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Zhang Y, Mou Y, Chen M, Lin X, Zhao Y, Luo X. Binary split fluorescent biosensor based on lettuce DNA aptamer for label-free and enzyme-free analysis of hepatitis B viral DNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4561-4569. [PMID: 38912590 DOI: 10.1039/d4ay00713a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Hepatitis B virus (HBV) acts as a severe public health threat, causing chronic liver diseases. Although the quantified evaluation of HBV infection can be obtained by estimating the capacity of the HBV DNA genome, it still lacks an effective and robust detection method without using enzymes or chemical labeling. Herein, we have designed a binary split fluorescent DNA aptasensor (bsFDA) by rationally splitting the lettuce aptamer into two functional DNA short chains and utilizing the HBV DNA segment complementary sequences (HDs). In this strategy, the bsFDA has been investigated to specifically recognize the HDs, forming a triplex DNA with the lettuce aptamer structure. Meanwhile, the turn-on fluorescence of bsFDA is obtained upon formation of a fluorescent complex between DFHO and the triplex DNA structure, allowing the enzyme-free, label-free, fast-responsive, and reliable fluorescence readout for detecting HDs and the potential HDs mutants. Moreover, bsFDA has been applied for spiked HDs analysis in different real matrixes, including human serum and cell lysate. The satisfactory recovery rates and reproducibility of the bsFDA reveal its potential detection efficacy for HDs analysis in biological samples. Overall, bsFDA holds great potential in developing functionalized aptasensors and realizing viral genome analysis in biological research.
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Affiliation(s)
- Yanfei Zhang
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Yue Mou
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Meiyun Chen
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Xinru Lin
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Yujie Zhao
- Medical College, Guangxi University, Nanning 530004, P. R. China.
| | - Xingyu Luo
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
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Ranga A, Gupta A, Yadav L, Kumar S, Jain P. Advancing beyond reverse transcriptase inhibitors: The new era of hepatitis B polymerase inhibitors. Eur J Med Chem 2023; 257:115455. [PMID: 37216809 DOI: 10.1016/j.ejmech.2023.115455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
Hepatitis B virus (HBV) is a genetically diverse blood-borne virus responsible for chronic hepatitis B. The HBV polymerase plays a key role in viral genome replication within the human body and has been identified as a potential drug target for chronic hepatitis B therapeutics. However, available nucleotide reverse transcriptase inhibitors only target the reverse transcriptase domain of the HBV polymerase; they also pose resistance issues and require lifelong treatment that can burden patients financially. In this study, various chemical classes are reviewed that have been developed to target different domains of the HBV polymerase: Terminal protein, which plays a vital role in the formation of the viral DNA; Reverse transcriptase, which is responsible for the synthesis of the viral DNA from RNA, and; Ribonuclease H, which is responsible for degrading the RNA strand in the RNA-DNA duplex formed during the reverse transcription process. Host factors that interact with the HBV polymerase to achieve HBV replication are also reviewed; these host factors can be targeted by inhibitors to indirectly inhibit polymerase functionality. A detailed analysis of the scope and limitations of these inhibitors from a medicinal chemistry perspective is provided. The structure-activity relationship of these inhibitors and the factors that may affect their potency and selectivity are also examined. This analysis will be useful in supporting the further development of these inhibitors and in designing new inhibitors that can inhibit HBV replication more efficiently.
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Affiliation(s)
- Abhishek Ranga
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Aarti Gupta
- Department of Pharmaceutical Biotechnology, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Laxmi Yadav
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Sachin Kumar
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
| | - Priti Jain
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
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Detectability of Hepatitis B Virus in Peripheral Blood Mononuclear Cells Among Naive Chronic Hepatitis B Patients With Negative Viremia. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2022. [DOI: 10.1097/ipc.0000000000001153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bianca C, Sidhartha E, Tiribelli C, El-Khobar KE, Sukowati CHC. Role of hepatitis B virus in development of hepatocellular carcinoma: Focus on covalently closed circular DNA. World J Hepatol 2022; 14:866-884. [PMID: 35721287 PMCID: PMC9157711 DOI: 10.4254/wjh.v14.i5.866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/31/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023] Open
Abstract
Chronic infection with hepatitis B virus (HBV) remains a major global health problem, especially in developing countries. It may lead to prolonged liver damage, fibrosis, cirrhosis, and hepatocellular carcinoma. Persistent chronic HBV infection is related to host immune response and the stability of the covalently closed circular DNA (cccDNA) in human hepatocytes. In addition to being essential for viral transcription and replication, cccDNA is also suspected to play a role in persistent HBV infections or hepatitis relapses since cccDNA is very stable in non-dividing human hepatocytes. Understanding the pathogenicity and oncogenicity of HBV components would be essential in the development of new diagnostic tools and treatment strategies. This review summarizes the role and molecular mechanisms of HBV cccDNA in hepatocyte transformation and hepatocarcinogenesis and current efforts to its detection and targeting.
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Affiliation(s)
- Claryssa Bianca
- Department of Biomedicine, Indonesia International Institute for Life Sciences, Jakarta 13210, Indonesia
| | - Elizabeth Sidhartha
- Department of Biomedicine, Indonesia International Institute for Life Sciences, Jakarta 13210, Indonesia
| | - Claudio Tiribelli
- Centro Studi Fegato, Fondazione Italiana Fegato ONLUS, Trieste 34149, Italy
| | - Korri Elvanita El-Khobar
- Eijkman Center for Molecular Biology, National Research and Innovation Agency (BRIN), Jakarta 10340, Indonesia
| | - Caecilia H C Sukowati
- Centro Studi Fegato, Fondazione Italiana Fegato ONLUS, Trieste 34149, Italy
- Eijkman Center for Molecular Biology, National Research and Innovation Agency (BRIN), Jakarta 10340, Indonesia
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Exonuclease I and III improve the detection efficacy of hepatitis B virus covalently closed circular DNA. Hepatobiliary Pancreat Dis Int 2019; 18:458-463. [PMID: 30522829 DOI: 10.1016/j.hbpd.2018.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/29/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND Hepatitis B virus covalently closed circular DNA (HBV cccDNA) is an important biomarker of hepatitis B virus infection. However, the current methods are not specific and sensitive. The present study aimed to develop a specific and sensitive assay method for the quantification of HBV cccDNA. METHODS Exonuclease I (Exo I) & Exonuclease III (Exo III) and specific primer probes are used in real-time PCR. The virus particles isolated from peripheral blood mononuclear cells were used as negative control and HBV1.3 recombinant plasmid 3.2 kb circular DNA fragment was used as positive control. The methods of cccDNA detection were evaluated in cell lines, plasmid, animal model, patient serum and liver biopsies. RESULTS A linear range of 101-107 copies/assay using specific primers for HBV cccDNA was established. HBV cccDNA were only detected in cell lines, animal model and liver tissue. It cannot be detected in serum samples. Intrahepatic HBV cccDNA level had good correlation with intrahepatic total HBV DNA level (r = 0.765, P < 0.001). CONCLUSIONS The real-time quantitative PCR is an effective and feasible method for sensitive and specific detection of low copy number of cccDNA. The novel detection method is fast, provides high sensitivity and specificity and can be used in clinical practice.
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Mouzannar K, Fusil F, Lacombe B, Ollivier A, Ménard C, Lotteau V, Cosset FL, Ramière C, André P. Farnesoid X receptor-α is a proviral host factor for hepatitis B virus that is inhibited by ligands in vitro and in vivo. FASEB J 2018; 33:2472-2483. [PMID: 30307769 DOI: 10.1096/fj.201801181r] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hepatitis B virus (HBV) infection and bile acid (BA) metabolism are interdependent: infection modifies the expression of the BA nuclear receptor farnesoid X receptor (FXR)-α, and modulation of FXRα activity by ligands alters HBV replication. Mechanisms of HBV control by FXRα remain to be unveiled. FXRα silencing in HBV-infected HepaRG cells decreased the viral covalently closed circular (ccc)DNA pool size and transcriptional activity. Treatment with the FXRα agonist GW4064 inhibited FXRα proviral effect on cccDNA similarly for wild-type and hepatitis B viral X protein (HBx)-deficient virus, whereas agonist-induced inhibition of pregenomic and precore RNA transcription and viral DNA secretion was HBx dependent. These data indicated that FXRα acts as a proviral factor by 2 different mechanisms, which are abolished by FXRα stimulation. Finally, infection of C3H/HeN mice by a recombinant adeno-associated virus-2/8-HBV vector induced a sustained HBV replication in young mice in contrast with the transient decline in adult mice. Four-week GW4064 treatment of infected C3H/HeN mice decreased secretion of HBV DNA and HB surface antigen in adult mice only. These results suggest that the physiologic balance of FXRα expression and activation by bile acid is a key host metabolic pathway in the regulation of HBV infection and that FXRα can be envisioned as a target for HBV treatment.-Mouzannar, K., Fusil, F., Lacombe, B., Ollivier, A., Ménard, C., Lotteau, V., Cosset, F.-L., Ramière, C., André, P. Farnesoid X receptor α is a proviral host factor for hepatitis B virus that is inhibited by ligands in vitro and in vivo.
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Affiliation(s)
- Karim Mouzannar
- Centre International de Recherche en Infectiologie (CIRI), Université Lyon, Université Claude Bernard Lyon 1, INSERM, Unité1111, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Floriane Fusil
- Centre International de Recherche en Infectiologie (CIRI), Université Lyon, Université Claude Bernard Lyon 1, INSERM, Unité1111, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Benoît Lacombe
- Centre International de Recherche en Infectiologie (CIRI), Université Lyon, Université Claude Bernard Lyon 1, INSERM, Unité1111, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Anaïs Ollivier
- Centre International de Recherche en Infectiologie (CIRI), Université Lyon, Université Claude Bernard Lyon 1, INSERM, Unité1111, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Camille Ménard
- Centre International de Recherche en Infectiologie (CIRI), Université Lyon, Université Claude Bernard Lyon 1, INSERM, Unité1111, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie (CIRI), Université Lyon, Université Claude Bernard Lyon 1, INSERM, Unité1111, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - François-Loïc Cosset
- Centre International de Recherche en Infectiologie (CIRI), Université Lyon, Université Claude Bernard Lyon 1, INSERM, Unité1111, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Christophe Ramière
- Centre International de Recherche en Infectiologie (CIRI), Université Lyon, Université Claude Bernard Lyon 1, INSERM, Unité1111, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5308, École Normale Supérieure (ENS) de Lyon, Lyon, France.,Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Patrice André
- Centre International de Recherche en Infectiologie (CIRI), Université Lyon, Université Claude Bernard Lyon 1, INSERM, Unité1111, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
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Li J, Sun X, Fang J, Wang C, Han G, Ren W. Analysis of intrahepatic total HBV DNA, cccDNA and serum HBsAg level in Chronic Hepatitis B patients with undetectable serum HBV DNA during oral antiviral therapy. Clin Res Hepatol Gastroenterol 2017; 41:635-643. [PMID: 28438570 DOI: 10.1016/j.clinre.2017.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 01/23/2017] [Accepted: 03/15/2017] [Indexed: 02/04/2023]
Abstract
BACKGROUND This study aimed to investigate the relationship between intrahepatic cccDNA and serum HBsAg in chronic Hepatitis B (CHB) patients with undetectable serum HBV DNA during antiviral therapy. METHODS We investigated HBsAg serum levels and their relationship to intrahepatic total cccDNA and HBV DNA in CHB patients with undetectable serum HBV DNA during oral antiviral therapy. Intrahepatic cccDNA and HBV DNA quantitation were performed in the same needle biopsy material, while serum HBsAg, HBeAg and HBV DNA levels were measured in samples drawn on the day of the liver biopsy. RESULTS A total of 90 patients who had a liver biopsy were enrolled, including 80 patients with CHB and 10 patients with liver cirrhosis (LC). All the CHB patients were divided into HBeAg-positive and HBeAg-negative group. By using real-time PCR detection, we found that intrahepatic cccDNA and HBV DNA levels were higher in CHB patients than those in LC patients (Intrahepatic cccDNA: 6.15±1.19 vs. 6.12±0.36, HBV DNA: 7.26±0.49 vs. 5.59±0.45, both P<0.05). Intrahepatic cccDNA level was positively correlated with serum HBsAg in HBeAg-negative (r=0.66, P=0.02) and lower serum HBeAg (≤50S/CO) CHB patients (r=0.47, P=0.03), but not in higher serum HBeAg (>50S/CO) CHB patients (both P>0.05). In HBeAg negative patients, serum HBsAg level was correlated with intrahepatic total HBV DNA level (r=0.52, P=0.006). However, no relationship between HBsAg level and intrahepatic total HBV DNA level was found in HBeAg positive patients (both P>0.05). CONCLUSIONS Serum HBsAg can be used to predict intrahepatic cccDNA and HBV DNA level in CHB patients with low serum HBeAg statues, especially in HBeAg negative patients.
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Affiliation(s)
- Jie Li
- Department of Infectious Disease, Shandong Provincial Hospital Affiliated to Shandong University, 324 Jingwu Road, Ji'nan, Shandong 250021, China; Division of Gastroenterology and Hepatology, Stanford University Medical Center, Palo Alto, CA, United States.
| | - Xizhen Sun
- Department of Infectious Disease, Shandong Provincial Hospital Affiliated to Shandong University, 324 Jingwu Road, Ji'nan, Shandong 250021, China.
| | - Jianting Fang
- Department of Infectious Disease, Shandong Provincial Hospital Affiliated to Shandong University, 324 Jingwu Road, Ji'nan, Shandong 250021, China.
| | - Chuanxi Wang
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong University, 324 Jingwu Road, Ji'nan, Shandong 250021, China.
| | - Guoqing Han
- Department of Infectious Disease, Shandong Provincial Hospital Affiliated to Shandong University, 324 Jingwu Road, Ji'nan, Shandong 250021, China.
| | - Wanhua Ren
- Department of Infectious Disease, Shandong Provincial Hospital Affiliated to Shandong University, 324 Jingwu Road, Ji'nan, Shandong 250021, China.
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Li X, Zhao J, Yuan Q, Xia N. Detection of HBV Covalently Closed Circular DNA. Viruses 2017; 9:E139. [PMID: 28587292 PMCID: PMC5490816 DOI: 10.3390/v9060139] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 12/19/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection affects approximately 240 million people worldwide and remains a serious public health concern because its complete cure is impossible with current treatments. Covalently closed circular DNA (cccDNA) in the nucleus of infected cells cannot be eliminated by present therapeutics and may result in persistence and relapse. Drug development targeting cccDNA formation and maintenance is hindered by the lack of efficient cccDNA models and reliable cccDNA detection methods. Southern blotting is regarded as the gold standard for quantitative cccDNA detection, but it is complicated and not suitable for high-throughput drug screening, so more sensitive and simple methods, including polymerase chain reaction (PCR)-based methods, Invader assays, in situ hybridization and surrogates, have been developed for cccDNA detection. However, most methods are not reliable enough, and there are no unified standards for these approaches. This review will summarize available methods for cccDNA detection. It is hoped that more robust methods for cccDNA monitoring will be developed and that standard operation procedures for routine cccDNA detection in scientific research and clinical monitoring will be established.
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Affiliation(s)
- Xiaoling Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Jinghua Zhao
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University, Xiamen 361102, China.
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University, Xiamen 361102, China.
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The recombined cccDNA produced using minicircle technology mimicked HBV genome in structure and function closely. Sci Rep 2016; 6:25552. [PMID: 27174254 PMCID: PMC4865889 DOI: 10.1038/srep25552] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/18/2016] [Indexed: 12/17/2022] Open
Abstract
HBV covalently closed circular DNA (cccDNA) is drug-resistant and responsible for viral persistence. To facilitate the development of anti-cccDNA drugs, we developed a minicircle DNA vector (MC)-based technology to produce large quantity of recombined cccDNA (rcccDNA) resembling closely to its wild-type counterpart both in structure and function. The rcccDNA differed to the wild-type cccDNA (wtcccDNA) only in that it carried an extra 36-bp DNA recombinant product attR upstream of the preC/C gene. Using a procedure similar to standard plasmid production, milligrams of rcccDNA can be generated in common laboratories conveniently. The rcccDNA demonstrated many essential biological features of wtcccDNA, including: (1) undergoing nucleation upon nucleus entry; (2) serving as template for production of all HBV RNAs and proteins; (3) deriving virions capable of infecting tree shrew, and subsequently producing viral mRNAs, proteins, rcccDNA and infectious virions. As an example to develop anti-cccDNA drugs, we used the Crispr/Cas9 system to provide clear-cut evidence that rcccDNA was cleaved by this DNA editing tool in vitro. In summary, we have developed a convenient technology to produce large quantity of rcccDNA as a surrogate of wtcccDNA for investigating HBV biology and developing treatment to eradicate this most wide-spreading virus.
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Becker N, Rimbaud L, Chiroleu F, Reynaud B, Thébaud G, Lett JM. Rapid accumulation and low degradation: key parameters of Tomato yellow leaf curl virus persistence in its insect vector Bemisia tabaci. Sci Rep 2015; 5:17696. [PMID: 26625871 PMCID: PMC4667217 DOI: 10.1038/srep17696] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 11/04/2015] [Indexed: 02/05/2023] Open
Abstract
Of worldwide economic importance, Tomato yellow leaf curl virus (TYLCV, Begomovirus) is responsible for one of the most devastating plant diseases in warm and temperate regions. The DNA begomoviruses (Geminiviridae) are transmitted by the whitefly species complex Bemisia tabaci. Although geminiviruses have long been described as circulative non-propagative viruses, observations such as long persistence of TYLCV in B. tabaci raised the question of their possible replication in the vector. We monitored two major TYLCV strains, Mild (Mld) and Israel (IL), in the invasive B. tabaci Middle East-Asia Minor 1 cryptic species, during and after the viral acquisition, within two timeframes (0-144 hours or 0-20 days). TYLCV DNA was quantified using real-time PCR, and the complementary DNA strand of TYLCV involved in viral replication was specifically quantified using anchored real-time PCR. The DNA of both TYLCV strains accumulated exponentially during acquisition but remained stable after viral acquisition had stopped. Neither replication nor vertical transmission were observed. In conclusion, our quantification of the viral loads and complementary strands of both Mld and IL strains of TYLCV in B. tabaci point to an efficient accumulation and preservation mechanism, rather than to a dynamic equilibrium between replication and degradation.
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Affiliation(s)
- Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE. Muséum National d’Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 50, F-75005, Paris, France
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’Irat, F-97410 Saint Pierre, Ile de La Réunion, France
| | - Loup Rimbaud
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’Irat, F-97410 Saint Pierre, Ile de La Réunion, France
- Montpellier SupAgro, UMR 385 BGPI, F-34398 Montpellier, France
| | - Frédéric Chiroleu
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’Irat, F-97410 Saint Pierre, Ile de La Réunion, France
| | - Bernard Reynaud
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’Irat, F-97410 Saint Pierre, Ile de La Réunion, France
| | | | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’Irat, F-97410 Saint Pierre, Ile de La Réunion, France
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A sensitive and accurate quantification method for the detection of hepatitis B virus covalently closed circular DNA by the application of a droplet digital polymerase chain reaction amplification system. Biotechnol Lett 2015; 37:2063-73. [DOI: 10.1007/s10529-015-1890-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 06/10/2015] [Indexed: 02/07/2023]
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Guo Y, Sheng S, Nie B, Tu Z. Development of magnetic capture hybridization and quantitative polymerase chain reaction for hepatitis B virus covalently closed circular DNA. HEPATITIS MONTHLY 2015; 15:e23729. [PMID: 25741372 PMCID: PMC4344652 DOI: 10.5812/hepatmon.23729] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/03/2014] [Accepted: 12/14/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) served as a vital role in the life cycle of the virus and persistent infection. However, specific and quantitative methods for cccDNA detection have not been available. OBJECTIVES Our aim was to develop and primarily evaluate a quantitative method for HBV cccDNA based on magnetic capture hybridization and quantitative PCR technology. MATERIALS AND METHODS The functionalized-nanoparticles specifically to capture HBV cccDNA, located on both sides of relaxed circle DNA (rcDNA) gap, were designed. Then, magnetic capture hybridization and quantitative PCR (MCH-qPCR) assay were developed and its performance was primarily evaluated with cccDNA standards and serum samples of patients with chronic hepatitis B. RESULTS Specific nanoparticles of cccDNA capture were prepared and a magnetic capture hybridization and quantitative assay method for cccDNA was developed successfully. The limit of detection was 90 IU/mL, and a good linear relationship in the range of 10(2)-10(6) IU/mL was revealed (r(2) = 0.994) with the MCH-qPCR. Compared with directly real-time PCR, a high content of HBV DNA did not affect the detection of cccDNA for the MCH-qPCR method, and there was no cross-reactivity between cccDNA and rcDNA. CONCLUSIONS The novel MCH-qPCR method has good sensitivity and specificity. It could meet the requirement of clinical routine detection.
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Affiliation(s)
- Yongcan Guo
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shangchun Sheng
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Bin Nie
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Zhiguang Tu
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
- Corresponding Author: Zhiguang Tu, The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China. Tel: +86-2368485759, Fax: +86-2368485239, E-mail:
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Association between HBV Pre-S mutations and the intracellular HBV DNAs in HBsAg-positive hepatocellular carcinoma in China. Clin Exp Med 2014; 15:483-91. [PMID: 25501679 DOI: 10.1007/s10238-014-0321-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/19/2014] [Indexed: 02/06/2023]
Abstract
This study aimed to investigate the association between HBV mutations and intrahepatic HBV status and to determine the clinical features and the contribution of HBV mutations to postoperative prognosis for hepatocellular carcinoma (HCC) patients with HBsAg (+) in China. Using TaqMan fluorescent real-time PCR, HBV covalently closed circular DNA (cccDNA) and total DNA (tDNA) were both quantified in 106 pairs of tumor tissues (TT) and adjacent non-tumor tissues (ANTT) obtained from HCC patients who received no antiviral treatment before surgical treatment. The prevalence of 19 hot spot mutations was evaluated by Sanger sequencing. HBV cccDNA and tDNA were lower in TT than in ANTT. The loads of cccDNA and tDNA in ANTT were associated with serum HBV DNA and HBeAg. Three Pre-S mutants (A2962G and C2964A in Pre-S1 and C105T in Pre-S2) were associated with higher tumor cccDNA levels (P < 0.05), and A2962G/C2964A mutants were associated with higher AFP levels. This would assist to disclose the virological features, to implement a more clinically personalized therapy and to improve the prognosis of HBV-related HCC patients.
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Zhang Z, Zhang J, Pei X, Zhang Q, Lu B, Zhang X, Liu J. An aptamer targets HBV core protein and suppresses HBV replication in HepG2.2.15 cells. Int J Mol Med 2014; 34:1423-9. [PMID: 25174447 DOI: 10.3892/ijmm.2014.1908] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 08/11/2014] [Indexed: 12/27/2022] Open
Abstract
Hepatitis B virus (HBV)-related hepatitis is a major health concern worldwide. As current anti-HBV therapies are limited, it is essential to develop new strategies. Aptamer, a newly developed adaptive molecule (single-strand DNA or RNA also known as nucleotide antibody), is a new strategy for clinical diagnosis and therapy due to its high affinity and specificity. In the present study, by systematic evolution of ligand by exponential enrichment (SELEX), aptamers were screened against the core protein of HBV (HBc) from a random ssDNA library. Quantitative PCR (qPCR) results showed that the binding proportions of the SELEX-enriched aptamer pools were increased with the SELEX rounds, until round seven. Thus, the pool of round seven was cloned. Following the sequence analysis of a total of 90 clones by Macaw software, five aptamer candidates were selected and their affinity to HBc was tested by dot blot. Apt.No.28, which had sequence replicates in the clones, was shown to have a high affinity. Furthermore, by agarose gel electrophoresis-capillary transfer-blotting and qPCR, Apt.No.28 was shown to inhibit the assembly of the nucleocapsid, reducing extracellular HBV DNA whose synthesis relied on the formation of the nucleocapsid, indicating its role in suppressing HBV replication. The results provided a new ideal targeting molecule and may facilitate the strategy for targeted therapy as well as drug development of HBV-related diseases.
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Affiliation(s)
- Zuowei Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Jun Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Xiaoyu Pei
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Qi Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Bin Lu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Xiaojiao Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Jie Liu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
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Chen C, Wang JCY, Zlotnick A. A kinase chaperones hepatitis B virus capsid assembly and captures capsid dynamics in vitro. PLoS Pathog 2011; 7:e1002388. [PMID: 22114561 PMCID: PMC3219723 DOI: 10.1371/journal.ppat.1002388] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 10/04/2011] [Indexed: 12/14/2022] Open
Abstract
The C-terminal domain (CTD) of Hepatitis B virus (HBV) core protein is involved in regulating multiple stages of the HBV lifecycle. CTD phosphorylation correlates with pregenomic-RNA encapsidation during capsid assembly, reverse transcription, and viral transport, although the mechanisms remain unknown. In vitro, purified HBV core protein (Cp183) binds any RNA and assembles aggressively, independent of phosphorylation, to form empty and RNA-filled capsids. We hypothesize that there must be a chaperone that binds the CTD to prevent self-assembly and nonspecific RNA packaging. Here, we show that HBV capsid assembly is stalled by the Serine Arginine protein kinase (SRPK) binding to the CTD, and reactivated by subsequent phosphorylation. Using the SRPK to probe capsids, solution and structural studies showed that SRPK bound to capsid, though the CTD is sequestered on the capsid interior. This result indicates transient CTD externalization and suggests that capsid dynamics could be crucial for directing HBV intracellular trafficking. Our studies illustrate the stochastic nature of virus capsids and demonstrate the appropriation of a host protein by a virus for a non-canonical function. A virus particle is a molecular machine that has evolved to self-assemble within the confines of a living cell. For hepatitis B virus (HBV), outside of a cell, the self-assembly process is very aggressive and consequently not specific for viral RNA. Here we show that HBV takes advantage of a host protein, SRPK, which acts like a molecular chaperone, to prevent the HBV core protein from binding RNA and to prevent the core protein from assembling at the wrong time and place. At the right time, SRPK can be removed in a regulated reaction to allow assembly. Once a virus is assembled, it must traffic to the right intracellular locale. Using SRPK, we show that HBV cores can transiently expose a segment of protein, normally inside the virus, that carries a signal for transport to the host nucleus. This is the first example we know of where a virus repurposes an enzyme for an alternative function. This sort of interplay between virus and host, where the virus hijacks and repurposes host proteins, is likely to be a common feature of viral infection.
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Affiliation(s)
- Chao Chen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Joseph Che-Yen Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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16
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Quantitation of HBV covalently closed circular DNA in micro formalin fixed paraffin-embedded liver tissue using rolling circle amplification in combination with real-time PCR. Clin Chim Acta 2011; 412:1905-11. [PMID: 21741960 DOI: 10.1016/j.cca.2011.06.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 06/15/2011] [Accepted: 06/23/2011] [Indexed: 02/07/2023]
Abstract
BACKGROUND The study aimed to develop an effective method to quantitate HBV covalently closed circular DNA (cccDNA) using small section of formalin fixed paraffin-embedded (FFPE) liver biopsy. METHODS Plasmid-safe ATP-dependent DNase (PSAD)-treated samples were subjected to rolling circle amplification (RCA) prior to real-time PCR mediated by cccDNA-selective primers. Human beta-actin gene was used as a reference control. RESULTS Compared to the classical method, i.e., PSAD digestion+real-time PCR, introduction of RCA increased the lower limit of detection for about 2 logs with good inter- and intra-assay reproducibility. HBV cccDNA was detected in 91.5% (119/130) of the FFPE samples. The cccDNA levels (copy/cell) between FFPE liver tissues and fresh frozen counterpart tissues were comparable. The median of cccDNA level in HBeAg-positive patients was higher than that in HBeAg-negative ones (52.60 vs. 31.25copies/cell, P<0.01). Intrahepatic cccDNA level was positively correlated with intrahepatic HBV total DNA level, but not obviously correlated with serum HBV DNA or alanine aminotransferase levels. CONCLUSIONS The method could sensitively and specifically quantitate intrahepatic HBV cccDNA in micro FFPE liver biopsy tissue for evaluation of HBV replication status in the liver.
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Kim JW, Lee SH, Park YS, Hwang JH, Jeong SH, Kim N, Lee DH. Replicative activity of hepatitis B virus is negatively associated with methylation of covalently closed circular DNA in advanced hepatitis B virus infection. Intervirology 2011; 54:316-25. [PMID: 21242658 DOI: 10.1159/000321450] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 09/20/2010] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES The aim of this study was to examine the methylation status of intrahepatic hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) and to elucidate the possible relationship between the cccDNA methylation and viral replicative activity in patients with HBV-related liver cirrhosis (HBV-LC). METHODS The methylation status of HBV cccDNA was investigated by bisulfite sequencing in nonneoplastic tissues from 12 patients with HBV-LC who underwent surgical resection for combined hepatocellular carcinoma. Clinical, biochemical and virologic factors were evaluated with respect to the degrees of cccDNA methylation. We also examined the effect of methylation of cccDNA on viral transcription by an in vitro transcription assay. RESULTS Variable degrees of CpG methylation were present in the HBV cccDNA from patients with HBV-LC. Old age, low serum HBV DNA levels and low virion productivity were significantly associated with elevated cccDNA methylation. Virion productivity of cccDNA was also lower in HepAD38 cells with a higher degree of cccDNA methylation. In vitro transcription assays showed that the transcriptional activity of HBV cccDNA was suppressed by increased methylation of cccDNA. CONCLUSIONS Increased CpG methylation of cccDNA is associated with old age, low serum HBV DNA levels and suppressed replicative activity in HBV-LC.
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Affiliation(s)
- Jin-Wook Kim
- Department of Medicine, Seoul National University Bundang Hospital, Seongnam, South
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18
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Gao YT, Han T, Li Y, Yang B, Wang YJ, Wang FM, Jing X, Du Z. Enhanced specificity of real-time PCR for measurement of hepatitis B virus cccDNA using restriction endonuclease and plasmid-safe ATP-dependent DNase and selective primers. J Virol Methods 2010; 169:181-7. [PMID: 20691734 DOI: 10.1016/j.jviromet.2010.07.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 07/27/2010] [Accepted: 07/29/2010] [Indexed: 11/24/2022]
Abstract
The persistence of covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) in hepatocytes plays a key role in viral persistence and resistance to therapy. Therefore, quantitative cccDNA measurement is of clinical importance for evaluating the efficacy of antiviral drugs, selecting an appropriate treatment strategy, and predicting the prognosis. Current established methods for measurement of cccDNA need further improvement. A modified method was developed using digestion with restriction endonucleases that do not recognize sites in the HBV DNA and plasmid-safe ATP-dependent DNase (PSAD), and using a cccDNA-specific primer set in a real-time PCR reaction. The cccDNA-specific primer has a similar amplification efficiency as a commercial kit. Treatment of samples with restriction endonuclease followed by PSAD digestion increased significantly the specificity of a cccDNA-selective primer set compared with other treatments (P<0.05). Analysis of 35 serum and liver DNA samples from patients with hepatocellular carcinoma demonstrated that the amount of serum cccDNA is beyond the minimum detection limit and that the liver cccDNA quantity is about 0-49.2 copies/cell, consistent with previous reports. Taken together, this method has the potential for evaluating the efficacy of antiviral drugs.
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Affiliation(s)
- Ying-Tang Gao
- Key Laboratory of Artificial Cell, Institute for Hepatobiliary Disease, Tianjin Third Central Hospital, Tianjin, China
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19
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Development of cell cultures that express hepatitis B virus to high levels and accumulate cccDNA. J Virol Methods 2010; 169:52-60. [PMID: 20600328 DOI: 10.1016/j.jviromet.2010.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 06/10/2010] [Accepted: 06/21/2010] [Indexed: 01/20/2023]
Abstract
Establishment of an infection with hepatitis B virus (HBV) requires synthesis and maintenance of a covalently closed circular DNA (cccDNA) form of the viral genome in the nucleus of host cells. To facilitate the investigation of the synthesis of cccDNA, cell cultures were developed that express HBV to high levels. Cell lines derived from hepatoma cells Huh7 and HepG2 were created that express Epstein-Barr virus (EBV) nuclear antigen-1 and a fusion protein of the Tet repressor and Kox1 transcriptional repression domain stably. Transfection of these cell lines with an expression plasmid for HBV that contains the origin of plasmid replication of EBV (oriP) led to increases in the intracellular levels of HBV core protein ( approximately 8- to 51-fold) and encapsidated HBV DNA ( approximately 3- to 12-fold) in comparison to Huh7 and HepG2 cells. Virion production was also increased ( approximately 3- to 12-fold) in these cell cultures and an increase in the level of cccDNA ( approximately 3-fold) was observed in the Huh7-derived cell lines. In addition, these cell lines maintained the HBV expression plasmid upon selection and expressed HBV conditionally. Thus, these cell cultures exhibit several features that facilitate study of the synthesis of cccDNA and other aspects of replication of HBV.
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20
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HBV life cycle: entry and morphogenesis. Viruses 2009; 1:185-209. [PMID: 21994545 PMCID: PMC3185491 DOI: 10.3390/v1020185] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Revised: 07/31/2009] [Accepted: 08/13/2009] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) is a major cause of liver disease. HBV primarily infects hepatocytes by a still poorly understood mechanism. After an endocytotic process, the nucleocapsids are released into the cytoplasm and the relaxed circular rcDNA genome is transported towards the nucleus where it is converted into covalently closed circular cccDNA. Replication of the viral genome occurs via an RNA pregenome (pgRNA) that binds to HBV polymerase (P). P initiates pgRNA encapsidation and reverse transcription inside the capsid. Matured, rcDNA containing nucleocapsids can re-deliver the RC-DNA to the nucleus, or be secreted via interaction with the envelope proteins as progeny virions.
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21
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Kim JW, Lee SH, Park YS, Jeong SH, Kim N, Lee DH. [Inhibition of in vitro hepatitis B virus replication by lentivirus-mediated short-hairpin RNA against HBx]. THE KOREAN JOURNAL OF HEPATOLOGY 2009; 15:15-24. [PMID: 19346782 DOI: 10.3350/kjhep.2009.15.1.15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUNDS/AIMS Hepatitis B virus (HBV) replicates via RNA intermediates, which could serve as targets for RNA interference (RNAi). Vector-mediated short-hairpin RNA (shRNA) can induce sustained RNAi in comparison to small interfering RNA. Lentiviral vector is known to induce prolonged RNAi with high transduction efficiency. In this study, we sought to test the in vitro efficacy of shRNA delivered by a lentiviral vector in suppressing the replication of HBV. METHODS Two shRNA sequences against the hepatitis B viral protein HBx (sh1580 and sh1685) were cloned downstream of the U6 promoter in an HIV-based plasmid to generate third-generation lentiviral vectors. HepAD38 cells were transduced with anti-HBx lentiviral vectors, and HBV replication was induced for 5 days. HBV DNA was isolated and quantified using real-time PCR. RESULTS Lentiviral vectors encoding the shRNA against HBV transduced HepAD38 cells with high efficacy. The total intracellular HBV DNA content was significantly reduced by both sh1580 and sh1685 (2.9% and 12.0%, respectively; P<0.05). HBV covalently closed circular DNA (cccDNA) was also suppressed significantly (19.7% and 25.5%, respectively; P<0.05). CONCLUSIONS Lentivirus-mediated delivery of shRNA against HBx can effectively suppress the replication of HBV and reduce HBV cccDNA in cell culture systems.
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Affiliation(s)
- Jin-Wook Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Seoul National University Bungdang Hospital, Seongnam, Korea.
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22
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Takkenberg RB, Zaaijer HL, Molenkamp R, Menting S, Terpstra V, Weegink CJ, Dijkgraaf MGW, Jansen PLM, Reesink HW, Beld MGHM. Validation of a sensitive and specific real-time PCR for detection and quantitation of hepatitis B virus covalently closed circular DNA in plasma of chronic hepatitis B patients. J Med Virol 2009; 81:988-95. [PMID: 19382261 DOI: 10.1002/jmv.21477] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) serves as a template for viral replication and plays a role in persistence of HBV infection. The origin and significance of cccDNA in plasma however, is not well understood. A sensitive, specific, and reproducible real-time PCR for detection and quantitation of cccDNA in plasma of chronic hepatitis B patients was developed and validated. Four HBV DNA reference panels, and 96 plasma samples of chronic hepatitis B patients were analyzed. Results were compared with total HBV DNA levels, individual ALT levels and the Histology Activity Index (HAI). This cccDNA assay had a lower limit of detection at 15 copies/PCR, a lower limit of quantitation at 91 copies/PCR and a correlation coefficient (R) of 0.98 (P < 0.0001). cccDNA was detected in two of four international panels. Significant correlation was found between cccDNA and total HBV DNA levels in both panels (R = 0.96, and R = 0.43) and in samples of the chronic hepatitis B patients (R = 0.88, P < 0.0001). In 57% of these samples cccDNA was detectable. Mean level of cccDNA was 0.16% of total HBV load. Plasma cccDNA levels were higher in HBeAg positive samples than in HBeAg negative samples (4.91 log copies/ml vs. 3.88 log copies/ml, P < 0.0001). Levels of total HBV DNA and HBV genotype did not influence cccDNA detection. ALT levels and HAI-score were not correlated with plasma cccDNA levels. These findings suggest that cccDNA levels in plasma are not the result of increased hepatocyte degeneration, but indicate that other mechanisms might be responsible.
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Affiliation(s)
- R B Takkenberg
- AMC Liver Center, Department of Gastroenterology and Hepatology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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23
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Pan XP, Li LJ, Du WB, Li MW, Cao HC, Sheng JF. Differences of YMDD mutational patterns, precore/core promoter mutations, serum HBV DNA levels in lamivudine-resistant hepatitis B genotypes B and C. J Viral Hepat 2007; 14:767-74. [PMID: 17927612 DOI: 10.1111/j.1365-2893.2007.00869.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The aims of this study were to investigate the viral differences among lamivudine-resistant hepatitis B virus (HBV) genotypes B and C in vivo. Fifty-three patients carrying lamivudine-resistant HBV were enrolled in this study. HBV genotypes, Levels of alanine aminotransferase (ALT), HBV DNA levels were monitored during therapy. The polymerase and precore/core promoter genes were amplified by polymerase chain reaction and their products were sequenced directly. Among 53 patients resistant HBV genotypes B and C accounted for 41.50% and 58.50%, respectively. The occurrence of reverse transcriptase rt204I mutants was lower in genotype B (36.36%) than that in genotype C (87.10%), whereas rt204V mutants was higher in genotype B (63.64%) than that in genotype C (12.90%). The occurrence of precore mutation (nt1896A) was higher in genotype B (77.27%) than that in genotype C (32.26%). Serum HBV DNA levels after emergence of lamivudine resistance were higher in genotype C (7.71 +/- 0.80 Log copies/mL) compared with genotype B (6.97 +/- 0.77 Log copies/mL). Multivariate analysis identified pretreatment HBV DNA levels, HBeAg status and HBV genotype as independent factors associated with a shorter time to lamivudine resistance(P = 0.035, P = 0.006 and P = 0.001, respectively). Multivariate analysis showed that HBV genotype (P = 0.004) and pretreatment ALT levels (P = 0.01) was independently associated with YMDD mutational patterns. The results showed that the YMDD mutational patterns, precore mutation and serum HBV DNA levels differ between lamivudine-resistant HBV genotypes B and C in vivo. It is valuable for treatment of lamivudine-resistant HBV in clinic.
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Affiliation(s)
- X P Pan
- Key Laboratory of Infectious Diseases, Ministry of Public Health, Department of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Mazet-Wagner AA, Baclet MC, Loustaud-Ratti V, Denis F, Alain S. Real-time PCR quantitation of hepatitis B virus total DNA and covalently closed circular DNA in peripheral blood mononuclear cells from hepatitis B virus-infected patients. J Virol Methods 2006; 138:70-9. [PMID: 16962180 DOI: 10.1016/j.jviromet.2006.07.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 07/12/2006] [Accepted: 07/19/2006] [Indexed: 12/29/2022]
Abstract
It remains unclear whether hepatitis B virus (HBV) replicates in extrahepatic tissues, and particularly in peripheral blood mononuclear cells (PBMCs), which may serve as a reservoir for the maintenance of infection. A real-time PCR assay for the quantitation of total and covalently closed circular (ccc) HBV DNA in serum and in PBMCs was developed. This assay was highly sensitive (detection limit: 27 IU/mL), linear over a wide range (9 log10), and was displayed high inter- and intra-assay reproducibility for the quantitation of total DNA. Genotypes A to E were detected and the results were consistent with those obtained with the COBAS Amplicor HBV Monitor Test. The specificity of the methodology was increased by prior treatment with an enzyme that digests relaxed circular DNA, and the elimination of background signals from virus adsorbed to the surface of PBMCs. HBV DNA was detected in the serum and PBMCs of 12 HBsAg-positive patients, with less than 1% in the cccDNA form. In conclusion, the quantitation of total and ccc HBV DNA in PBMCs is potentially useful as a non-invasive marker, and may help to increase our knowledge of the natural history of hepatitis B.
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Affiliation(s)
- A A Mazet-Wagner
- Laboratoire de Bactériologie-Virologie EA3175, Faculté de Médecine, Université de Limoges, 2 rue du Dr Marcland, 87000 Limoges, France
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25
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Laras A, Koskinas J, Dimou E, Kostamena A, Hadziyannis SJ. Intrahepatic levels and replicative activity of covalently closed circular hepatitis B virus DNA in chronically infected patients. Hepatology 2006; 44:694-702. [PMID: 16941694 DOI: 10.1002/hep.21299] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) is responsible for viral persistence in the natural course of chronic HBV infection and during prolonged antiviral therapy and serves as the template for the production of HBV pregenomic RNA (pgRNA), the primary step in HBV replication. In this study, we have developed and applied sensitive and specific quantitative real-time polymerase chain reaction (PCR) assays for the measurement of intrahepatic concentration, pgRNA production, and replicative activity of cccDNA in liver biopsy samples from 34 non-treated patients with chronic hepatitis B (CHB); 12 hepatitis B e antigen (HBeAg)(+) and 22 HBeAg(-). Median copy number for cccDNA was 1.5 per cell and for pgRNA significantly higher, 6.5 copies per cell, with a good correlation between cccDNA and pgRNA levels in all samples. In HBeAg(-) patients, median values of cccDNA and pgRNA levels were 10-fold and 200-fold lower than in HBeAg(+), respectively, reflecting the differences in viral activity and clinical characteristics of the two groups. Furthermore, the replicative activity of intrahepatic cccDNA was significantly lower in HBeAg(-) patients harboring mutant HBV strains than in HBeAg(+) patients: median 3.5 versus 101 pgRNA copies per cccDNA molecule. In conclusion, the levels of both HBV cccDNA, a marker of HBV persistence, and pgRNA, an indicator of viral replication, in the liver of chronically infected patients correlate with viral activity and the phase of HBV infection. The combined measurement of cccDNA and pgRNA levels provides valuable information on the presence and replicative activity of intrahepatic HBV cccDNA.
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Affiliation(s)
- Andreas Laras
- Hepatitis Research Laboratory, Athens University School of Medicine, and Henry Dunant Hospital, Athens, Greece
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26
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N/A, 秦 波. N/A. Shijie Huaren Xiaohua Zazhi 2006; 14:1999-2002. [DOI: 10.11569/wcjd.v14.i20.1999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Abstract
The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.
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Affiliation(s)
| | | | - T. Lion
- Corresponding author. Tel.: +43 1 40470 489; fax: +43 1 40470 437.
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28
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Takehara T, Suzuki T, Ohkawa K, Hosui A, Jinushi M, Miyagi T, Tatsumi T, Kanazawa Y, Hayashi N. Viral covalently closed circular DNA in a non-transgenic mouse model for chronic hepatitis B virus replication. J Hepatol 2006; 44:267-74. [PMID: 16226822 DOI: 10.1016/j.jhep.2005.07.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2004] [Revised: 07/27/2005] [Accepted: 07/29/2005] [Indexed: 01/04/2023]
Abstract
BACKGROUND/AIMS The lack of small animal models supporting chronic hepatitis B virus (HBV) infection impedes the assessment of anti-viral drugs in the whole animal. Although transgenic mice have been used for this purpose, these models are clearly different from natural infection, because HBV is produced from the integrated HBV sequence harbored in all hepatocytes. METHODS Balb/cA nude mice were hydrodynamically injected with a plasmid having 1.5-fold over-length of HBV DNA and analyzed for HBV replication. RESULTS Hydrodynamically injected mice showed substantial levels of antigenemia and viremia for more than 1 year. Covalently closed circular DNA (cccDNA), the template of viral replication in natural infection, was produced in the livers and was critically involved in the long-term HBV production, because disruption of the pol gene of the inoculated DNA resulted in transient expression of HBV genes for less than 2 months. Administration of the IFNalpha gene transiently suppressed HBV DNA replication, but was not capable of eliminating HBV in this model. CONCLUSIONS In vivo gene transfer of a plasmid encoding HBV DNA can establish chronic viral replication in mice, which involves, at least in part, new synthesis of the HBV cccDNA episome, thus recapitulating a part of human HBV infection.
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Affiliation(s)
- Tetsuo Takehara
- Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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Tang B, Wang YM, Liu J, Zhang R. Detection of hepatitis B virus cccDNA with modified polymerase chain reaction. Shijie Huaren Xiaohua Zazhi 2005; 13:2188-2192. [DOI: 10.11569/wcjd.v13.i18.2188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To establish a simple and fast hepatitis B virus covalently closed circular DNA(cccDNA) detecting method based on polymerase chain reaction(PCR) with satisfactory sensitivity and specificity.
METHODS: The cccDNA and the relaxed circular DNA (rcDNA) were extracted from HepG2.2.15 cells and supernatant, respectively, and then purified. Two pairs of specific PCR primes were designed to cover the single strand area of rcDNA. And two pairs of non-specific PCR primes were designed to cover the double strand area of rcDNA. Before and after digested by single-strand-specific mung bean nuclease(MBN), cccDNA and rcDNA samples were amplified by specific primes and non-specific primes. Whether the digested cccDNA can be amplified by specific primes, without amplifying the digested rcDNA, was observed. The PCR parameters such as substrate amount and circulation times were changed during amplification. The HBV genome plasmid was used as control; and the HBV samples from patient with hepatitis B was used for practical test.
RESULTS: Different amounts of rcDNA template were amplified by specific and non-specific primes. More than 104 and 102 rcDNA template molecules were amplified by two pairs of specific and non-specific primes, respectively. The specific primes could not discriminate between rcDNA and cccDNA when the template molecules were overabundant. Before and after the digestion by MBN, different amounts of cccDNA were amplified by specific and non-specific primes; and after the digestion, rcDNA templates were amplified by non-specific primes, but not by specific primes. With this strategy, we found the virus samples from the serum of the patient with chronic hepatitis B contained mainly rcDNA and a small quantity of cccDNA, while the samples from hepatocytes contained mainly cccDNA.
CONCLUSION: The combination of MBN selective digestion and specific PCR amplification of the cccDNA is a simple, fast, sensitive and specific method for the detection of HBV cccDNA.
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Guo HY, Tan DM, Xu XW. Predictive value of HBV cccDNA in PBMC of response to lamivudine therapy in patients with chronic hepatitis B. Shijie Huaren Xiaohua Zazhi 2005; 13:1202-1205. [DOI: 10.11569/wcjd.v13.i10.1202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To assess the value of hepatitis B virus (HBV) covalently closed circle DNA (cccDNA) in peripheral blood mononuclear cells (PBMC) for the prediction of the sustained response to lamivudine therapy in patients with chronic hepatitis B.
METHODS: Seventeen chronic hepatitis B patients with complete or partial response (serum HBV DNA turned negative, and ALT was normalized with or without HBeAg/anti-HBe seroconversion) were selected. HBV cccDNA in PBMC was detected at the end of lamivudine treatment, and 1 year after treatment.
RESULTS: Nine out of 17 patients were positive for HBV cccDNA in their PBMC at the end of lamivudine treatment. Virological relapse were found during 1-year follow-up in all of these 9 patients; whereas only 1 relapse was observed among the 8 patients without HBV cccDNA.
CONCLUSION: HBV cccDNA in PBMC at the end of treatment is of good predictive value for the sustained response to lamivudine treatment in chronic hepatitis B patients.
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Wong DKH, Yuen MF, Yuan H, Sum SSM, Hui CK, Hall J, Lai CL. Quantitation of covalently closed circular hepatitis B virus DNA in chronic hepatitis B patients. Hepatology 2004; 40:727-37. [PMID: 15349913 DOI: 10.1002/hep.20353] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This study examined a signal amplification assay, the Invader assay, for the quantitation of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) in liver biopsies and sera. DNA was extracted from liver biopsy and serum samples were collected from 16 hepatitis B e antigen (HBeAg)-positive and 36 antibody-to-HBeAg-positive (anti-HBe-positive) chronic hepatitis B patients. The amount of total HBV DNA and cccDNA was measured using the Invader assay. Anti-HBe-positive patients had lower median total intrahepatic HBV DNA (P < .001) and intrahepatic cccDNA levels (P = .001) than HBeAg-positive patients. Intrahepatic cccDNA correlated positively with the total intrahepatic HBV DNA (r = 0.950, P < .001). However, the proportion of intrahepatic HBV DNA in the form of cccDNA was inversely related to the amount of total intrahepatic HBV DNA (r = -0.822, P < .001). A small amount of cccDNA was detected in 39 of 52 (75%) serum samples. Anti-HBe-positive patients had lower median serum cccDNA levels than HBeAg-positive patients (P = .002). Serum HBV DNA correlated positively with intrahepatic total HBV DNA (r = 0.778, P < .001) and intrahepatic cccDNA (r = 0.481, P = .002). In conclusion, the Invader assay is a reliable assay for the quantitation of cccDNA. Serum and intrahepatic total HBV DNA and cccDNA levels become lower as the disease progresses from HBeAg-positive to anti-HBe-positive phase, with cccDNA becoming the predominant form of intrahepatic HBV DNA.
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Affiliation(s)
- Danny Ka-Ho Wong
- Division of Gastroenterology and Hepatology, Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
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Singh M, Dicaire A, Wakil AE, Luscombe C, Sacks SL. Quantitation of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) in the liver of HBV-infected patients by LightCycler real-time PCR. J Virol Methods 2004; 118:159-67. [PMID: 15081611 DOI: 10.1016/j.jviromet.2004.02.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2003] [Revised: 02/11/2004] [Accepted: 02/16/2004] [Indexed: 02/07/2023]
Abstract
Antivirals for hepatitis B virus (HBV) reduce viral load and improve liver histology, however, their effect on covalently closed circular DNA (cccDNA), the HBV transcriptional template, has not been extensively examined. This study evaluated a newly designed LightCycler based quantitative cccDNA PCR assay. A linear range of 2.5 x 10(1) to 1 x 10(9) copies/assay using primers specific for HBV cccDNA and 2.5 x 10(1) to 2.5 x 10(9) copies/assay using primers specific for total HBV DNA (tDNA) was established. beta-Globin was used to estimate the number of cells in each PCR reaction. Enzymatic digestion with an ATP-dependent DNase improved the analytic specificity to a greater than 1:10000 ratio of cccDNA:RC DNA (relaxed circular DNA). One-tenth of the extracted DNA from 1mg of liver biopsy, was analyzed from six patients, three HBV-infected and three uninfected individuals, under blinded conditions; three were found positive and three negative for cccDNA and tDNA. Approximately 6 x 10(3) copies of cccDNA/mg of tissue were detected in a pre-transplant biopsy from an HBV-infected patient treated with lamivudine. Sequential post-transplant liver biopsies were negative for both HBV cccDNA and tDNA. An HBV-infected patient with cirrhosis who was antiviral therapy naïve had 3.7 x 10(4) copies of cccDNA/mg of liver tissue. Another treatment-naïve patient with a history of high HBV viral load had 1 x 10(5) copies of cccDNA/mg of tissue (4 x 10 (6) copies of tDNA/mg of tissue). Further studies are warranted but the high level of sensitivity, specificity, rapidity and accuracy provided by this novel assay with the LightCycler system indicate that it could be useful for monitoring antiviral therapy.
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Affiliation(s)
- Madhu Singh
- Viridae Clinical Sciences Inc., 1134 Burrard Street, Vancouver, BC, Canada V6Z 1Y8
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