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Xie C, Lu D. Evolution and diversity of the hepatitis B virus genome: Clinical implications. Virology 2024; 598:110197. [PMID: 39098184 DOI: 10.1016/j.virol.2024.110197] [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: 05/23/2024] [Revised: 07/14/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
Hepatitis B virus (HBV) infection remains a significant global health burden. The genetic variation of HBV is complex. HBV can be divided into nine genotypes, which show significant differences in geographical distribution, clinical manifestations, transmission routes and treatment response. In recent years, substantial progress has been made through various research methods in understanding the development, pathogenesis, and antiviral treatment response of clinical disease associated with HBV genetic variants. This progress provides important theoretical support for a deeper understanding of the natural history of HBV infection, virus detection, drug treatment, vaccine development, mother-to-child transmission, and surveillance management. This review summarizes the mechanisms of HBV diversity, discusses methods used to detect viral diversity in current studies, and the impact of viral genome variation during infection on the development of clinical disease.
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Affiliation(s)
- Chengzuo Xie
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Daiqiang Lu
- Institute of Molecular and Medical Virology, Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, School of Medicine, Jinan University, Guangzhou, Guangdong Province, 510632, China.
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2
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Zhu C, Tang M, Fu Y, Xun Z, Lin C, Wu S, Chen T, Zeng Y, Yang B, Ou Q, Liu C. Characterization of BCP/PreC/C region quasispecies in treatment-naive patients with different phases of HBV infection using next-generation sequencing. Int J Med Microbiol 2024; 315:151619. [PMID: 38564936 DOI: 10.1016/j.ijmm.2024.151619] [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: 02/25/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND To analysis of quasispecies (QS) changes and high-frequency mutations in the BCP/PreC/C region of patients at different phases of hepatitis B virus (HBV) infection and provides novel biomarkers for the diagnosis of chronic hepatitis B (CHB) patients. METHODS With the application of next-generation sequencing technology, we were able to sequence the HBV BCP/PreC/C regions in 40 patients, each at different phases of the HBV infection. The heterogeneity of QS and the frequency of mutations were calculated using MEGA 7 software. RESULTS Our results show that the complexity and diversity of the BCP/PreC/C QS in HBeAg-positive CHB patients are significantly higher than those in HBeAg-positive chronic infection patients, while HBeAg-negative chronic infection patients had significantly higher QS complexity and diversity than HBeAg-negative CHB patients. In addition, HBeAg-negative patients showed reduced complexity but increased diversity compared with HBeAg-positive patients. Receiver operating characteristic curves showed that G1764A, C2102T, dN and complexity of QS could be used as potential biomarkers for diagnosing HBeAg-positive CHB, while the A2189C, dS and complexity of QS could be used as potential biomarkers for diagnosing HBeAg-negative chronic hepatitis. Finally, our study also found that G1896A and A2159G may be hotspot mutations affecting HBeAg seroconversion. CONCLUSION Our research elucidates the evolution of HBV by analyzing QS heterogeneity and mutation patterns, offering novel serum biomarkers for enhancing clinical diagnosis and disease prognosis. This comprehensive approach sheds light on the intricate dynamics of HBV progression and paves the way for more precise medical interventions.
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Affiliation(s)
- Chenggong Zhu
- Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Minjie Tang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ya Fu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhen Xun
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Caorui Lin
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Songhang Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yongbin Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
| | - Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
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3
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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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5
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Kasianchuk N, Dobrowolska K, Harkava S, Bretcan A, Zarębska-Michaluk D, Jaroszewicz J, Flisiak R, Rzymski P. Gene-Editing and RNA Interference in Treating Hepatitis B: A Review. Viruses 2023; 15:2395. [PMID: 38140636 PMCID: PMC10747710 DOI: 10.3390/v15122395] [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: 10/28/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The hepatitis B virus (HBV) continues to cause substantial health and economic burdens, and its target of elimination may not be reached in 2030 without further efforts in diagnostics, non-pharmaceutical prevention measures, vaccination, and treatment. Current therapeutic options in chronic HBV, based on interferons and/or nucleos(t)ide analogs, suppress the virus replication but do not eliminate the pathogen and suffer from several constraints. This paper reviews the progress on biotechnological approaches in functional and definitive HBV treatments, including gene-editing tools, i.e., zinc-finger proteins, transcription activator-like effector nucleases, and CRISPR/Cas9, as well as therapeutics based on RNA interference. The advantages and challenges of these approaches are also discussed. Although the safety and efficacy of gene-editing tools in HBV therapies are yet to be demonstrated, they show promise for the revitalization of a much-needed advance in the field and offer viral eradication. Particular hopes are related to CRISPR/Cas9; however, therapeutics employing this system are yet to enter the clinical testing phases. In contrast, a number of candidates based on RNA interference, intending to confer a functional cure, have already been introduced to human studies. However, larger and longer trials are required to assess their efficacy and safety. Considering that prevention is always superior to treatment, it is essential to pursue global efforts in HBV vaccination.
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Affiliation(s)
- Nadiia Kasianchuk
- Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | | | - Sofiia Harkava
- Junior Academy of Sciences of Ukraine, Regional Branch in Dnipro, 49000 Dnipro, Ukraine;
| | - Andreea Bretcan
- National College “Ienăchiță Văcărescu”, 130016 Târgoviște, Romania;
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases and Allergology, Jan Kochanowski University, 25-317 Kielce, Poland;
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia in Katowice, 41-902 Bytom, Poland;
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland;
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland
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6
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Evolutional transition of HBV genome during the persistent infection determined by single-molecule real-time sequencing. Hepatol Commun 2023; 7:e0047. [PMID: 36848123 PMCID: PMC9974078 DOI: 10.1097/hc9.0000000000000047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/20/2022] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Although HBV infection is a serious health issue worldwide, the landscape of HBV genome dynamics in the host has not yet been clarified. This study aimed to determine the continuous genome sequence of each HBV clone using a single-molecule real-time sequencing platform, and clarify the dynamics of structural abnormalities during persistent HBV infection without antiviral therapy. PATIENTS AND METHODS Twenty-five serum specimens were collected from 10 untreated HBV-infected patients. Continuous whole-genome sequencing of each clone was performed using a PacBio Sequel sequencer; the relationship between genomic variations and clinical information was analyzed. The diversity and phylogeny of the viral clones with structural variations were also analyzed. RESULTS The whole-genome sequences of 797,352 HBV clones were determined. The deletion was the most common structural abnormality and concentrated in the preS/S and C regions. Hepatitis B e antibody (anti-HBe)-negative samples or samples with high alanine aminotransferase levels have significantly diverse deletions than anti-HBe-positive samples or samples with low alanine aminotransferase levels. Phylogenetic analysis demonstrated that various defective and full-length clones evolve independently and form diverse viral populations. CONCLUSIONS Single-molecule real-time long-read sequencing revealed the dynamics of genomic quasispecies during the natural course of chronic HBV infections. Defective viral clones are prone to emerge under the condition of active hepatitis, and several types of defective variants can evolve independently of the viral clones with the full-length genome.
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7
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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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8
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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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9
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Vaillant A. Oligonucleotide-Based Therapies for Chronic HBV Infection: A Primer on Biochemistry, Mechanisms and Antiviral Effects. Viruses 2022; 14:v14092052. [PMID: 36146858 PMCID: PMC9502277 DOI: 10.3390/v14092052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/21/2022] Open
Abstract
Three types of oligonucleotide-based medicines are under clinical development for the treatment of chronic HBV infection. Antisense oligonucleotides (ASOs) and synthetic interfering RNA (siRNA) are designed to degrade HBV mRNA, and nucleic acid polymers (NAPs) stop the assembly and secretion of HBV subviral particles. Extensive clinical development of ASOs and siRNA for a variety of liver diseases has established a solid understanding of their pharmacodynamics, accumulation in different tissue types in the liver, pharmacological effects, off-target effects and how chemical modifications and delivery approaches affect these parameters. These effects are highly conserved for all ASO and siRNA used in human studies to date. The clinical assessment of several ASO and siRNA compounds in chronic HBV infection in recent years is complicated by the different delivery approaches used. Moreover, these assessments have not considered the large clinical database of ASO/siRNA function in other liver diseases and known off target effects in other viral infections. The goal of this review is to summarize the current understanding of ASO/siRNA/NAP pharmacology and integrate these concepts into current clinical results for these compounds in the treatment of chronic HBV infection.
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Affiliation(s)
- Andrew Vaillant
- Replicor Inc., 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada
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10
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Lin J, Li J, Xie P, Han Y, Yu D, Chen J, Zhang X. Hepatitis B virus middle surface antigen loss promotes clinical variant persistence in mouse models. Virulence 2021; 12:2868-2882. [PMID: 34738866 PMCID: PMC8632123 DOI: 10.1080/21505594.2021.1999130] [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: 11/30/2022] Open
Abstract
Hepatitis B virus (HBV) middle surface antigen (MHBs) mutation or deletion occurs in patients with chronic HBV infection. However, the functional role of MHBs in HBV infection is still an enigma. Here, we reported that 7.33% (11/150) isolates of CHB patients had MHBs start codon mutations compared with 0.00% (0/146) in acute hepatitis B (AHB) patients. Interestingly, MHBs loss accounted for 11.88% (126/1061) isolates from NCBI GenBank, compared with 0.09% (1/1061) and 0.00% (0/1061) for HBV large surface antigen (LHBs) loss and HBV small surface antigen (SHBs) loss, respectively. One persistent HBV clone of genotype B (B56, MHBs loss) from a CHB patient was hydrodynamically injected into BALB/c mice. B56 persisted for >70 weeks in BALB/c mice, whereas B56 with restored MHBs (B56M+) was quickly cleared within 28 days. Serum cytokine assays demonstrated that CXCL1, CXCL2, IL-6 and IL-33 were significantly increased during rapid HBV clearance in B56M+ mice. Furthermore, the enhancers and promoters of B56 were proved to be required for B56 persistence in mice. Ablating MHBs expression improved the persistence of a new clone (HBV1.3, genotype B) which was recreated by using enhancers and promoters of B56. These data demonstrated that MHBs deletion can promote the persistence of specific HBV variants in a hydrodynamic mouse model. MHBs re-expression restored a rapid clearance of HBV, which was accompanied by cytokine responses including the elevation of CXCL1, CXCL2, IL-6 and IL-33.
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Affiliation(s)
- Junyu Lin
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Li
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peilin Xie
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Han
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Demin Yu
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Chen
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinxin Zhang
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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Chen Z, Eggerman TL, Bocharov AV, Baranova IN, Vishnyakova TG, Patterson AP. APOBEC3-induced mutation of the hepatitis virus B DNA genome occurs during its viral RNA reverse transcription into (-)-DNA. J Biol Chem 2021; 297:100889. [PMID: 34181944 PMCID: PMC8321922 DOI: 10.1016/j.jbc.2021.100889] [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: 05/24/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/17/2022] Open
Abstract
APOBEC3s are innate single-stranded DNA cytidine-to-uridine deaminases that catalyze mutations in both pathogen and human genomes with significant roles in human disease. However, how APOBEC3s mutate a single-stranded DNA that is available momentarily during DNA transcription or replication in vivo remains relatively unknown. In this study, utilizing hepatitis B virus (HBV) viral mutations, we evaluated the mutational characteristics of individual APOBEC3s with reference to the HBV replication process through HBV whole single-strand (-)-DNA genome mutation analyses. We found that APOBEC3s induced C-to-T mutations from the HBV reverse transcription start site continuing through the whole (-)-DNA transcript to the termination site with variable efficiency, in an order of A3B >> A3G > A3H-II or A3C. A3B had a 3-fold higher mutation efficiency than A3H-II or A3C with up to 65% of all HBV genomic cytidines being converted into uridines in a single mutation event, consistent with the A3B localized hypermutation signature in cancer, namely, kataegis. On the other hand, A3C expression led to a 3-fold higher number of mutation-positive HBV genome clones, although each individual clone had a lower number of C-to-T mutations. Like A3B, A3C preferred both 5'-TC and 5'-CC sequences, but to a lesser degree. The APOBEC3-induced HBV mutations were predominantly detected in the HBV rcDNA but were not detectable in other intermediates including HBV cccDNA and pgRNA by primer extension of their PCR amplification products. These data demonstrate that APOBEC3-induced HBV genome mutations occur predominantly when the HBV RNA genome was reversely transcribed into (-)-DNA in the viral capsid.
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Affiliation(s)
- Zhigang Chen
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas L Eggerman
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Division of Diabetes, Endocrinology and Metabolic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alexander V Bocharov
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Irina N Baranova
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Tatyana G Vishnyakova
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Amy P Patterson
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
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12
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Campos-Valdez M, Monroy-Ramírez HC, Armendáriz-Borunda J, Sánchez-Orozco LV. Molecular Mechanisms during Hepatitis B Infection and the Effects of the Virus Variability. Viruses 2021; 13:v13061167. [PMID: 34207116 PMCID: PMC8235420 DOI: 10.3390/v13061167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/16/2022] Open
Abstract
The immunopathogenesis and molecular mechanisms involved during a hepatitis B virus (HBV) infection have made the approaches for research complex, especially concerning the patients’ responses in the course of the early acute stage. The study of molecular bases involved in the viral clearance or persistence of the infection is complicated due to the difficulty to detect patients at the most adequate points of the disease, especially in the time lapse between the onset of the infection and the viral emergence. Despite this, there is valuable data obtained from animal and in vitro models, which have helped to clarify some aspects of the early immune response against HBV infection. The diversity of the HBV (genotypes and variants) has been proven to be associated not only with the development and outcome of the disease but also with the response to treatments. That is why factors involved in the virus evolution need to be considered while studying hepatitis B infection. This review brings together some of the published data to try to explain the immunological and molecular mechanisms involved in the different stages of the infection, clinical outcomes, viral persistence, and the impact of the variants of HBV in these processes.
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Affiliation(s)
- Marina Campos-Valdez
- Centro Universitario de Ciencias de la Salud, Departamento de Biología Molecular y Genómica, Instituto de Biología Molecular en Medicina, Universidad de Guadalajara, Guadalajara 44340, Jalisco, México; (M.C.-V.); (H.C.M.-R.); (J.A.-B.)
| | - Hugo C. Monroy-Ramírez
- Centro Universitario de Ciencias de la Salud, Departamento de Biología Molecular y Genómica, Instituto de Biología Molecular en Medicina, Universidad de Guadalajara, Guadalajara 44340, Jalisco, México; (M.C.-V.); (H.C.M.-R.); (J.A.-B.)
| | - Juan Armendáriz-Borunda
- Centro Universitario de Ciencias de la Salud, Departamento de Biología Molecular y Genómica, Instituto de Biología Molecular en Medicina, Universidad de Guadalajara, Guadalajara 44340, Jalisco, México; (M.C.-V.); (H.C.M.-R.); (J.A.-B.)
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Campus Guadalajara, Zapopan 45201, Jalisco, México
| | - Laura V. Sánchez-Orozco
- Centro Universitario de Ciencias de la Salud, Departamento de Biología Molecular y Genómica, Instituto de Biología Molecular en Medicina, Universidad de Guadalajara, Guadalajara 44340, Jalisco, México; (M.C.-V.); (H.C.M.-R.); (J.A.-B.)
- Correspondence: ; Tel.: +52-33-3954-5677
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13
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Vaillant A. HBsAg, Subviral Particles, and Their Clearance in Establishing a Functional Cure of Chronic Hepatitis B Virus Infection. ACS Infect Dis 2021; 7:1351-1368. [PMID: 33302622 DOI: 10.1021/acsinfecdis.0c00638] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In diverse viral infections, the production of excess viral particles containing only viral glycoproteins (subviral particles or SVP) is commonly observed and is a commonly evolved mechanism for immune evasion. In hepatitis B virus (HBV) infection, spherical particles contain the hepatitis B surface antigen, outnumber infectious virus 10 000-100 000 to 1, and have diverse inhibitory effects on the innate and adaptive immune response, playing a major role in the chronic nature of HBV infection. The current goal of therapies in development for HBV infection is a clinical outcome called functional cure, which signals a persistent and effective immune control of the infection. Although removal of spherical SVP (and the HBsAg they carry) is an important milestone in achieving functional cure, this outcome is rarely achieved with current therapies due to distinct mechanisms for assembly, secretion, and persistence of SVP, which are poorly targeted by direct acting antivirals or immunotherapies. In this Review, the current understanding of the distinct mechanisms involved in the production and persistence of spherical SVP in chronic HBV infection and their immunoinhibitory activity will be reviewed as well as current therapies in development with the goal of clearing spherical SVP and achieving functional cure.
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Affiliation(s)
- Andrew Vaillant
- Replicor Inc., 6100 Royalmount Avenue, Montreal, Quebec H8Y 3E6, Canada
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14
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Wagner J, Yuen L, Littlejohn M, Sozzi V, Jackson K, Suri V, Tan S, Feierbach B, Gaggar A, Marcellin P, Buti Ferret M, Janssen HLA, Gane E, Chan HLY, Colledge D, Rosenberg G, Bayliss J, Howden BP, Locarnini SA, Wong D, Thompson AT, Revill PA. Analysis of Hepatitis B Virus Haplotype Diversity Detects Striking Sequence Conservation Across Genotypes and Chronic Disease Phase. Hepatology 2021; 73:1652-1670. [PMID: 32780526 DOI: 10.1002/hep.31516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/01/2020] [Accepted: 06/29/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS We conducted haplotype analysis of complete hepatitis B virus (HBV) genomes following deep sequencing from 368 patients across multiple phases of chronic hepatitis B (CHB) infection from four major genotypes (A-D), analyzing 4,110 haplotypes to identify viral variants associated with treatment outcome and disease progression. APPROACH AND RESULTS Between 18.2% and 41.8% of nucleotides and between 5.9% and 34.3% of amino acids were 100% conserved in all genotypes and phases examined, depending on the region analyzed. Hepatitis B e antigen (HBeAg) loss by week 192 was associated with different haplotype populations at baseline. Haplotype populations differed across the HBV genome and CHB history, this being most pronounced in the precore/core gene. Mean number of haplotypes (frequency) per patient was higher in immune-active, HBeAg-positive chronic hepatitis phase 2 (11.8) and HBeAg-negative chronic hepatitis phase 4 (16.2) compared to subjects in the "immune-tolerant," HBeAg-positive chronic infection phase 1 (4.3, P< 0.0001). Haplotype frequency was lowest in genotype B (6.2, P< 0.0001) compared to the other genotypes (A = 11.8, C = 11.8, D = 13.6). Haplotype genetic diversity increased over the course of CHB history, being lowest in phase 1, increasing in phase 2, and highest in phase 4 in all genotypes except genotype C. HBeAg loss by week 192 of tenofovir therapy was associated with different haplotype populations at baseline. CONCLUSIONS Despite a degree of HBV haplotype diversity and heterogeneity across the phases of CHB natural history, highly conserved sequences in key genes and regulatory regions were identified in multiple HBV genotypes that should be further investigated as targets for antiviral therapies and predictors of treatment response.
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Affiliation(s)
- Josef Wagner
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
| | - Lilly Yuen
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
| | - Margaret Littlejohn
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
| | - Vitina Sozzi
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
| | - Kathy Jackson
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | | | | | - Maria Buti Ferret
- Liver Unit, Valle d'Hebron University Hospital, Ciberehd del Insituto Carlos III Barcelona, Barcelona, Spain
| | - Harry L A Janssen
- Toronto Center for Liver Diseases, Toronto General Hospital, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Ed Gane
- New Zealand Liver Transplant Unit, Auckland City Hospital, Auckland, New Zealand
| | - Henry L Y Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Danni Colledge
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
| | - Gillian Rosenberg
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
| | - Julianne Bayliss
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stephen A Locarnini
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
| | - Darren Wong
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia.,Department of Gastroenterology, St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Alexander T Thompson
- Department of Gastroenterology, St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Peter A Revill
- Division of Molecular Research and Development, Victorian Infectious Diseases, Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne Healthy, University of Melbourne, Melbourne, VIC, Australia
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15
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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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16
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Li Q, Wang J, Lu M, Qiu Y, Lu H. Acute-on-Chronic Liver Failure From Chronic-Hepatitis-B, Who Is the Behind Scenes. Front Microbiol 2020; 11:583423. [PMID: 33365018 PMCID: PMC7750191 DOI: 10.3389/fmicb.2020.583423] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022] Open
Abstract
Acute-on-chronic liver failure (ACLF) is an acute syndrome accompanied with decompensation of cirrhosis, organ failure with high 28-day mortality rate. Systemic inflammation is the main feature of ACLF, and poor outcome is closely related with exacerbated systemic inflammatory responses. It is well known that severe systemic inflammation is an important event in chronic hepatitis B (CHB)-ACLF, which eventually leads to liver injury. However, the initial CHB-ACLF events are unclear; moreover, the effect of these events on host immunity as well as that of immune imbalance on CHB-ACLF progression are unknown. Here, we investigate the initial events of ACLF progression, discuss possible mechanisms underlying ACLF progression, and provide a new model for ACLF prediction and treatment. We review the characteristics of ACLF, and consider its plausible immune predictors and alternative treatment strategies.
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Affiliation(s)
- Qian Li
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, China
| | - Jun Wang
- Center of Clinical Laboratory, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
| | - Mengji Lu
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Yuanwang Qiu
- Department of Hepatology, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
| | - Hongzhou Lu
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, China
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17
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Fergusson JR, Wallace Z, Connolly MM, Woon AP, Suckling RJ, Hine DW, Barber C, Bunjobpol W, Choi B, Crespillo S, Dembek M, Dieckmann N, Donoso J, Godinho LF, Grant T, Howe D, McCully ML, Perot C, Sarkar A, Seifert FU, Singh PK, Stegmann KA, Turner B, Verma A, Walker A, Leonard S, Maini MK, Wiederhold K, Dorrell L, Simmons R, Knox A. Immune-Mobilizing Monoclonal T Cell Receptors Mediate Specific and Rapid Elimination of Hepatitis B-Infected Cells. Hepatology 2020; 72:1528-1540. [PMID: 32770836 PMCID: PMC7702151 DOI: 10.1002/hep.31503] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/17/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS Therapies for chronic hepatitis B virus (HBV) infection are urgently needed because of viral integration, persistence of viral antigen expression, inadequate HBV-specific immune responses, and treatment regimens that require lifelong adherence to suppress the virus. Immune mobilizing monoclonal T Cell receptors against virus (ImmTAV) molecules represent a therapeutic strategy combining an affinity-enhanced T Cell receptor with an anti-CD3 T Cell-activating moiety. This bispecific fusion protein redirects T cells to specifically lyse infected cells expressing the target virus-derived peptides presented by human leukocyte antigen (HLA). APPROACH AND RESULTS ImmTAV molecules specific for HLA-A*02:01-restricted epitopes from HBV envelope, polymerase, and core antigens were engineered. The ability of ImmTAV-Env to activate and redirect polyclonal T cells toward cells containing integrated HBV and cells infected with HBV was assessed using cytokine secretion assays and imaging-based killing assays. Elimination of infected cells was further quantified using a modified fluorescent hybridization of viral RNA assay. Here, we demonstrate that picomolar concentrations of ImmTAV-Env can redirect T cells from healthy and HBV-infected donors toward hepatocellular carcinoma (HCC) cells containing integrated HBV DNA resulting in cytokine release, which could be suppressed by the addition of a corticosteroid in vitro. Importantly, ImmTAV-Env redirection of T cells induced cytolysis of antigen-positive HCC cells and cells infected with HBV in vitro, causing a reduction of hepatitis B e antigen and specific loss of cells expressing viral RNA. CONCLUSIONS The ImmTAV platform has the potential to enable the elimination of infected cells by redirecting endogenous non-HBV-specific T cells, bypassing exhausted HBV-specific T cells. This represents a promising therapeutic option in the treatment of chronic hepatitis B, with our lead candidate now entering trials.
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MESH Headings
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal/therapeutic use
- CD3 Complex/antagonists & inhibitors
- Cell Line, Tumor
- Epitopes/immunology
- HLA-A2 Antigen/immunology
- Hepatitis B Surface Antigens/immunology
- Hepatitis B virus/immunology
- Hepatitis B virus/isolation & purification
- Hepatitis B, Chronic/drug therapy
- Hepatitis B, Chronic/immunology
- Hepatitis B, Chronic/virology
- Hepatocytes
- Humans
- Immunoconjugates/genetics
- Immunoconjugates/immunology
- Immunoconjugates/pharmacology
- Immunoconjugates/therapeutic use
- Lymphocyte Activation/drug effects
- Primary Cell Culture
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/therapeutic use
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/immunology
- Recombinant Fusion Proteins/pharmacology
- Recombinant Fusion Proteins/therapeutic use
- T-Lymphocytes/drug effects
- T-Lymphocytes/immunology
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dawn Howe
- Immunocore LtdAbingdonUnited Kingdom
| | | | | | | | | | | | - Kerstin A. Stegmann
- Division of Infection and ImmunityInstitute of Immunity and TransplantationUniversity College LondonLondonUnited Kingdom
| | | | | | | | | | - Mala K. Maini
- Division of Infection and ImmunityInstitute of Immunity and TransplantationUniversity College LondonLondonUnited Kingdom
| | | | - Lucy Dorrell
- Immunocore LtdAbingdonUnited Kingdom
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUnited Kingdom
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18
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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: 0.4] [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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Yasen A, Aini A, Wang H, Li W, Zhang C, Ran B, Tuxun T, Maimaitinijiati Y, Shao Y, Aji T, Wen H. Progress and applications of single-cell sequencing techniques. INFECTION GENETICS AND EVOLUTION 2020; 80:104198. [PMID: 31958516 DOI: 10.1016/j.meegid.2020.104198] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 01/06/2023]
Abstract
Single-cell sequencing (SCS) is a next-generation sequencing method that is mainly used to analyze differences in genetic and protein information between cells, to obtain genetic information on microorganisms that are difficult to cultivate at a single-cell level and to better understand their specific roles in the microenvironment. By sequencing the whole genome, transcriptome and epigenome of a single cell, the complex heterogeneous mechanisms involved in disease occurrence and progression can be revealed, further improving disease diagnosis, prognosis prediction and monitoring of the therapeutic effects of drugs. In this study, we mainly summarized the methods and application fields of SCS, which may provide potential references for its future clinical applications, including the analysis of embryonic and organ development, the immune system, cancer progression, and parasitic and infectious diseases as well as stem cell research, antibody screening, and therapeutic research and development.
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Affiliation(s)
- Aimaiti Yasen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, 393 Xin Yi Road, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Abudusalamu Aini
- The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Hui Wang
- Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Wending Li
- The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Chuanshan Zhang
- Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Bo Ran
- Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Tuerhongjiang Tuxun
- Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Yusufukadier Maimaitinijiati
- The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Yingmei Shao
- Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Tuerganaili Aji
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, 393 Xin Yi Road, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China.
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, 393 Xin Yi Road, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China.
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20
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Trinks J, Marciano S, Esposito I, Franco A, Mascardi MF, Mendizabal M, Livellara B, Arrigo D, Calzetta P, Vujacich C, Giunta D, Gadano A, Flichman D. The genetic variability of hepatitis B virus subgenotype F1b precore/core gene is related to the outcome of the acute infection. Virus Res 2019; 277:197840. [PMID: 31846615 DOI: 10.1016/j.virusres.2019.197840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/03/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023]
Abstract
AIM To assess the association of viral and host genetic variability with the outcome of acute infection with hepatitis B virus subgenotype F1b (HBV/F1b). METHODS The cohort consisted of 26 patients with acute HBV/F1b infection who exhibit different outcomes: spontaneous resolution (n = 10), progression to chronic hepatitis (n = 10) and acute liver failure (n = 6). HLA SNPs (rs3077, rs9277542, rs2856718 and rs7453920) were determined. The S gene and core promoter/precore/core region were direct sequenced, and this latter region was also ultra-deep sequenced. Mean number of mutations, mutation rate, Shannon entropy, positive selection sites and mutational patterns of quasispecies were compared between groups. RESULTS HLA SNPs were associated with spontaneous resolution or progression to chronic hepatitis, but not with the development of acute liver failure. The mean number of mutations in the S gene was similar among the three groups. Patients with spontaneous resolution had the lowest number of mutations, mutation rates and Shannon entropy values in the precore/core compared to the other two groups. Ten positive selection sites mapped on HLA-restricted epitopes were related to progression to chronic hepatitis and acute liver failure. Mutations T1753C, A1762T, G1764A, C1766T, T1768A G1896A, G2092T and T2107C were associated with acute liver failure and progression to chronic hepatitis. CONCLUSION Highly heterogeneous and complex HBV precore/core carrying specific point mutations, combined with the host HLA background, were associated with a worse clinical outcome of acute HBV/F1b infection.
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Affiliation(s)
- Julieta Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Sebastián Marciano
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina; Departamento de Investigación, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Isabella Esposito
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - Alejandra Franco
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - Maria Florencia Mascardi
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - Manuel Mendizabal
- Unidad de Hígado y Trasplante Hepático, Hospital Universitario Austral, Buenos Aires, Argentina
| | - Beatriz Livellara
- Laboratorio Central, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Diego Arrigo
- Laboratorio Central, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Pablo Calzetta
- División de Gastroenterología, Hospital Juan A. Fernández, Buenos Aires, Argentina
| | - Claudia Vujacich
- Fundación Centro de Estudios Infectológicos (FUNCEI), Buenos Aires, Argentina
| | - Diego Giunta
- Departamento de Investigación, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina; Área de Investigación de Medicina Interna, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Adrián Gadano
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina; Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina; Departamento de Investigación, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Diego Flichman
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina
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21
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Liu C, Lin J, Xun Z, Huang J, Huang E, Chen T, He Y, Lin N, Yang B, Ou Q. Establishment of Coamplification at Lower Denaturation Temperature PCR/Fluorescence Melting Curve Analysis for Quantitative Detection of Hepatitis B Virus DNA, Genotype, and Reverse Transcriptase Mutation and Its Application in Diagnosis of Chronic Hepatitis B. J Mol Diagn 2019; 21:1106-1116. [PMID: 31607557 DOI: 10.1016/j.jmoldx.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022] Open
Abstract
Dynamic and real-time hepatitis B virus (HBV) DNA, genotype, and reverse transcriptase mutation analysis plays an important role in diagnosing and monitoring chronic hepatitis B (CHB) and in assessing the therapeutic response. We established a highly sensitive coamplification at lower denaturation temperature PCR (COLD-PCR) coupled with probe-based fluorescence melting curve analysis (FMCA) for precision diagnosis of CHB patients. The imprecision with %CV and detection limit of HBV DNA detected by COLD-PCR/FMCA were 2.58% to 4.42% and 500 IU/mL, respectively. For mutation, the imprecision and detection limit were 3.35% to 6.49% and 1%, respectively. Compared with Sanger sequencing, the coincidence rates of genotype and mutation were 96.0% and 82.5%, respectively, whereas the inconsistent data resulted from a low proportion (<20%) of mixed genotypes or mixed mutations. The mutation ratio in HBV infection patients was as follows: hepatitis B e antigen (HBeAg)-positive infection (0/0.0%) < HBeAg-negative infection (16/4.5%) < HBeAg-positive hepatitis (30/5.5%) < HBeAg-negative hepatitis (36/6.5%). In patients with entecavir therapy, the proportion of mutation at baseline or week 4 in virologic response (VR) group was <4%, whereas in the partial VR group, it was mostly ≥4%. COLD-PCR/FMCA provides a novel tool with high sensitivity, convenience, and practicability for the simultaneous quantification of HBV DNA, genotype, and mutation. It might be used for distinguishing the different phases of HBV infection and predicting VR of CHB patients.
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Affiliation(s)
- Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Jinpiao Lin
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Zhen Xun
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Jinlan Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Er Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Yujue He
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Ni Lin
- School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, People's Republic of China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China.
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22
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McNaughton AL, D'Arienzo V, Ansari MA, Lumley SF, Littlejohn M, Revill P, McKeating JA, Matthews PC. Insights From Deep Sequencing of the HBV Genome-Unique, Tiny, and Misunderstood. Gastroenterology 2019; 156:384-399. [PMID: 30268787 PMCID: PMC6347571 DOI: 10.1053/j.gastro.2018.07.058] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/27/2018] [Accepted: 07/23/2018] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) is a unique, tiny, partially double-stranded, reverse-transcribing DNA virus with proteins encoded by multiple overlapping reading frames. The substitution rate is surprisingly high for a DNA virus, but lower than that of other reverse transcribing organisms. More than 260 million people worldwide have chronic HBV infection, which causes 0.8 million deaths a year. Because of the high burden of disease, international health agencies have set the goal of eliminating HBV infection by 2030. Nonetheless, the intriguing HBV genome has not been well characterized. We summarize data on the HBV genome structure and replication cycle, explain and quantify diversity within and among infected individuals, and discuss advances that can be offered by application of next-generation sequencing technology. In-depth HBV genome analyses could increase our understanding of disease pathogenesis and allow us to better predict patient outcomes, optimize treatment, and develop new therapeutics.
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Affiliation(s)
- Anna L McNaughton
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Valentina D'Arienzo
- Nuffield Department of Medicine, NDM Research Building, Oxford, United Kingdom
| | - M Azim Ansari
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Sheila F Lumley
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia; Department of Microbiology and Immunology, University of Melbourne. Melbourne, Australia
| | - Peter Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia; Department of Microbiology and Immunology, University of Melbourne. Melbourne, Australia
| | - Jane A McKeating
- Nuffield Department of Medicine, NDM Research Building, Oxford, United Kingdom
| | - Philippa C Matthews
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.
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Caballero A, Tabernero D, Buti M, Rodriguez-Frias F. Hepatitis B virus: The challenge of an ancient virus with multiple faces and a remarkable replication strategy. Antiviral Res 2018; 158:34-44. [PMID: 30059722 DOI: 10.1016/j.antiviral.2018.07.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 02/07/2023]
Abstract
The hepatitis B virus (HBV) is the prototype member of the Hepadnaviridae, an ancient family of hepatotropic DNA viruses, which may have originated from 360 to 430 million years ago and with evidence of endogenization in reptilian genomes >200 million years ago. The virus is currently estimated to infect more than 250 million humans. The extremely successful spread of this pathogen among the human population is explained by its multiple particulate forms, effective transmission strategies (particularly perinatal transmission), long induction period and low associated mortality. These characteristics confer selective advantages, enabling the virus to persist in small, disperse populations and spread worldwide, with high prevalence rates in many countries. The HBV replication strategy is remarkably complex and includes a multiplicity of particulate structures. In addition to the common virions containing DNA in a relaxed circular (rcDNA) or double-stranded linear (dslDNA) forms, the viral population includes virion-like particles containing RNA or "empty" (viral envelopes and capsids without genomes), subviral particles (only an envelope) and even naked capsids. Consequently, several forms of the genome coexist in a single infection: (i) the "traveler" forms found in serum, including rcDNA and dslDNA, which originate from retrotranscription of a messenger RNA (the pregenomic RNA, another form of the viral genome itself) and (ii) forms confined to the host cell nucleus, including covalently closed circular DNA (cccDNA), which leads to a minichromosome form associated with histones and viral proteins, and double-stranded DNA integrated into the host genome. This complex composition lends HBV a kind of "multiple personality". Are these additional particles and genomic forms simple intermediaries/artifacts or do they play a role in the viral life cycle?
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Affiliation(s)
- Andrea Caballero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, Clinical Laboratories, 08035 Barcelona, Spain.
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, Clinical Laboratories, 08035 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 3-5 Avenida Monforte de Lemos, pavilion 11, 28029 Madrid, Spain.
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 3-5 Avenida Monforte de Lemos, pavilion 11, 28029 Madrid, Spain; Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, General Hospital, Internal Medicine 2, 08035 Barcelona, Spain.
| | - Francisco Rodriguez-Frias
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, Clinical Laboratories, 08035 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 3-5 Avenida Monforte de Lemos, pavilion 11, 28029 Madrid, Spain.
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24
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Zhao RH, Shi Y, Zhao H, Wu W, Sheng JF. Acute-on-chronic liver failure in chronic hepatitis B: an update. Expert Rev Gastroenterol Hepatol 2018; 12:341-350. [PMID: 29334786 DOI: 10.1080/17474124.2018.1426459] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Acute-on-chronic liver failure is a common pattern of end-stage liver disease in clinical practice and occurs frequently in patients with chronic hepatitis B or HBV-related cirrhosis. New progress in recent years leads to a better understanding of this disease. Areas covered: This review updates the current comprehensive knowledge about HBV-ACLF from epidemiological studies, experimental studies, and clinical studies and provide new insights into the definition, diagnostic criteria, epidemiology, nature history, pathogenesis, treatment and prognostication of HBV-ACLF. Expert commentary: Patients with chronic hepatitis B or HBV-related cirrhosis are at risk of developing acute-on-chronic liver failure, with multi-organ failure and high short-term mortality. The precipitating events can be intra-hepatic or extra-hepatic and the underlying chronic liver injury can be cirrhotic or non-cirrhotic. Host and viral factors contribute to the susceptibility of developing HBV-ACLF. Systemic inflammation is the driver of HBV-ACLF, which can be attributed to non-sterile and sterile factors. Liver transplantation is the definitive treatment for HBV-ACLF. Cell therapy is a promising alternative to LT, but requires validation and still has concern of long-term safety. Other medical therapies, such as nucleoside analogue, artificial liver supporting and glucocorticoid may improve survival in a specific subgroup. New scoring systems improve the accuracy of prognostication in HBV-ACLF, which is critical for early identification of candidates for LT.
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Affiliation(s)
- Rui-Hong Zhao
- a Department of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine , Zhejiang University , Hangzhou , China
| | - Yu Shi
- a Department of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine , Zhejiang University , Hangzhou , China
| | - Hong Zhao
- a Department of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine , Zhejiang University , Hangzhou , China
| | - Wei Wu
- a Department of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine , Zhejiang University , Hangzhou , China
| | - Ji-Fang Sheng
- a Department of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine , Zhejiang University , Hangzhou , China
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25
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A comparative study on the characterization of hepatitis B virus quasispecies by clone-based sequencing and third-generation sequencing. Emerg Microbes Infect 2017; 6:e100. [PMID: 29116219 PMCID: PMC5717089 DOI: 10.1038/emi.2017.88] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/12/2017] [Accepted: 09/17/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) has a high mutation rate due to the extremely high replication rate and the proofreading deficiency during reverse transcription. The generated variants with genetic heterogeneity are described as viral quasispecies (QS). Clone-based sequencing (CBS) is thought to be the ‘gold standard’ for assessing QS complexity and diversity of HBV, but an important issue about CBS is cost-effectiveness and laborious. In this study, we investigated the utility of the third-generation sequencing (TGS) DNA sequencing to characterize genetic heterogeneity of HBV QS and assessed the possible contribution of TGS technology in HBV QS studies. Parallel experiments including 3 control samples, which consisted of HBV full gene genotype B and genotype C plasmids, and 10 patients samples were performed by using CBS and TGS to analyze HBV whole-genome QS. Characterization of QS heterogeneity was conducted by using comprehensive statistical analysis. The results showed that TGS had a high consistency with CBS when measuring the complexity and diversity of QS. In addition, to detect rare variants, there were strong advantages conferred by TGS. In summary, TGS was considered to be practicable in HBV QS studies and it might have a relevant role in the clinical management of HBV infection in the future.
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26
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Jia J, Liang X, Chen S, Wang H, Li H, Fang M, Bai X, Wang Z, Wang M, Zhu S, Sun F, Gao C. Next-generation sequencing revealed divergence in deletions of the preS region in the HBV genome between different HBV-related liver diseases. J Gen Virol 2017; 98:2748-2758. [PMID: 29022863 DOI: 10.1099/jgv.0.000942] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In order to investigate if deletion patterns of the preS region can predict liver disease advancement, the preS region of the hepatitis B virus (HBV) genome in 45 chronic hepatitis B (CHB) and 94 HBV-related hepatocellular carcinoma (HCC) patients was sequenced by next-generation sequencing (NGS) and the percentages of nucleotide deletion in the preS region were analysed. Hierarchical clustering and heatmaps based on deletion percentages of preS revealed different deletion patterns between CHB and HCC patients. Intergenotype comparison also indicated divergence in preS deletions between HBV genotype B and C. No significant difference was found in preS deletion patterns between sera and matched adjacent non-tumour tissues. Based on hierarchical clustering, HCC patients were classed into two groups with different preS deletion patterns and different clinical features. Finally, the support vector machine (SVM) model was trained on preS nucleotide deletion percentages and used to predict HCC versus CHB patients. The prediction performance was assessed with fivefold cross-validation and independent cohort validation. The median area under the curve (AUC) was 0.729 after repeating SVM 500 times with fivefold cross-validations. After parameter optimization, the SVM model was used to predict an independent cohort with 51 CHB patients and 72 HCC patients and the AUC was 0.727. In conclusion, the use of the NGS method revealed a prominent divergence in preS deletion patterns between disease groups and virus genotypes, but not between different tissue types. Quantitative NGS data combined with a machine learning method could be a powerful approach for prediction of the status of different diseases.
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Affiliation(s)
- Jian'an Jia
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China.,Department of Laboratory Medicine, The 105th Hospital of PLA, Hefei 230031, PR China
| | - Xiaotao Liang
- Shanghai Key Lab of Intelligent Information Processing and School of Computer Science, Fudan University, Shanghai, PR China.,Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, PR China
| | - Shipeng Chen
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
| | - Hui Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China.,Department of Clinical Laboratory, The First Affiliated Hospital of Chinese PLA's General Hospital, Beijing 100048, PR China
| | - Huiming Li
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
| | - Meng Fang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
| | - Xin Bai
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, PR China
| | - Ziyi Wang
- Shanghai Institute of Technology, Shanghai 201418, PR China
| | - Mengmeng Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
| | - Shanfeng Zhu
- Shanghai Key Lab of Intelligent Information Processing and School of Computer Science, Fudan University, Shanghai, PR China.,Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, PR China
| | - Fengzhu Sun
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, PR China.,Molecular and Computational Program Department of Biological Sciences, University of Southern California, LA 90089, USA
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China
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27
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Zhou TC, Li X, Li L, Li XF, Zhang L, Wei J. Evolution of full-length genomes of HBV quasispecies in sera of patients with a coexistence of HBsAg and anti-HBs antibodies. Sci Rep 2017; 7:661. [PMID: 28386078 PMCID: PMC5428874 DOI: 10.1038/s41598-017-00694-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/08/2017] [Indexed: 02/07/2023] Open
Abstract
Although the evolutionary changes of viral quasispecies are correlated to the pathological status of a disease, little is known in the coexistence of hepatitis B surface antigen (HBsAg) and antibodies to these antigens (anti-HBs). To examine evolutionary changes in hepatitis B virus (HBV) and their relationship to the coexistence of HBsAg and anti-HBs antibodies, HBV genomes in patients with a coexistence of HBsAg and anti-HBs antibodies (experimental group) and HBsAg positive without anti-HBs (control group) were assessed. Our results showed that quasispecies diversity was significantly higher in the experimental group for large HBsAg (LHBsAg), middle HBsAg (MHBsAg), and HBsAg genes. LHBsAg harbored dN/dS values eight times higher in the experimental group; however, the mean dN/dS ratios in genes HbxAg, Pol and PreC/C of the experimental patients had an opposite trend. Phylogenetic trees in the experimental group were more complex than the control group. More positive selection sites, mutations and deletions were observed in the experimental group in specific regions. Furthermore, several amino acid variants in epitopes were potentially associated with the immune evasion. In conclusion, cumulative evolutionary changes in HBV genome that facilitate immune evasion provide insights into the genetic mechanism of a coexistence of HBsAg and anti-HBs antibodies.
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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
| | - Xiao Li
- Central lab, Liver disease research center, the second people's hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Long Li
- Central lab, Liver disease research center, the second people's hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Xiao-Fei Li
- Clinical laboratory, the third people's hospital of Kunming City, 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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28
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Xue Y, Wang MJ, Huang SY, Yang ZT, Yu DM, Han Y, Zhu MY, Huang D, Zhang DH, Gong QM, Zhang XX. Characteristics of CpG Islands and their quasispecies of full-length hepatitis B virus genomes from patients at different phases of infection. SPRINGERPLUS 2016; 5:1630. [PMID: 27722049 PMCID: PMC5031574 DOI: 10.1186/s40064-016-3192-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/01/2016] [Indexed: 12/23/2022]
Abstract
BACKGROUND CpG islands in hepatitis B virus (HBV) genome are potential targets for methylation mediated gene silencing, and may be involved in the pathogenesis of HBV infection. To date, their characteristics in HBV quasispecies (QS) remain largely unknown. The purpose of this study was to investigate the characteristics of CpG islands in HBV QS. METHODS Forty patients diagnosed as acute hepatitis B (AHB, n = 10), immune-tolerant HBV carriers (IT, n = 9), chronic hepatitis B (CHB, n = 11), or acute on chronic liver failure (ACLF, n = 10), were enrolled in this case-control study. A total of 599 clones were isolated, and full-length HBV genomes were sequenced. RESULTS CpG island II (CGII) in AHB group was shorter in length and its QS heterogeneity was lower than that in the chronic infection group. Among the chronic infection subgroups, CGII and CpG island III (CGIII) in IT group were longer and their heterogeneity was lower compared to CHB and ACLF groups. Length of CGII correlated with HBV DNA levels positively while the complexity and diversity of CGII correlated with HBV DNA levels negatively. Moreover, CGII and CGIII were shorter in genotype B than those in genotype C, while QS complexity and diversity of either CGII or CGIII had no significant difference between genotype B and C. CONCLUSIONS Overall, our results suggest that the distribution, length and QS heterogeneity of CpG islands in full-length HBV genome differ across clinical phases of infection, of which the mechanism warrants further study.
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Affiliation(s)
- Yuan Xue
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Ming-Jie Wang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Su-Yuan Huang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Zhi-Tao Yang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - De-Min Yu
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Yue Han
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Ming-Yu Zhu
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Dao Huang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Dong-Hua Zhang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Qi-Ming Gong
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Xin-Xin Zhang
- Clinical Virology Research Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, No. 197, Ruijin Er Road, Shanghai, 200025 China.,Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiaotong University, School of Medicine, Shanghai, China.,Pôle Sino-Français de Recherches en Science du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
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29
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Single-Cell Genomics for Virology. Viruses 2016; 8:v8050123. [PMID: 27153082 PMCID: PMC4885078 DOI: 10.3390/v8050123] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/15/2016] [Accepted: 04/21/2016] [Indexed: 12/25/2022] Open
Abstract
Single-cell sequencing technologies, i.e., single cell analysis followed by deep sequencing investigate cellular heterogeneity in many biological settings. It was only in the past year that single-cell sequencing analyses has been applied in the field of virology, providing new ways to explore viral diversity and cell response to viral infection, which are summarized in the present review.
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