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Lago BV, Portilho MM, Mello VM, De Sousa PSF, Angelice GP, Marques BCL, da Silva Andrade LT, Marques VA, Lewis-Ximenez LL, Mello FCDA, Villar LM. Genetic variability of hepatitis B virus in acute and in different phases of chronic infection in Brazil. Sci Rep 2024; 14:10742. [PMID: 38730249 PMCID: PMC11087654 DOI: 10.1038/s41598-024-60900-2] [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: 12/22/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
The selection pressure imposed by the host immune system impacts on hepatitis B virus (HBV) variability. This study evaluates HBV genetic diversity, nucleos(t)ide analogs resistance and HBsAg escape mutations in HBV patients under distinct selective pressures. One hundred and thirteen individuals in different phases of HBV infection were included: 13 HBeAg-positive chronic infection, 9 HBeAg-positive chronic hepatitis, 47 HBeAg-negative chronic infection (ENI), 29 HBeAg-negative chronic hepatitis (ENH) and 15 acute infected individuals. Samples were PCR amplified, sequenced and genetically analyzed for the overlapping POL/S genes. Most HBV carriers presented genotype A (84/113; 74.3%), subgenotype A1 (67/84; 79.7%), irrespective of group, followed by genotypes D (20/113; 17.7%), F (8/113; 7.1%) and E (1/113; 0.9%). Clinically relevant mutations in polymerase (tL180M/M204V) and in the Major Hydrophilic Region of HBsAg (sY100C, T118A/M, sM133T, sD144A and sG145R) were observed. Our findings, however, indicated that most polymorphic sites were located in the cytosolic loops (CYL1-2) and transmembrane domain 4 (TMD4) of HBsAg. Lower viral loads and higher HBV genetic diversity were observed in ENI and ENH groups (p < 0.001), suggesting that these groups are subjected to a higher selective pressure. Our results provide information on the molecular characteristics of HBV in a diverse clinical setting, and may guide future studies on the balance of HBV quasispecies at different stages of infection.
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Affiliation(s)
- Barbara Vieira Lago
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil.
- Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Fiocruz, Rio de Janeiro, Brazil.
| | - Moyra Machado Portilho
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Vinicius Motta Mello
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil.
| | - Paulo Sergio Fonseca De Sousa
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Giovana Paula Angelice
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Bianca Cristina Leires Marques
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Larissa Tropiano da Silva Andrade
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Vanessa Alves Marques
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Lia Laura Lewis-Ximenez
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Francisco Campello do Amaral Mello
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Livia Melo Villar
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
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Duchen D, Clipman SJ, Vergara C, Thio CL, Thomas DL, Duggal P, Wojcik GL. A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction. PLoS One 2024; 19:e0301069. [PMID: 38669259 PMCID: PMC11051683 DOI: 10.1371/journal.pone.0301069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/09/2024] [Indexed: 04/28/2024] Open
Abstract
Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference a priori remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative 'genome graph' can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual's infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research.
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Affiliation(s)
- Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Center for Biomedical Data Science, Yale School of Medicine, New Haven, CT, United States of America
| | - Steven J. Clipman
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Candelaria Vergara
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Chloe L. Thio
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David L. Thomas
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Genevieve L. Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
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Yekani M, Azargun R, Sharifi S, Nabizadeh E, Nahand JS, Ansari NK, Memar MY, Soki J. Collateral sensitivity: An evolutionary trade-off between antibiotic resistance mechanisms, attractive for dealing with drug-resistance crisis. Health Sci Rep 2023; 6:e1418. [PMID: 37448730 PMCID: PMC10336338 DOI: 10.1002/hsr2.1418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Background The discovery and development of antimicrobial drugs were one of the most significant advances in medicine, but the evolution of microbial resistance limited the efficiency of these drugs. Aim This paper reviews the collateral sensitivity in bacteria and its potential and limitation as a new target for treating infections. Results and Discussion Knowledge mechanisms of resistance to antimicrobial agents are useful to trace a practical approach to treat and control of resistant pathogens. The effect of a resistance mechanism to certain antibiotics on the susceptibility or resistance to other drugs is a key point that may be helpful for applying a strategy to control resistance challenges. In an evolutionary trade-off known as collateral sensitivity, the resistance mechanism to a certain drug may be mediated by the hypersensitivity to other drugs. Collateral sensitivity has been described for different drugs in various bacteria, but the molecular mechanisms affecting susceptibility are not well demonstrated. Collateral sensitivity could be studied to detect its potential in the battle against resistance crisis as well as in the treatment of pathogens adapting to antibiotics. Collateral sensitivity-based antimicrobial therapy may have the potential to limit the emergence of antibiotic resistance.
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Affiliation(s)
- Mina Yekani
- Department of Microbiology, Faculty of MedicineKashan University of Medical SciencesKashanIran
- Infectious and Tropical Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Student Research CommitteeKashan University of Medical SciencesKashanIran
| | - Robab Azargun
- Department of Microbiology, Faculty of MedicineMaragheh University of Medical ScienceMaraghehIran
| | - Simin Sharifi
- Dental and Periodontal Research CenterTabriz University of Medical SciencesTabrizIran
| | - Edris Nabizadeh
- Infectious and Tropical Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Navideh Karimi Ansari
- Department of Microbiology, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Jozsef' Soki
- Institute of Medical Microbiology, Albert Szent‐Györgyi Faculty of MedicineUniversity of SzegedSzegedHungary
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Yu T, Zhang M, Zhang H, Zheng J, Shen C, Jiang N, Zou L, Wang J, Yu Y, Zhang Q, Yu S, Huang Y, Huang Y, Zhang J, Qiu C, Zhang W, Meng Z. Evidence of Residual Ongoing Viral Replication in Chronic Hepatitis B Patients Successfully Treated With Nucleos(t)ide Analogues. J Infect Dis 2023; 227:675-685. [PMID: 36546708 DOI: 10.1093/infdis/jiac493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/17/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Chronic hepatitis B is usually treated with nucleos(t)ide analogues (NAs). However, a cure is rarely achieved, even with years of treatment. Here, we investigated whether viral replication is completely halted and how long covalently closed circular DNA (cccDNA) persists in patients successfully treated with NAs. METHODS A series of longitudinal serum samples and a collection of cross-sectional liver biopsies were obtained from patients successfully treated with NAs. Viral variants in serum HBV RNA were enumerated by deep sequencing. Viral replication intermediates in hepatocytes were directly visualized by in situ hybridization. The apparent half-life of each cccDNA was estimated. RESULTS Three of 6 successfully treated patients demonstrated clear evidence of a small proportion of virus evolution, although the overwhelming proportion of variants were identical or possessed a similar degree of divergence through time. The apparent half-life of variants was estimated to be from approximately 7.42 weeks to infinite. Hepatocytes remained positive for cytoplasmic nucleocapsids-associated relaxed circular DNA in 4 of 7 liver needle biopsies. CONCLUSIONS We conclude that even after prolonged treatment, a small proportion of the cccDNA reservoir is constantly replenished by continued low-level HBV replication, whereas a large proportion of the cccDNA reservoir persists over time.
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Affiliation(s)
- Tong Yu
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Miaoqu Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Hanyue Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Jianming Zheng
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Chuan Shen
- Department of Infectious Disease, The Third Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
- Clinical Research Center for Infectious Disease of Hebei Province, Shijiazhuang, China
| | - Ning Jiang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Lei Zou
- Department of Infectious Disease, Yancheng Second People's Hospital, Yancheng, China
| | - Jing Wang
- Department of Infectious Disease, Jingan District Central Hospital of Shanghai, Shanghai, China
| | - Yiqi Yu
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Qiran Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Shuili Yu
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Yanfang Huang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Yuxian Huang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Jiming Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Chao Qiu
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Zhefeng Meng
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
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5
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Duchen D, Clipman S, Vergara C, Thio CL, Thomas DL, Duggal P, Wojcik GL. A hepatitis B virus (HBV) sequence variation graph improves sequence alignment and sample-specific consensus sequence construction for genetic analysis of HBV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523611. [PMID: 36711598 PMCID: PMC9882026 DOI: 10.1101/2023.01.11.523611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Hepatitis B virus (HBV) remains a global public health concern, with over 250 million individuals living with chronic HBV infection (CHB) and no curative therapy currently available. Viral diversity is associated with CHB pathogenesis and immunological control of infection. Improved methods to characterize the viral genome at both the population and intra-host level could aid drug development efforts. Conventionally, HBV sequencing data are aligned to a linear reference genome and only sequences capable of aligning to the reference are captured for analysis. Reference selection has additional consequences, including sample-specific 'consensus' sequence construction. It remains unclear how to select a reference from available sequences and whether a single reference is sufficient for genetic analyses. Using simulated short-read sequencing data generated from full-length publicly available HBV genome sequences and HBV sequencing data from a longitudinally sampled individual with CHB, we investigate alternative graph-based alignment approaches. We demonstrate that using a phylogenetically representative 'genome graph' for alignment, rather than linear reference sequences, avoids issues of reference ambiguity, improves alignment, and facilitates the construction of sample-specific consensus sequences genetically similar to an individual's infection. Graph-based methods can therefore improve efforts to characterize the genetics of viral pathogens, including HBV, and may have broad implications in host pathogen research.
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Affiliation(s)
- Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Steven Clipman
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Candelaria Vergara
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Chloe L Thio
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - David L Thomas
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
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Fu Y, Fang F, Guo H, Xiao X, Hu Y, Zeng Y, Chen T, Wu S, Lin N, Huang J, Jiang L, Ou Q, Liu C. Compartmentalisation of Hepatitis B virus X gene evolution in hepatocellular carcinoma microenvironment and the genotype-phenotype correlation of tumorigenicity in HBV-related patients with hepatocellular carcinoma. Emerg Microbes Infect 2022; 11:2486-2501. [PMID: 36102940 PMCID: PMC9621239 DOI: 10.1080/22221751.2022.2125344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/26/2022] [Accepted: 09/12/2022] [Indexed: 02/08/2023]
Abstract
Hepatitis B virus (HBV) exists as quasispecies (QS). However, the evolutionary characteristics of haplotypes of HBV X gene in the hepatocellular carcinoma (HCC) microenvironment remain unclear. Mutations across X gene are essential for the tumorigenicity of HBV X protein (HBx). However, the functional phenotypes of many mutant HBx remain unknown. This study aims to compare the characteristics of X gene evolution between tumour and non-tumour tissues in HCC patients and investigate the tumorigenic phenotype of HBx harbouring mutation T81P/S101P/L123S. This study included 24 HCC patients. Molecular cloning of X gene was performed to analyse characteristics of haplotypes in liver tissues. HCC cell lines stably expressing wild-type or mutant HBx and subcutaneous tumour xenograft mouse model were used to assess HBx-T81P/S101P/L123S tumorigenicity. The mean heterogeneity of HBV QS across X gene in tumour tissues was lower than that in non-tumour tissues. A location bias was observed in X gene clones with genotype C or D in tumour tissues compared to those with genotype B. Mutations in genotype-C or - D clones were mainly clustered in the dimerization region and aa110-aa140 within the transactivation region. A novel mutation combination at residues 81, 101 and 123 was identified in tumour tissues. Further, HBx-T81P/S101P/L123S promotes cell proliferation and increases genomic instability, which was mediated by MYC. This study elucidates the compartmentalized evolution patterns of HBV X gene between intra tumour and non-tumour tissues in HCC patients and provides a new mechanism underlying HBV-driven hepatocarcinogenesis, suggesting a potential viral marker for monitoring HCC.
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Affiliation(s)
- Ya Fu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Fengling Fang
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Hongyan Guo
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Xialin Xiao
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Yuhai Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Yongbin Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Songhang Wu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Ni Lin
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Jinlan Huang
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Ling Jiang
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
- Qishui Ou Department of Laboratory Medicine, The First Affiliated Hospital, Clinical Laboratory Diagnostics, The First Clinical College, Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, People’s Republic of China
- Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
- Can Liu Department of Laboratory Medicine, The First Affiliated Hospital, Clinical Laboratory Diagnostics, The First Clinical College, Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, People’s Republic of China
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7
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Liver Histology of Treatment-Naïve Children with Chronic Hepatitis B Virus Infection in Shanghai China. Int J Infect Dis 2022; 123:112-118. [PMID: 36028208 DOI: 10.1016/j.ijid.2022.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND & AIMS Chronic hepatitis B (CHB) is associated with high morbidity and mortality. We aimed to investigate associations between hepatic histology and clinical characteristics in treatment-naïve children with CHB in Shanghai, China. METHODS The liver biopsy specimens of 278 treatment-naïve children with CHB virus infection were scored for inflammation and fibrosis, and correlations with clinical and laboratory data were determined. RESULTS CHB clinical, virologic and pathologic features were studied in 278 treatment-naïve children (177 males (63.7%)) from Shanghai, China. Maternal sera were hepatitis B surface antigen (HBsAg) positive for 277 children. At biopsy, 87.4% of patients were hepatitis B e antigen positive. The median age at biopsy was 5.1 years (interquartile range 2.8-8.4 years). Hepatitis B virus (HBV) DNA levels were generally high (mean 7.4 log10 IU/ml), as were levels of serum alanine aminotransferase (ALT, median 105 U/L). Using the Metavir histology activity index scoring system, no, mild, moderate and severe inflammation was seen in 2.9%, 22.3%, 73.4%, and 1.4% of patients, respectively. No fibrosis, mild fibrosis, moderate fibrosis, and cirrhosis was seen in 11.5%, 32.7%, 47.5%, and 8.3% of patients, respectively. When the serum ALT level was ≤80 (2× the upper limit of normal) and >80 U/L, the inflammation score (P<0.0001) was significantly different. And the fibrosis score was significantly different (P<0.0001), either. Inflammation and fibrosis were aggravated with increasing ALT levels. Fibrosis scores were significantly higher in children aged ≤3 than aged >3 years (P<0.0001). The rates of moderate fibrosis and cirrhosis were higher in children aged ≤3 years at biopsy. No correlations were found between histologic changes and sex, HBV genotype or HBV DNA level. CONCLUSION Substantial heterogeneity in inflammatory and fibrotic levels was observed in treatment-naïve children with CHB in Shanghai, China. Serum ALT levels >80 U/L may be a strong indicator of the degree of hepatic inflammation and fibrosis severity. Moderate fibrosis and cirrhosis can appear in children aged <3 years or younger.
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8
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Li Y, Xiao Y, Li L, Song Y, Zhai X, Liu J, Duan Z, Yan L, Ding F, Liu J, Zhu L, Jiang J, Zou H, Li L, Liang C, Wang J, Li J. The dynamic changes of HBV quasispecies diversity in infancy after immunoprophylaxis failure: a prospective cohort study. Virol J 2021; 18:236. [PMID: 34844612 PMCID: PMC8628401 DOI: 10.1186/s12985-021-01707-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Previous works have observed that younger infants with chronic hepatitis B virus (HBV) infection are more responsive to antiviral treatment. However, the underlying mechanism remains unclear. In this study, the dynamic changes of HBV quasispecies in infants with immunoprophylaxis failure were investigated to provide virological explanations for clinical management on infantile antiviral therapy. METHODS Thirteen 7-month-old infants with immunoprophylaxis failure and their mothers were enrolled from a prospective cohort, and 8 of them were followed up to 3 years old. The sequences of HBV quasispecies were analyzed by the full-length genome clone-based sequencing, and compared among mothers and their infants at different ages. RESULTS The results revealed that the complexity, mutation frequency and genetic distance of HBV quasispecies decreased significantly at full-length, partial open reading frames and regulatory regions of HBV genome at nucleotide level in 7-month-old infants comparing with their mothers, whereas increased significantly to near the maternal level when infants grew up to 3 years old. Furthermore, similar changes were also found in Core, PreS2, RT and P regions of HBV genome at amino acid level, especially for potential NAs-resistant mutants in RT region and immune-escape mutants in Core and PreS2 regions. CONCLUSIONS This study uncovered the evolution of HBV quasispecies in infancy after mother-to-child transmission, which may provide the virological evidence for explaning that younger children are more responsive to antiviral therapy.
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Affiliation(s)
- Yi Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Yiwei Xiao
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Lili Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Yarong Song
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Xiangjun Zhai
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Jianxun Liu
- Zhengzhou Municipal Center for Disease Control and Prevention, Zhengzhou, 450053, China
| | - Zhongping Duan
- Beijing Youan Hospital, Capital Medical University, Beijing, 100054, China
| | - Ling Yan
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Feng Ding
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Jia Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Liguo Zhu
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Jie Jiang
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Huaibin Zou
- Beijing Youan Hospital, Capital Medical University, Beijing, 100054, China
| | - Lingxiang Li
- Gongyi City Maternal and Child Health Hospital, Zhengzhou, 451200, China
| | - Caihong Liang
- Zhongmu County Maternal and Child Health Hospital, Zhengzhou, 451450, China
| | - Jie Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Jie Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100083, China.
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9
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Tang X, Huang W, Kang J, Ding K. Early dynamic changes of quasispecies in the reverse transcriptase region of hepatitis B virus in telbivudine treatment. Antiviral Res 2021; 195:105178. [PMID: 34509461 DOI: 10.1016/j.antiviral.2021.105178] [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: 05/24/2021] [Revised: 08/03/2021] [Accepted: 09/08/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Telbivudine (LdT) - a synthetic thymidine β-L-nucleoside analogue (NA) - is an effective inhibitor for hepatitis B virus (HBV) replication. The quasispecies spectra in the reverse transcriptase (RT) region of the HBV genome and their dynamic changes associated with LdT treatment remains largely unknown. METHODS We prospectively recruited a total of 21 treatment-naive patients with chronic HBV infection and collected sequential serum samples at five time points (baseline, weeks 1, 3, 12, and 24 after LdT treatment). The HBV RT region was amplified and shotgun-sequenced by the Ion Torrent Personal Genome Machine (PGM)® system. We reconstructed full-length haplotypes of the RT region using an integrated bioinformatics framework, including de novo contig assembly and full-length haplotype reconstruction. In addition, we investigated the quasispecies' dynamic changes and evolution history and characterized potential NAs resistant mutations over the treatment course. RESULTS Viral quasispecies differed obviously between patients with complete (n = 8) and incomplete/no response (n = 13) at 12 weeks after LdT treatment. A reduced dN/dS ratio in quasispecies demonstrated a selective constraint resulting from antiviral therapy. The temporal clustering of sequential quasispecies showed different patterns along with a 24-week observation, although its statistic did not differ significantly. Several patients harboring pre-existing resistant mutations showed different clinical responses, while NAs resistant mutations were rare within a short-term treatment. CONCLUSION A complete profile of quasispecies reconstructed from in-depth shotgun sequencing may has important implications for enhancing clinical decision in adjusting antiviral therapy timely.
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Affiliation(s)
- Xia Tang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Wenxun Huang
- Department of Infectious Diseases, Chongqing Three Gorges Central Hospital, Chongqing, 404000, PR China
| | - Juan Kang
- Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400003, PR China
| | - Keyue Ding
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, Henan Province, 450003, PR China.
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10
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Yin J, Chen X, Li N, Han X, Liu W, Pu R, Wu T, Ding Y, Zhang H, Zhao J, Han X, Wang H, Cheng S, Cao G. Compartmentalized evolution of hepatitis B virus contributes differently to the prognosis of hepatocellular carcinoma. Carcinogenesis 2021; 42:461-470. [PMID: 33247709 DOI: 10.1093/carcin/bgaa127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/26/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Serum hepatitis B virus (HBV) mutations can predict hepatocellular carcinoma (HCC) occurrence. We aimed to clarify if HBV evolves synchronously in the sera, adjacent liver and tumors and predict HCC prognosis equally. A total of 203 HBV-positive HCC patients with radical hepatectomy in Shanghai, China, during 2011-15 were enrolled in this prospective study. Quasispecies complexity (QC) in HBV core promoter region was assessed using clone-based sequencing. We performed RNA sequencing on tumors and paired adjacent tissues of another 15 HCC patients and analyzed it with three public data sets containing 127 samples. HBV QC was positively correlated to APOBEC3s' expression level (r = 0.28, P < 0.001), higher in the adjacent tissues than in the tumors (P = 6.50e-3), and higher in early tumors than in advanced tumors (P = 0.039). The evolutionary distance between the sera-derived HBV strains and the tumor-derived ones was significantly longer than that between the sera-derived ones and the adjacent tissue-derived ones (P < 0.001). Multivariate Cox regression analyses indicated that high HBV QC in the sera predicted an unfavorable overall survival (P = 0.002) and recurrence-free survival (RFS; P = 0.004) in HCC, whereas, in the tumors, it predicted a favorable RFS (P < 0.001). APOBECs-related HBV mutations, including G1764A, were more frequent in the sera than in the adjacent tissues. High-frequent A1762T/G1764A in the sera predicted an unfavorable RFS (P < 0.001), whereas, in the tumors, it predicted a favorable RFS (P = 0.035). In conclusion, HBV evolves more advanced in the sera than in the tumors. HBV QC and A1762T/G1764A in the sera and tumors have contrary prognostic effects in HCC.
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Affiliation(s)
- Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Xi Chen
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Nan Li
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Xuewen Han
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Wenbin Liu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Rui Pu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Ting Wu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Yibo Ding
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Hongwei Zhang
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Jun Zhao
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Xue Han
- Division of Chronic Diseases, Center for Disease Control and Prevention of Yangpu District, Shanghai, China
| | - Hongyang Wang
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, China
| | - Shuqun Cheng
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China.,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China.,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, China
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11
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Fu Y, Wu S, Hu Y, Chen T, Zeng Y, Liu C, Ou Q. Mutational characterization of HBV reverse transcriptase gene and the genotype-phenotype correlation of antiviral resistance among Chinese chronic hepatitis B patients. Emerg Microbes Infect 2021; 9:2381-2393. [PMID: 33124952 PMCID: PMC7605321 DOI: 10.1080/22221751.2020.1835446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background and Aims: The drug resistance of hepatitis B virus (HBV) originates from mutations within HBV reverse transcriptase (RT) region during the prolonged antiviral therapy. So far, the characteristics of how these mutations distribute and evolve in the process of therapy have not been clarified yet. Thus we aimed to investigate these characteristics and discuss their contributing factors. Methods: HBV RT region was direct-sequenced in 285 treatment-naive and 214 post-treatment patients. Mutational frequency and Shannon entropy were calculated to identify the specific mutations differing between genotypes or treatment status. A typical putative resistance mutation rtL229V was further studied using in-vitro susceptibility assays and molecular modeling. Results: The classical resistance mutations were rarely detected among treatment-naive individuals, while the putative resistance mutations were observed at 8 AA sites. rtV191I and rtA181T/V were the only resistance mutations identified as genotype-specific mutation. Selective pressure of drug usage not only contributed to the classical resistance mutations, but also induced the changes at a putative resistance mutation site rt229. rtL229V was the major substitution at the site of rt229. It contributed to the most potent suppression of viral replication and reduced the in-vitro drug susceptibility to entecavir (ETV) when coexisting with rtM204V, consistent with the hypothesis based on the molecular modeling and clinical data analysis. Conclusions: The analysis of mutations in RT region under the different circumstances of genotypes and therapy status might pave the way for a better understanding of resistance evolution, thus providing the basis for a rational administration of antiviral therapy.
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Affiliation(s)
- Ya Fu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Songhang Wu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Yuhai Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Yongbin Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
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12
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Deng H, Guo F, Yu W, Li L, Xia Y, Guan Y, Li J. Dynamic changes of HCV genomes under selective pressure from DAAs therapy in relapsed patients. Virus Res 2021; 302:198453. [PMID: 33991622 DOI: 10.1016/j.virusres.2021.198453] [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: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022]
Abstract
Currently, direct-acting antiviral drugs (DAAs) are widely used as therapeutic methods for hepatitis C virus (HCV)-positive patients, however, patients may experience treatment failure, and the dynamic changes of HCV genomes in these patients are unknown. In this study, three real-world DAAs cohorts were enrolled to observe clinical efficacy. In addition, serum samples from treatment failure patients at baseline and relapse were used to analyze changes of the HCV genomes at near full-length genome level, including resistance-associated variants (RAVs), viral quasispecies diversity and selection analysis. Next-generation sequencing was used as the detection method. The overall sustained virological response at 12 w after the end of treatment was achieved in 91.9% (57/62) of HCV patients, and 3 paired samples obtained from relapsed patients. All the 3 patients harbored baseline NS5A RAVs, the frequency of NS5A RAVs increased in 2 patients and a new NS5A RAV emerged in 1 patient at relapse, and almost all the viral strains existed with NS5A RAVs at relapse. The results of the viral quasispecies diversity analysis revealed that viral quasispecies diversity decreased at relapse compared to baseline, and the results of selection analysis indicated that the virus population experienced a bottleneck phenomenon, recent selective sweep and population expansion or was under purification selection after DAAs treatment. This study indicated that the clinical efficacy was excellent in real-world DAAs cohorts, and the viral strains existed at relapse were selective by DAAs therapy.
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Affiliation(s)
- Haohui Deng
- Department of Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Fengxia Guo
- Department of Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Weihua Yu
- Department of Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Linghua Li
- Department of Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yang Xia
- Department of Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yujuan Guan
- Department of Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jianping Li
- Department of Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China.
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13
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Wang M, Chen L, Dong M, Li J, Zhu B, Yang Z, Gong Q, Han Y, Yu D, Zhang D, Zoulim F, Zhang J, Zhang X. Viral quasispecies quantitative analysis: a novel approach for appraising the immune tolerant phase of chronic hepatitis B virus infection. Emerg Microbes Infect 2021; 10:842-851. [PMID: 33870846 PMCID: PMC8812768 DOI: 10.1080/22221751.2021.1919033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Few non-invasive models were established for precisely identifying the immune tolerant (IT) phase from chronic hepatitis B (CHB). This study aimed to develop a novel approach that combined next-generation sequencing (NGS) and machine learning algorithms using our recently published viral quasispecies (QS) analysis package. 290 HBeAg positive patients from whom liver biopsies were taken were enrolled and divided into a training group (n = 148) and a validation group (n = 142). HBV DNA was extracted and QS sequences were obtained by NGS. Hierarchical clustering analysis (HCA) and principal component analysis (PCA) based on viral operational taxonomic units (OTUs) were performed to explore the correlations among QS and clinical phenotypes. Three machine learning algorithms, including K-nearest neighbour, support vector machine, and random forest algorithm, were used to construct diagnostic models for IT phase classification. Based on histopathology, 90 IT patients and 200 CHB patients were diagnosed. HBsAg titres for IT patients were higher than those of CHB patients (p < 0.001). HCA and PCA analysis grouped IT and CHB patients into two distinct clusters. The relative abundance of viral OTUs differed mainly within the BCP/precore/core region and was significantly correlated with liver inflammation and fibrosis. For the IT phase classification, all machine-learning models showed higher AUC values compared to models based on HBsAg, APRI, and FIB-4. The relative abundance of viral OTUs reflects the severity of liver inflammation and fibrosis. The novel QS quantitative analysis approach could be used to diagnose IT patients more precisely and reduce the need for liver biopsy.
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Affiliation(s)
- Mingjie Wang
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China.,Department of Gastroenterology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China
| | - Li Chen
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China
| | - MinHui Dong
- Department of Infectious Diseases, Huashan Hospital and Key Laboratory of Medical Molecular Virology (MOH & MOE), Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Jing Li
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China
| | - Beidi Zhu
- Department of Infectious Diseases, Huashan Hospital and Key Laboratory of Medical Molecular Virology (MOH & MOE), Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Zhitao Yang
- Department of Emergency, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China
| | - Qiming Gong
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China
| | - Yue Han
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China
| | - Demin Yu
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China
| | - Donghua Zhang
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China
| | - Fabien Zoulim
- INSERM U1052, Cancer Research Centre of Lyon (CRCL), Lyon, France
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital and Key Laboratory of Medical Molecular Virology (MOH & MOE), Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xinxin Zhang
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People's Republic of China
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14
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Yin GQ, Li J, Zhong B, Yang YF, Wang MR. New therapeutic options for persistent low-level viremia in patients with chronic hepatitis B virus infection: Increase of entecavir dosage. World J Gastroenterol 2021; 27:666-676. [PMID: 33716446 PMCID: PMC7934007 DOI: 10.3748/wjg.v27.i8.666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/25/2020] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection (CHB) is a public health concern worldwide. Current therapies utilizing nucleos(t)ide analogs (NA) have not resulted in a complete cure for CHB. Furthermore, patients on long-term NA treatment often develop low-level viremia (LLV). Persistent LLV, in addition to causing the progression of liver disease or hepatocellular carcinoma, may shed light on the current plight of NA therapy. Here, we review the literature on LLV, NA treatment, and various doses of entecavir to find a strategy for improving the efficacy of this antiviral agent. For LLV patients, three therapeutic options are available, switching to another antiviral monotherapy, interferon-α switching therapy, and continuing monotherapy. In real-world clinical practice, entecavir overdose has been used in antiviral therapy for CHB patients with NA refractory and persistent LLV, which encouraged us to conduct further in-depth literature survey on dosage and duration related entecavir studies. The studies of pharmacodynamics and pharmacokinetics show that entecavir has the maximal selected index for safety, and has great potential in inhibiting HBV replication, in all of the NAs. In the particular section of the drug approval package published by the United States Food and Drug Administration, entecavir doses 2.5-20 mg/d do not increase adverse events, and entecavir doses higher than 1.0 mg/d might improve the antiviral efficacy. The literature survey led us to two suggestions: (1) Increasing entecavir dose to 1.0 mg/d for the treatment of NA naïve patients with HBV DNA >2 × 106 IU/mL is feasible and would provide better prognosis; and (2) Further research is needed to assess the long-term toxic effects of higher entecavir doses (2.5 and 5.0 mg/d), which may prove beneficial in treating patients with prior NA treatment, partial virological response, or LLV state.
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Affiliation(s)
- Guo-Qing Yin
- Department of Infectious Diseases, Nanjing Zhong-Da Hospital, Southeast University School of Medicine, Nanjing 210009, Jiangsu Province, China
| | - Jun Li
- Department of Infectious Diseases, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Bei Zhong
- The Sixth Affiliated Hospital, Guangzhou Medical University/Qingyuan People’s Hospital, Qingyuan 511518, Guangdong Province, China
| | - Yong-Fong Yang
- Department of Liver Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, Jiangsu Province, China
| | - Mao-Rong Wang
- Department of Infectious Diseases and Liver Disease Center, The Affiliated Nanjing Jinling Hospital, Nanjing University, Nanjing 210002, Jiangsu Province, China
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15
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Zhou TC, Liu FW, Fan JH, Zhang SH, Lv SQ, Yu ZY, Zhang YM, Zhang L, Wei J. The association of the heterogeneity of HBV reverse transcriptase quasispecies with antiviral efficacy after treatment with nucleos(t)ide analogues for 10 years. INFECTION GENETICS AND EVOLUTION 2021; 89:104706. [PMID: 33418145 DOI: 10.1016/j.meegid.2021.104706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022]
Abstract
To assess the heterogeneity of HBV reverse transcriptase (RT) quasispecies during 10 years of antiviral therapy and their association with antiviral efficacy. Nineteen patients with chronic hepatitis B (CHB) infection receiving nucleos(t)ide analogues (NAs) were enrolled. Based on the antiviral efficacy after 1 year of treatment, 5 patients were grouped into an early virologic response (EVR) group, while 8 patients were grouped into a late virologic response (LVR) group. Furthermore, 6 CHB patients that had undergone antiviral treatment for 10 years were grouped into a virologic breakthrough (VBT) group. The HBV RT from each patient were amplified, cloned, and sequenced. The complexity of the RT gene in the EVR group was significantly higher than that in the LVR (P = 0.0393) and VBT groups (P = 0.0141). Phylogenetic tree analysis showed that the average branch length of the EVR and LVR groups were significantly greater than that of VBT group (P < 0.001). The complexity (at the nucleotide level) of the RT quasispecies was negatively correlated with the corresponding HBV DNA load (P = 0.0163) at one year post-antiviral treatment. Moreover, both the LVR and VBT groups accumulated more deleterious mutations than the EVR group. After 1 year of NAs treatment, the increased HBV quasispecies complexity and evolutionary topologies, coupled with less deleterious mutations, are likely associated with a favorable efficacy during long-term antiviral treatment.
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Affiliation(s)
- Tai-Cheng Zhou
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Feng-Wei Liu
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Jing-Hua Fan
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China; The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Si-Hang Zhang
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Song-Qin Lv
- Clinical Lab, The Third People's Hospital of Kunming City, Kunming, Yunnan Province, China
| | - Zhi-Yong Yu
- Hepatopancreatobiliary Surgery Department, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Yan-Mei Zhang
- The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Liang Zhang
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China.
| | - Jia Wei
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China.
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Nie Y, Deng X, Lan Y, Li L, Li F, Hu F. Comparison and Correlation of Genetic Variability of the HBV Pre-S Region in HIV/HBV Co-Infected Patients: Quasispecies Perspective. Infect Drug Resist 2020; 13:4327-4334. [PMID: 33293836 PMCID: PMC7719043 DOI: 10.2147/idr.s278415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/17/2020] [Indexed: 11/23/2022] Open
Abstract
Background Human immunodeficiency virus (HIV)/hepatitis B virus (HBV) co-infection can accelerate HBV-induced liver disease. A previous study showed that variation in the HBV pre-S region and quasispecies heterogeneity (Sn, mean genetic distance, dS, dN, and dS/dN) are both related to HBV-induced terminal liver disease in HBV mono-infection. Currently, data are lacking on quasispecies variation of the HBV pre-S region in HIV/HBV co-infection. Investigating the quasispecies variation of the HBV pre-S region and its related factors in HIV/HBV co-infection will help to better explore the pathogenic mechanism of HIV/HBV co-infection. Methods According to the HIV antibody results obtained before treatment, chronic HBV-infected patients were divided into HIV/HBV co-infected and HBV mono-infected groups. The clinical characteristics of all patients were collected, and DNA was extracted from the serum. The HBV pre-S region was amplified by nested PCR and was further TA cloned. BioEdit software 7.0 was used for sequence alignment with reference to the standard sequence of the matched HBV genotype. We used 1:1 propensity score matching (PSM) to control for baseline confounding factors between the two groups. Results After 1:1 PSM, we identified 100 patients with similar propensities: 50 HIV/HBV co-infected patients and 50 HBV mono-infected patients. HBV quasispecies indices were lower in the HIV/HBV co-infected group than those in the HBV mono-infected group. A significant correlation was observed between all quasispecies indices and soluble cluster of differentiation 163 (sCD163) and interleukin-18 (IL-18) in the HIV/HBV co-infected group; however, this phenomenon was not found in the HBV mono-infected group. Conclusion Combined HIV infection reduces quasispecies heterogeneity in the HBV pre-S region, and the quasispecies heterogeneity is related to the sCD163 and IL-18 levels.
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Affiliation(s)
- Yuan Nie
- Research Institute, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Xizi Deng
- Research Institute, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yun Lan
- Research Institute, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Linghua Li
- Research Institute, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Feng Li
- Research Institute, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Fengyu Hu
- Research Institute, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
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Comparison of Serum Hepatitis B Virus RNA Levels and Quasispecies Evolution Patterns between Entecavir and Pegylated-Interferon Mono-treatment in Chronic Hepatitis B Patients. J Clin Microbiol 2020; 58:JCM.00075-20. [PMID: 32554476 PMCID: PMC7448659 DOI: 10.1128/jcm.00075-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) RNA may independently predict virological and serological response. This study aimed to compare dynamic changes in serum HBV RNA levels and HBV quasispecies evolution patterns between entecavir and pegylated-interferon mono-treatment in chronic hepatitis B patients and to determine the clinical significance during treatment. TaqMan real-time PCR was used for quantitative analysis. HBV RNA levels were retrospectively determined in serial serum samples from 178 chronic hepatitis B patients who received either entecavir or pegylated-interferon treatment. Hepatitis B virus (HBV) RNA may independently predict virological and serological response. This study aimed to compare dynamic changes in serum HBV RNA levels and HBV quasispecies evolution patterns between entecavir and pegylated-interferon mono-treatment in chronic hepatitis B patients and to determine the clinical significance during treatment. TaqMan real-time PCR was used for quantitative analysis. HBV RNA levels were retrospectively determined in serial serum samples from 178 chronic hepatitis B patients who received either entecavir or pegylated-interferon treatment. Both serum HBV DNA and RNA quasispecies were analyzed via next-generation sequencing. Receiver operating characteristics (ROC) analysis was performed to evaluate the prediction value of individual biomarkers for hepatitis B e antigen (HBeAg) seroconversion. Patients who received pegylated-interferon treatment showed stronger declines in HBV RNA levels than did those who received entecavir treatment. Serum HBV RNA levels were lower in patients with subsequent HBeAg seroconversion. At baseline, the level of HBV RNA was better than other indicators in predicting HBeAg seroconversion. Moreover, the predictive value of serum HBV RNA levels was better in the entecavir group. Baseline HBV RNA exhibited a significantly higher genetic diversity than HBV DNA and had a significant decline after 4 weeks of entecavir treatment. Higher baseline genetic diversity may result in a better outcome in pegylated-interferon-treated patients. Serum HBV RNA levels showed different decline kinetics, and HBV RNA quasispecies showed different evolution patterns in entecavir and pegylated-interferon mono-treatment. Taken together, serum HBV RNA may serve as a promising biomarker of HBeAg seroconversion in patients during antiviral treatment.
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Nie Y, Deng XZ, Lan Y, Li F, Hu FY. Pre-S Deletions are Predominant Quasispecies in HIV/HBV Infection: Quasispecies Perspective. Infect Drug Resist 2020; 13:1643-1649. [PMID: 32606815 PMCID: PMC7294102 DOI: 10.2147/idr.s255473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/16/2020] [Indexed: 12/15/2022] Open
Abstract
Background Combined HIV infection can accelerate HBV-induced liver disease. It is known that HBV Pre-S deletion is closely related to HBV-associated terminal liver disease in HBV mono-infection. Currently, data on HBV Pre-S quasispecies feature deletion in HIV/HBV co-infected patients are lacking. Methods The characteristics and blood samples of patients with chronic HBV infection were collected and classified into an HIV/HBV co-infection group and an HBV mono-infection group according to HIV antibody results before treatment. HBV DNA in serum was extracted. The HBV Pre-S region was amplified by nested-PCR and was further T-A cloned. Using the standard sequence of the matched genotype HBV as a reference, BioEdit 7.0 software was employed for sequence alignment. Results HBV Pre-S regions were successfully amplified from 147 patients, including 71 cases in the HIV/HBV co-infected group and 76 cases in the HBV mono-infected group. The proportion of the HIV/HBV co-infected group with Pre-S quasispecies deletion was lower than that of the HBV mono-infected group. By analyzing the frequency of Pre-S quasispecies in the two groups, the frequency of Pre-S quasispecies in HIV/HBV co-infected patients with Pre-S quasispecies was higher than HBV mono-infected patients. The frequency of Pre-S quasispecies deletion of the S protein promoter region in the HIV/HBV co-infected group was significantly higher than that in the HBV mono-infected group. Conclusion High-frequency Pre-S quasispecies deletions are predominant in HIV/HBV co-infected patients; however, low-frequency Pre-S deletions are predominant in HBV mono-infected patients, providing a reference for the pathogenesis of the accelerated progression of liver disease in HIV/HBV co-infection.
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Affiliation(s)
- Yuan Nie
- Research Institute, Guangzhou Eighth People's Hospital Affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China.,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xi-Zi Deng
- Research Institute, Guangzhou Eighth People's Hospital Affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yun Lan
- Research Institute, Guangzhou Eighth People's Hospital Affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Feng Li
- Research Institute, Guangzhou Eighth People's Hospital Affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Feng-Yu Hu
- Research Institute, Guangzhou Eighth People's Hospital Affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
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Wang M, Li J, Zhang X, Han Y, Yu D, Zhang D, Yuan Z, Yang Z, Huang J, Zhang X. An integrated software for virus community sequencing data analysis. BMC Genomics 2020; 21:363. [PMID: 32414327 PMCID: PMC7227348 DOI: 10.1186/s12864-020-6744-4] [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: 02/12/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND A virus community is the spectrum of viral strains populating an infected host, which plays a key role in pathogenesis and therapy response in viral infectious diseases. However automatic and dedicated pipeline for interpreting virus community sequencing data has not been developed yet. RESULTS We developed Quasispecies Analysis Package (QAP), an integrated software platform to address the problems associated with making biological interpretations from massive viral population sequencing data. QAP provides quantitative insight into virus ecology by first introducing the definition "virus OTU" and supports a wide range of viral community analyses and results visualizations. Various forms of QAP were developed in consideration of broader users, including a command line, a graphical user interface and a web server. Utilities of QAP were thoroughly evaluated with high-throughput sequencing data from hepatitis B virus, hepatitis C virus, influenza virus and human immunodeficiency virus, and the results showed highly accurate viral quasispecies characteristics related to biological phenotypes. CONCLUSIONS QAP provides a complete solution for virus community high throughput sequencing data analysis, and it would facilitate the easy analysis of virus quasispecies in clinical applications.
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Affiliation(s)
- Mingjie Wang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China
| | - Jianfeng Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xiaonan Zhang
- Key Lab of Medicine Molecular Virology of MOE/MOH, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Yue Han
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China
| | - Demin Yu
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China
| | - Donghua Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China
| | - Zhenghong Yuan
- Key Lab of Medicine Molecular Virology of MOE/MOH, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Zhitao Yang
- Emergency Department, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China.
| | - Jinyan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
| | - Xinxin Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China. .,Clinical Research Center, Ruijin Hospital North, Shanghai Jiaotong University, School of Medicine, Shanghai, 201821, China.
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Xiao Y, Sun K, Duan Z, Liu Z, Li Y, Yan L, Song Y, Zou H, Zhuang H, Wang J, Li J. Quasispecies characteristic in "a" determinant region is a potential predictor for the risk of immunoprophylaxis failure of mother-to-child-transmission of sub-genotype C2 hepatitis B virus: a prospective nested case-control study. Gut 2020; 69:933-941. [PMID: 31446427 PMCID: PMC7229894 DOI: 10.1136/gutjnl-2019-318278] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 08/05/2019] [Accepted: 08/17/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE This study was performed to explore the correlation between the characteristics of hepatitis B virus (HBV) quasispecies in HBV-infected pregnant women and the risk of immunoprophylaxis failure for their infants. DESIGN In this prospective nested case-control study, the characteristics of HBV quasispecies in mothers whose infants were immunoprophylaxis success (control group) and those whose infants were immunoprophylaxis failure (case group) were analysed by the clone-based sequencing of full-length HBV genome and next-generation sequencing (NGS) of "a" determinant region, and were compared between the two groups. RESULTS The quasispecies characteristics including mutant frequency, Shannon entropy and mean genetic distance at amino acid level of "a" determinant region were significantly lower in case group than that in control group, using the full-length HBV genome clone-based sequencing assay. These results were confirmed by NGS assay. Notably, we discovered that the differences were also significant at nucleotide level by NGS assay. Furthermore, the risk of immunoprophylaxis failure could be predicted by analysing the three HBV quasispecies characteristics either at nucleotide level or at amino acid level of "a" determinant region, and the corresponding predictive values were tentatively set up. CONCLUSIONS HBV quasispecies with a more complex mutant spectrum in "a" determinant region might be more vulnerable to extinct through mother-to-child-transmission (MTCT). More importantly, analysing HBV quasispecies characteristics in pregnant women with high HBV DNA load might be helpful to predict the high-risk population of immunoprophylaxis failure, and consequently provide accurate intervention against MTCT of HBV.
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Affiliation(s)
- Yiwei Xiao
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Kuixia Sun
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China,Department of Clinical Laboratory, Peking University First Hospital, Beijing, 100034, P.R. China
| | - Zhongping Duan
- Artificial Liver Center, Beijing Youan Hospital, Capital Medical University, Beijing, 100054, P.R. China
| | - Zhixiu Liu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Yi Li
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Ling Yan
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Yarong Song
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Huaibin Zou
- Artificial Liver Center, Beijing Youan Hospital, Capital Medical University, Beijing, 100054, P.R. China
| | - Hui Zhuang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Jie Wang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Jie Li
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
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Liu C, Lin J, Xun Z, Huang J, Huang E, Chen T, He Y, Lin N, Yang B, Ou Q. Establishment of Coamplification at Lower Denaturation Temperature PCR/Fluorescence Melting Curve Analysis for Quantitative Detection of Hepatitis B Virus DNA, Genotype, and Reverse Transcriptase Mutation and Its Application in Diagnosis of Chronic Hepatitis B. J Mol Diagn 2019; 21:1106-1116. [PMID: 31607557 DOI: 10.1016/j.jmoldx.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022] Open
Abstract
Dynamic and real-time hepatitis B virus (HBV) DNA, genotype, and reverse transcriptase mutation analysis plays an important role in diagnosing and monitoring chronic hepatitis B (CHB) and in assessing the therapeutic response. We established a highly sensitive coamplification at lower denaturation temperature PCR (COLD-PCR) coupled with probe-based fluorescence melting curve analysis (FMCA) for precision diagnosis of CHB patients. The imprecision with %CV and detection limit of HBV DNA detected by COLD-PCR/FMCA were 2.58% to 4.42% and 500 IU/mL, respectively. For mutation, the imprecision and detection limit were 3.35% to 6.49% and 1%, respectively. Compared with Sanger sequencing, the coincidence rates of genotype and mutation were 96.0% and 82.5%, respectively, whereas the inconsistent data resulted from a low proportion (<20%) of mixed genotypes or mixed mutations. The mutation ratio in HBV infection patients was as follows: hepatitis B e antigen (HBeAg)-positive infection (0/0.0%) < HBeAg-negative infection (16/4.5%) < HBeAg-positive hepatitis (30/5.5%) < HBeAg-negative hepatitis (36/6.5%). In patients with entecavir therapy, the proportion of mutation at baseline or week 4 in virologic response (VR) group was <4%, whereas in the partial VR group, it was mostly ≥4%. COLD-PCR/FMCA provides a novel tool with high sensitivity, convenience, and practicability for the simultaneous quantification of HBV DNA, genotype, and mutation. It might be used for distinguishing the different phases of HBV infection and predicting VR of CHB patients.
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Affiliation(s)
- Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Jinpiao Lin
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Zhen Xun
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Jinlan Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Er Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Yujue He
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Ni Lin
- School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, People's Republic of China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China.
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22
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Mei F, Ren J, Long L, Li J, Li K, Liu H, Tang Y, Fang X, Wu H, Xiao C, Huang T, Deng W. Analysis of HBV X gene quasispecies characteristics by next-generation sequencing and cloning-based sequencing and its association with hepatocellular carcinoma progression. J Med Virol 2019; 91:1087-1096. [PMID: 30712269 DOI: 10.1002/jmv.25421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVES This study aimed to describe the differences between next-generation sequencing (NGS) and cloning-based sequencing (CBS) in HBX quasispecies research and primitively investigate the relationship between the dominant HBX quasispecies and hepatocellular carcinoma (HCC). METHODS A total of 12 serum samples were collected. Serum hepatitis B virus (HBV) DNA was extracted, and the HBV X-region (HBX) was amplified by nested polymerase chain reaction (PCR). The PCR products were simultaneously tested with NGS and CBS to detect quasispecies of the HBX. RESULTS A total of 9348 eligible quasispecies sequences were obtained by NGS, which were much larger than the 98 of that by CBS. By the phylogenetic tree, the dominant quasispecies sequence of each sample could be found, although they had several nucleotides differences between the dominant quasispecies sequences found by CBS and NGS. By comparing the quasispecies heterogeneity, it was found that the quasispecies complexity value of HBV X-region obtained by NGS was higher than CBS (P < 0.05). The diversity values, including d, dS, dN, an d d N/ dS obtained by NGS were lower than by CBS (all of P < 0.01). The relativity of Spearman(rs) in d, dS, and dN were statistically significant (rs_ d = 0.865, P = 0.001; rs_ dS = 0.722, P = 0.014; and rs_ dN = 0.738, P = 0.011, respectively). There were 21 different bases between the HBX quasispecies of case A and control B. CONCLUSION The results of this can be used as guidance when researchers plan to choose a suitable method to study quasispecies, especially the HBV X gene quasispecies. Some high-risk mutations of HBX quasispecies were also found in this study and their relationship with HCC need deeper exploration.
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Affiliation(s)
- Fanbiao Mei
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jingjing Ren
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Long Long
- The Faculty of Big Data, Guangxi Teachers Education University, Nanning, Guangxi, China
| | - Jilin Li
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Kezhi Li
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Haizhou Liu
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yanping Tang
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiang Fang
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hanghang Wu
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Chanchan Xiao
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Tianren Huang
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wei Deng
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Wang C, Yu S, Zhang Y, Zhang M, Lv L, Huang C, Li X, Li J, Zhang Z. Viral quasispecies of hepatitis B virus in patients with YMDD mutation and lamivudine resistance may not predict the efficacy of lamivudine/adefovir rescue therapy. Exp Ther Med 2019; 17:2473-2484. [PMID: 30906435 PMCID: PMC6425149 DOI: 10.3892/etm.2019.7255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 12/03/2018] [Indexed: 02/07/2023] Open
Abstract
The association between hepatitis B virus (HBV) quasispecies (QS) and the efficacy of nucleos(t)ide analog therapy is currently not well defined, particularly in the case of lamivudine (LAM)/adefovir (ADV) combination rescue therapy for patients with chronic HBV infection (CHB) presenting with LAM resistance. In the present study, 16 CHB patients with the rtM204I/V mutation in the tyrosine-methionine-aspartate-aspartate motif of the C domain of the polymerase gene who switched to LAM/ADV treatment due to LAM resistance were assessed. HBV DNA was isolated from these patients and the reverse transcriptase (RT) region was sequenced. The QS heterogeneity and distribution was analyzed, the mutation sites were recorded and the phylogenetic trees were constructed. The results indicated that QS heterogeneity and distribution in the RT and S regions were not significantly different between responders (RS) and non-RS (NRS) at baseline (P>0.05), except for the higher frequency of a dominant strain in the RT region at the nucleotide level in the RS group (P=0.039). In addition, in NRS, no significant difference in QS heterogeneity or distribution in these regions was identified at six months vs. the baseline. Furthermore, although in the non-responder group the frequency of the LAM resistance-associated mutations (rtM204V/I) decreased at 6 months compared with the baseline, it did not disappear in any of the patients after six months of treatment. Analysis of individual patients did not indicate any consistent selection of specific HBV mutants during LAM/ADV rescue therapy. In conclusion, the baseline HBV QS within the RT and S regions may not be a valid predictor of the response to LAM/ADV rescue treatment in CHB patients with LAM resistance.
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Affiliation(s)
- Changtai Wang
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China.,Department of Infectious Diseases, The Affiliated Anqing Hospital of Anhui Medical University, Anqing, Anhui 246000, P.R. China
| | - Shu Yu
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Yafei Zhang
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Min Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Liying Lv
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Cheng Huang
- College of Pharmacy, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xu Li
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Jun Li
- College of Pharmacy, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Zhenhua Zhang
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China.,College of Pharmacy, Anhui Medical University, Hefei, Anhui 230022, P.R. China
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24
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Clinical Manifestations and Laboratory Tests of AECHB and Severe Hepatitis (Liver Failure). ACUTE EXACERBATION OF CHRONIC HEPATITIS B 2019. [PMCID: PMC7418529 DOI: 10.1007/978-94-024-1603-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This chapter describes the clinical symptoms and signs of AECHB and HBV ACLF, classification, grading of HBV ACLF and their features, diagnostic principles and standards in liver pathology, biochemistry, and virology of HBV ACLF.Liver failure is defined as serious damage to the liver cause by a variety of etiologies, leading to liver function disorder or even decompensation, and clinical syndromes with coagulopathy, jaundice, hepatic encephalopathy, and ascites. Severe hepatitis B can be indicated pathologically by apparent hepatocellular necrosis, including extensive multifocal, confluent, bridging, sub-massive or massive necrosis. Laboratory tests during the course of severe exacerbation of chronic hepatitis B can reflect pathological changes and liver function in a timely manner, providing objective and informative reference data for evaluation of disease severity and treatment efficacy. Among the most important laboratory tests are those for prothrombin activity, international normalized ratio, and increases in total bilirubin concentration. Severe hepatitis B is associated with interactions between the virus and host factors. Detection of HBV DNA, HBV genotype, quasispecies and HBV mutation can provide important theoretical bases for the prevention, control or mitigation of the progress of severe hepatitis B. Noninvasive imaging modalities can be used to visualize the entire liver and parts of it. Measuring liver volume to evaluate liver size and liver reserve capacity is regarded as important in diagnosis, surgical approach and prognostic evaluation of patients with severe exacerbation of chronic hepatitis B and liver failure. Model for End-Stage Liver Disease (MELD) is the first quantitative method developed to assess whether a patient with liver failure requires a liver transplant. The predictive value of the MELD model has been improved by the MELD-Na, iMELD, and MESO models. Several other valuable prognostic models have been developed. For example, for patients with HBV-ACLF, the established TPPM scoring system was found to be more predictive than MELD score.
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Hou J, Wang G, Wang F, Cheng J, Ren H, Zhuang H, Sun J, Li L, Li J, Meng Q, Zhao J, Duan Z, Jia J, Tang H, Sheng J, Peng J, Lu F, Xie Q, Wei L. Guideline of Prevention and Treatment for Chronic Hepatitis B (2015 Update). J Clin Transl Hepatol 2017; 5:297-318. [PMID: 29226097 PMCID: PMC5719188 DOI: 10.14218/jcth.2016.00019] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 01/14/2017] [Accepted: 01/16/2017] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jinlin Hou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence to: Jinlin Hou, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou avenue, Guangzhou 510515, China. E-mail: ; Lai Wei, Peking University People’s Hospital, Peking University Hepatology Institute, No. 11 Xizhimen South Street, Beijing 100044, China. E-mail:
| | - Guiqiang Wang
- Department of Infectious Diseases, Center for Liver Diseases, Peking University First Hospital, Beijing, China
| | - Fusheng Wang
- The Institute of Translational Hepatology, 302 Hospital of PLA, Peking University, Beijing, China
| | - Jun Cheng
- Center of Liver Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Hong Ren
- Institute for Viral Hepatitis, the Key Laboratory of Molecular Biology for Infectious Diseases, the second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hui Zhuang
- Department of Microbiology of Peking University Health Science Center, Beijing, China
| | - Jian Sun
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jie Li
- Department of Microbiology of Peking University Health Science Center, Beijing, China
| | - Qinghua Meng
- Serious Illness Medicine Inpatient Area, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jingmin Zhao
- Department of Pathology, 302 Hospital of PLA, Peking University, Beijing, China
| | - Zhongping Duan
- Artificial Liver Center, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jidong Jia
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hong Tang
- Center of Infectious Diseases, West China Hospital of Sichuan University, Division of Infectious Diseases, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Jifang Sheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jie Peng
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fengmin Lu
- Department of Microbiology of Peking University Health Science Center, Beijing, China
| | - Qing Xie
- Department of Infectious Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Lai Wei
- Hepatology Institute, Peking University People’s Hospital, Beijing, China
- *Correspondence to: Jinlin Hou, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou avenue, Guangzhou 510515, China. E-mail: ; Lai Wei, Peking University People’s Hospital, Peking University Hepatology Institute, No. 11 Xizhimen South Street, Beijing 100044, China. E-mail:
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Rajoriya N, Combet C, Zoulim F, Janssen HLA. How viral genetic variants and genotypes influence disease and treatment outcome of chronic hepatitis B. Time for an individualised approach? J Hepatol 2017; 67:1281-1297. [PMID: 28736138 DOI: 10.1016/j.jhep.2017.07.011] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 06/27/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022]
Abstract
Chronic hepatitis B virus (HBV) infection remains a global problem. Several HBV genotypes exist with different biology and geographical prevalence. Whilst the future aim of HBV treatment remains viral eradication, current treatment strategies aim to suppress the virus and prevent the progression of liver disease. Current strategies also involve identification of patients for treatment, namely those at risk of progressive liver disease. Identification of HBV genotype, HBV mutants and other predictive factors allow for tailoured treatments, and risk-surveillance pathways, such as hepatocellular cancer screening. In the future, these factors may enable stratification not only of treatment decisions, but also of patients at risk of higher relapse rates when current therapies are discontinued. Newer technologies, such as next-generation sequencing, to assess drug-resistant or immune escape variants and quasi-species heterogeneity in patients, may allow for more information-based treatment decisions between the clinician and the patient. This article serves to discuss how HBV genotypes and genetic variants impact not only upon the disease course and outcomes, but also current treatment strategies. Adopting a personalised genotypic approach may play a role in future strategies to combat the disease. Herein, we discuss new technologies that may allow more informed decision-making for response guided therapy in the battle against HBV.
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Affiliation(s)
- Neil Rajoriya
- Toronto Centre for Liver Diseases, Toronto General Hospital, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
| | - Christophe Combet
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69XXX, France
| | - Fabien Zoulim
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69XXX, France; Department of Hepatology, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Harry L A Janssen
- Toronto Centre for Liver Diseases, Toronto General Hospital, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada.
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A comparative study on the characterization of hepatitis B virus quasispecies by clone-based sequencing and third-generation sequencing. Emerg Microbes Infect 2017; 6:e100. [PMID: 29116219 PMCID: PMC5717089 DOI: 10.1038/emi.2017.88] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/12/2017] [Accepted: 09/17/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) has a high mutation rate due to the extremely high replication rate and the proofreading deficiency during reverse transcription. The generated variants with genetic heterogeneity are described as viral quasispecies (QS). Clone-based sequencing (CBS) is thought to be the ‘gold standard’ for assessing QS complexity and diversity of HBV, but an important issue about CBS is cost-effectiveness and laborious. In this study, we investigated the utility of the third-generation sequencing (TGS) DNA sequencing to characterize genetic heterogeneity of HBV QS and assessed the possible contribution of TGS technology in HBV QS studies. Parallel experiments including 3 control samples, which consisted of HBV full gene genotype B and genotype C plasmids, and 10 patients samples were performed by using CBS and TGS to analyze HBV whole-genome QS. Characterization of QS heterogeneity was conducted by using comprehensive statistical analysis. The results showed that TGS had a high consistency with CBS when measuring the complexity and diversity of QS. In addition, to detect rare variants, there were strong advantages conferred by TGS. In summary, TGS was considered to be practicable in HBV QS studies and it might have a relevant role in the clinical management of HBV infection in the future.
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Wang J, Yu Y, Li G, Shen C, Meng Z, Zheng J, Jia Y, Chen S, Zhang X, Zhu M, Zheng J, Song Z, Wu J, Shao L, Qian P, Mao X, Wang X, Huang Y, Zhao C, Zhang J, Qiu C, Zhang W. Relationship between serum HBV-RNA levels and intrahepatic viral as well as histologic activity markers in entecavir-treated patients. J Hepatol 2017; 68:S0168-8278(17)32261-4. [PMID: 28870671 DOI: 10.1016/j.jhep.2017.08.021] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS In diagnostics, serum hepatitis B virus (HBV)-RNA levels are valuable when the HBV-DNA load in circulation is effectively suppressed by nucleos(t)ide analogue (NUC) therapy. This study aimed to determine the intrahepatic viral replication activity reflected in serum HBV-RNA and whether HBV-RNA contributes to liver histological changes in patients treated with NUC. METHODS A cross-sectional set of serum and liver biopsy samples was obtained from patients treated with entecavir, who had undetectable levels of serum HBV-DNA. The correlations between serum HBV-RNA concentration and levels of peripheral and intrahepatic viral replicative forms, as well as histological scores, were analyzed. Quasispecies of serum HBV-RNA and intrahepatic viral replicative forms were examined by deep sequencing. HBV-RNA-positive hepatocytes were visualized by in situ hybridization. RESULTS Serum HBV-RNA was detected in 35 of 47 patients (74.47%, 2.33-4.80log10copies/ml). These levels correlated not only with the intrahepatic HBV-RNA level and the ratio of intrahepatic HBV-RNA to covalently closed circular DNA (cccDNA), but also with the histological scores for grading and staging. Regarding quasispecies, serum HBV-RNA was dynamic and more genetically homogenous to simultaneously sampled intrahepatic HBV-RNA than to the cccDNA pool. In situ histology revealed that HBV-RNA-positive hepatocytes were clustered in foci, sporadically distributed across the lobules, and co-localized with hepatitis B surface antigen. CONCLUSION Serum HBV-RNA levels reflect intrahepatic viral transcriptional activity and are associated with liver histopathology in patients receiving NUC therapy. Our study sheds light on the nature of HBV-RNA in the pathogenesis of chronic HBV infection and has implications for the management of chronic hepatitis B during NUC therapy. LAY SUMMARY Serum HBV-RNA levels are indicative of the intrahepatic transcriptional activity of covalently closed circular DNA and are associated with liver histological changes in patients with chronic B hepatitis who are receiving nucleos(t)ide analogue therapy.
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Affiliation(s)
- Jing Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yiqi Yu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Guojun Li
- Department of Hepatology, The Second Hospital of Yinzhou of Ningbo, Ningbo, China
| | - Chuan Shen
- Department of Infectious Diseases, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhefeng Meng
- Minhang Hospital, Fudan University, Shanghai, China
| | - Jianming Zheng
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yanhong Jia
- Department of Infectious Diseases, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Shaolong Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiao Zhang
- Continuing Education Office, Healthy School of Huangpu District, Shanghai, China
| | - Mengqi Zhu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiangjiang Zheng
- Department of Pathology, The Second Hospital of Yinzhou of Ningbo, Ningbo, China
| | - Zhangzhang Song
- Department of Hepatology, The Second Hospital of Yinzhou of Ningbo, Ningbo, China
| | - Jing Wu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Lingyun Shao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Peiyu Qian
- Minhang Hospital, Fudan University, Shanghai, China
| | - Xiaona Mao
- Department of Clinical Laboratory, The Second Hospital of Yinzhou of Ningbo, Ningbo, China
| | - Xuanyi Wang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Key Laboratory of Medical Molecular Virology, Fudan University, Shanghai, China
| | - Yuxian Huang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Caiyan Zhao
- Department of Infectious Diseases, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Chao Qiu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China; Minhang Hospital, Fudan University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Key Laboratory of Medical Molecular Virology, Fudan University, Shanghai, China.
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
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Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing. Sci Rep 2017; 7:10168. [PMID: 28860476 PMCID: PMC5578979 DOI: 10.1038/s41598-017-10591-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 08/11/2017] [Indexed: 02/07/2023] Open
Abstract
Despite full immunoprophylaxis, mother-to-child transmission (MTCT) of Hepatitis B Virus still occurs in approximately 2–5% of HBsAg positive mothers. Little is known about the bottleneck of HBV transmission and the evolution of viral quasispecies in the context of MTCT. Here we adopted a newly developed tag linkage deep sequencing method and analyzed the quasispecies of four MTCT pairs that broke through immunoprophylaxis. By assigning unique tags to individual viral sequences, we accurately reconstructed HBV haplotypes in a region of 836 bp, which contains the major immune epitopes and drug resistance mutations. The detection limit of minor viral haplotypes reached 0.1% for individual patient sample. Dominance of “a determinant” polymorphisms were observed in two children, which pre-existed as minor quasispecies in maternal samples. In all four pairs of MTCT samples, we consistently observed a significant overlap of viral haplotypes shared between mother and child. We also demonstrate that the data can be potentially useful to estimate the bottleneck effect during HBV MTCT, which provides information to optimize treatment for reducing the frequency of MTCT.
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Yang G, Liu Z, Yang J, Luo K, Xu Y, He H, Fu Q, Yu S, Wang Z. Quasispecies characteristics in mother-to-child transmission of hepatitis B virus by next-generation sequencing. J Infect 2017; 75:48-58. [PMID: 28483405 DOI: 10.1016/j.jinf.2017.04.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 02/24/2017] [Accepted: 04/26/2017] [Indexed: 12/19/2022]
Abstract
OBJECTIVES To identify within-host quasispecies characteristics of hepatitis B virus (HBV) in mothers and children infected via mother-to-child transmission (MTCT). METHODS Using next-generation sequencing (NGS), we analyzed sequences within the non-overlapping pre-core/core (pre-C/C) gene in 37 mother-child pairs. RESULTS Phylogenetic and Highlighter analyses suggested that both a single strain and multiple distinct strains may be transmitted in MTCT of HBV. However, analysis of reassembled viral sequences revealed a relatively narrow distribution of variants in children, which was confirmed by a lower viral diversity in children than that in mothers. New closely related variants with combinations of two to five high-frequency mutations were observed in seven children with elevated ALT levels; the new variants out-competed the transmitted maternal variants to become the dominant strains in five of them. Furthermore, 30 mutations with a frequency >1% of all viruses within-host were present in those children; the mutations caused 19 amino-acid substitutions. Interestingly, almost all were located within the well-known T-cell or B-cell epitopes. CONCLUSIONS There are restrictive changes that occur in the early stages of chronic HBV infection through MTCT with different clinical consequences. These data might have important implications for future investigations of interrelated immunopathogenesis and therapeutic strategies.
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Affiliation(s)
- Guifeng Yang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China
| | - Zhihua Liu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Juncheng Yang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kangxian Luo
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Xu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haitang He
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qunfang Fu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shouyi Yu
- Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China.
| | - Zhanhui Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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Clinical features and viral quasispecies characteristics associated with infection by the hepatitis B virus G145R immune escape mutant. Emerg Microbes Infect 2017; 6:e15. [PMID: 28325923 PMCID: PMC5378923 DOI: 10.1038/emi.2017.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 12/12/2022]
Abstract
Coexistence of the hepatitis B surface antigen (HBsAg) and hepatitis B surface antibody (anti-HBs) is an uncommon phenomenon, and the underlying mechanisms remain largely unknown. Amino-acid (aa) substitution from glycine to arginine at aa 145 (G145R), in the major hydrophilic region, has been reported in patients with HBsAg and anti-HBs coexistence. However, there is limited knowledge about the clinical features and viral quasispecies characteristics associated with G145R mutant hepatitis B virus (HBV) infection. We herein describe the dynamic changes in the serological and virological markers in a case of hepatitis B with coexisting HBsAg and anti-HBs, caused by a G145R immune escape mutant (genotype C). Entecavir was administered during the 4th week after admission. Alanine aminotransferase peaked in the 16th week, while both the HBsAg and HBeAg declined rapidly. HBsAg clearance and hepatitis B e antigen (HBeAg)/hepatitis B e antibody (anti-HBe) seroconversion were achieved in the 36th week, and then entecavir was withdrawn. A follow-up of 96 weeks showed that HBV DNA remained undetectable and that anti-HBs was maintained above 100 mIU/mL. The quasispecies characteristics of the G145R mutant HBV were investigated via ultra-deep sequencing. The complexity and genetic distance of the S and RT regions were much higher in the 8th week than at baseline or in the 4th week. Moreover, the frequencies of mutations (L173P, Q181R and A184V) in cytotoxic T lymphocyte epitopes increased before entecavir treatment. These findings extend understanding of the evolution of HBV under host immune pressure and of the clinical outcomes of affected patients.
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HBV quasispecies composition in Lamivudine-failed chronic hepatitis B patients and its influence on virological response to Tenofovir-based rescue therapy. Sci Rep 2017; 7:44742. [PMID: 28303969 PMCID: PMC5356183 DOI: 10.1038/srep44742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/13/2017] [Indexed: 12/15/2022] Open
Abstract
The present study sought to evaluate the structure of HBV quasispecies in Lamivudine (LMV)-failed chronic hepatitis B (CHB) patients and its impact in defining the subsequent virological responses to Tenofovir (TDF)-based rescue-therapy. By analyzing HBV clones encompassing reverse transcriptase (RT) and surface (S) region from LMV-failed and treatment-naïve CHB patients, we identified 5 classical and 12 novel substitutions in HBV/RT and 9 substitutions in immune-epitopes of HBV/S that were significantly associated with LMV failure. In silico analysis showed spatial proximity of some of the newly-identified, mutated RT residues to the RT catalytic centre while most S-substitutions caused alteration in epitope hydrophobicity. TDF administration resulted in virological response in 60% of LMV-failed patients at 24-week but non-response in 40% of patients even after 48-weeks. Significantly high frequencies of 6 S-substitutions and one novel RT-substitution, rtH124N with 6.5-fold-reduced susceptibility to TDF in vitro, were noted at baseline in TDF non-responders than responders. Follow-up studies depicted greater evolutionary drift of HBV quasispecies and significant decline in frequencies of 3 RT and 6 S-substitutions in responder-subgroup after 24-week TDF-therapy while most variants persisted in non-responders. Thus, we identified the HBV-RT/S variants that could potentially predict unfavorable response to LMV/TDF-therapy and impede immune-mediated viral clearance.
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Xue Y, Wang MJ, Huang SY, Yang ZT, Yu DM, Han Y, Zhu MY, Huang D, Zhang DH, Gong QM, Zhang XX. Characteristics of CpG Islands and their quasispecies of full-length hepatitis B virus genomes from patients at different phases of infection. SPRINGERPLUS 2016; 5:1630. [PMID: 27722049 PMCID: PMC5031574 DOI: 10.1186/s40064-016-3192-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/01/2016] [Indexed: 12/23/2022]
Abstract
BACKGROUND CpG islands in hepatitis B virus (HBV) genome are potential targets for methylation mediated gene silencing, and may be involved in the pathogenesis of HBV infection. To date, their characteristics in HBV quasispecies (QS) remain largely unknown. The purpose of this study was to investigate the characteristics of CpG islands in HBV QS. METHODS Forty patients diagnosed as acute hepatitis B (AHB, n = 10), immune-tolerant HBV carriers (IT, n = 9), chronic hepatitis B (CHB, n = 11), or acute on chronic liver failure (ACLF, n = 10), were enrolled in this case-control study. A total of 599 clones were isolated, and full-length HBV genomes were sequenced. RESULTS CpG island II (CGII) in AHB group was shorter in length and its QS heterogeneity was lower than that in the chronic infection group. Among the chronic infection subgroups, CGII and CpG island III (CGIII) in IT group were longer and their heterogeneity was lower compared to CHB and ACLF groups. Length of CGII correlated with HBV DNA levels positively while the complexity and diversity of CGII correlated with HBV DNA levels negatively. Moreover, CGII and CGIII were shorter in genotype B than those in genotype C, while QS complexity and diversity of either CGII or CGIII had no significant difference between genotype B and C. CONCLUSIONS Overall, our results suggest that the distribution, length and QS heterogeneity of CpG islands in full-length HBV genome differ across clinical phases of infection, of which the mechanism warrants further study.
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Affiliation(s)
- Yuan Xue
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Ming-Jie Wang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Su-Yuan Huang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Zhi-Tao Yang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - De-Min Yu
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Yue Han
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Ming-Yu Zhu
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Dao Huang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Dong-Hua Zhang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Qi-Ming Gong
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Xin-Xin Zhang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
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Li H, Song XF, Hu TT, Ren H, Hu P. A strong conservative tendency in HBV transcriptase (RT): a majority of natural RT mutations derived from the S gene. Liver Int 2016; 36:963-70. [PMID: 26707356 DOI: 10.1111/liv.13051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/11/2015] [Indexed: 12/28/2022]
Abstract
BACKGROUND & AIMS Little is known about natural mutations in the HBV reverse transcriptase (RT) region. Our study aimed to characterize the natural RT mutation along the natural course of chronic Hepatitis B (CHB). METHODS Sixty CHB patients (immune-tolerant phase, IT, n = 20; immune-active phase, IA, n = 20 and inactive carriers phase, IC, n = 20) were selected from the Focal study, including 25 subjects with median 18 months follow-up. Mutations were evaluated at both RT and main S protein encoding region by clone-based sequencing. RESULTS The HBV RT quasispecies had significant lower heterogeneity in IT than IA and IC phases (P < 0.05), but not between IA and IC phases (P > 0.05). Limited heterogeneity over time was further confirmed in a longitudinal study. Locations of RT mutations were primarily located in the interdomians and the lowest in functional domains in each phase. Mutations in human leukocyte antigen (HLA) I epitopes (IT, 0.95%; IA, 1.31%; IC, 1.28%, P < 0.05) and HLA II epitopes (IT, 0.70%; IA, 0.90%; IC, 1.45%, P < 0.01) varied significantly over time. More frequent mutations were detected in the ORF of S gene from the same clones (HBsAg vs. RT: IT, 75 vs. 45; IA, 83 vs. 64; IC, 80 vs. 65). The majority of RT mutations were shared with genetic changes in the main S gene. CONCLUSIONS Our findings suggested that HBV RT showed a strong conservative tendency and a majority of their natural mutations were derived from the same genetic changes in the S gene.
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Affiliation(s)
- Hu Li
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiao-Fei Song
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ting-Ting Hu
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Ren
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Hu
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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35
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Yin GQ, Zhong B. Efficacy of interferon for chronic hepatitis B in patients with nucleoside and nucleotide combination therapy failure. J Gastroenterol Hepatol 2016; 31:248-55. [PMID: 26456953 DOI: 10.1111/jgh.13191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/12/2015] [Accepted: 09/17/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIM In China, inappropriate therapies with nucleos(t)ide analogues (NA) have induced hepatitis B virus resistance, combination therapy with nucleoside and nucleotide (ComTNsNt) failure, or multi-drug resistant mutations. However, the efficacy of combination therapy with entecavir plus tenofovir for ComTNsNt failure is limited. In the current study, the regimens of interferon-α (IFN-α) therapy, switching from NAs to IFN-α, and subsequent re-treatment with IFN-α were applied to treat ComTNsNt failure. We further evaluated the efficacy of this therapy. METHODS Eleven patients with ComTNsNt failure were enrolled in this study. Nine subjects (9/11) received IFN-α switching therapy. Combination therapy with IFN-α and ComTNsNt was administered in the first 4 weeks. Then, ComTNsNt was discontinued at the end of Week 4, and IFN-α monotherapy was continued for 6 months. Two (2/11) patients discontinued ComTNsNt without receiving IFN-α treatment. All 11 patients received the first re-treatment of IFN-α when they experienced hepatitis relapses after the withdrawal of IFN-α or ComTNsNt. Six (6/11) patients received a second re-treatment of IFN-α. Follow up was conducted after IFN-α therapy in all 11 patients. RESULTS Two patients (2/9) receiving IFN-α switching therapy experienced alanine aminotransferase (ALT) flare. In contrast, the two patients without IFN-α switching therapy experienced ALT flare. Multiple re-treatments with IFN-α resulted in a sustained response. CONCLUSIONS Interferon-α switching therapy and IFN-α re-treatment might be applied for treatment of ComTNsNt failure. IFN-α switching therapy resulted in safe ComTNsNt cessation, and IFN-α re-treatment induced a sustained response of IFN-α in all patients. This IFN-α treatment is an optional treatment for ComTNsNt failure.
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Affiliation(s)
- Guo Qing Yin
- Department of Infectious Disease, Nanjing Zhong-Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Bei Zhong
- The Affiliated Qingyuan Hospital, Jinan University Medical School, Qingyuan, Guangdong, China
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36
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Zhang XX, Li MR, Cao Y, Zhang RW, Zhang Y, Li F, Xi HL, Xu XY. Dynamics of Genotypic Mutations of the Hepatitis B Virus Associated With Long-Term Entecavir Treatment Determined With Ultradeep Pyrosequencing: A Retrospective Observational Study. Medicine (Baltimore) 2016; 95:e2614. [PMID: 26825915 PMCID: PMC5291585 DOI: 10.1097/md.0000000000002614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The aim of the study is to explore the evolution of genotypic mutations within the reverse transcriptase region in partial virological responders (PVRs) receiving long-term entecavir (ETV) treatment. A total of 32 patients were classified as completely virological responders (CVRs) (n = 12) or PVRs (n = 20). Five partial responders were hepatitis B virus (HBV)-DNA positive after long-term therapy, which lasted for >3 years. A total of 71 serum samples from these 32 patients were assayed by ultra-deep pyrosequencing (UDPS): 32 samples were from all patients at baseline, and 39 were from PVRs with sequential inter-treatment. Approximately 84,708 sequences were generated per sample. At baseline, the quasispecies heterogeneity did not significantly differ between the 2 groups. The frequencies of substitutions indicating pre-existence of nucleos(t)ide analog resistant (NAr) mutants ranged from 0.10% to 6.70%, which did not statistically differ between groups either. However, the substitutions associated with the NAr mutants were significantly different from those associated with the non-NAr mutants in 13 patients; 6 of these patients were PVRs and the others were CVRs. Five patients were HBV DNA positive after regular ETV monotherapy for >3 years, and 4 of these patients underwent mild NAr substitution fluctuations (<20%). One patient developed virological breakthrough while bearing single, double, and triple (rtL180 M, rtM204 V, rtS202G) substitutions. In addition to the common substitutions, unknown amino acid substitutions, such as rtL145 M/S, rtF151Y/L, rtR153Q, rtI224 V, rtN248H, rtS223A, rtS256C, need to be further verified. NAr substitutions are observed at frequencies of 0.10% to 6.7% before therapy. Long-term ETV therapy generally results in virological responses, as long as the proportion of resistance mutations remains at a relatively low level. Genotypic resistance to ETV is detected in all PVRs receiving long-term ETV therapy.
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Affiliation(s)
- Xia-Xia Zhang
- From the Department of Infectious Disease, Peking University First Hospital, No.8 Xishiku Street, Xicheng District, Beijing, China
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Homs M, Rodriguez-Frias F, Gregori J, Ruiz A, Reimundo P, Casillas R, Tabernero D, Godoy C, Barakat S, Quer J, Riveiro-Barciela M, Roggendorf M, Esteban R, Buti M. Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection. PLoS One 2016; 11:e0158557. [PMID: 27362848 PMCID: PMC4928832 DOI: 10.1371/journal.pone.0158557] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/19/2016] [Indexed: 02/07/2023] Open
Abstract
Chronic HDV infection can cause a severe form of viral hepatitis for which there is no specific treatment. Characterization of the hepatitis B or C viral quasispecies has provided insight into treatment failure and disease recurrence following liver transplantation, has proven useful to understand hepatitis B e antigen seroconversion, and has helped to predict whether hepatitis C infection will resolve or become chronic. It is likely that characterization of the hepatitis delta virus (HDV) quasispecies will ultimately have similar value for the management of this infection. This study sought to determine the RNA evolution rates in serum of chronic hepatitis delta (CHD) treatment-naïve patients, using next-generation sequencing methods. The region selected for study encompassed nucleotide positions 910 to 1270 of the genome and included the amber/W codon. Amber/W is a substrate of the editing process by the ADAR1 host enzyme and is essential for encoding the 2 delta antigens (HDAg). The amber codon encodes the small (unedited) HDAg form and the W codon the large (edited) HDAg form. The evolution rate was analyzed taking into account the time elapsed between samples, the percentage of unedited and edited genomes, and the complexity of the viral population. The longitudinal studies included 29 sequential samples from CHD patients followed up for a mean of 11.5 years. In total, 121,116 sequences were analyzed. The HDV evolution rate ranged from 9.5x10-3 to 1.2x10-3 substitutions/site/year and showed a negative correlation with the time elapsed between samples (p<0.05). An accumulation of transition-type changes was found to be responsible for higher evolution rates. The percentages of unedited and edited genomes and the quasispecies complexity showed no relationships with the evolution rate, but the fluctuations in the percentages of genomes and in complexity suggest continuous adaptation of HDV to the host conditions.
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Affiliation(s)
- Maria Homs
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- * E-mail:
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Diseases Unit, Vall d’Hebron Research Institute, Barcelona, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès, Spain
| | - Alicia Ruiz
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Pilar Reimundo
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rosario Casillas
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Liver Diseases Unit, Vall d’Hebron Research Institute, Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Cristina Godoy
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Salma Barakat
- Gastroenterology Department, National Centre for Gastrointestinal and Liver disease, Khartoum, Sudan
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Diseases Unit, Vall d’Hebron Research Institute, Barcelona, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Michael Roggendorf
- Institut of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, 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, Barcelona, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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Zhou B, Dong H, He Y, Sun J, Jin W, Xie Q, Fan R, Wang M, Li R, Chen Y, Xie S, Shen Y, Huang X, Wang S, Lu F, Jia J, Zhuang H, Locarnini S, Zhao GP, Jin L, Hou J. Composition and Interactions of Hepatitis B Virus Quasispecies Defined the Virological Response During Telbivudine Therapy. Sci Rep 2015; 5:17123. [PMID: 26599443 PMCID: PMC4657086 DOI: 10.1038/srep17123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/26/2015] [Indexed: 01/08/2023] Open
Abstract
Reverse transcriptase (RT) mutations contribute to hepatitis B virus resistance during antiviral therapy with nucleos(t)ide analogs. However, the composition of the RT quasispecies and their interactions during antiviral treatment have not yet been thoroughly defined. In this report, 10 patients from each of 3 different virological response groups, i.e., complete virological response, partial virological response and virological breakthrough, were selected from a multicenter trial of Telbivudine treatment. Variations in the drug resistance-related critical RT regions in 107 serial serum samples from the 30 patients were examined by ultra-deep sequencing. A total of 496,577 sequence reads were obtained, with an average sequencing coverage of 4,641X per sample. The phylogenies of the quasispecies revealed the independent origins of two critical quasispecies, i.e., the rtA181T and rtM204I mutants. Data analyses and theoretical modeling showed a cooperative-competitive interplay among the quasispecies. In particular, rtM204I mutants compete against other quasispecies, which eventually leads to virological breakthrough. However, in the absence of rtM204I mutants, synergistic growth of the drug-resistant rtA181T mutants with the wild-type quasispecies could drive the composition of the viral population into a state of partial virological response. Furthermore, we demonstrated that the frequency of drug-resistant mutations in the early phase of treatment is important for predicting the virological response to antiviral therapy.
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Affiliation(s)
- Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hui Dong
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yungang He
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology; CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jian Sun
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weirong Jin
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China.,Shanghai Shenyou Biotechnology Co., Ltd., Shanghai, China
| | - Qing Xie
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Rong Fan
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Minxian Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology; CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ran Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology; CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yangyi Chen
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Shaoqing Xie
- Shanghai Shenyou Biotechnology Co., Ltd., Shanghai, China
| | - Yan Shen
- Shanghai Shenyou Biotechnology Co., Ltd., Shanghai, China
| | - Xin Huang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology; CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shengyue Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Fengming Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jidong Jia
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hui Zhuang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Stephen Locarnini
- Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
| | - Guo-Ping Zhao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology; CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences; Key Laboratory of Medical Molecular Virology affiliated to the Ministries of Education and Health, Shanghai Medical College and Department of Microbiology, School of Life Sciences; Fudan University, Shanghai, China
| | - Li Jin
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology; CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences; Key Laboratory of Medical Molecular Virology affiliated to the Ministries of Education and Health, Shanghai Medical College and Department of Microbiology, School of Life Sciences; Fudan University, Shanghai, China
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
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Yin F, Wu Z, Fang W, Wu C, Rayner S, Han M, Deng F, Du R, Liu J, Wang M, Wang H, Ning Q, Hu Z. Resistant mutations and quasispecies complexity of hepatitis B virus during telbivudine treatment. J Gen Virol 2015; 96:3302-3312. [DOI: 10.1099/jgv.0.000285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Feifei Yin
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zeguang Wu
- Department of Infectious Disease, Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Fang
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Chunchen Wu
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Simon Rayner
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Meifang Han
- Department of Infectious Disease, Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Deng
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ruikun Du
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jinliang Liu
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Manli Wang
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hualin Wang
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qin Ning
- Department of Infectious Disease, Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhihong Hu
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Increased intrahepatic quasispecies heterogeneity correlates with off-treatment sustained response to nucleos(t)ide analogues in e antigen-positive chronic hepatitis B patients. Clin Microbiol Infect 2015; 22:201-207. [PMID: 26493847 DOI: 10.1016/j.cmi.2015.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 12/16/2022]
Abstract
Finite treatment with nucleos(t)ide analogues (NAs) remains a great challenge for chronic hepatitis B in the clinic. This study aimed to investigate the relationship between intrahepatic quasispecies heterogeneity and the NAs off-treatment outcomes in a prospective cohort. Eighteen HBeAg-positive patients with chronic hepatitis B who achieved the cessation criteria underwent liver biopsy, and stopped treatment thereafter. Patients were followed up prospectively for 1 year. The reverse transcriptase (RT) gene of intrahepatic hepatitis B virus (HBV) was cloned and sequenced. Intrahepatic quasispecies heterogeneity and specific gene mutations were analysed using bioinformatic methods. Ten patients achieved sustained response, and eight patients developed viral relapse. The intrahepatic quasispecies Shannon entropy and nucleotide diversity within either RT or the surface (S) region of patients with sustained response were significantly higher (p < 0.05) than those of patients who had a viral relapse. Intrahepatic quasispecies Shannon entropy at the nucleotide level predicted the sustained off-treatment response (area under receiver operating characteristics curve 0.925; 95% CI 0.807-1.000; p 0.003). More positive selection sites and N-glycosylation mutations within the S region were found in patients with sustained response than in the patients with viral relapse (p < 0.01). Most of the positive selection sites in patients with sustained response were located in reported HLA-I-restricted or HLA-II-restricted epitopes. Intrahepatic quasispecies heterogeneity at the end of treatment was correlated with off-treatment outcomes in HBeAg-positive patients with chronic hepatitis B. More immune escape mutations were found within the S region in patients with sustained response. The higher intrahepatic quasispecies heterogeneity indicated a more robust immune control over HBV, which in turn maintained a sustained response after withdrawal of NAs.
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41
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Han Y, Gong L, Sheng J, Liu F, Li XH, Chen L, Yu DM, Gong QM, Hao P, Zhang XX. Prediction of virological response by pretreatment hepatitis B virus reverse transcriptase quasispecies heterogeneity: the advantage of using next-generation sequencing. Clin Microbiol Infect 2015; 21:797.e1-8. [PMID: 25882357 DOI: 10.1016/j.cmi.2015.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/18/2015] [Accepted: 03/28/2015] [Indexed: 02/07/2023]
Abstract
Prediction of antiviral efficacy prior to treatment remains largely unavailable. We have previously demonstrated the clinical value of on-treatment hepatitis B virus (HBV) reverse transcriptase (RT) quasispecies (QS) evolution patterns. In this study, we aimed to elucidate the relevance for prediction of pretreatment HBV RT QS characteristics by comparing the performance of next-generation sequencing (NGS) and clone-based Sanger sequencing (CBS). Thirty-six lamivudine-treated patients were retrospectively studied, including 18 responders and 18 non-responders. CBS and NGS data of pretreatment serum HBV were used to generate RT QS genetic complexity and diversity scores, according to our previous studies. The ability of both methods to predict responsiveness was evaluated with receiver operating characteristic (ROC) curves. A cut-off value was generated on the basis of prediction ability. Responders had significantly higher pretreatment RT QS genetic complexity and diversity (in the first two parts, which overlapped with the S gene, at both the nucleotide and amino acid levels) than non-responders by NGS-based testing. NGS-based algorithms predicted response better than CBS in the ROC curve analysis. The mean distance of the second contig had the highest area under the curve (AUC) value. When the cut-off value was set to 0.007186, the difference between survival curves was significant (p 0.0090). Pretreatment HBV RT QS heterogeneity in the overlapping region of the RT and S genes could be a predictor of antiviral efficacy. NGS improves the predictions of virological outcomes relative to CBS algorithms. This may have important implications for the clinical management of subjects chronically infected with HBV.
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Affiliation(s)
- Y Han
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - L Gong
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Department of Liver Diseases, the Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - J Sheng
- Shanghai Centre for Bioinformation Technology, China
| | - F Liu
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - X-H Li
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - L Chen
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - D-M Yu
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Q-M Gong
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - P Hao
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, China
| | - X-X Zhang
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Translational Medicine Research Centre, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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Hao R, Xiang K, Peng Y, Hou J, Sun J, Li Y, Su M, Yan L, Zhuang H, Li T. Naturally occurring deletion/insertion mutations within HBV whole genome sequences in HBeAg-positive chronic hepatitis B patients are correlated with baseline serum HBsAg and HBeAg levels and might predict a shorter interval to HBeAg loss and seroconversion during antiviral treatment. INFECTION GENETICS AND EVOLUTION 2015; 33:261-8. [DOI: 10.1016/j.meegid.2015.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/10/2015] [Accepted: 05/11/2015] [Indexed: 12/26/2022]
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Prolonged entecavir therapy is not effective for HBeAg seroconversion in treatment-naive chronic hepatitis B patients with a partial virological response. Antimicrob Agents Chemother 2015; 59:5348-56. [PMID: 26100697 DOI: 10.1128/aac.01017-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/10/2015] [Indexed: 02/07/2023] Open
Abstract
The aims of this study were to investigate the efficacy of prolonged entecavir (ETV) therapy in treatment-naive chronic hepatitis B (CHB) patients and to determine whether continuous ETV therapy is feasible to achieve HBeAg seroconversion, particularly in patients with partial virological response (PVR). A total of 142 treatment-naive patients with CHB were enrolled. The mean duration of treatment was 65 (range, 26 to 90) months, and 86 patients (60.6%) were HBeAg positive. PVR was defined as detectable hepatitis B virus (HBV) DNA (>116 copies/ml) at year 1. The cumulative incidence of virological response (VR) increased from 54.9% at year 1 to 98.2% at year 7. HBeAg positivity (odds ratio [OR], 4.146; P = 0.001) and initial alanine aminotransferase (ALT) (OR, 0.997; P = 0.004) were independent risk factors for PVR. Among the 64 patients with PVR, 47 patients (73.4%) achieved VR within 4 years after prolonged ETV therapy without treatment adaptation. Three patients (2.1%) experienced virological breakthrough and HBV variants with genotypic resistance. The cumulative rate of HBeAg seroconversion was significantly higher in the patients with VR than in the patients with PVR (P = 0.018). None of the PVR patients with HBV DNA at ≥5,000 copies/ml at year 1 ever experienced HBeAg seroconversion. Multivariate analysis identified VR at year 1 as the only determinant of HBeAg seroconversion (hazard ratio [HR], 3.009; P = 0.010). In conclusion, although there were patients with PVR, prolonged ETV therapy showed excellent VR, with only 2.1% emergence of viral resistance during a 7-year follow-up. However, to achieve HBeAg seroconversion, drug modification is needed for HBeAg-positive patients with PVR (especially those with HBV DNA at ≥5,000 copies/ml at year 1).
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Characterization of Full-Length Genomes of Hepatitis B Virus Quasispecies in Sera of Patients at Different Phases of Infection. J Clin Microbiol 2015; 53:2203-14. [PMID: 25926495 DOI: 10.1128/jcm.00068-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/24/2015] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B virus (HBV) infection results in different clinical presentation due to different levels of immune response. Our study aimed to characterize HBV full-length genome quasispecies (QS) in patients with different phases of infection to better understand its pathogenesis. Forty treatment-naive HBV-infected patients were enrolled, including 10 cases of acute hepatitis B (AHB), 9 cases of immunotolerant (IT) HBV carriers, 11 cases of chronic hepatitis B (CHB), and 10 cases of acute-on-chronic liver failure (ACLF). The present study was conducted by clone-based sequencing. QS heterogeneity within each open reading frame was calculated. The mutation frequency index (MFI) and amino acid variations within the large HBsAg, HBcAg, and HBxAg regions were analyzed based on the different infection phases. In total, 606 HBV full-length sequences were obtained. HBV QS had higher heterogeneity in ACLF and CHB than that in IT among chronically infected individuals. AHB patients had the lower QS heterogeneity at onset than those with chronic infection. ACLF patients had the highest frequency of mutations in the core promoter and precore region. A triple mutation (A1762T/G1764A/G1896A) was observed more frequently in genotype C than in genotype B. The MFI indicated that specific peptides of the studied regions had more frequent mutations in ACLF. Furthermore, several amino acid variations, known as T- and B-cell epitopes, were potentially associated with the immunoactive phase of infection. More HBV genome mutations and deletions were observed in patients with more severe diseases, particularly in specific regions of the core and preS regions, the clinical significance and mechanism of which need to be further investigated.
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Coffin CS, Osiowy C, Gao S, Nishikawa S, van der Meer F, van Marle G. Hepatitis B virus (HBV) variants fluctuate in paired plasma and peripheral blood mononuclear cells among patient cohorts during different chronic hepatitis B (CHB) disease phases. J Viral Hepat 2015; 22:416-26. [PMID: 25203736 DOI: 10.1111/jvh.12308] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hepatitis B virus is classically considered a hepatotropic virus but also infects peripheral blood mononuclear cells. Chronic hepatitis B has different disease phases modulated by host immunity. We compared HBV variability, drug resistance and immune escape mutations in the overlapping HBV polymerase/surface gene in plasma and peripheral blood mononuclear cells in different disease phases. Plasma and peripheral blood mononuclear cells were isolated from 22 treatment naïve patient cohorts (five inactive, six immune-active, nine HBeAg negative and two immune-tolerant). HBV was genotyped via line probe assay, hepatitis B surface antigen titres were determined by an in-house immunoassay, and HBV DNA was quantified by kinetic PCR. The HBV polymerase/surface region, including full genome in some, was PCR-amplified and cloned, and ~20 clones/sample were sequenced. The sequences were subjected to various mutational and phylogenetic analyses. Clonal sequencing showed that only three of 22 patients had identical HBV genotype profiles in both sites. In immune-active chronic hepatitis B, viral diversity in plasma was higher compared with peripheral blood mononuclear cells. Mutations at residues, in a minority of clones, associated with drug resistance, and/or immune escape were found in both compartments but were more common in plasma. Immune escape mutations were more often observed in the peripheral blood mononuclear cells of immune-active CHB carriers, compared with other disease phases. During all CHB disease phases, differences exist between HBV variants found in peripheral blood mononuclear cells and plasma. Moreover, these data indicate that HBV evolution occurs in a compartment and disease phase-specific fashion.
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Affiliation(s)
- C S Coffin
- Liver Unit, Division of Gastroenterology and Hepatology, University of Calgary, Calgary, AB, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Application of a hybrid method combining grey model and back propagation artificial neural networks to forecast hepatitis B in china. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015; 2015:328273. [PMID: 25815044 PMCID: PMC4357037 DOI: 10.1155/2015/328273] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 01/22/2015] [Accepted: 01/22/2015] [Indexed: 01/08/2023]
Abstract
Accurate incidence forecasting of infectious disease provides potentially valuable insights in its own right. It is critical for early prevention and may contribute to health services management and syndrome surveillance. This study investigates the use of a hybrid algorithm combining grey model (GM) and back propagation artificial neural networks (BP-ANN) to forecast hepatitis B in China based on the yearly numbers of hepatitis B and to evaluate the method's feasibility. The results showed that the proposal method has advantages over GM (1, 1) and GM (2, 1) in all the evaluation indexes.
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Wong DKH, Kopaniszen M, Omagari K, Tanaka Y, Fong DYT, Seto WK, Fung J, Huang FY, Zhang AY, Hung IFN, Lai CL, Yuen MF. Effect of hepatitis B virus reverse transcriptase variations on entecavir treatment response. J Infect Dis 2014; 210:701-707. [PMID: 24610871 DOI: 10.1093/infdis/jiu133] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Entecavir therapy often reduces hepatitis B virus (HBV) DNA to an undetectable level, but HBV DNA remain detectable in some patients. We investigated whether baseline HBV reverse transcriptase (rt) polymorphism and quasispecies complexity and diversity were associated with treatment response. METHODS Pretreatment HBV DNA levels, HBV rt sequence, serology, and quasispecies complexity and diversity from 305 entecavir-treated patients were determined. These data were tested for their association with year 1 virological outcome, defined by optimal response (undetectable HBV DNA; lower limit of detection, ≤12 IU/mL) or partial response (detectable HBV DNA). RESULTS Four rt variants were more frequently detected in the 64 partial responders than in the 241 optimal responders (all P < .05). Multivariate analysis revealed that high baseline HBV DNA level (P < .0001; odds ratio [OR], 2.32), HBV e antigen (HBeAg) positivity (P < .001; OR, 3.70), and rt124N (P = .002; OR, 3.06) were associated with a partial entecavir response. Compared with the optimal responders, the partial responders had a lower quasispecies complexity and diversity. CONCLUSIONS Apart from the known factors (high baseline HBV DNA level and HBeAg positivity), a novel single nucleotide polymorphism (rt124N) and lower quasispecies complexity and diversity were associated with partial entecavir response at year 1.
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Affiliation(s)
| | | | - Katsumi Omagari
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Japan
| | | | | | - James Fung
- Department of Medicine State Key Laboratory for Liver Research
| | | | | | | | - Ching-Lung Lai
- Department of Medicine State Key Laboratory for Liver Research
| | - Man-Fung Yuen
- Department of Medicine State Key Laboratory for Liver Research
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Shan C, Yin GQ, Wu P. Efficacy and safety of tenofovir in a kidney transplant patient with chronic hepatitis B and nucleos(t)ide multidrug resistance: a case report. J Med Case Rep 2014; 8:281. [PMID: 25146249 PMCID: PMC4155764 DOI: 10.1186/1752-1947-8-281] [Citation(s) in RCA: 9] [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: 02/07/2014] [Accepted: 06/26/2014] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Five nucleos(t)ide analogs are used to treat chronic hepatitis B. Ideal nucleos(t)ide analog therapy in chronic hepatitis B patients with kidney transplantation must ensure virological suppression and minimize renal injury. However, resistance to nucleos(t)ide analogs frequently results in virological breakthrough, hepatitis flare, and complicated deterioration of the transplanted kidney. Inappropriate rescue therapy for drug resistance may subsequently cause hepatitis B virus multidrug resistance. Currently, tenofovir is used to treat chronic hepatitis B patients with kidney transplantation. In the field, we first reported combination therapy with tenofovir plus entecavir in a kidney transplant chronic hepatitis B patient with nucleos(t)ide analog multidrug resistance. CASE PRESENTATION A 50-year-old Chinese man with chronic hepatitis B and kidney transplantation received nucleos(t)ide analog therapy with sequential monotherapy and combination therapy. Virological parameters, hepatic enzymology and renal function were monitored. Drug-resistance mutations were detected by sequence analysis. Our patient received sequential nucleos(t)ide analog monotherapy and inappropriate combination therapy during 132 months, which caused multidrug resistance and renal functional injury. Entecavir plus adefovir was administered in month 106, resulting in decreased hepatitis B virus load, normal hepatic function, and stabilized creatinine clearance. As a result of rebounded viral load and significantly declining creatinine clearance, tenofovir plus entecavir was administered in month 133. After eight weeks, undetectable hepatitis B virus DNA, normal hepatic function and improved creatinine clearance were present. Compared with combination therapy with adefovir plus entecavir, tenofovir plus entecavir showed a potent antiviral effect for multidrug resistance and minimized renal injury. CONCLUSIONS In chronic hepatitis B patients with kidney transplantation, sequential monotherapy with antiviral agents with low barriers to resistance should be avoided, and initial therapy with entecavir is a better option. Combination therapy with tenofovir plus entecavir in this setting with multidrug resistance is safe and effective.
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Affiliation(s)
- Chun Shan
- Department of Infectious Disease, Nanjing Zhong-Da Hospital, Southeast University School of Medicine, 87 Ding Jia Qiao, Nanjing 210009, Jiangsu, China
| | - Guo Qing Yin
- Department of Infectious Disease, Nanjing Zhong-Da Hospital, Southeast University School of Medicine, 87 Ding Jia Qiao, Nanjing 210009, Jiangsu, China
| | - Pei Wu
- Department of Infectious Disease, Nanjing Zhong-Da Hospital, Southeast University School of Medicine, 87 Ding Jia Qiao, Nanjing 210009, Jiangsu, China
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Tu Z, Hu Y, Xu L, Huang Y, Luo X, Hu JL, Huang AL. An improved method for simple and efficient hepatitis B virus genome cloning. J Virol Methods 2014; 205:75-80. [PMID: 24833122 DOI: 10.1016/j.jviromet.2014.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/24/2014] [Accepted: 05/02/2014] [Indexed: 12/28/2022]
Abstract
The genetic variation of hepatitis B virus (HBV) is associated with a natural history of infection and with a response to antiviral therapy. Current attempts to investigate the genetic variation within patients infected with HBV have characterized only the subgenomic region or a limited number of full-length genomes. In this study, a simple and efficient full-length HBV cloning method, which is independent of restriction digestion and ligation, from a clinical sample is presented. The full-length HBV amplified from patients' sera serves as two megaprimers and contains two ends that are homologous to the insertion site of a newly constructed plasmid. This method could enable the extension of the plasmid backbone by DNA polymerase. To improve the cloning efficiency, a LacZ gene fragment was incorporated into the middle of the insertion site in the plasmid and was used for blue-white screening. Through optimization and evaluation, a high success rate of positive clones (90%) from an individual patient was obtained. Thus, this study provides a simple, efficient, and convenient method for full-length HBV cloning from many clinical samples, and this method could greatly facilitate studies concerning the genetic variation of HBV.
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Affiliation(s)
- Zeng Tu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Department of Microbiology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yuan Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China
| | - Lei Xu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Department of Microbiology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yong Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China
| | - Xuan Luo
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China
| | - Jie-Li Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China.
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China.
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Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics 2014; 30:1104-1111. [PMID: 24389655 DOI: 10.1093/bioinformatics/btt768] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/25/2013] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Given the inherent dynamics of a viral quasispecies, we are often interested in the comparison of diversity indices of sequential samples of a patient, or in the comparison of diversity indices of virus in groups of patients in a treated versus control design. It is then important to make sure that the diversity measures from each sample may be compared with no bias and within a consistent statistical framework. In the present report, we review some indices often used as measures for viral quasispecies complexity and provide means for statistical inference, applying procedures taken from the ecology field. In particular, we examine the Shannon entropy and the mutation frequency, and we discuss the appropriateness of different normalization methods of the Shannon entropy found in the literature. By taking amplicons ultra-deep pyrosequencing (UDPS) raw data as a surrogate of a real hepatitis C virus viral population, we study through in-silico sampling the statistical properties of these indices under two methods of viral quasispecies sampling, classical cloning followed by Sanger sequencing (CCSS) and next-generation sequencing (NGS) such as UDPS. We propose solutions specific to each of the two sampling methods-CCSS and NGS-to guarantee statistically conforming conclusions as free of bias as possible. CONTACT josep.gregori@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Josep Gregori
- Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain
| | - Miquel Salicrú
- Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain
| | - Esteban Domingo
- Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain
| | - Alex Sanchez
- Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain
| | - Juan I Esteban
- Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain
| | - Josep Quer
- Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain
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