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Li CL, Hsu CL, Lin YY, Ho MC, Hu RH, Tzeng ST, Wang YC, Tanaka Y, Chen PJ, Yeh SH. HBV DNA integration and somatic mutations in HCC patients with HBV-HCV dual infection reveals profiles intermediate between HBV- and HCV-related HCC. J Biomed Sci 2025; 32:2. [PMID: 39743539 PMCID: PMC11694426 DOI: 10.1186/s12929-024-01094-7] [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: 06/06/2024] [Accepted: 11/09/2024] [Indexed: 01/04/2025] Open
Abstract
BACKGROUND In regions with a high prevalence of chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, coinfected patients face a heightened risk of developing hepatocellular carcinoma (HCC), termed HBV/HCV-related HCC (HBCV-HCC). We aimed to investigate the contribution of preexisting chronic hepatitis B (CHB) and subsequent chronic hepatitis C (CHC) to the development of HBCV-HCC. METHODS We examined HBV's involvement in 93 HBCV-HCC cases by analyzing HBV DNA integration as an indicator of HCC originating from HBV-infected hepatocytes, compared with 164 HBV-HCCs and 56 HCV-HCCs as controls. RESULTS Next generation sequencing revealed that 55% of HBCV-HCCs exhibited clonal HBV integration, which falls between the rates observed in HBV-HCCs (88%) and HCV-HCCs (7%), with similar integration patterns to HBV-HCCs. Common HCC somatic mutation analysis indicated HCV superinfection in HBCV-HCCs correlated with increased mutation rates in the telomerase reverse transcriptase (TERT) promoter and beta-catenin genes. Transcriptome analysis showed a prevalence of replicating HCV over HBV in HBCV-HCCs, with preexisting HBV exerting a proliferative role. The comparison of clinical characteristics revealed similarities between HBCV-HCC and HCV-HCC patients, including later onset for HBCV-HCC, possibly due to HCV superinfection slowing carcinogenesis. Notably, HBCV-HCCs with the same driver mutation, HBV integration at the TERT promoter, tended to develop later and showed a better prognosis post-tumor resection than HBV-HCCs. CONCLUSIONS Our findings shed light on the interplay between preexisting CHB and subsequent CHC in elevating the risk of HBCV-HCC. These insights are crucial for understanding viral etiology-specific carcinogenesis and guiding surveillance policies for HBCV-HCC post-antiviral therapy.
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Affiliation(s)
- Chiao-Ling Li
- Graduate Institute of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - You-Yu Lin
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Ming-Chih Ho
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
- Department of Surgery, National Taiwan University Hospital Hsinchu Branch, Hsinchu, Taiwan
| | - Rey-Heng Hu
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
- Department of Surgery, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | | | | | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Science, Nagoya, Japan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
- Center of Precision Medicine, National Taiwan University, Taipei, Taiwan.
| | - Shiou-Hwei Yeh
- Graduate Institute of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan.
- Center of Precision Medicine, National Taiwan University, Taipei, Taiwan.
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan.
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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] [MESH Headings] [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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Rzymski P, Zarębska-Michaluk D, Flisiak R. Could chronic HBV infection explain Beethoven's hearing loss? Implications for patients currently living with hepatitis B. J Infect 2023; 87:171-176. [PMID: 37302659 DOI: 10.1016/j.jinf.2023.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
The cause of Ludwig van Beethoven's health deterioration, i.e., hearing loss and cirrhosis, have been subject to various studies. The genomic analysis of his hair indicates infection with the hepatitis B virus (HBV) at least 6 months prior to death. However, considering his first documented case of jaundice in the summer of 1821, second jaundice months prior to his death, and increased risk of hearing loss in HBV-infected patients, we offer an alternative hypothesis of chronic HBV infection as a cause of deafness and cirrhosis. According to it, HBV was acquired early, progressed from immune-tolerant to an immune-reactive phase, and triggered Beethoven's hearing issues when aged 28. Later, HBV infection entered the non-replication phase with at least two episodes of reactivation in the fifth decade of life accompanied by jaundice. More studies examining hearing loss in patients with chronic HBV infection are encouraged to better understand their potential otologic needs.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland.
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases and Allergology, Jan Kochanowski University, 25-317 Kielce, Poland
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland
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Tung TT, Schmid J, Nghia VX, Cao LC, Linh LTK, Rungsung I, Sy BT, My TN, The NT, Hoan NX, Meyer CG, Wedemeyer H, Kremsner PG, Toan NL, Song LH, Bock CT, Velavan TP. Low Risk of Occult Hepatitis B Infection among Vietnamese Blood Donors. Pathogens 2022; 11:1524. [PMID: 36558858 PMCID: PMC9786887 DOI: 10.3390/pathogens11121524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Occult hepatitis B infection (OBI) is characterized by the presence of low levels of hepatitis B virus (HBV) DNA and undetectable HBsAg in the blood. The prevalence of OBI in blood donors in Asia ranges from 0.013% (China) to 10.9% (Laos), with no data available from Vietnam so far. We aimed to investigate the prevalence of OBI among Vietnamese blood donors. A total of 623 (114 women and 509 men) HBsAg-negative blood donors were screened for anti-HBc and anti-HBs by ELISA assays. In addition, DNA from sera was isolated and nested PCR was performed for the HBV surface gene (S); a fragment of the S gene was then sequenced in positive samples. The results revealed that 39% (n = 242) of blood donors were positive for anti-HBc, and 70% (n = 434) were positive for anti-HBs, with 36% (n = 223) being positive for both anti-HBc and anti-HBs. In addition, 3% of blood donors (n = 19) were positive for anti-HBc only, and 34% (n = 211) had only anti-HBs as serological marker. A total of 27% (n = 170) were seronegative for any marker. Two of the blood donors (0.3%) were OBI-positive and sequencing revealed that HBV sequences belonged to HBV genotype B, which is the predominant genotype in Vietnam.
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Affiliation(s)
- Tran Thanh Tung
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 10000, Vietnam
| | - Jürgen Schmid
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
| | | | - Le Chi Cao
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
- Department of Parasitology, Hue University of Medicine and Pharmacy (HUMP), Hue 52000, Vietnam
| | - Le Thi Kieu Linh
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 10000, Vietnam
| | - Ikrormi Rungsung
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
| | - Bui Tien Sy
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
- 108 Military Central Hospital, Hanoi 10000, Vietnam
| | - Truong Nhat My
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 10000, Vietnam
| | - Nguyen Trong The
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 10000, Vietnam
- 108 Military Central Hospital, Hanoi 10000, Vietnam
| | - Nghiem Xuan Hoan
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 10000, Vietnam
- 108 Military Central Hospital, Hanoi 10000, Vietnam
| | - Christian G. Meyer
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 10000, Vietnam
| | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30623 Hannover, Germany
- German Center for Infection Research, Partner Hannover-Braunschweig, 38104 Braunschweig, Germany
| | - Peter G. Kremsner
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
- Centre de Recherches Medicales de Lambarene, Lambaréné B.P. 242, Gabon
| | - Nguyen Linh Toan
- Department of Pathophysiology, Vietnam Military Medical University, Hanoi 10000, Vietnam
| | - Le Huu Song
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 10000, Vietnam
- 108 Military Central Hospital, Hanoi 10000, Vietnam
| | - C.-Thomas Bock
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
- Division of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Thirumalaisamy P. Velavan
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 10000, Vietnam
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Lundgren E, Romero-Severson E, Albert J, Leitner T. Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification. PLoS Comput Biol 2022; 18:e1009741. [PMID: 36026480 PMCID: PMC9455879 DOI: 10.1371/journal.pcbi.1009741] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 09/08/2022] [Accepted: 08/02/2022] [Indexed: 01/07/2023] Open
Abstract
To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. HIV biomarkers are measurable biological quantities that have some relationship to the amount of time someone has been infected with HIV. To train our model, we used five biomarkers based on real data from serological assays, HIV sequence data, and target cell counts in longitudinally followed, untreated patients with known infection times. The biomarkers were modeled with a mixed effects framework to allow for patient specific variation and general trends, and fit to patient data using Markov Chain Monte Carlo (MCMC) methods. Subsequently, the density of the unobserved infection time conditional on observed biomarkers were obtained by integrating out the random effects from the model fit. This probabilistic information about infection times was incorporated into the likelihood function for the transmission history and phylogenetic tree reconstruction, informed by the HIV sequence data. To critically test our methodology, we developed a coalescent-based simulation framework that generates phylogenies and biomarkers given a specific or general transmission history. Testing on many epidemiological scenarios showed that biomarker augmented phylogenetics can reach 90% accuracy under idealized situations. Under realistic within-host HIV-1 evolution, involving substantial within-host diversification and frequent transmission of multiple lineages, the average accuracy was at about 50% in transmission clusters involving 5-50 hosts. Realistic biomarker data added on average 16 percentage points over using the phylogeny alone. Using more biomarkers improved the performance. Shorter temporal spacing between transmission events and increased transmission heterogeneity reduced reconstruction accuracy, but larger clusters were not harder to get right. More sequence data per infected host also improved accuracy. We show that the method is robust to incomplete sampling and that adding biomarkers improves reconstructions of real HIV-1 transmission histories. The technology presented here could allow for better prevention programs by providing data for locally informed and tailored strategies.
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Affiliation(s)
- Erik Lundgren
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ethan Romero-Severson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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6
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Liver Histology of Treatment-Naïve Children with Chronic Hepatitis B Virus Infection in Shanghai China. Int J Infect Dis 2022; 123:112-118. [PMID: 36028208 DOI: 10.1016/j.ijid.2022.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND & AIMS Chronic hepatitis B (CHB) is associated with high morbidity and mortality. We aimed to investigate associations between hepatic histology and clinical characteristics in treatment-naïve children with CHB in Shanghai, China. METHODS The liver biopsy specimens of 278 treatment-naïve children with CHB virus infection were scored for inflammation and fibrosis, and correlations with clinical and laboratory data were determined. RESULTS CHB clinical, virologic and pathologic features were studied in 278 treatment-naïve children (177 males (63.7%)) from Shanghai, China. Maternal sera were hepatitis B surface antigen (HBsAg) positive for 277 children. At biopsy, 87.4% of patients were hepatitis B e antigen positive. The median age at biopsy was 5.1 years (interquartile range 2.8-8.4 years). Hepatitis B virus (HBV) DNA levels were generally high (mean 7.4 log10 IU/ml), as were levels of serum alanine aminotransferase (ALT, median 105 U/L). Using the Metavir histology activity index scoring system, no, mild, moderate and severe inflammation was seen in 2.9%, 22.3%, 73.4%, and 1.4% of patients, respectively. No fibrosis, mild fibrosis, moderate fibrosis, and cirrhosis was seen in 11.5%, 32.7%, 47.5%, and 8.3% of patients, respectively. When the serum ALT level was ≤80 (2× the upper limit of normal) and >80 U/L, the inflammation score (P<0.0001) was significantly different. And the fibrosis score was significantly different (P<0.0001), either. Inflammation and fibrosis were aggravated with increasing ALT levels. Fibrosis scores were significantly higher in children aged ≤3 than aged >3 years (P<0.0001). The rates of moderate fibrosis and cirrhosis were higher in children aged ≤3 years at biopsy. No correlations were found between histologic changes and sex, HBV genotype or HBV DNA level. CONCLUSION Substantial heterogeneity in inflammatory and fibrotic levels was observed in treatment-naïve children with CHB in Shanghai, China. Serum ALT levels >80 U/L may be a strong indicator of the degree of hepatic inflammation and fibrosis severity. Moderate fibrosis and cirrhosis can appear in children aged <3 years or younger.
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7
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Sirilert S, Tongsong T, Kumfu S, Chattipakorn SC, Chattipakorn N. Effects of intrauterine exposure to hepatitis B virus in foetuses. J Med Microbiol 2021; 70. [PMID: 34779762 DOI: 10.1099/jmm.0.001455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Foetal response to hepatitis B viral infection is still unknown. The mechanisms of persistent infection that occurs more often in mother-to-child transmission than adult transmission are also unclear. Various aspects of the environmental factors that accelerate or inhibit infection and the cytokine responses are associated with the persistence of infection. Several studies showed that the cytokine poor immune response in immaturity causes the persistence of the infection. However, some reports suggested that a mature immune response was the cause of this persistent infection. This review comprehensively summarized the reports from in vitro, in vivo as well as clinical reports regarding the responses of the foetuses of hepatitis B infected mothers to the micro-organism. The mechanism of more opportunities to be persistently infected via the mother-to-child transmission route is also summarized and discussed. Since there are limited clinical reports at this time, this review will provide evidence for future studies regarding the intrauterine infection mechanism and foetal response to hepatitis B virus to elucidate the mechanisms responsible for mother-to-child transmission. This understanding may lead to effective interventions to control mother-to-child hepatitis B infection in the future.
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Affiliation(s)
- Sirinart Sirilert
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Theera Tongsong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Sirinart Kumfu
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, Thailand
| | - Siriporn C Chattipakorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, Thailand
| | - Nipon Chattipakorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, Thailand
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8
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Ghosh S, Chakraborty A, Banerjee S. Persistence of Hepatitis B Virus Infection: A Multi-Faceted Player for Hepatocarcinogenesis. Front Microbiol 2021; 12:678537. [PMID: 34526974 PMCID: PMC8435854 DOI: 10.3389/fmicb.2021.678537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) infection has a multi-dimensional effect on the host, which not only alters the dynamics of immune response but also persists in the hepatocytes to predispose oncogenic factors. The virus exists in multiple forms of which the nuclear localized covalently closed circular DNA (cccDNA) is the most stable and the primary reason for viral persistence even after clearance of surface antigen and viral DNA. The second reason is the existence of pregenomic RNA (pgRNA) containing virion particles. On the other hand, the integration of the viral genome in the host chromosome also leads to persistent production of viral proteins along with the chromosomal instabilities. The interferon treatment or administration of nucleot(s)ide analogs leads to reduction in the viral DNA load, but the pgRNA and surface antigen clearance are a slow process and complete loss of serological HBsAg is rare. The prolonged exposure of immune cells to the viral antigens, particularly HBs antigen, in the blood circulation results in T-cell exhaustion, which disrupts immune clearance of the virus and virus-infected cells. In addition, it predisposes immune-tolerant microenvironment, which facilitates the tumor progression. Thus cccDNA, pgRNA, and HBsAg along with the viral DNA could be the therapeutic targets in the early disease stages that may improve the quality of life of chronic hepatitis B patients by impeding the progression of the disease toward hepatocellular carcinoma.
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Affiliation(s)
| | | | - Soma Banerjee
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
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Increased hepatitis B virus quasispecies diversity is correlated with liver fibrosis progression. INFECTION GENETICS AND EVOLUTION 2021; 93:104938. [PMID: 34029727 DOI: 10.1016/j.meegid.2021.104938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/08/2021] [Accepted: 05/12/2021] [Indexed: 12/30/2022]
Abstract
Host immune response and viral factors are involved in disease progression in patients with chronic hepatitis B virus (HBV) infection. However, the relationship between HBV quasispecies and liver fibrosis progression remains unclear. In this study, 447 patients with chronic HBV infection, including 239 with chronic hepatitis B (CHB), 104 with liver cirrhosis (LC) and 104 with hepatocellular carcinoma (HCC) were enrolled. The 239 CHB patients were divided into groups F1, F2, and F3 according to liver fibrosis score. Four fragments of the HBV genome were determined and analyzed using next-generation sequencing. Specific mutations, such as A1762T, G1764A and G1896A, in the BCP/PC region were more common in patients with advanced liver disease and formed the majority of the viral quasispecies pool in patients with LC and HCC. The viral complexity and diversity increased as the fibrosis progressed, especially in patients with CHB who were comparable in age but at different stages of fibrosis. Patients with early-stage fibrosis experienced higher purifying selection pressure in the four sequenced regions, whereas different protein-coding region experienced different negative selection with disease progression. HBV quasispecies diversity may increase fibrosis progression in CHB patients with aging under immune selection.
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10
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Cheng HR, Yang HC, Lin SR, Yang TY, Lin YY, Su TH, Tseng TC, Liu CJ, Kao JH. Combined viral quasispecies diversity and hepatitis B core-related antigen predict off-nucleos(t)ide analog durability in HBeAg-negative patients. Hepatol Int 2021; 15:582-592. [PMID: 33886088 DOI: 10.1007/s12072-021-10186-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/31/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Viral quasispecies dynamics between pre- and post-nucleos(t)ide analog (NA) therapy remains unclear. AIM This study aimed to investigate the HBV quasispecies evolution and its relationship with durability of off-therapy responses in HBeAg-negative chronic hepatitis B (CHB) patients who stopped NA therapy. METHODS Fifty-four HBeAg-negative CHB patients who stopped NAs, including 19 virological controllers (VC) who maintained serum HBV DNA < 2000 IU/mL beyond 1-year off-therapy, and 35 virological relapsers (VR) experiencing virological relapse within 1-year off-therapy were recruited. Viral quasispecies was analyzed by deep sequencing. Hepatitis B core-related antigen (HBcrAg) and HBsAg were also measured. RESULTS VC had significantly higher baseline viral quasispecies diversity of the precore/core gene, measured by nucleotide diversity, than VR. Low baseline viral nucleotide diversity (< 0.01) and high HBcrAg (≧ 2.0 KU/mL), but not HBsAg, at end of treatment (EOT) were significantly associated with higher risk of 1-year virological relapse (hazard ratio [HR] 6.09 and 3.31, respectively). Combination of low baseline viral nucleotide diversity and high HBcrAg at EOT could identify patients at high risk (HR 15.82). Further analysis of the evolution of HBV whole genome showed that HBV nucleotide diversity negatively correlated with serum HBV DNA levels. Notably, the viral quasispecies diversity between pre- and post-NA treatment remained relatively unchanged. CONCLUSION Higher baseline HBV quasispecies diversity associates with more durable off-therapy viral suppression in HBeAg-negative CHB patients. Combination of baseline viral nucleotide diversity and HBcrAg at EOT can identify patients at high risk for virological relapse after stopping NAs.
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Affiliation(s)
- Huei-Ru Cheng
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan
| | - Hung-Chih Yang
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Su-Ru Lin
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan
| | - Ta-Yu Yang
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - You-Yu Lin
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan
| | - Tung-Hung Su
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Tai-Chung Tseng
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Jen Liu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Jia-Horng Kao
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan.
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11
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Jeon MY, Kim BK, Lee JS, Lee HW, Park JY, Kim DY, Ahn SH, Han KH, Kim SU. Negligible risks of hepatocellular carcinoma during biomarker-defined immune-tolerant phase for patients with chronic hepatitis B. Clin Mol Hepatol 2021; 27:295-304. [PMID: 33317247 PMCID: PMC8046628 DOI: 10.3350/cmh.2020.0216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND/AIMS The immune-tolerant (IT) phase of chronic hepatitis B (CHB) patients is not generally indicative of antiviral therapy (AVT). We assessed and compared the risk of hepatocellular carcinoma (HCC) during the IT-phase stringently defined by a low fibrosis-4 (FIB-4) index, compared to that in patients undergoing AVT. METHODS Among 125 untreated patients that were hepatitis B e-antigen positive, hepatitis B virus-DNA >20,000 IU/mL, with normal alanine aminotransferase level from 2012 to 2018, those with a FIB-4 index of <1.45 were classified into the IT-group. The cumulative probability of HCC was estimated using Kaplan-Meier analysis. All patients were assessed until HCC development (intention-to-treat [ITT] analysis), whereas those suspected of experiencing CHB phase switch were assessed using the per-protocol (PP) and censored at the time of phase switch. RESULTS The cumulative probability of HCC at 1-, 3-, and 5-years among the IT-group was zero, compared to AVT-treated patients with FIB-4 indices <1.45 during the same period: 0.2%, 0.6%, and 1.4%, respectively (P=0.264 for ITT and P=0.533 for PP). Among the initially screened 125 untreated patients, those with a FIB-4 index of ≥1.45 had a higher risk of HCC compared to the IT-group (P=0.005). Furthermore, among AVT-treated patients, those with a FIB-4 index of ≥1.45 had a higher risk of HCC compared to their counterpart (P<0.001). CONCLUSION The risk of HCC was negligible in the IT-group stringently defined by a low FIB-4 index. However, given that a higher HCC risk exists among untreated patients with higher FIB-4, appropriate criteria for AVT should be established.
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Affiliation(s)
- Mi Young Jeon
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Yonsei Liver Center, Severance Hospital, Seoul, Korea
| | - Beom Kyung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Yonsei Liver Center, Severance Hospital, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Seung Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Yonsei Liver Center, Severance Hospital, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Hye Won Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Yonsei Liver Center, Severance Hospital, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Jun Yong Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Yonsei Liver Center, Severance Hospital, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Do Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Yonsei Liver Center, Severance Hospital, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Hoon Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Yonsei Liver Center, Severance Hospital, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Kwang-Hyub Han
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Yonsei Liver Center, Severance Hospital, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Up Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Yonsei Liver Center, Severance Hospital, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
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12
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Lin SR, Yang TY, Peng CY, Lin YY, Dai CY, Wang HY, Su TH, Tseng TC, Liu IJ, Cheng HR, Shen YC, Wu FY, Liu CJ, Chen DS, Chen PJ, Yang HC, Kao JH. Whole genome deep sequencing analysis of viral quasispecies diversity and evolution in HBeAg seroconverters. JHEP Rep 2021; 3:100254. [PMID: 33870157 PMCID: PMC8042178 DOI: 10.1016/j.jhepr.2021.100254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/21/2022] Open
Abstract
Background & Aims We aimed to investigate how viral quasispecies of the HBV whole genome evolves and diversifies in response to HBeAg seroconversion and viral control utilising next-generation sequencing (NGS). Methods Fifty HBeAg-positive chronic hepatitis B patients, including 18 treatment-naïve and 32 interferon (IFN)-treated individuals, were recruited. Serial HBV whole genomes in serum were analysed by NGS to determine sequence characteristics and viral quasispecies. Results HBV quasispecies diversity, measured by nucleotide diversity, was negatively correlated with viral load and hepatitis activity. Spontaneous HBeAg seroconverters exhibited significantly greater viral quasispecies diversity than treatment-naïve non-seroconverters from >1 year before seroconversion (0.0112 vs. 0.0060, p <0.01) to >1 year after seroconversion (0.0103 vs. 0.0068, p <0.01). IFN-induced HBeAg seroconverters tended to have higher viral genetic diversity than non-seroconverters along with treatment. Particularly, the IFN responders, defined as IFN-induced HBeAg seroconversion with low viraemia, exhibited significantly greater genetic diversity of whole HBV genome at 6 months post-IFN treatment than IFN non-responders (0.0148 vs. 0.0106, p = 0.048). Moreover, spontaneous HBeAg seroconverters and IFN responders exhibited significantly higher evolutionary rates and more intra-host single-nucleotide variants. Interestingly, in spontaneous HBeAg seroconverters and IFN responders, there were distinct evolutionary patterns in the HBV genome. Conclusions Higher HBV quasispecies diversity is associated with spontaneous HBeAg seroconversion and IFN-induced HBeAg seroconversion with low viraemia, conferring a favourable clinical outcome. Lay summary HBeAg seroconversion is a landmark in the natural history of chronic HBV infection. Using next-generation sequencing, we found that the nucleotide diversity of HBV was negatively correlated with viral load and hepatitis activity. Patients undergoing HBeAg seroconversion had more diverse HBV genomes and a faster viral evolution rate. Our findings suggest HBeAg seroconversion is driven by host selection pressure, likely immune selection pressure.
Deep sequencing of whole HBV genome uncovers the quasispecies changes in chronic hepatitis B patients. The nucleotide diversity of HBV negatively correlates with viraemia during HBeAg loss/seroconversion. Viral quasispecies diversity is greater in spontaneous HBeAg seroconverters before and after seroconversion than in treatment-naïve non-seroconverters. Responders to IFN have greater viral quasispecies diversity than non-responders at 24 weeks after treatment. The genome positions of non-synonymous intra-host single nucleotide variants (iSNVs) of HBV tend to be located at possible T cell epitopes.
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Key Words
- ALT, alanine aminotransferase
- AUC, area under curve
- BCP, basal core promoter
- C, core
- CHB, chronic hepatitis B
- Chronic hepatitis B
- EOT, end of treatment
- HBeAg seroconversion
- IFN, interferon
- IFN-NR, IFN-non-responders
- IFN-No-eSC, IFN-treated HBeAg non-seroconverters
- IFN-RS, IFN-responders
- IFN-eSC, IFN-treated HBeAg seroconverters
- Intra-host single nucleotide variants
- NGS, next-generation sequencing
- ORFs, open reading frames
- P, polymerase
- S, surface
- TN-No-eSC, treatment-naïve non-seroconverters
- TN-eSC, treatment-naïve HBeAg seroconverters
- dN, nonsynonymous substitution rate
- dS, synonymous substitution rate
- iSNVs, intra-host single-nucleotide variants
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Affiliation(s)
- Su-Ru Lin
- Department of Microbiology, National Taiwan University, Taipei, Taiwan
| | - Ta-Yu Yang
- Department of Microbiology, National Taiwan University, Taipei, Taiwan
| | - Cheng-Yuan Peng
- School of Medicine, China Medical University, Taichung, Taiwan.,Department of Internal Medicine, Center for Digestive Medicine, China Medical University Hospital, Taichung, Taiwan
| | - You-Yu Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Yen Dai
- Department of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Hepato-Biliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tung-Hung Su
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tai-Chung Tseng
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - I-Jung Liu
- Cardinal Tien Junior College of Healthcare and Management, New Taipei City, Taiwan
| | - Huei-Ru Cheng
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yueh-Chi Shen
- Department of Microbiology, National Taiwan University, Taipei, Taiwan
| | - Fang-Yi Wu
- Department of Microbiology, National Taiwan University, Taipei, Taiwan
| | - Chun-Jen Liu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Ding-Shinn Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Chih Yang
- Department of Microbiology, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jia-Horng Kao
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
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13
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Zhou TC, Liu FW, Fan JH, Zhang SH, Lv SQ, Yu ZY, Zhang YM, Zhang L, Wei J. The association of the heterogeneity of HBV reverse transcriptase quasispecies with antiviral efficacy after treatment with nucleos(t)ide analogues for 10 years. INFECTION GENETICS AND EVOLUTION 2021; 89:104706. [PMID: 33418145 DOI: 10.1016/j.meegid.2021.104706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022]
Abstract
To assess the heterogeneity of HBV reverse transcriptase (RT) quasispecies during 10 years of antiviral therapy and their association with antiviral efficacy. Nineteen patients with chronic hepatitis B (CHB) infection receiving nucleos(t)ide analogues (NAs) were enrolled. Based on the antiviral efficacy after 1 year of treatment, 5 patients were grouped into an early virologic response (EVR) group, while 8 patients were grouped into a late virologic response (LVR) group. Furthermore, 6 CHB patients that had undergone antiviral treatment for 10 years were grouped into a virologic breakthrough (VBT) group. The HBV RT from each patient were amplified, cloned, and sequenced. The complexity of the RT gene in the EVR group was significantly higher than that in the LVR (P = 0.0393) and VBT groups (P = 0.0141). Phylogenetic tree analysis showed that the average branch length of the EVR and LVR groups were significantly greater than that of VBT group (P < 0.001). The complexity (at the nucleotide level) of the RT quasispecies was negatively correlated with the corresponding HBV DNA load (P = 0.0163) at one year post-antiviral treatment. Moreover, both the LVR and VBT groups accumulated more deleterious mutations than the EVR group. After 1 year of NAs treatment, the increased HBV quasispecies complexity and evolutionary topologies, coupled with less deleterious mutations, are likely associated with a favorable efficacy during long-term antiviral treatment.
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Affiliation(s)
- Tai-Cheng Zhou
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Feng-Wei Liu
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Jing-Hua Fan
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China; The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Si-Hang Zhang
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Song-Qin Lv
- Clinical Lab, The Third People's Hospital of Kunming City, Kunming, Yunnan Province, China
| | - Zhi-Yong Yu
- Hepatopancreatobiliary Surgery Department, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Yan-Mei Zhang
- The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Liang Zhang
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China.
| | - Jia Wei
- Central Lab, Liver Disease Research Center, The Second People's Hospital of Yunnan Province, Kunming, Yunnan Province, China.
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14
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Chaw SM, Tai JH, Chen SL, Hsieh CH, Chang SY, Yeh SH, Yang WS, Chen PJ, Wang HY. The origin and underlying driving forces of the SARS-CoV-2 outbreak. J Biomed Sci 2020; 27:73. [PMID: 32507105 PMCID: PMC7276232 DOI: 10.1186/s12929-020-00665-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/28/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND SARS-CoV-2 began spreading in December 2019 and has since become a pandemic that has impacted many aspects of human society. Several issues concerning the origin, time of introduction to humans, evolutionary patterns, and underlying force driving the SARS-CoV-2 outbreak remain unclear. METHOD Genetic variation in 137 SARS-CoV-2 genomes and related coronaviruses as of 2/23/2020 was analyzed. RESULT After correcting for mutational bias, the excess of low frequency mutations on both synonymous and nonsynonymous sites was revealed which is consistent with the recent outbreak of the virus. In contrast to adaptive evolution previously reported for SARS-CoV during its brief epidemic in 2003, our analysis of SARS-CoV-2 genomes shows signs of relaxation. The sequence similarity in the spike receptor binding domain between SARS-CoV-2 and a sequence from pangolin is probably due to an ancient intergenomic introgression that occurred approximately 40 years ago. The current outbreak of SARS-CoV-2 was estimated to have originated on 12/11/2019 (95% HPD 11/13/2019-12/23/2019). The effective population size of the virus showed an approximately 20-fold increase from the onset of the outbreak to the lockdown of Wuhan (1/23/2020) and ceased to increase afterwards, demonstrating the effectiveness of social distancing in preventing its spread. Two mutations, 84S in orf8 protein and 251 V in orf3 protein, occurred coincidentally with human intervention. The former first appeared on 1/5/2020 and plateaued around 1/23/2020. The latter rapidly increased in frequency after 1/23/2020. Thus, the roles of these mutations on infectivity need to be elucidated. Genetic diversity of SARS-CoV-2 collected from China is two times higher than those derived from the rest of the world. A network analysis found that haplotypes collected from Wuhan were interior and had more mutational connections, both of which are consistent with the observation that the SARS-CoV-2 outbreak originated in China. CONCLUSION SARS-CoV-2 might have cryptically circulated within humans for years before being discovered. Data from the early outbreak and hospital archives are needed to trace its evolutionary path and determine the critical steps required for effective spreading.
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Affiliation(s)
- Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jui-Hung Tai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shi-Lun Chen
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Hung Hsieh
- Department of Forestry and Nature Conservation, Chinese Culture University, Taipei, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shiou-Hwei Yeh
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wei-Shiung Yang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.
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15
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Li Y, Shen C, Yang L, Yang Y, Wang M, Li S, Chen F, Yang M, Peng L, Ma J, Duan Z, Li L, Liu Y. Intra-host diversity of hepatitis B virus during mother-to-child transmission: the X gene may play a key role in virus survival in children after transmission. Arch Virol 2020; 165:1279-1288. [PMID: 32240369 DOI: 10.1007/s00705-020-04597-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/21/2020] [Indexed: 12/23/2022]
Abstract
Mother-to-child transmission of hepatitis B virus (HBV) is the main route of transmission in Asia, and characterization of HBV quasispecies is needed to further understand virus evolution and adaptation. To understand changes in HBV during mother-to-child transmission, we enrolled nine pairs of mothers and children in the study, including a set of twins. Three groups were infected with HBV genotype C, and six groups were infected with HBV genotype B. The full-length HBV genome was amplified by PCR from serum samples before antiviral treatment, the whole viral genomes from each pair were sequenced, and the complexity and diversity of the quasispecies were analyzed. The entropy of transmitted HBV in children was found to be lower than their mothers, suggesting that there was a bottleneck effect during HBV transmission from the mother to the child. Selective evolution was shown by calculating πN and πS in the whole genomes, and the highest values were obtained for the X gene, which plays a role in viral replication and immune escape. All genotype C patients and only one genotype B pair had a πN/πS greater than 1 ratio, indicating that positive selection had occurred. In addition, quasispecies were found to be different between the twin children despite having the same mother, indicating that virus evolution is host-specific.
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Affiliation(s)
- Yanjie Li
- Department of Infectious Diseases, Shenzhen Third People's Hospital, University of South China, Shenzhen, 518112, China
| | - Chenguang Shen
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Liuqing Yang
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Yang Yang
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Miao Wang
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Shanqin Li
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Feng Chen
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Min Yang
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Ling Peng
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Jinmin Ma
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhongping Duan
- Difficult and complicated liver diseases and artificial liver center, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
| | - Liqiang Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Yingxia Liu
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China.
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16
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Luo Y, Zhang L, Dai Y, Hu Y, Xu B, Zhou YH. Conservative Evolution of Hepatitis B Virus Precore and Core Gene During Immune Tolerant Phase in Intrafamilial Transmission. Virol Sin 2020; 35:388-397. [PMID: 32124248 DOI: 10.1007/s12250-020-00194-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/06/2019] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) is characterized with high mutations, which is attributed to the lack of proof-reading of the viral reverse transcriptase and host immune pressure. In this study, 31 HBV chronic carriers from 14 families were enrolled to investigate the evolution of the same original HBV sources in different hosts. Sequences of pre-C and C (pre-C/C) genes were analyzed in eight pairs of HBV-infected mothers with longitudinal sera (at an interval of 6.0-7.2 years) and their children (5.5-6.7 years old), and in 15 adults (21-78 years old) from six families with known intrafamilial HBV infection. The pre-C/C sequences had almost no change in eight mothers during 6.0-7.2 years and their children who were in immune tolerant phase. The pre-C/C sequences from the 15 adults of six families, mostly in the immune-clearance phase or the low replicative phase, showed various diversified mutations between individuals from each family. Compared to a reference stain (GQ205441) isolated nearby, the pre-C/C in individuals in immune tolerant phase showed 98.56%-99.52% homology at nucleotide level and 99.5%-100% homology at amino acid level. In contrast, multiple mutations were developed in the immune-clearance phase or the low replicative phase, affecting immune epitopes in core gene and G1896 in pre-C gene. The results indicate that the evolution of new HBV variants is not mainly resulted from the spontaneous error rate of viral reverse transcription, but from the host immune pressure.
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Affiliation(s)
- Yuqian Luo
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital and Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, 210008, China
| | - Le Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital and Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, 210008, China
| | - Yimin Dai
- Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China
| | - Yali Hu
- Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China
| | - Biyun Xu
- Department of Biostatistics, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China
| | - Yi-Hua Zhou
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital and Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, 210008, China. .,Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing Medical University, Nanjing, 210008, China.
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17
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McNaughton AL, Revill PA, Littlejohn M, Matthews PC, Ansari MA. Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences. J Gen Virol 2020; 101:271-283. [PMID: 32134374 PMCID: PMC7416611 DOI: 10.1099/jgv.0.001387] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), characterized thus far. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level. All of the generated data, including the alignments, phylogenies and chosen reference sequences, are available online (https://doi.org/10.6084/m9.figshare.8851946) as a simple open-access resource.
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Affiliation(s)
- Anna L. McNaughton
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Peter A. Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Philippa C. Matthews
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - M. Azim Ansari
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
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18
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Domingo E. Long-term virus evolution in nature. VIRUS AS POPULATIONS 2020. [PMCID: PMC7153321 DOI: 10.1016/b978-0-12-816331-3.00007-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Viruses spread to give rise to epidemics and pandemics, and some key parameters that include virus and host population numbers determine virus persistence or extinction in nature. Viruses evolve at different rates depending on the polymerase copying fidelity during genome replication and a number of environmental influences. Calculated rates of evolution in nature vary depending on the time interval between virus isolations. In particular, intrahost evolution is generally more rapid that interhost evolution, and several possible mechanisms for this difference are considered. The mechanisms by which the error-prone viruses evolve are very unlikely to render the operation of a molecular clock (constant rate of incorporation of mutations in the evolving genomes), although a clock is assumed in many calculations. Several computational tools permit the alignment of viral sequences and the establishment of phylogenetic relationships among viruses. The evolution of the virus in the form of dynamic mutant clouds in each infected individual, together with multiple environmental parameters renders the emergence and reemergence of viral pathogens an unpredictable event, another facet of biological complexity.
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Immunopathogenesis of HBV Infection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1179:71-107. [DOI: 10.1007/978-981-13-9151-4_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Highly diversified shrew hepatitis B viruses corroborate ancient origins and divergent infection patterns of mammalian hepadnaviruses. Proc Natl Acad Sci U S A 2019; 116:17007-17012. [PMID: 31371507 DOI: 10.1073/pnas.1908072116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Shrews, insectivorous small mammals, pertain to an ancient mammalian order. We screened 693 European and African shrews for hepatitis B virus (HBV) homologs to elucidate the enigmatic genealogy of HBV. Shrews host HBVs at low prevalence (2.5%) across a broad geographic and host range. The phylogenetically divergent shrew HBVs comprise separate species termed crowned shrew HBV (CSHBV) and musk shrew HBV (MSHBV), each containing distinct genotypes. Recombination events across host orders, evolutionary reconstructions, and antigenic divergence of shrew HBVs corroborated ancient origins of mammalian HBVs dating back about 80 million years. Resurrected CSHBV replicated in human hepatoma cells, but human- and tupaia-derived primary hepatocytes were resistant to hepatitis D viruses pseudotyped with CSHBV surface proteins. Functional characterization of the shrew sodium taurocholate cotransporting polypeptide (Ntcp), CSHBV/MSHBV surface peptide binding patterns, and infection experiments revealed lack of Ntcp-mediated entry of shrew HBV. Contrastingly, HBV entry was enabled by the shrew Ntcp. Shrew HBVs universally showed mutations in their genomic preCore domains impeding hepatitis B e antigen (HBeAg) production and resembling those observed in HBeAg-negative human HBV. Deep sequencing and in situ hybridization suggest that HBeAg-negative shrew HBVs cause intense hepatotropic monoinfections and low within-host genomic heterogeneity. Geographical clustering and low MSHBV/CSHBV-specific seroprevalence suggest focal transmission and high virulence of shrew HBVs. HBeAg negativity is thus an ancient HBV infection pattern, whereas Ntcp usage for entry is not evolutionarily conserved. Shrew infection models relying on CSHBV/MSHBV revertants and human HBV will allow comparative assessments of HBeAg-mediated HBV pathogenesis, entry, and species barriers.
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Feld JJ, Terrault NA, Lin HHS, Belle SH, Chung RT, Tsai N, Khalili M, Perrillo R, Cooper SL, Ghany MG, Janssen HL, Lok AS. Entecavir and Peginterferon Alfa-2a in Adults With Hepatitis B e Antigen-Positive Immune-Tolerant Chronic Hepatitis B Virus Infection. Hepatology 2019; 69:2338-2348. [PMID: 30549279 PMCID: PMC6541521 DOI: 10.1002/hep.30417] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/06/2018] [Indexed: 12/23/2022]
Abstract
Monotherapy with interferon or nucleoside analog is generally not recommended during the immune-tolerant (IT) phase of chronic hepatitis B virus (HBV) infection. Recognition that high HBV DNA levels are associated with hepatocellular carcinoma has increased interest in treating HBV in the IT phase. Small pediatric studies reported efficacy with combination nucleoside analog and interferon therapy. The aim of this study was to evaluate the safety and efficacy of the combination of entecavir and peginterferon in adults in the IT phase of chronic HBV infection. Hepatitis B e antigen (HBeAg)-positive adults with HBV DNA > 107 IU/mL and alanine aminotransferase (ALT) ≤ 1.5 times the upper limit of normal (ULN) (male: ≤ 45, female: ≤ 30 U/L) received entecavir 0.5 mg daily for 8 weeks followed by the addition of peginterferon alfa-2a 180 µg/week to entecavir for an additional 40 weeks. The primary endpoint was HBeAg loss and HBV DNA ≤ 1,000 IU/mL 48 weeks after end of treatment (EOT). Among 28 participants from 11 sites, the median age was 37.2 (range: 22-61) years, 54% were male, and 96% were Asian. Nearly all were infected with genotype C (64%) or B (32%). Median baseline HBV DNA was 8.2 log10 IU/mL, and ALT was 0.9 times the ULN. Although one (4%) participant cleared HBeAg, none met the primary endpoint of both HBeAg loss AND HBV DNA ≤ 1,000 IU/mL 48 weeks post-EOT. ALT elevations > 5 times the ULN occurred in eight (29%) participants, and none were associated with icterus. Forty-eight weeks posttreatment, HBV DNA rebounded to baseline levels in all participants, including the participant who lost HBeAg, and ALT values returned to near baseline levels in all but four participants. Conclusion: A lead-in strategy of 8 weeks of entecavir followed by combination peginterferon and entecavir therapy for 40 weeks had limited efficacy in adults in the IT phase of chronic HBV infection and cannot be recommended.
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Affiliation(s)
| | | | - Hsing-Hua S. Lin
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Steven H. Belle
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | | | | | | | | | - Stewart L. Cooper
- San Francisco Center for Liver Disease, California Pacific Medical Centre, San Francisco CA
| | - Marc G. Ghany
- Liver Diseases Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
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22
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Gauder C, Mojsiejczuk LN, Tadey L, Mammana L, Bouzas MB, Campos RH, Flichman DM. Role of viral load in Hepatitis B virus evolution in persistently normal ALT chronically infected patients. INFECTION GENETICS AND EVOLUTION 2018; 67:17-22. [PMID: 30393187 DOI: 10.1016/j.meegid.2018.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/10/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023]
Abstract
Chronic HBV infection has been associated with severe liver disease although most of them do not progress to this stage. Even though low replicative carriers form the largest group of HBV chronically infected patients, there is a paucity of longitudinal studies to evaluate the molecular evolution of the whole genome in this subset of patients. In this study, longitudinal samples from 10 patients with persistently normal ALT levels were collected. HBV full-length genome sequences were obtained from 3 samples per patient (baseline, 5 and 10-years of follow-up). Patients were grouped according to HBV-DNA level into <103 IU/ml (group A) or > 103 IU/ml (group B). The substitution rate was inversely related with HBV-DNA levels. Moreover, the rate in the 10-year follow-up was significantly higher in group A (6.9 × 10-4 ± 1.3 × 10-4) than group B (2.7 × 10-4 ± 7.4 × 10-5 substitution/site/year, p < .001). Most of the substitutions were in the Core region and the majority were non-synonymous changes. The rate of nucleotide substitution was inversely related to HBV-DNA levels, highlighting the role of viral load in the HBV intra-host dynamics, even in low replicative state patients. Moreover, the difference in the substitution rate between the analysed groups was mainly consequence of substitutions restricted to the Core region, particularly in the simple coding region and antigenic epitopes, which suggest that the immune pressure drives the different evolutionary behaviour of groups.
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Affiliation(s)
- C Gauder
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina
| | - L N Mojsiejczuk
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - L Tadey
- Unidad de Virología Hospital F.J. Muñiz, Uspallata 2272, Ciudad Autónoma de Buenos Aires, Argentina
| | - L Mammana
- Unidad de Virología Hospital F.J. Muñiz, Uspallata 2272, Ciudad Autónoma de Buenos Aires, Argentina
| | - M B Bouzas
- Unidad de Virología Hospital F.J. Muñiz, Uspallata 2272, Ciudad Autónoma de Buenos Aires, Argentina
| | - R H Campos
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - D M Flichman
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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Lumley SF, McNaughton AL, Klenerman P, Lythgoe KA, Matthews PC. Hepatitis B Virus Adaptation to the CD8+ T Cell Response: Consequences for Host and Pathogen. Front Immunol 2018; 9:1561. [PMID: 30061882 PMCID: PMC6054973 DOI: 10.3389/fimmu.2018.01561] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022] Open
Abstract
Chronic viral hepatitis infections are a major public health concern, with an estimated 290 million individuals infected with hepatitis B virus (HBV) globally. This virus has been a passenger in human populations for >30,000 years, and remains highly prevalent in some settings. In order for this endemic pathogen to persist, viral adaptation to host immune responses is pre-requisite. Here, we focus on the interplay between HBV infection and the CD8+ T cell response. We present the evidence that CD8+ T cells play an important role in control of chronic HBV infection and that the selective pressure imposed on HBV through evasion of these immune responses can potentially influence viral diversity, chronicity, and the outcome of infection, and highlight where there are gaps in current knowledge. Understanding the nature and mechanisms of HBV evolution and persistence could shed light on differential disease outcomes, including cirrhosis and hepatocellular carcinoma, and help reach the goal of global HBV elimination by guiding the design of new strategies, including vaccines and therapeutics.
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Affiliation(s)
- Sheila F. Lumley
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Anna L. McNaughton
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford BRC, John Radcliffe Hospital, Oxford, United Kingdom
| | - Katrina A. Lythgoe
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Philippa C. Matthews
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford BRC, John Radcliffe Hospital, Oxford, United Kingdom
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24
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Kim GA, Lim YS, Han S, Choi J, Shim JH, Kim KM, Lee HC, Lee YS. High risk of hepatocellular carcinoma and death in patients with immune-tolerant-phase chronic hepatitis B. Gut 2018; 67:945-952. [PMID: 29055908 DOI: 10.1136/gutjnl-2017-314904] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/05/2017] [Accepted: 09/26/2017] [Indexed: 02/06/2023]
Abstract
OBJECTIVE High serum HBV DNA levels are associated with high risks of hepatocellular carcinoma (HCC) and cirrhosis in patients with chronic hepatitis B (CHB). Although the immune-tolerant (IT) phase is characterised by high circulating HBV DNA levels, it remains unknown whether antiviral treatment reduces risks of HCC and mortality. DESIGN This historical cohort study included HBeAg-positive patients with CHB with high HBV DNA levels (≥20 000 IU/mL) and no evidence of cirrhosis at a tertiary referral hospital in Korea from 2000 to 2013. The clinical outcomes of 413 untreated IT-phase patients with normal alanine aminotransferase (ALT) levels (females, <19 IU/mL; males, <30 IU/mL) were compared with those of 1497 immune-active (IA)-phase patients (ALT ≥80 IU/mL) treated with nucleos(t)ide analogues. RESULTS The IT group was significantly younger than the IA group (mean age, 38 vs 40 years at baseline, p=0.04). The 10-year estimated cumulative incidences of HCC (12.7% vs 6.1%; p=0.001) and death/transplantation (9.7% vs 3.4%; p<0.001) were significantly higher in the IT group than the IA group. In multivariable analyses, the IT group showed a significantly higher risk of HCC (HR 2.54; 95% CI 1.54 to 4.18) and death/transplantation (HR 3.38; 95% CI 1.85 to 6.16) than the IA group, which was consistently identified through inverse probability treatment weighting, propensity score-matched and competing risks analyses. CONCLUSIONS Untreated IT-phase patients with CHB had higher risks of HCC and death/transplantation than treated IA-phase patients. Unnecessary deaths could be prevented through earlier antiviral intervention in select IT-phase patients.
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Affiliation(s)
- Gi-Ae Kim
- Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Young-Suk Lim
- Department of Gastroenterology, Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seungbong Han
- Department of Applied Statistics, Gachon University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jonggi Choi
- Department of Gastroenterology, Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ju Hyun Shim
- Department of Gastroenterology, Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kang Mo Kim
- Department of Gastroenterology, Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Han Chu Lee
- Department of Gastroenterology, Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yung Sang Lee
- Department of Gastroenterology, Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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25
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Dusheiko G. Current and future directions of management of hepatitis B: steps toward a cure. Future Virol 2018. [DOI: 10.2217/fvl-2017-0103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Universal hepatitis B virus vaccination has been effective in reducing incident chronic hepatitis B but will not have the requisite effect on the prevalence of end-stage liver disease in chronically infected persons. The natural history and immunological stages of hepatitis B virus infection are still being defined. Over three decades, current therapies have reduced morbidity from chronic hepatitis B. The majority require nucleoside analog maintenance therapy. The preferential preservation of covalently closed circular DNA (cccDNA), and capsid reverse transcriptase–cccDNA interactions currently precludes cure in most. A functional cure in the host may require several synergistic antiviral and immunological intercessions. The correct sequencing and combinations of treatment with either host or viral targeting agents have yet to be determined. Proven surrogates for cccDNA for clinical trials are required. Different strategies may become apparent for patients at different stages of the disease. Curative therapies will require affordability. This review focuses on steps toward a cure.
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Affiliation(s)
- Geoffrey Dusheiko
- Kings College Hospital & University College London Medical School, Denmark Hill, London SE5 9RS, UK
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Hou J, Wang G, Wang F, Cheng J, Ren H, Zhuang H, Sun J, Li L, Li J, Meng Q, Zhao J, Duan Z, Jia J, Tang H, Sheng J, Peng J, Lu F, Xie Q, Wei L. Guideline of Prevention and Treatment for Chronic Hepatitis B (2015 Update). J Clin Transl Hepatol 2017; 5:297-318. [PMID: 29226097 PMCID: PMC5719188 DOI: 10.14218/jcth.2016.00019] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 01/14/2017] [Accepted: 01/16/2017] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jinlin Hou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence to: Jinlin Hou, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou avenue, Guangzhou 510515, China. E-mail: ; Lai Wei, Peking University People’s Hospital, Peking University Hepatology Institute, No. 11 Xizhimen South Street, Beijing 100044, China. E-mail:
| | - Guiqiang Wang
- Department of Infectious Diseases, Center for Liver Diseases, Peking University First Hospital, Beijing, China
| | - Fusheng Wang
- The Institute of Translational Hepatology, 302 Hospital of PLA, Peking University, Beijing, China
| | - Jun Cheng
- Center of Liver Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Hong Ren
- Institute for Viral Hepatitis, the Key Laboratory of Molecular Biology for Infectious Diseases, the second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hui Zhuang
- Department of Microbiology of Peking University Health Science Center, Beijing, China
| | - Jian Sun
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jie Li
- Department of Microbiology of Peking University Health Science Center, Beijing, China
| | - Qinghua Meng
- Serious Illness Medicine Inpatient Area, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jingmin Zhao
- Department of Pathology, 302 Hospital of PLA, Peking University, Beijing, China
| | - Zhongping Duan
- Artificial Liver Center, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jidong Jia
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hong Tang
- Center of Infectious Diseases, West China Hospital of Sichuan University, Division of Infectious Diseases, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Jifang Sheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jie Peng
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fengmin Lu
- Department of Microbiology of Peking University Health Science Center, Beijing, China
| | - Qing Xie
- Department of Infectious Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Lai Wei
- Hepatology Institute, Peking University People’s Hospital, Beijing, China
- *Correspondence to: Jinlin Hou, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou avenue, Guangzhou 510515, China. E-mail: ; Lai Wei, Peking University People’s Hospital, Peking University Hepatology Institute, No. 11 Xizhimen South Street, Beijing 100044, China. E-mail:
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Tu T, Bühler S, Bartenschlager R. Chronic viral hepatitis and its association with liver cancer. Biol Chem 2017; 398:817-837. [PMID: 28455951 DOI: 10.1515/hsz-2017-0118] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/13/2017] [Indexed: 02/06/2023]
Abstract
Chronic infection with hepatitis viruses represents the major causative factor for end-stage liver diseases, including liver cirrhosis and primary liver cancer (hepatocellular carcinoma, HCC). In this review, we highlight the current understanding of the molecular mechanisms that drive the hepatocarcinogenesis associated with chronic hepatitis virus infections. While chronic inflammation (associated with a persistent, but impaired anti-viral immune response) plays a major role in HCC initiation and progression, hepatitis viruses can also directly drive liver cancer. The mechanisms by which hepatitis viruses induce HCC include: hepatitis B virus DNA integration into the host cell genome; metabolic reprogramming by virus infection; induction of the cellular stress response pathway by viral gene products; and interference with tumour suppressors. Finally, we summarise the limitations of hepatitis virus-associated HCC model systems and the development of new techniques to circumvent these shortcomings.
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28
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Tolerance and immunity to pathogens in early life: insights from HBV infection. Semin Immunopathol 2017; 39:643-652. [PMID: 28685270 PMCID: PMC5711997 DOI: 10.1007/s00281-017-0641-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 06/19/2017] [Indexed: 02/06/2023]
Abstract
Immunity is not static but varies with age. The immune system of a newborn infant is not "defective" or "immature." Rather, there are distinct features of innate and adaptive immunity from fetal life to adulthood, which may alter the susceptibility of newborn infants to infections compared to adults. Increased protection to certain infectious diseases during early life may benefit from a dampened immune response as a result of decreased immune pathology. This concept may offer an alternative interpretation of the different pathological manifestations clinically observed in hepatitis B virus (HBV)-infected patients during the natural history of infection. Herein, we review the immune pathological features of HBV infection from early life to adulthood and challenge the concept of a generic immune tolerant state in young people. We then discuss how the different clinical and virological manifestations during HBV infection may be related to the differential antiviral immunity and pro-inflammatory capacity generated at different ages. Lastly, we address the potential to consider earlier therapeutic intervention in HBV-infected young patients to achieve effective immune control leading to better outcomes.
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29
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Yang G, Liu Z, Yang J, Luo K, Xu Y, He H, Fu Q, Yu S, Wang Z. Quasispecies characteristics in mother-to-child transmission of hepatitis B virus by next-generation sequencing. J Infect 2017; 75:48-58. [PMID: 28483405 DOI: 10.1016/j.jinf.2017.04.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 02/24/2017] [Accepted: 04/26/2017] [Indexed: 12/19/2022]
Abstract
OBJECTIVES To identify within-host quasispecies characteristics of hepatitis B virus (HBV) in mothers and children infected via mother-to-child transmission (MTCT). METHODS Using next-generation sequencing (NGS), we analyzed sequences within the non-overlapping pre-core/core (pre-C/C) gene in 37 mother-child pairs. RESULTS Phylogenetic and Highlighter analyses suggested that both a single strain and multiple distinct strains may be transmitted in MTCT of HBV. However, analysis of reassembled viral sequences revealed a relatively narrow distribution of variants in children, which was confirmed by a lower viral diversity in children than that in mothers. New closely related variants with combinations of two to five high-frequency mutations were observed in seven children with elevated ALT levels; the new variants out-competed the transmitted maternal variants to become the dominant strains in five of them. Furthermore, 30 mutations with a frequency >1% of all viruses within-host were present in those children; the mutations caused 19 amino-acid substitutions. Interestingly, almost all were located within the well-known T-cell or B-cell epitopes. CONCLUSIONS There are restrictive changes that occur in the early stages of chronic HBV infection through MTCT with different clinical consequences. These data might have important implications for future investigations of interrelated immunopathogenesis and therapeutic strategies.
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Affiliation(s)
- Guifeng Yang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China
| | - Zhihua Liu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Juncheng Yang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kangxian Luo
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Xu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haitang He
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qunfang Fu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shouyi Yu
- Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China.
| | - Zhanhui Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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30
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Lythgoe KA, Gardner A, Pybus OG, Grove J. Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections. Trends Microbiol 2017; 25:336-348. [PMID: 28377208 PMCID: PMC5405858 DOI: 10.1016/j.tim.2017.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/03/2017] [Accepted: 03/03/2017] [Indexed: 12/24/2022]
Abstract
With extremely short generation times and high mutability, many viruses can rapidly evolve and adapt to changing environments. This ability is generally beneficial to viruses as it allows them to evade host immune responses, evolve new behaviours, and exploit ecological niches. However, natural selection typically generates adaptation in response to the immediate selection pressures that a virus experiences in its current host. Consequently, we argue that some viruses, particularly those characterised by long durations of infection and ongoing replication, may be susceptible to short-sighted evolution, whereby a virus' adaptation to its current host will be detrimental to its onward transmission within the host population. Here we outline the concept of short-sighted viral evolution and provide examples of how it may negatively impact viral transmission among hosts. We also propose that viruses that are vulnerable to short-sighted evolution may exhibit strategies that minimise its effects. We speculate on the various mechanisms by which this may be achieved, including viral life history strategies that result in low rates of within-host evolution, or the establishment of a 'germline' lineage of viruses that avoids short-sighted evolution. These concepts provide a new perspective on the way in which some viruses have been able to establish and maintain global pandemics.
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Affiliation(s)
| | - Andy Gardner
- School of Biology, University of St Andrews, St Andrews, KY16 9TH, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Joe Grove
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, WC1E 6BT, UK
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Lin YY, Hsieh CH, Chen JH, Lu X, Kao JH, Chen PJ, Chen DS, Wang HY. De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline. BMC Bioinformatics 2017; 18:223. [PMID: 28446139 PMCID: PMC5406902 DOI: 10.1186/s12859-017-1630-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 04/12/2017] [Indexed: 12/18/2022] Open
Abstract
Background The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data. Results In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods. Conclusions Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1630-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- You-Yu Lin
- Department of Life Science, National Taiwan University, Taipei, 106, Taiwan. .,Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan.
| | - Chia-Hung Hsieh
- Department of Forestry and Nature Conservation, Chinese Culture University, Taipei, 111, Taiwan
| | - Jiun-Hong Chen
- Department of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Xuemei Lu
- Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Jia-Horng Kao
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Ding-Shinn Chen
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan. .,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 106, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 100, Taiwan.
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Tu T, Budzinska MA, Shackel NA, Urban S. HBV DNA Integration: Molecular Mechanisms and Clinical Implications. Viruses 2017; 9:v9040075. [PMID: 28394272 PMCID: PMC5408681 DOI: 10.3390/v9040075] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 02/06/2023] Open
Abstract
Chronic infection with the Hepatitis B Virus (HBV) is a major cause of liver-related morbidity and mortality. One peculiar observation in cells infected with HBV (or with closely‑related animal hepadnaviruses) is the presence of viral DNA integration in the host cell genome, despite this form being a replicative dead-end for the virus. The frequent finding of somatic integration of viral DNA suggests an evolutionary benefit for the virus; however, the mechanism of integration, its functions, and the clinical implications remain unknown. Here we review the current body of knowledge of HBV DNA integration, with particular focus on the molecular mechanisms and its clinical implications (including the possible consequences of replication-independent antigen expression and its possible role in hepatocellular carcinoma). HBV DNA integration is likely to influence HBV replication, persistence, and pathogenesis, and so deserves greater attention in future studies.
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Affiliation(s)
- Thomas Tu
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
| | - Magdalena A Budzinska
- Centenary Institute, The University of Sydney, Sydney, NSW 2050, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Nicholas A Shackel
- Centenary Institute, The University of Sydney, Sydney, NSW 2050, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
- Liverpool Hospital, Gastroenterology, Sydney, NSW 2170, Australia.
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
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Mason WS, Gill US, Litwin S, Zhou Y, Peri S, Pop O, Hong ML, Naik S, Quaglia A, Bertoletti A, Kennedy PT. HBV DNA Integration and Clonal Hepatocyte Expansion in Chronic Hepatitis B Patients Considered Immune Tolerant. Gastroenterology 2016; 151:986-998.e4. [PMID: 27453547 PMCID: PMC8406433 DOI: 10.1053/j.gastro.2016.07.012] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/30/2016] [Accepted: 07/07/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Chronic infection with hepatitis B virus (HBV) progresses through different phases. The first, called the immune-tolerant phase, has been associated with a lack of disease activity. We examined HBV-DNA integration, clonal hepatocyte expansion, HBV antigen expression, and HBV-specific immune responses in patients in the immune-tolerant phase to assess whether this designation is appropriate or if there is evidence of disease activity. METHODS We studied HBV-DNA integration, clonal hepatocyte expansion, and expression of hepatitis B surface antigen and core antigen in liver tissues from 26 patients with chronic HBV infection (ages, 14-39 y); 9 patients were positive for hepatitis B e antigen (HBeAg) in the immune-tolerant phase and were matched for age with 10 HBeAg-positive patients with active disease and 7 HBeAg-negative patients with active disease. Peripheral blood samples were collected and HBV-specific T cells were quantified for each group. RESULTS Detection of HBV antigens differed among groups. However, unexpectedly high numbers of HBV-DNA integrations, randomly distributed among chromosomes, were detected in all groups. Clonal hepatocyte expansion in patients considered immune tolerant also was greater than expected, potentially in response to hepatocyte turnover mediated by HBV-specific T cells, which were detected in peripheral blood cells from patients in all phases of infection. CONCLUSIONS We measured HBV-specific T cells, HBV-DNA integration, and clonal hepatocyte expansion in different disease phases of young patients with chronic hepatitis B, with emphasis on the so-called immune-tolerant phase. A high level of HBV-DNA integration and clonal hepatocyte expansion in patients considered immune tolerant indicated that hepatocarcinogenesis could be underway-even in patients with early stage chronic HBV infection. Our findings do not support the concepts that this phase is devoid of markers of disease progression or that an immune response has not been initiated. We propose that this early phase be called a high-replication, low-inflammation stage. The timing of therapeutic interventions to minimize further genetic damage to the hepatocyte population should be reconsidered.
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Affiliation(s)
| | - Upkar S. Gill
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine & Dentistry, QMUL, London, UK
| | - Samuel Litwin
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Yan Zhou
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Suraj Peri
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Oltin Pop
- Histopathology, Institute of Liver Studies, Kings College Hospital, London, UK
| | - Michelle L.W. Hong
- Emerging Infectious Diseases Program, Duke-NUS Graduate Medical School, Singapore
| | - Sandhia Naik
- Department of Paediatric Gastroenterology & Hepatology, The Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Alberto Quaglia
- Histopathology, Institute of Liver Studies, Kings College Hospital, London, UK
| | - Antonio Bertoletti
- Emerging Infectious Diseases Program, Duke-NUS Graduate Medical School, Singapore
| | - Patrick T.F. Kennedy
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine & Dentistry, QMUL, London, UK
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Pereira-Gómez M, Bou JV, Andreu I, Sanjuán R. Lamivudine/Adefovir Treatment Increases the Rate of Spontaneous Mutation of Hepatitis B Virus in Patients. PLoS One 2016; 11:e0163363. [PMID: 27649318 PMCID: PMC5029863 DOI: 10.1371/journal.pone.0163363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/06/2016] [Indexed: 12/19/2022] Open
Abstract
The high levels of genetic diversity shown by hepatitis B virus (HBV) are commonly attributed to the low fidelity of its polymerase. However, the rate of spontaneous mutation of human HBV in vivo is currently unknown. Here, based on the evolutionary principle that the population frequency of lethal mutations equals the rate at which they are produced, we have estimated the mutation rate of HBV in vivo by scoring premature stop codons in 621 publicly available, full-length, molecular clone sequences derived from patients. This yielded an estimate of 8.7 × 10-5 spontaneous mutations per nucleotide per cell infection in untreated patients, which should be taken as an upper limit estimate because PCR errors and/or lack of effective lethality may inflate observed mutation frequencies. We found that, in patients undergoing lamivudine/adefovir treatment, the HBV mutation rate was elevated by more than sixfold, revealing a mutagenic effect of this treatment. Genome-wide analysis of single-nucleotide polymorphisms indicated that lamivudine/adefovir treatment increases the fraction of A/T-to-G/C base substitutions, consistent with recent work showing similar effects of lamivudine in cellular DNA. Based on these data, the rate at which HBV produces new genetic variants in treated patients is similar to or even higher than in RNA viruses.
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Affiliation(s)
- Marianoel Pereira-Gómez
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain
| | - Juan-Vicente Bou
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain
| | - Iván Andreu
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain
- Departament de Genètica, Universitat de València, València, Spain
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Mojsiejczuk LN, Torres C, Sevic I, Badano I, Malan R, Flichman DM, Liotta DJ, Campos RH. Molecular epidemiology of hepatitis B virus in Misiones, Argentina. INFECTION GENETICS AND EVOLUTION 2016; 44:34-42. [PMID: 27321439 DOI: 10.1016/j.meegid.2016.06.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 12/18/2022]
Abstract
Hepatitis B virus (HBV) infection is a major public health problem worldwide. The aims of this study were to describe the molecular epidemiology of HBV in the Province of Misiones, Argentina and estimate the phylodynamic of the main groups in a Bayesian coalescent framework. To this end, partial or complete genome sequences were obtained from 52 blood donor candidates. The phylogenetic analysis based on partial sequences of S/P region showed a predominance of genotype D (65.4%), followed by genotype F (30.8%) and genotype A as a minority (3.8%). At subgenotype level, the circulation of subgenotypes D3 (42.3%), D2 (13.5%), F1b (11.5%) and F4 (9.6%) was mainly identified. The Bayesian coalescent analysis of 29 complete genome sequences for the main groups revealed that the subgenotypes D2 and D3 had several introductions to the region, with ancestors dating back from 1921 to 1969 and diversification events until the late '70s. The genotype F in Misiones has a more recent history; subgenotype F4 isolates were intermixed with sequences from Argentina and neighboring countries and only one significant cluster dated back in 1994 was observed. Subgenotype F1b isolates exhibited low genetic distance and formed a closely related monophyletic cluster, suggesting a very recent introduction. In conclusion, the phylogenetic and coalescent analyses showed that the European genotype D has a higher circulation, a longer history of diversification and may be responsible for the largest proportion of chronic HBV infections in the Province of Misiones. Genotype F, especially subgenotype F1b, had a more recent introduction and its diversification in the last 20years might be related to its involvement in new transmission events.
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Affiliation(s)
- Laura Noelia Mojsiejczuk
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Carolina Torres
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Ina Sevic
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Argentina
| | - Inés Badano
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas Químicas y Naturales. Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Richard Malan
- Banco de Sangre Central de Misiones, Av. Cabred y Av. López Torres, Posadas, Misiones, Argentina
| | - Diego Martin Flichman
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Domingo Javier Liotta
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas Químicas y Naturales. Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas, Misiones, Argentina
| | - Rodolfo Hector Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
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Domingo E. Long-Term Virus Evolution in Nature. VIRUS AS POPULATIONS 2016. [PMCID: PMC7149407 DOI: 10.1016/b978-0-12-800837-9.00007-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Viruses spread to give rise to epidemics and pandemics, and some key parameters that include virus and host population numbers determine virus persistence or extinction in nature. Viruses evolve at different rates of evolution depending on the polymerase copying fidelity during genome replication. Calculated rates of evolution in nature vary depending on the time interval between virus isolations. In particular, intra-host evolution is generally more rapid that inter-host evolution and several possible mechanisms for this difference are considered. The mechanisms by which the error-prone viruses evolve render very unlikely the operation of a molecular clock (constant rate of incorporation of mutations in the evolving genomes). Several computational methods are reviewed that permit the alignment of viral sequences and the establishment of phylogenetic relationships among viruses. The evolution of virus in the form of dynamic mutant clouds in each infected individual, together with multiple environmental influences, render the emergence and reemergence of viral pathogens an unpredictable event, another example of biological complexity.
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Tu T, Mason WS, Clouston AD, Shackel NA, McCaughan GW, Yeh MM, Schiff ER, Ruszkiewicz AR, Chen JW, Harley HAJ, Stroeher UH, Jilbert AR. Clonal expansion of hepatocytes with a selective advantage occurs during all stages of chronic hepatitis B virus infection. J Viral Hepat 2015; 22:737-53. [PMID: 25619231 DOI: 10.1111/jvh.12380] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/15/2014] [Indexed: 12/23/2022]
Abstract
Hepatocyte clone size was measured in liver samples of 21 patients in various stages of chronic hepatitis B virus (HBV) infection and from 21 to 76 years of age. Hepatocyte clones containing unique virus-cell DNA junctions formed by the integration of HBV DNA were detected using inverse nested PCR. The maximum hepatocyte clone size tended to increase with age, although there was considerable patient-to-patient variation in each age group. There was an upward trend in maximum clone size with increasing fibrosis, inflammatory activity and with seroconversion from HBV e-antigen (HBeAg)-positive to HBeAg-negative, but these differences did not reach statistical significance. Maximum hepatocyte clone size did not differ between patients with and without a coexisting hepatocellular carcinoma. Thus, large hepatocyte clones containing integrated HBV DNA were detected during all stages of chronic HBV infection. Using laser microdissection, no significant difference in clone size was observed between foci of HBV surface antigen (HBsAg)-positive and HBsAg-negative hepatocytes, suggesting that expression of HBsAg is not a significant factor in clonal expansion. Laser microdissection also revealed that hepatocytes with normal-appearing histology make up a major fraction of the cells undergoing clonal expansion. Thus, preneoplasia does not appear to be a factor in the clonal expansion detected in our assays. Computer simulations suggest that the large hepatocyte clones are not produced by random hepatocyte turnover but have an as-yet-unknown selective advantage that drives increased clonal expansion in the HBV-infected liver.
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Affiliation(s)
- T Tu
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.,Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - W S Mason
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - A D Clouston
- Centre for Liver Disease Research, School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, QLD, Australia
| | - N A Shackel
- Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,A. W. Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - G W McCaughan
- Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,A. W. Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - M M Yeh
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - E R Schiff
- Schiff Liver Institute and Center for Liver Diseases, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - A R Ruszkiewicz
- Department of Anatomical Pathology and Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
| | - J W Chen
- South Australian Liver Transplant Unit, Flinders Medical Centre, Adelaide, SA, Australia
| | - H A J Harley
- Department of Gastroenterology and Hepatology, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - U H Stroeher
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - A R Jilbert
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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Hong LZ, Hong S, Wong HT, Aw PPK, Cheng Y, Wilm A, de Sessions PF, Lim SG, Nagarajan N, Hibberd ML, Quake SR, Burkholder WF. BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads. Genome Biol 2015; 15:517. [PMID: 25406369 DOI: 10.1186/preaccept-6768001251451949] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Indexed: 12/16/2022] Open
Abstract
We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-specific barcode onto random segments of the template molecule and assembling the barcoded short reads into complete haplotypes. We applied BAsE-Seq on mixed clones of hepatitis B virus and accurately identified haplotypes occurring at frequencies greater than or equal to 0.4%, with >99.9% specificity. Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases.
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Abstract
We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-specific barcode onto random segments of the template molecule and assembling the barcoded short reads into complete haplotypes. We applied BAsE-Seq on mixed clones of hepatitis B virus and accurately identified haplotypes occurring at frequencies greater than or equal to 0.4%, with >99.9% specificity. Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases.
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Tu T, Budzinska MA, Shackel NA, Jilbert AR. Conceptual models for the initiation of hepatitis B virus-associated hepatocellular carcinoma. Liver Int 2015; 35:1786-800. [PMID: 25640596 DOI: 10.1111/liv.12773] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022]
Abstract
Although chronic hepatitis B virus (HBV) infection is a known risk factor for the development of hepatocellular carcinoma (HCC), the steps involved in the progression from normal liver to HCC are poorly understood. In this review, we apply five conceptual models, previously proposed by Vineis et al. to explain carcinogenesis in general, to explore the possible steps involved in the initiation and evolution of HBV-associated HCC. Available data suggest that the most suitable and inclusive model is based on evolution of hepatocyte subpopulations. In this evolutionary model, HCC-associated changes are driven by selection and subsequent clonal expansion of phenotypically altered hepatocyte subpopulations in the microenvironment of the HBV-infected liver. This model can incorporate the wide range of mechanisms proposed to play a role in the initiation of HCC including oncogenic HBV proteins, integration of HBV DNA and chronic inflammation of the liver. The model may assist in the early prevention, detection and treatment of HCC and may guide future studies of the initiation of HBV-associated HCC.
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Affiliation(s)
- Thomas Tu
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.,Liver Cell Biology, Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Magdalena A Budzinska
- Liver Cell Biology, Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Nicholas A Shackel
- Liver Cell Biology, Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,A.W. Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Allison R Jilbert
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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Vanwolleghem T, Hou J, van Oord G, Andeweg AC, Osterhaus ADME, Pas SD, Janssen HLA, Boonstra A. Re-evaluation of hepatitis B virus clinical phases by systems biology identifies unappreciated roles for the innate immune response and B cells. Hepatology 2015; 62:87-100. [PMID: 25808668 DOI: 10.1002/hep.27805] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/20/2015] [Indexed: 12/11/2022]
Abstract
UNLABELLED To identify immunological mechanisms that govern distinct clinical phases of a chronic hepatitis B virus (HBV) infection-immune tolerant (IT), immune active (IA), inactive carrier (IC), and hepatitis B e antigen (HBeAg)-negative (ENEG) hepatitis phases-we performed a systems biology study. Serum samples from untreated chronic HBV patients (n = 71) were used for multiplex cytokine measurements, quantitative hepatitis B surface antigen (HBsAg), HBeAg levels, HBV genotype, and mutant analysis. Leukocytes were phenotyped using multicolor flow cytometry, and whole-blood transcriptome profiles were generated. The latter were compared with liver biopsy transcriptomes from IA (n = 16) and IT (n = 3) patients. HBV viral load as well as HBeAg and HBsAg levels (P < 0.001), but not leukocyte composition, differed significantly between distinct phases. Serum macrophage chemotactic protein 1, interleukin-12p40, interferon (IFN)-gamma-inducible protein 10, and macrophage inflammatory protein 1 beta levels were different between two or more clinical phases (P < 0.05). Comparison of blood transcriptomes identified 64 differentially expressed genes. The gene signature distinguishing IA from IT and IC patients was predominantly composed of highly up-regulated immunoglobulin-encoding genes. Modular repertoire analysis using gene sets clustered according to similar expression patterns corroborated the abundant expression of B-cell function-related genes in IA patients and pointed toward increased (ISG) transcript levels in IT patients, compared to subsequent phases. Natural killer cell activities were clustered in clinical phases with biochemical liver damage (IA and ENEG phases), whereas T-cell activities were higher in all phases, compared to IT patients. B-cell-related transcripts proved to be higher in biopsies from IA versus IT patients. CONCLUSION HBV clinical phases are characterized by distinct blood gene signatures. Innate IFN and B-cell responses are highly active during the IT and IA phases, respectively. This suggests that the presumed immune tolerance in chronic HBV infections needs to be redefined.
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Affiliation(s)
- Thomas Vanwolleghem
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jun Hou
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Gertine van Oord
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arno C Andeweg
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A D M E Osterhaus
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Suzan D Pas
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Harry L A Janssen
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Liver Clinic, University Health Network, Toronto, Ontario, Canada
| | - Andre Boonstra
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
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Mojsiejczuk LN, Torres C, Fainboin HA, Galdame OA, Campos RH, Flichman DM. Identification of a new clade of hepatitis B virus genotype F. INFECTION GENETICS AND EVOLUTION 2015; 34:122-5. [PMID: 26073681 DOI: 10.1016/j.meegid.2015.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/05/2015] [Accepted: 06/05/2015] [Indexed: 12/23/2022]
Abstract
Hepatitis B virus (HBV) is classified into eight main genotypes (A-H) and several subgenotypes. Here, three new genotype F complete genome sequences isolated from patients from Buenos Aires city are reported. The new sequences form a separate monophyletic group from the previously known subgenotype F4 strains. Based on results of phylogenetic, genetic distance and evolutionary analyses, the name F4b is proposed for these isolates and F4a for the formerly known as F4. The identification of new clusters allows deepening the knowledge about the diversification process and evolutionary history of HBV.
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Affiliation(s)
- Laura Noelia Mojsiejczuk
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Carolina Torres
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina
| | - Hugo Alberto Fainboin
- Unidad de Hepatopatías Infecciosas, Hospital F.J. Muñiz, Uspallata 2272, Ciudad Autónoma de Buenos Aires, Argentina
| | - Omar Andres Galdame
- Sección Hepatología, Hospital Italiano, Juan D. Perón 4190, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rodolfo Hector Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina
| | - Diego Martin Flichman
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina
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Gao S, Duan ZP, Coffin CS. Clinical relevance of hepatitis B virus variants. World J Hepatol 2015; 7:1086-1096. [PMID: 26052397 PMCID: PMC4450185 DOI: 10.4254/wjh.v7.i8.1086] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/28/2015] [Accepted: 02/12/2015] [Indexed: 02/06/2023] Open
Abstract
The hepatitis B virus (HBV) is a global public health problem with more than 240 million people chronically infected worldwide, who are at risk for end-stage liver disease and hepatocellular carcinoma. There are an estimated 600000 deaths annually from complications of HBV-related liver disease. Antiviral therapy with nucleos/tide analogs (NA) targeting the HBV polymerase (P) can inhibit disease progression by long-term suppression of HBV replication. However, treatment may fail with first generation NA therapy due to the emergence of drug-resistant mutants, as well as incomplete medication adherence. The HBV replicates via an error-prone reverse transcriptase leading to quasispecies. Due to overlapping open reading frames mutations within the HBV P can cause concomitant changes in the HBV surface gene (S) and vice versa. HBV quasispecies diversity is associated with response to antiviral therapy, disease severity and long-term clinical outcomes. Specific mutants have been associated with antiviral drug resistance, immune escape, liver fibrosis development and tumorgenesis. An understanding of HBV variants and their clinical relevance may be important for monitoring chronic hepatitis B disease progression and treatment response. In this review, we will discuss HBV molecular virology, mechanism of variant development, and their potential clinical impact.
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Tseng TC, Liu CJ, Chen CL, Yang WT, Yang HC, Su TH, Wang CC, Kuo SFT, Liu CH, Chen PJ, Chen DS, Kao JH. Higher lifetime chance of spontaneous surface antigen loss in hepatitis B carriers with genotype C infection. Aliment Pharmacol Ther 2015; 41:949-960. [PMID: 25809540 DOI: 10.1111/apt.13170] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/18/2014] [Accepted: 03/02/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Clearance of hepatitis B surface antigen (HBsAg) indicates clinical control of hepatitis B virus (HBV) infection. However, little is known about the impact of viral genomic variations on HBsAg loss. METHODS We explored the association between viral genomic factors and HBsAg loss in 2121HBeAg-negative patients. HBV pre-core stop codon (1896) and basal core promoter (BCP) (1762/1764) sequences were determined in patients with HBV DNA ≥200 IU/mL (N = 1693). The effect of HBV genotype on HBsAg loss was further validated in the whole cohort of 3445 HBsAg carriers. RESULTS The cumulative lifetime (age 28-75 years) incidence of HBsAg loss was 50.4% in 2121 HBeAg-negative patients. We found that genotype C, but not pre-core stop codon or BCP mutants, was associated with HBsAg loss. Compared to genotype B patients, genotype C patients had higher lifetime chance of HBsAg loss, with hazard ratio of 1.8 (95% confidence interval: 1.4-2.4). Multivariable analysis showed that male sex, elevated ALT levels, lower serum HBV DNA and HBsAg levels, and genotype C infection were associated with higher chance of HBsAg loss independently. We then performed sensitivity analysis, which re-included HBeAg-positive, cirrhotic and treatment-experienced patients, and confirmed the robustness of our results in 3445 HBsAg carriers. CONCLUSION Genotype C infection, compared to genotype B, is associated with a higher lifetime chance of HBsAg loss in Asian HBV carriers.
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Affiliation(s)
- T-C Tseng
- Division of Gastroenterology, Department of Internal Medicine, Taipei Tzuchi Hospital, The Buddhist Tzuchi Medical Foundation, Taipei, Taiwan; School of Medicine, Tzu Chi University, Hualien, Taiwan
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Seeger C, Mason WS. Molecular biology of hepatitis B virus infection. Virology 2015; 479-480:672-86. [PMID: 25759099 PMCID: PMC4424072 DOI: 10.1016/j.virol.2015.02.031] [Citation(s) in RCA: 618] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/09/2015] [Accepted: 02/16/2015] [Indexed: 02/06/2023]
Abstract
Human hepatitis B virus (HBV) is the prototype of a family of small DNA viruses that productively infect hepatocytes, the major cell of the liver, and replicate by reverse transcription of a terminally redundant viral RNA, the pregenome. Upon infection, the circular, partially double-stranded virion DNA is converted in the nucleus to a covalently closed circular DNA (cccDNA) that assembles into a minichromosome, the template for viral mRNA synthesis. Infection of hepatocytes is non-cytopathic. Infection of the liver may be either transient (<6 months) or chronic and lifelong, depending on the ability of the host immune response to clear the infection. Chronic infections can cause immune-mediated liver damage progressing to cirrhosis and hepatocellular carcinoma (HCC). The mechanisms of carcinogenesis are unclear. Antiviral therapies with nucleoside analog inhibitors of viral DNA synthesis delay sequelae, but cannot cure HBV infections due to the persistence of cccDNA in hepatocytes.
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Characterization of Full-Length Genomes of Hepatitis B Virus Quasispecies in Sera of Patients at Different Phases of Infection. J Clin Microbiol 2015; 53:2203-14. [PMID: 25926495 DOI: 10.1128/jcm.00068-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/24/2015] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B virus (HBV) infection results in different clinical presentation due to different levels of immune response. Our study aimed to characterize HBV full-length genome quasispecies (QS) in patients with different phases of infection to better understand its pathogenesis. Forty treatment-naive HBV-infected patients were enrolled, including 10 cases of acute hepatitis B (AHB), 9 cases of immunotolerant (IT) HBV carriers, 11 cases of chronic hepatitis B (CHB), and 10 cases of acute-on-chronic liver failure (ACLF). The present study was conducted by clone-based sequencing. QS heterogeneity within each open reading frame was calculated. The mutation frequency index (MFI) and amino acid variations within the large HBsAg, HBcAg, and HBxAg regions were analyzed based on the different infection phases. In total, 606 HBV full-length sequences were obtained. HBV QS had higher heterogeneity in ACLF and CHB than that in IT among chronically infected individuals. AHB patients had the lower QS heterogeneity at onset than those with chronic infection. ACLF patients had the highest frequency of mutations in the core promoter and precore region. A triple mutation (A1762T/G1764A/G1896A) was observed more frequently in genotype C than in genotype B. The MFI indicated that specific peptides of the studied regions had more frequent mutations in ACLF. Furthermore, several amino acid variations, known as T- and B-cell epitopes, were potentially associated with the immunoactive phase of infection. More HBV genome mutations and deletions were observed in patients with more severe diseases, particularly in specific regions of the core and preS regions, the clinical significance and mechanism of which need to be further investigated.
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