐particulate viral protein, is a marker of HBV replication. This is the only HBV antigen to cross the placenta, leading to specific unresponsiveness of helper T cells to the capsid protein and HBeAg in newborns. HBeAg is tolerated in utero and acts as a tolerogen after birth. Perinatal transmission is frequent when mothers are HBeAg‐positive, whereas it occurs less frequently when mothers are HBeAg‐negative. Sequence heterogeneity is a feature of HBV. Based on an intergroup divergence >7.5% across the complete genome, HBV is classified phylogenetically into at least nine genotypes. With between ~4% and 8% intergroup nucleotide divergence, genotypes A–D, F, H and I are classified further into subgenotypes. HBV genotypes/subgenotypes may have distinct geographical distribution and can develop different mutations in the regions of the HBV genome that code for HBeAg. These differences can be related to the role of HBV genotypes to the natural history of infection and mode of transmission. Thus genotypes/subgenotypes of HBV can be responsible for the different natural history of infection and modes of transmission in children, found in various regions of the world, where different genotypes/subgenotypes prevail. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Anna Kramvis
- Hepatitis Virus Diversity Research Unit (HVDRU), Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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21
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Tong S, Revill P. Overview of hepatitis B viral replication and genetic variability. J Hepatol 2016; 64:S4-S16. [PMID: 27084035 PMCID: PMC4834849 DOI: 10.1016/j.jhep.2016.01.027] [Citation(s) in RCA: 276] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 02/06/2023]
Abstract
Chronic infection with hepatitis B virus (HBV) greatly increases the risk for liver cirrhosis and hepatocellular carcinoma (HCC). HBV isolates worldwide can be divided into ten genotypes. Moreover, the immune clearance phase selects for mutations in different parts of the viral genome. The outcome of HBV infection is shaped by the complex interplay of the mode of transmission, host genetic factors, viral genotype and adaptive mutations, as well as environmental factors. Core promoter mutations and mutations abolishing hepatitis B e antigen (HBeAg) expression have been implicated in acute liver failure, while genotypes B, C, subgenotype A1, core promoter mutations, preS deletions, C-terminal truncation of envelope proteins, and spliced pregenomic RNA are associated with HCC development. Our efforts to treat and prevent HBV infection are hampered by the emergence of drug resistant mutants and vaccine escape mutants. This paper provides an overview of the HBV life cycle, followed by review of HBV genotypes and mutants in terms of their biological properties and clinical significance.
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Affiliation(s)
- Shuping Tong
- Liver Research Center, Rhode Island Hospital, The Alpert Warren School of Medicine, Brown University, Providence, RI, USA; Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Peter Revill
- Research and Molecular Development, Victorian Infectious Diseases Reference Laboratory, Doherty Institute, Melbourne, VIC, Australia ()
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22
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Zhang ZH, Wu CC, Chen XW, Li X, Li J, Lu MJ. Genetic variation of hepatitis B virus and its significance for pathogenesis. World J Gastroenterol 2016; 22:126-144. [PMID: 26755865 PMCID: PMC4698480 DOI: 10.3748/wjg.v22.i1.126] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) has a worldwide distribution and is endemic in many populations. Due to its unique life cycle which requires an error-prone reverse transcriptase for replication, it constantly evolves, resulting in tremendous genetic variation in the form of genotypes, sub-genotypes, and mutations. In recent years, there has been considerable research on the relationship between HBV genetic variation and HBV-related pathogenesis, which has profound implications in the natural history of HBV infection, viral detection, immune prevention, drug treatment and prognosis. In this review, we attempted to provide a brief account of the influence of HBV genotype on the pathogenesis of HBV infection and summarize our current knowledge on the effects of HBV mutations in different regions on HBV-associated pathogenesis, with an emphasis on mutations in the preS/S proteins in immune evasion, occult HBV infection and hepatocellular carcinoma (HCC), mutations in polymerase in relation to drug resistance, mutations in HBV core and e antigen in immune evasion, chronicalization of infection and hepatitis B-related acute-on-chronic liver failure, and finally mutations in HBV x proteins in HCC.
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23
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Buti M, Tabernero D, Mas A, Homs M, Prieto M, Rodríguez-Frías F, Casafont F, Casillas R, González A, Miras M, Herrero JI, Castells L, Esteban R. Hepatitis B virus quasispecies evolution after liver transplantation in patients under long-term lamivudine prophylaxis with or without hepatitis B immune globulin. Transpl Infect Dis 2015; 17:208-20. [PMID: 25641570 DOI: 10.1111/tid.12360] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/23/2014] [Accepted: 01/18/2015] [Indexed: 12/22/2022]
Abstract
AIMS To investigate an optimal long-term prophylactic strategy for prevention of hepatitis B virus (HBV) recurrence after liver transplantation, we conducted a randomized study of 29 transplant recipients receiving a short course of hepatitis B immune globulin (HBIg) + lamivudine (LAM), followed by randomization to long-term prophylaxis with LAM with or without HBIg. METHODS The efficacy and safety, and impact on survival and HBV recurrence of these 2 prophylactic regimens were compared over a mean period of 10 years. In patients with viral recurrence, the HBV quasispecies in the surface/polymerase region were studied by ultra-deep pyrosequencing (UDPS). RESULTS The 10-year survival rate was 76% and was not affected by the type of prophylaxis. Four patients had hepatitis B surface antigen (HBsAg) recurrence within the first 48 months after orthotopic liver transplantation (OLT). HBsAg-positive and -negative patients showed similar mean survival times, with no differences between the 2 regimens. Low HBV DNA levels were transiently detected in 32% of HBsAg-negative patients. UDPS showed major changes after OLT in the HBV quasispecies of patients with viral recurrence, which may be explained by a "bottleneck" effect of OLT together with prophylactic therapy. CONCLUSION Long-term survival after OLT in end-stage chronic hepatitis B patients was good with both prophylactic strategies. However, low, transient HBV DNA levels were detected even in the absence of HBsAg, showing the importance of continuing HBV prophylaxis.
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Affiliation(s)
- M Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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24
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Araujo NM. Hepatitis B virus intergenotypic recombinants worldwide: An overview. INFECTION GENETICS AND EVOLUTION 2015; 36:500-510. [PMID: 26299884 DOI: 10.1016/j.meegid.2015.08.024] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/11/2015] [Accepted: 08/19/2015] [Indexed: 02/07/2023]
Abstract
Novel variants generated by recombination events between different hepatitis B virus (HBV) genotypes have been increasingly documented worldwide, and the role of recombination in the evolutionary history of HBV is of significant research interest. In the present study, large-scale data retrieval and analysis on HBV intergenotypic recombinant genomes were performed. The geographical distribution of HBV recombinants as well as the molecular processes involved in recombination were examined. After review of published data, a total of 436 complete HBV sequences, previously identified as recombinants, were included in the recombination detection analysis. About 60% of HBV recombinants were B/C (n=179) and C/D (n=83) hybrids. A/B/C, A/C, A/C/G, A/D, A/E, A/G, B/C/U (U=unknown genotype), C/F, C/G, C/J, D/E, D/F, and F/G hybrids were additionally identified. HBV intergenotypic sequences were reported in almost all geographical regions with similar circulation patterns as their original genotypes, indicating the potential for spreading in a wide range of human populations and developing their own epidemiology. Recombination breakpoints were non-randomly distributed in the genome, and specific favored sites detected, such as within nt 1700-2000 and 2100-2300 regions, which displayed a statistically significant difference in comparison with the remaining genome. Elucidation of the effects of recombination events on the evolutionary history of HBV is critical to understand current and future evolution trends.
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Affiliation(s)
- Natalia M Araujo
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, 21040-360 Rio de Janeiro, RJ, Brazil.
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Hou Z, Huang J, Zhong C, Li L, Xie Q, Ma M, Han T, Wang D, Maldonado M, Xu L, Huang T, Zhong Y. CpG islands of hepatitis B virus genome isolated from Chinese patients. Gene 2015; 561:261-7. [PMID: 25688883 DOI: 10.1016/j.gene.2015.02.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/22/2015] [Accepted: 02/13/2015] [Indexed: 02/05/2023]
Abstract
There are differences in the distribution and length of HBV CpG islands and the viral mutations contribute greatly to the development of HBV-related diseases. However, little is known regarding the effects of such difference and mutations in HBV genotypes B and C sequences on the regulation of HBV gene expression and their clinical outcomes. To study the distribution, length and genetic trait of CpG islands in normal and mutant sequences of HBV genotypes B and C, 320 HBV isolates from Chinese patients were retrieved from GenBank. Programs CLUSTALX 1.83 and MethPrimer were employed to perform multiple sequence alignments and to predict CpG islands, respectively. 72.0% genotype B isolates contained three conventional CpG islands, and 76.1% genotype C only contained CpG islands II and III. 14.6% genotype B and 7.5% genotype C contained three novel CpG islands. In genotype B, lengths of conventional CpG islands between normal and mutant isolates exhibited substantial variations, but in genotype C, those were relatively stable. CpG island II could be "truncated" or "split". "Truncated" region mutations were associated with structural and functional abnormalities of HBV genes. Rate of "split" CpG island II in genotype B was much higher than that in genotype C. In the majority of isolates from HCC and HBV-ACLF, genotype C lacked CpG island I and novel islands. Distribution, length and genetic trait of CpG islands in HBV genotypes B and C might affect their methylation status, and further affect regulation of HBV gene expression, leading to different clinical outcomes.
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Affiliation(s)
- Zhiwei Hou
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Research Center for Reproductive Medicine, Shantou University Medical College, Shantou 515041, China
| | - Jihua Huang
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, Chengdu 610000, China
| | - Chengyao Zhong
- Faculty of Science and Engineering, University Paul Sabatier, Toulouse 31062, France
| | - Lianbing Li
- Key Laboratory of Birth Defects and Reproductive Health of National Health and Family Planning Commission, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 400020, China
| | - Qingdong Xie
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Research Center for Reproductive Medicine, Shantou University Medical College, Shantou 515041, China
| | - Mingfu Ma
- Key Laboratory of Birth Defects and Reproductive Health of National Health and Family Planning Commission, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 400020, China
| | - Tingting Han
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, Chengdu 610000, China
| | - Degang Wang
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Research Center for Reproductive Medicine, Shantou University Medical College, Shantou 515041, China
| | - Martin Maldonado
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Research Center for Reproductive Medicine, Shantou University Medical College, Shantou 515041, China
| | - Lan Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Research Center for Reproductive Medicine, Shantou University Medical College, Shantou 515041, China
| | - Tianhua Huang
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Research Center for Reproductive Medicine, Shantou University Medical College, Shantou 515041, China.
| | - Ying Zhong
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, Chengdu 610000, China.
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Qian Z, Jianqiong W, Hongmei L, Rong Z, Li L, Jinping Z, Tao S. Distribution and epidemiologic trends of HBV genotypes and subtypes in 14 countries neighboring china. HEPATITIS MONTHLY 2015; 15:e24422. [PMID: 26045702 PMCID: PMC4451280 DOI: 10.5812/hepatmon.15(5)2015.24422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 03/10/2015] [Accepted: 04/14/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND The number of cases of HBV infection reported by the WHO for each district and country is positively correlated with the number of HBV sequences in the database isolated from the corresponding district and country. OBJECTIVES This study determined distribution characteristics of HBV genotypes and subtypes in 14 countries neighboring China. The progress made in genomic research involving HBV was also reviewed. MATERIALS AND METHODS Nine hundred fifty-one complete genome sequences of HBV from 14 countries neighboring China were selected from NCBI. The sequence-related information was analyzed and recorded. One hundred seventy-two sequences of HBV genotype B were screened for alignment using DNA star and MEGA 5.1. RESULTS Dominant HBV genotypes in the countries neighboring China were genotypes B, C and D and dominant subtypes were adw2 and adrq+. The association between genotype and serotype of HBV in these countries was shown to differ from previous research results. As shown by sequence alignment, the sequence divergence between five subgenotypes (B3, B5, B7, B8 and B9) was below 4%. The B subgenotypes shared six common specific amino acid sites in the S region. CONCLUSIONS The B3, B5, B7, B8 and B9 subgenotypes can be clustered into quasi-sub-genotype B3 and the open reading frame of HBV has a start codon preference; however, whether a mutation in the start codon in the pre-S2 region has an impact on survival and replication of HBV remains to be determined.
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Affiliation(s)
- Zhao Qian
- Kunming Medical College, Kunming, Yunnan, China
- Institute of Basic and Clinical Medicine, Provincial Key Laboratory for Birth Defects and Genetic Diseases, the First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming Science and Technology University, Kunming, Yunnan Province, China
| | - Wang Jianqiong
- Clinical Laboratory, the First People’s Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Li Hongmei
- Institute of Basic and Clinical Medicine, Provincial Key Laboratory for Birth Defects and Genetic Diseases, the First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming Science and Technology University, Kunming, Yunnan Province, China
- Kunming Science and Technology University, Kunming, Yunnan, China
| | - Zeng Rong
- Institute of Basic and Clinical Medicine, Provincial Key Laboratory for Birth Defects and Genetic Diseases, the First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming Science and Technology University, Kunming, Yunnan Province, China
| | - Li Li
- Institute of Basic and Clinical Medicine, Provincial Key Laboratory for Birth Defects and Genetic Diseases, the First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming Science and Technology University, Kunming, Yunnan Province, China
| | - Zhang Jinping
- Institute of Basic and Clinical Medicine, Provincial Key Laboratory for Birth Defects and Genetic Diseases, the First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming Science and Technology University, Kunming, Yunnan Province, China
| | - Shen Tao
- Institute of Basic and Clinical Medicine, Provincial Key Laboratory for Birth Defects and Genetic Diseases, the First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming Science and Technology University, Kunming, Yunnan Province, China
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27
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Universal Primers for Detection and Sequencing of Hepatitis B Virus Genomes across Genotypes A to G. J Clin Microbiol 2015; 53:1831-5. [PMID: 25788548 DOI: 10.1128/jcm.03449-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/12/2015] [Indexed: 01/05/2023] Open
Abstract
Hepatitis B virus (HBV) has been divided into 10 genotypes, A to J, based on an 8% nucleotide sequence divergence between genotypes. The conventional practice of using a single set of primers to amplify a near-complete HBV genome is hampered by its low analytical sensitivity. The current practice of using overlapping conserved primer sets to amplify a complete HBV genome in a clinical sample is limited by the lack of pan-primers to detect all HBV genotypes. In this study, we designed six highly conserved, overlapping primer sets to cover the complete HBV genome. We based our design on the sequences of 5,154 HBV genomes of genotypes A to I downloaded from the GenBank nucleotide database. These primer sets were tested on 126 plasma samples from Malaysia, containing genotypes A to D and with viral loads ranging from 20 to >79,780,000 IU/ml. The overall success rates for PCR amplification and sequencing were >96% and >94%, respectively. Similarly, there was 100% amplification and sequencing success when the primer sets were tested on an HBV reference panel of genotypes A to G. Thus, we have established primer sets that gave a high analytical sensitivity for PCR-based detection of HBV and a high rate of sequencing success for HBV genomes in most of the viral genotypes, if not all, without prior known sequence data for the particular genotype/genome.
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Zhong C, Hou Z, Huang J, Xie Q, Zhong Y. Mutations and CpG islands among hepatitis B virus genotypes in Europe. BMC Bioinformatics 2015; 16:38. [PMID: 25652331 PMCID: PMC4339741 DOI: 10.1186/s12859-015-0481-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 01/27/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) genotypes have a distinct geographical distribution and influence disease progression and treatment outcomes. The purpose of this study was to investigate the distribution of HBV genotypes in Europe, the impact of mutation of different genotypes on HBV gene abnormalities, the features of CpG islands in each genotype and their potential role in epigenetic regulation. RESULTS Of 383 HBV isolates from European patients, HBV genotypes A-G were identified, with the most frequent being genotype D (51.96%) in 12 countries, followed by A (39.16%) in 7 countries, and then E (3.66%), G (2.87%), B (1.57%), F (0.52%) and C (0.26%). A higher rate of mutant isolates were identified in those with genotype D (46.7%) followed by G (45.5%), and mutations were associated with structural and functional abnormalities of HBV genes. Conventional CpG island I was observed in genotypes A, B, C, D and E. Conventional islands II and III were detected in all A-G genotypes. A novel CpG island IV was found in genotypes A, D and E, and island V was only observed in genotype F. The A-G genotypes lacked the novel CpG island VI. "Split" CpG island I in genotypes D and E and "split" island II in genotypes A, D, E, F and G were observed. Two mutant isolates from genotype D and one from E were found to lack both CpG islands I and III. CONCLUSIONS HBV genotypes A-G were identified in European patients. Structural and functional abnormalities of HBV genes were caused by mutations leading to the association of genotypes D and G with increased severity of liver disease. The distribution, length and genetic traits of CpG islands were different between genotypes and their biological and clinical significances warrant further study, which will help us better understand the potential role of CpG islands in epigenetic regulation of the HBV genome.
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Affiliation(s)
- Chengyao Zhong
- Faculty of Science and Engineering, University Paul Sabatier, Toulouse, 31062, France.
| | - Zhiwei Hou
- Key Laboratory of Birth Defects and Reproductive Health of National Health and Family Planning Commission, Chongqing Research Institute for Population and Family Planning Science and Technology, Chongqing, 400020, China.
| | - Jihua Huang
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, Chengdu, 610066, China.
| | - Qingdong Xie
- Research Center for Reproductive Medicine, Shantou University Medical College, Shantou, 515041, China.
| | - Ying Zhong
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, Chengdu, 610066, China.
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Caballero A, Gregori J, Homs M, Tabernero D, Gonzalez C, Quer J, Blasi M, Casillas R, Nieto L, Riveiro-Barciela M, Esteban R, Buti M, Rodriguez-Frias F. Complex Genotype Mixtures Analyzed by Deep Sequencing in Two Different Regions of Hepatitis B Virus. PLoS One 2015; 10:e0144816. [PMID: 26714168 PMCID: PMC4695080 DOI: 10.1371/journal.pone.0144816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023] Open
Abstract
This study assesses the presence and outcome of genotype mixtures in the polymerase/surface and X/preCore regions of the HBV genome in patients with chronic hepatitis B virus (HBV) infection. Thirty samples from ten chronic hepatitis B patients were included. The polymerase/surface and X/preCore regions were analyzed by deep sequencing (UDPS) in the first available sample at diagnosis, a pre-treatment sample, and a sample while under treatment. HBV genotype was determined by phylogenesis. Quasispecies complexity was evaluated by mutation frequency and nucleotide diversity. The polymerase/surface and X/preCore regions were validated for genotyping from 113 GenBank reference sequences. UDPS yielded a median of 10,960 sequences per sample (IQR 16,645) in the polymerase/surface region and 11,595 sequences per sample (IQR 14,682) in X/preCore. Genotype mixtures were more common in X/preCore (90%) than in polymerase/surface (30%) (p<0.001). On X/preCore genotyping, all samples were genotype A, whereas polymerase/surface yielded genotypes A (80%), D (16.7%), and F (3.3%) (p = 0.036). Genotype changes in polymerase/surface were observed in four patients during natural quasispecies dynamics and in two patients during treatment. There were no genotype changes in X/preCore. Quasispecies complexity was higher in X/preCore than in polymerase/surface (p = 0.004). The results provide evidence of genotype mixtures and differential genotype proportions in the polymerase/surface and X/preCore regions. The genotype dynamics in HBV infection and the different patterns of quasispecies complexity in the HBV genome suggest a new paradigm for HBV genotype classification.
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Affiliation(s)
- Andrea Caballero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Diseases Unit, Vall d’Hebron Research Institute, Barcelona, Spain
- Roche Diagnostics S.L., Sant Cugat del Vallès, Spain
| | - Maria Homs
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Carolina Gonzalez
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Diseases Unit, Vall d’Hebron Research Institute, Barcelona, Spain
| | - Maria Blasi
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosario Casillas
- Liver Diseases Unit, Vall d’Hebron Research Institute, Barcelona, Spain
| | - Leonardo Nieto
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- * E-mail:
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Abstract
Sequence heterogeneity is a feature of hepatitis B virus (HBV), the prototype member of the family Hepadnaviridae. Based on an intergroup divergence of greater than 7.5% across the complete genome, HBV has been classified phylogenetically into 9 genotypes, A-I, with a putative 10th genotype 'J', isolated from a single individual. With between approximately 4 and 8% intergroup nucleotide divergence across the complete genome and good bootstrap support, genotypes A-D, F, H, and I are classified further into subgenotypes. There is a broad and highly statistically significant correlation between serological subtypes and genotypes, and in some cases, serological subtypes can be used to differentiate subgenotypes. The genotypes, and certain subgenotypes, have distinct geographical distributions and are important in both the clinical manifestation of infection and response to antiviral therapy. HBV genotypes/subgenotypes and genetic variability of HBV are useful in epidemiological and transmission studies, tracing human migrations, and in predicting the risk for the development of severe liver disease and response to antiviral therapy. Moreover, knowledge of the genotype/subgenotype is important in implementing preventative strategies. Thus, it is crucial that new strains are correctly assigned to their respective genotype/subgenotype and consistent, unambiguous, and generally accepted nomenclature is utilized.
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Affiliation(s)
- Anna Kramvis
- Hepatitis Virus Diversity Research Programme (HVDRP), Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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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: 144] [Impact Index Per Article: 14.4] [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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Trinks J, Sugiyama M, Tanaka Y, Kurbanov F, Benetucci J, Giménez E, Weissenbacher MC, Mizokami M, Oubiña JR. In vitro replication competence of a hepatitis B genotype D/A recombinant virus: dissimilar biological behaviour regarding its parental genotypes. J Gen Virol 2013; 94:2724-2728. [PMID: 24026673 DOI: 10.1099/vir.0.053595-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
Hepatitis B virus (HBV) DNA recombinants contribute to ~30% of the overall full-length sequences already deposited in GenBank. However, their biological behaviour has not been analysed so far. In this study, the in vitro replication kinetics of the first D/A recombinant from the American continent differed from its parental genotypes, exhibiting higher extracellular levels of HBV DNA and hepatitis B e antigen. Southern blots of intracellular core-associated HBV DNA were in agreement with such results. Because this recombinant was obtained from an Argentinian injecting drug user belonging to a vulnerable community, these results are of singular relevance for regional public health. Further in vivo studies are urgently needed to determine the pathogenicity of these replicative competent clones.
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Affiliation(s)
- Julieta Trinks
- Instituto de Microbiología y Parasitología Médica (IMPAM), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, Piso 11, 1121, Buenos Aires, Argentina
| | - Masaya Sugiyama
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1, Kohnodai, Ichikawa 272-8516, Japan
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Fuat Kurbanov
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Jorge Benetucci
- Fundación de Ayuda al Inmunodeficiente (FUNDAI), Uspallata 2272, 1282, Buenos Aires, Argentina
| | - Edgardo Giménez
- Hospital Zonal General de Agudos 'Dr Isidoro G. Iriarte', Allison Bell 770, 1878, Quilmes, Argentina
| | - Mercedes C Weissenbacher
- National Academy of Medicine, Av. Las Heras 3092, 1425, Buenos Aires, Argentina
- Instituto de Microbiología y Parasitología Médica (IMPAM), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, Piso 11, 1121, Buenos Aires, Argentina
| | - Masashi Mizokami
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1, Kohnodai, Ichikawa 272-8516, Japan
| | - José R Oubiña
- Instituto de Microbiología y Parasitología Médica (IMPAM), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, Piso 11, 1121, Buenos Aires, Argentina
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Rethwilm A, Bodem J. Evolution of foamy viruses: the most ancient of all retroviruses. Viruses 2013; 5:2349-74. [PMID: 24072062 PMCID: PMC3814592 DOI: 10.3390/v5102349] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 08/27/2013] [Accepted: 09/18/2013] [Indexed: 12/24/2022] Open
Abstract
Recent evidence indicates that foamy viruses (FVs) are the oldest retroviruses (RVs) that we know and coevolved with their hosts for several hundred million years. This coevolution may have contributed to the non-pathogenicity of FVs, an important factor in development of foamy viral vectors in gene therapy. However, various questions on the molecular evolution of FVs remain still unanswered. The analysis of the spectrum of animal species infected by exogenous FVs or harboring endogenous FV elements in their genome is pivotal. Furthermore, animal studies might reveal important issues, such as the identification of the FV in vivo target cells, which than require a detailed characterization, to resolve the molecular basis of the accuracy with which FVs copy their genome. The issues of the extent of FV viremia and of the nature of the virion genome (RNA vs. DNA) also need to be experimentally addressed.
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Affiliation(s)
- Axel Rethwilm
- Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Str.7, Würzburg 97078, Germany.
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Mayaphi SH, Martin DJ, Mphahlele MJ, Blackard JT, Bowyer SM. Variability of the preC/C region of hepatitis B virus genotype A from a South African cohort predominantly infected with HIV. J Med Virol 2013; 85:1883-92. [PMID: 23925707 DOI: 10.1002/jmv.23695] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2013] [Indexed: 12/22/2022]
Abstract
Hepatitis B virus (HBV) is a serious global health problem, and HBV genotype is an important determinant of disease progression and treatment outcome. The aim of this study was to assess variations of the precore/core (preC/C) region in HBV genotype A. Sequencing of the preC/C and surface (S) genes of HBV was performed on plasma samples from 20 HBV/HIV co-infected and 5 HBV mono-infected individuals. All preC/C study sequences clustered with subgenotype A1, except for two which clustered with subgenotype D4 reference strains. The nucleotide and amino acid variability was far higher in the preC/C region than in the S region. Mutations associated with reduction or failure of HBV e-antigen (HBeAg) production were observed, with a preC start codon mutation being common (24%). Other mutations (e.g., P5H/L and I97L) associated with severe liver disease were also noticed, some of which were located in the major histocompatibility restricted sites. PreC/C intergenotype nucleotide divergence was >7%, while subgenotypes differed by 2.5-7%. Several study sequences were highly divergent from other African subgenotype A1 strains. This study showed that HBeAg-negative chronic hepatitis B is underestimated in subgenotype A1, and also highlighted the variant South African A1 strains. The major advantage of preC/C sequencing is that it informs patient management as HBeAg-negative chronic hepatitis B responds poorly to conventional interferon-α therapy, and some guidelines treat HBeAg-negative chronic hepatitis B differently from HBeAg-positive chronic hepatitis B. These data suggest that subgenotype A1 may be more involved in severe HBV-related diseases.
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Affiliation(s)
- Simnikiwe H Mayaphi
- Department of Medical Virology, University of Pretoria/Tshwane Academic Division of NHLS, Pretoria, South Africa.
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35
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Martinez AA, Zaldivar Y, Hong CC, Alvarado-Mora MV, Smith R, Ortiz AY, Pinho JRR, Cristina J, Pascale JM. Molecular characterisation of hepatitis B virus in the resident Chinese population in Panama City. Mem Inst Oswaldo Cruz 2013; 108:541-7. [PMID: 23903967 PMCID: PMC3970604 DOI: 10.1590/s0074-02762013000500002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/26/2013] [Indexed: 02/06/2023] Open
Abstract
Despite the effectiveness of current hepatitis B virus (HBV) vaccines, it is estimated that 350 million individuals suffer from chronic HBV infection and more than 50% of these affected individuals live on the Asian continent. Panama is a country with a great diversity of foreign groups; the Chinese community is a large example of this phenomenon. There is an urgent need to perform studies that evaluate the prevalence and the genetic diversity of HBV in this community. This study aimed to evaluate the prevalence of HBV and its genotypes and mutant variants in the Chinese population residing in Panama. In total, 320 subjects were enrolled in the study. Forty-two subjects (13.1%) were positive for HBsAg and HBV-DNA from 18 subjects revealed the presence of genotypes B2 and C1. Secondary mutations associated with drug resistance at positions rtV207L and rtN239T of the reverse transcriptase gene were identified. Additionally, the mutation pair A1762T/G1764A was found in three samples and the mutation G1896A was detected in an HBeAg-negative subject. In conclusion, to our knowledge, this is the first study to report high HBV prevalence rates in resident ethnic Chinese in Central America and the presence of genotypes B2 and C1 in this region.
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Affiliation(s)
- Alexander Augusto Martinez
- Gorgas Memorial Institute for Health Studies, Panama, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur,
India
- Instituto de Investigaciones Científicas y Servicios de Alta
Tecnología-AIP, Ciudad del Saber, Clayton, Panama
| | | | - Chen Ch Hong
- Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Monica Viviana Alvarado-Mora
- Laboratório de Gastroenterologia e Hepatologia Tropical,
Departamento de Gastroenterologia, Instituto de Medicina Tropical, Faculdade de
Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Rebecca Smith
- Gorgas Memorial Institute for Health Studies, Panama, Panama
| | - Alma Y Ortiz
- Gorgas Memorial Institute for Health Studies, Panama, Panama
| | - João Renato Rebello Pinho
- Laboratório de Gastroenterologia e Hepatologia Tropical,
Departamento de Gastroenterologia, Instituto de Medicina Tropical, Faculdade de
Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones
Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Juan Miguel Pascale
- Gorgas Memorial Institute for Health Studies, Panama, Panama
- School of Medicine, University of Panama, Panama, Panama
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36
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Jiang Y, Wang M, Zheng H, Wang WR, Jin L, He Y. Resolving ambiguity in the phylogenetic relationship of genotypes A, B, and C of hepatitis B virus. BMC Evol Biol 2013; 13:120. [PMID: 23758960 PMCID: PMC3682936 DOI: 10.1186/1471-2148-13-120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 06/05/2013] [Indexed: 01/05/2023] Open
Abstract
Background Hepatitis B virus (HBV) is an important infectious agent that causes widespread concern because billions of people are infected by at least 8 different HBV genotypes worldwide. However, reconstruction of the phylogenetic relationship between HBV genotypes is difficult. Specifically, the phylogenetic relationships among genotypes A, B, and C are not clear from previous studies because of the confounding effects of genotype recombination. In order to clarify the evolutionary relationships, a rigorous approach is required that can effectively explore genetic sequences with recombination. Result In the present study, phylogenetic relationship of the HBV genotypes was reconstructed using a consensus phylogeny of phylogenetic trees of HBV genome segments. Reliability of the reconstructed phylogeny was extensively evaluated in agreements of local phylogenies of genome segments. The reconstructed phylogenetic tree revealed that HBV genotypes B and C had a closer phylogenetic relationship than genotypes A and B or A and C. Evaluations showed the consensus method was capable to reconstruct reliable phylogenetic relationship in the presence of recombinants. Conclusion The consensus method implemented in this study provides an alternative approach for reconstructing reliable phylogenetic relationships for viruses with possible genetic recombination. Our approach revealed the phylogenetic relationships of genotypes A, B, and C of HBV.
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Affiliation(s)
- Yueming Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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37
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Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections. INFECTION GENETICS AND EVOLUTION 2013; 16:355-61. [PMID: 23538336 DOI: 10.1016/j.meegid.2013.03.021] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/23/2022]
Abstract
Hepatitis B virus (HBV) has evolved into phylogenetically separable genotypes and subgenotypes. Accurately assigning the subgenotype for an HBV strain is of clinical and epidemiological significance. In this paper, we review the recommendations currently employed for HBV subgenotyping, the history of HBV subgenotyping, the effects of recombination on HBV subgenotyping, misclassifications in HBV subgenotyping, and suggestions are made to correct the misclassifications. Finally, proposals are made to guide future HBV subgenotyping.
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38
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Zhang Y, Li C, Zhang Y, Zhu H, Kang Y, Liu H, Wang J, Qin Y, Mao R, Xie Y, Huang Y, Zhang J. Comparative analysis of CpG islands among HBV genotypes. PLoS One 2013; 8:e56711. [PMID: 23451072 PMCID: PMC3579858 DOI: 10.1371/journal.pone.0056711] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/14/2013] [Indexed: 12/18/2022] Open
Abstract
DNA methylation is being increasingly recognized to play a role in regulation of hepatitis B virus (HBV) gene expression. The aim of this study was to compare the CpG island distribution among different HBV genotypes. We analyzed 176 full-length HBV genomic sequences obtained from the GenBank database, belonging to genotypes A through J, to identify the CpG islands in the HBV genomes. Our results showed that while 79 out of 176 sequences contained three conventional CpG islands (I–III) as previously described, 83 HBV sequences harbored only two of the three known islands. Novel CpG islands were identified in the remaining 14 HBV isolates and named as CpG island IV, V, and VI. Among the eight known HBV genotypes and two putative genotypes, while HBV genomes containing three CpG islands were predominant in genotypes A, B, D, E, and I; genotypes C, F, G, and H tended to contain only two CpG islands (II and III). In conclusion, the CpG islands, which are potential targets for DNA methylation mediated by the host functions, differ among HBV genotypes, and these genotype-specific differences in CpG island distribution could provide new insights into the understanding of epigenetic regulation of HBV gene expression and hepatitis B disease outcome.
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Affiliation(s)
- Yongmei Zhang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenxiao Li
- Department of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yijun Zhang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haoxiang Zhu
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yaoyue Kang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongyan Liu
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jinyu Wang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanli Qin
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Richeng Mao
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Xie
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuxian Huang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- * E-mail: (JZ) (YH); (YH) (JZ)
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOH & MOE), Shanghai Medical College, Fudan University, Shanghai, China
- * E-mail: (JZ) (YH); (YH) (JZ)
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Shi W, Zhu C, Zheng W, Zheng W, Ling C, Carr MJ, Higgins DG, Zhang Z. Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype. PLoS One 2012; 7:e47271. [PMID: 23077582 PMCID: PMC3471840 DOI: 10.1371/journal.pone.0047271] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/10/2012] [Indexed: 12/23/2022] Open
Abstract
Background More than ten subgenotypes of genotype C Hepatitis B virus (HBV) have been reported, including C1 to C16 and two C/D recombinant subgenotypes (CD1 and CD2), however, inconsistent designations of these subgenotypes still exist. Methodology/Principal Findings We performed a phylogenetic analysis of all full-length genotype C HBV genome sequences to correct the misclassifications of HBV subgenotypes and to study the influence of recombination on HBV subgenotyping. Our results showed that although inclusion of the recombinant sequences changed the topology of the phylogenetic tree, it did not affect the subgenotyping of the non-recombinant sequences, except subgenotype C2. In addition, most of the subgenotypes have been properly designated. However, several misclassifications of HBV subgenotypes have been identified and corrected. For example, C11 proposed by Utsumi and colleagues in 2011 was found to be grouped with C12 proposed by Mulyanto and colleagues. Two sequences, GQ358157 and GU721029, previously designated as C6 have been re-designated as C12 and C7, respectively. Moreover, a quasi-subgenotype C2 was proposed, which included the old C2, several previously unclassified sequences and previously designated C14. In particular, we identified a novel subgenotype, tentative C14, which was well supported by phylogenetic analysis and sequence divergence of >4%. Conclusions/Significance A number of misclassifications in the subgenotyping of genotype C HBV have been identified in this study. After correcting the misclassifications, we proposed a better classification for the subgenotyping of genotype C HBV, in which a novel quasi-subgenotype C2 and a novel subgenotype, tentative C14, were described. Based on this large-scale analysis, we propose that a novel subgenotype should only be reported after a complete comparison of all relevant sequences rather than a few representative sequences only.
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Affiliation(s)
- Weifeng Shi
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (WS); (ZZ)
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Weimin Zheng
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China
| | - Wei Zheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Ling
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China
| | - Michael J. Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Desmond G. Higgins
- The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Zhong Zhang
- Department of Basic Medicine, Taishan Medical College, Taian, Shandong, China
- * E-mail: (WS); (ZZ)
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40
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Shi W, Zhu C, Zheng W, Carr MJ, Higgins DG, Zhang Z. Subgenotype reclassification of genotype B hepatitis B virus. BMC Gastroenterol 2012; 12:116. [PMID: 22925657 PMCID: PMC3523008 DOI: 10.1186/1471-230x-12-116] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 08/24/2012] [Indexed: 02/06/2023] Open
Abstract
Background Nine subgenotypes from genotype B have been identified for hepatitis B virus (HBV). However, these subgenotypes were less conclusive as they were often designated based on a few representative strains. In addition, subgenotype B6 was designated twice for viruses of different origin. Methods All complete genome sequences of genotype B HBV were phylogenetically analyzed. Sequence divergences between different potential subgenotypes were also assessed. Results Both phylogenetic and sequence divergence analyses supported the designation of subgenotypes B1, B2, B4, and B6 (from Arctic). However, sequence divergences between previously designated B3, B5, B7, B8, B9 and another B6 (from China) were mostly less than 4%. In addition, subgenotype B3 did not form a monophyly. Conclusion Current evidence failed to classify original B5, B7, B8, B9, and B6 (from China) as subgenotypes. Instead, they could be considered as a quasi-subgenotype B3 of Southeast Asian and Chinese origin. In addition, previously designated B6 (from Arctic) should be renamed as B5 for continuous numbering. This novel classification is well supported by both the phylogeny and sequence divergence of > 4%.
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Affiliation(s)
- Weifeng Shi
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Nansha, 511458, Guangzhou, China.
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41
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Shi W, Freitas IT, Zhu C, Zheng W, Hall WW, Higgins DG. Recombination in hepatitis C virus: identification of four novel naturally occurring inter-subtype recombinants. PLoS One 2012; 7:e41997. [PMID: 22911872 PMCID: PMC3404033 DOI: 10.1371/journal.pone.0041997] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 06/28/2012] [Indexed: 12/13/2022] Open
Abstract
Recombination in Hepatitis C virus (HCV) is considered to be rare. In this study, we performed a phylogenetic analysis of 1278 full-length HCV genome sequences to identify potential recombination events. Nine inter-genotype recombinants were identified, all of which have been previously reported. This confirms the rarity of inter-genotype HCV recombinants. The analysis also identified five inter-subtype recombinants, four of which are documented for the first time (EU246930, EU246931, EU246932, and EU246937). Specifically, the latter represent four different novel recombination types (6a/6o, 6e/6o, 6e/6h, and 6n/6o), and this was well supported by seven independent methods embedded in RDP. The breakpoints of the four novel HCV recombinants are located within the NS5B coding region and were different from all previously reported breakpoints. While the locations of the breakpoints identified by RDP were not identical, they are very close. Our study suggests that while recombination in HCV is rare, this warrants further investigation.
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Affiliation(s)
- Weifeng Shi
- The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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