1
|
Wu Y, Zheng S, Liu T, Liu X, Tang H, He Y, Xu W, Li L, Yu W, Xing K, Xia X. Viral Haplotypes in COVID-19 Patients Associated With Prolonged Viral Shedding. Front Cell Infect Microbiol 2021; 11:715143. [PMID: 34858866 PMCID: PMC8631178 DOI: 10.3389/fcimb.2021.715143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background Recently, more patients who recovered from the novel coronavirus disease 2019 (COVID-19) may later test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) again using reverse transcription-polymerase chain reaction (RT-PCR) testing. Even though it is still controversial about the possible explanation for clinical cases of long-term viral shedding, it remains unclear whether the persistent viral shedding means re-infection or recurrence. Methods Specimens were collected from three COVID-19-confirmed patients, and whole-genome sequencing was performed on these clinical specimens during their first hospital admission with a high viral load of SARS-CoV-2. Laboratory tests were examined and analyzed throughout the whole course of the disease. Phylogenetic analysis was carried out for SARS-CoV-2 haplotypes. Results We found haplotypes of SARS-CoV-2 co-infection in two COVID-19 patients (YW01 and YW03) with a long period of hospitalization. However, only one haplotype was observed in the other patient with chronic lymphocytic leukemia (YW02), which was verified as one kind of viral haplotype. Patients YW01 and YW02 were admitted to the hospital after being infected with COVID-19 as members of a family cluster, but they had different haplotype characteristics in the early stage of infection; YW01 and YW03 were from different infection sources; however, similar haplotypes were found together. Conclusion These findings show that haplotype diversity of SARS-CoV-2 may result in viral adaptation for persistent shedding in multiple recurrences of COVID-19 patients, who met the discharge requirement. However, the correlation between haplotype diversity of SARS-CoV-2 virus and immune status is not absolute. It showed important implications for the clinical management strategies for COVID-19 patients with long-term hospitalization or cases of recurrence.
Collapse
Affiliation(s)
- Yingping Wu
- Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Jinhua, China
| | - Shufa Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Tian Liu
- Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Jinhua, China
| | - Xueke Liu
- Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Jinhua, China
| | - Huina Tang
- Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Jinhua, China
| | - Yutong He
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Wei Xu
- Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Jinhua, China
| | - Lele Li
- Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Jinhua, China
| | - Wenxu Yu
- Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Jinhua, China
| | - Ke Xing
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaoping Xia
- Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Jinhua, China
| |
Collapse
|
2
|
Garcia-Garcia S, Cortese MF, Rodríguez-Algarra F, Tabernero D, Rando-Segura A, Quer J, Buti M, Rodríguez-Frías F. Next-generation sequencing for the diagnosis of hepatitis B: current status and future prospects. Expert Rev Mol Diagn 2021; 21:381-396. [PMID: 33880971 DOI: 10.1080/14737159.2021.1913055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Hepatitis B virus (HBV) causes a complex and persistent infection with a major impact on patients health. Viral-genome sequencing can provide valuable information for characterizing virus genotype, infection dynamics and drug and vaccine resistance. AREAS COVERED This article reviews the current literature to describe the next-generation sequencing progress that facilitated a more comprehensive study of HBV quasispecies in diagnosis and clinical monitoring. EXPERT OPINION HBV variability plays a key role in liver disease progression and treatment efficacy. Second-generation sequencing improved the sensitivity for detecting and quantifying mutations, mixed genotypes and viral recombination. Third-generation sequencing enables the analysis of the entire HBV genome, although the high error rate limits its use in clinical practice.
Collapse
Affiliation(s)
- Selene Garcia-Garcia
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
- Clinical Biochemistry Research Group, Vall d'Hebron Institut Recerca (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
- Clinical Biochemistry Research Group, Vall d'Hebron Institut Recerca (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francisco Rodríguez-Algarra
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David Tabernero
- Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas, Instituto De Salud Carlos III, Madrid Spain
| | - Ariadna Rando-Segura
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
| | - Josep Quer
- Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas, Instituto De Salud Carlos III, Madrid Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
| | - Maria Buti
- Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas, Instituto De Salud Carlos III, Madrid Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
| | - Francisco Rodríguez-Frías
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
- Clinical Biochemistry Research Group, Vall d'Hebron Institut Recerca (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas, Instituto De Salud Carlos III, Madrid Spain
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Comparison of Serum Hepatitis B Virus RNA Levels and Quasispecies Evolution Patterns between Entecavir and Pegylated-Interferon Mono-treatment in Chronic Hepatitis B Patients. J Clin Microbiol 2020; 58:JCM.00075-20. [PMID: 32554476 PMCID: PMC7448659 DOI: 10.1128/jcm.00075-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) RNA may independently predict virological and serological response. This study aimed to compare dynamic changes in serum HBV RNA levels and HBV quasispecies evolution patterns between entecavir and pegylated-interferon mono-treatment in chronic hepatitis B patients and to determine the clinical significance during treatment. TaqMan real-time PCR was used for quantitative analysis. HBV RNA levels were retrospectively determined in serial serum samples from 178 chronic hepatitis B patients who received either entecavir or pegylated-interferon treatment. Hepatitis B virus (HBV) RNA may independently predict virological and serological response. This study aimed to compare dynamic changes in serum HBV RNA levels and HBV quasispecies evolution patterns between entecavir and pegylated-interferon mono-treatment in chronic hepatitis B patients and to determine the clinical significance during treatment. TaqMan real-time PCR was used for quantitative analysis. HBV RNA levels were retrospectively determined in serial serum samples from 178 chronic hepatitis B patients who received either entecavir or pegylated-interferon treatment. Both serum HBV DNA and RNA quasispecies were analyzed via next-generation sequencing. Receiver operating characteristics (ROC) analysis was performed to evaluate the prediction value of individual biomarkers for hepatitis B e antigen (HBeAg) seroconversion. Patients who received pegylated-interferon treatment showed stronger declines in HBV RNA levels than did those who received entecavir treatment. Serum HBV RNA levels were lower in patients with subsequent HBeAg seroconversion. At baseline, the level of HBV RNA was better than other indicators in predicting HBeAg seroconversion. Moreover, the predictive value of serum HBV RNA levels was better in the entecavir group. Baseline HBV RNA exhibited a significantly higher genetic diversity than HBV DNA and had a significant decline after 4 weeks of entecavir treatment. Higher baseline genetic diversity may result in a better outcome in pegylated-interferon-treated patients. Serum HBV RNA levels showed different decline kinetics, and HBV RNA quasispecies showed different evolution patterns in entecavir and pegylated-interferon mono-treatment. Taken together, serum HBV RNA may serve as a promising biomarker of HBeAg seroconversion in patients during antiviral treatment.
Collapse
|
5
|
Next generation sequencing identifies baseline viral mutants associated with treatment response to pegylated interferon in HBeAg-positive chronic hepatitis B. Virus Genes 2019; 55:610-618. [PMID: 31359359 DOI: 10.1007/s11262-019-01689-5] [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: 03/26/2019] [Accepted: 07/18/2019] [Indexed: 12/27/2022]
Abstract
Current data of hepatitis B virus (HBV) variants associated with treatment outcome identified by next generation sequencing (NGS) are limited. This study was aimed at determining the role of baseline sequence variations in the enhancer II (EnhII), basal core promotor (BCP) and pre-core (PC) regions of HBV genotype C in patients treated with pegylated interferon (PEG-IFN). Patients with HBeAg-positive chronic hepatitis B (CHB) treated with 48-week PEG-IFN were enrolled. Combined response (CR) at week 96 was defined by HBeAg seroconversion plus HBV DNA < 2000 IU/mL and HBsAg < 1000 IU/mL. Pre-treatment viral mutations were characterized by Sanger sequencing and NGS (Miseq Illumina platform). Among 47 patients (32 male, mean age 32.4 years), CR was achieved in 12 (25.5%) individuals. Overall, NGS was superior to Sanger sequencing in detecting mutations (61.7% vs. 38.3%, P < 0.001). Based on NGS, the prevalence of T1753V (T1753C/A/G) and A1762T/G1764A variants were significantly lower in responders compared to non-responders (8.3% vs. 51.4%, P = 0.009 and 33.3% vs. 68.6%, P = 0.032, respectively). No significant difference between groups was found regarding C1653T and G1896A mutants. The absence of T1753V and A1762T/G1764A mutations were factors associated with CR (OR 11.65, 95%CI 1.36-100.16, P = 0.025, and OR 4.36, 95%CI 1.08-17.63, P = 0.039, respectively). The existence of pre-treatment T1753V, A1762T/G1764A mutations and their combination yielded negative predictive values of 94.7%, 85.7% and 93.8%, respectively. The presence of HBV mutants in the BCP region determined by NGS at baseline was associated with poor treatment outcome in patients with HBeAg-positive CHB receiving PEG-IFN.
Collapse
|
6
|
Wang C, Yu S, Zhang Y, Zhang M, Lv L, Huang C, Li X, Li J, Zhang Z. Viral quasispecies of hepatitis B virus in patients with YMDD mutation and lamivudine resistance may not predict the efficacy of lamivudine/adefovir rescue therapy. Exp Ther Med 2019; 17:2473-2484. [PMID: 30906435 PMCID: PMC6425149 DOI: 10.3892/etm.2019.7255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 12/03/2018] [Indexed: 02/07/2023] Open
Abstract
The association between hepatitis B virus (HBV) quasispecies (QS) and the efficacy of nucleos(t)ide analog therapy is currently not well defined, particularly in the case of lamivudine (LAM)/adefovir (ADV) combination rescue therapy for patients with chronic HBV infection (CHB) presenting with LAM resistance. In the present study, 16 CHB patients with the rtM204I/V mutation in the tyrosine-methionine-aspartate-aspartate motif of the C domain of the polymerase gene who switched to LAM/ADV treatment due to LAM resistance were assessed. HBV DNA was isolated from these patients and the reverse transcriptase (RT) region was sequenced. The QS heterogeneity and distribution was analyzed, the mutation sites were recorded and the phylogenetic trees were constructed. The results indicated that QS heterogeneity and distribution in the RT and S regions were not significantly different between responders (RS) and non-RS (NRS) at baseline (P>0.05), except for the higher frequency of a dominant strain in the RT region at the nucleotide level in the RS group (P=0.039). In addition, in NRS, no significant difference in QS heterogeneity or distribution in these regions was identified at six months vs. the baseline. Furthermore, although in the non-responder group the frequency of the LAM resistance-associated mutations (rtM204V/I) decreased at 6 months compared with the baseline, it did not disappear in any of the patients after six months of treatment. Analysis of individual patients did not indicate any consistent selection of specific HBV mutants during LAM/ADV rescue therapy. In conclusion, the baseline HBV QS within the RT and S regions may not be a valid predictor of the response to LAM/ADV rescue treatment in CHB patients with LAM resistance.
Collapse
Affiliation(s)
- Changtai Wang
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China.,Department of Infectious Diseases, The Affiliated Anqing Hospital of Anhui Medical University, Anqing, Anhui 246000, P.R. China
| | - Shu Yu
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Yafei Zhang
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Min Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Liying Lv
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Cheng Huang
- College of Pharmacy, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xu Li
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Jun Li
- College of Pharmacy, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Zhenhua Zhang
- Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China.,College of Pharmacy, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| |
Collapse
|
7
|
McNaughton AL, D’Arienzo V, Ansari MA, Lumley SF, Littlejohn M, Revill P, McKeating JA, Matthews PC. Insights From Deep Sequencing of the HBV Genome-Unique, Tiny, and Misunderstood. Gastroenterology 2019; 156:384-399. [PMID: 30268787 PMCID: PMC6347571 DOI: 10.1053/j.gastro.2018.07.058] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/27/2018] [Accepted: 07/23/2018] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) is a unique, tiny, partially double-stranded, reverse-transcribing DNA virus with proteins encoded by multiple overlapping reading frames. The substitution rate is surprisingly high for a DNA virus, but lower than that of other reverse transcribing organisms. More than 260 million people worldwide have chronic HBV infection, which causes 0.8 million deaths a year. Because of the high burden of disease, international health agencies have set the goal of eliminating HBV infection by 2030. Nonetheless, the intriguing HBV genome has not been well characterized. We summarize data on the HBV genome structure and replication cycle, explain and quantify diversity within and among infected individuals, and discuss advances that can be offered by application of next-generation sequencing technology. In-depth HBV genome analyses could increase our understanding of disease pathogenesis and allow us to better predict patient outcomes, optimize treatment, and develop new therapeutics.
Collapse
Affiliation(s)
- Anna L. McNaughton
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Valentina D’Arienzo
- Nuffield Department of Medicine, NDM Research Building, Oxford, United Kingdom
| | - M. Azim Ansari
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Sheila F. Lumley
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia,Department of Microbiology and Immunology, University of Melbourne. Melbourne, Australia
| | - Peter Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia,Department of Microbiology and Immunology, University of Melbourne. Melbourne, Australia
| | - Jane A. McKeating
- Nuffield Department of Medicine, NDM Research Building, Oxford, United Kingdom
| | - Philippa C. Matthews
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom,Reprint requests Address requests for reprints to: Philippa C. Matthews, BMBS, PhD, Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom.
| |
Collapse
|
8
|
Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC. PLoS Genet 2018; 14:e1007206. [PMID: 29474353 PMCID: PMC5841821 DOI: 10.1371/journal.pgen.1007206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 03/07/2018] [Accepted: 01/17/2018] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a common problem in the world, especially in China. More than 60–80% of hepatocellular carcinoma (HCC) cases can be attributed to HBV infection in high HBV prevalent regions. Although traditional Sanger sequencing has been extensively used to investigate HBV sequences, NGS is becoming more commonly used. Further, it is unknown whether word pattern frequencies of HBV reads by Next Generation Sequencing (NGS) can be used to investigate HBV genotypes and predict HCC status. In this study, we used NGS to sequence the pre-S region of the HBV sequence of 94 HCC patients and 45 chronic HBV (CHB) infected individuals. Word pattern frequencies among the sequence data of all individuals were calculated and compared using the Manhattan distance. The individuals were grouped using principal coordinate analysis (PCoA) and hierarchical clustering. Word pattern frequencies were also used to build prediction models for HCC status using both K-nearest neighbors (KNN) and support vector machine (SVM). We showed the extremely high power of analyzing HBV sequences using word patterns. Our key findings include that the first principal coordinate of the PCoA analysis was highly associated with the fraction of genotype B (or C) sequences and the second principal coordinate was significantly associated with the probability of having HCC. Hierarchical clustering first groups the individuals according to their major genotypes followed by their HCC status. Using cross-validation, high area under the receiver operational characteristic curve (AUC) of around 0.88 for KNN and 0.92 for SVM were obtained. In the independent data set of 46 HCC patients and 31 CHB individuals, a good AUC score of 0.77 was obtained using SVM. It was further shown that 3000 reads for each individual can yield stable prediction results for SVM. Thus, another key finding is that word patterns can be used to predict HCC status with high accuracy. Therefore, our study shows clearly that word pattern frequencies of HBV sequences contain much information about the composition of different HBV genotypes and the HCC status of an individual. HBV infection can lead to many liver complications including hepatocellular carcinoma (HCC), one of the most common liver cancers in China. High-throughput sequencing technologies have recently been used to study the genotype sequence compositions of HBV infected individuals and to distinguish chronic HBV (CHB) infection from HCC. We used NGS to sequence the pre-S region of a large number of CHB and HCC individuals and designed novel word pattern based approaches to analyze the data. We have several surprising key findings. First, most HBV infected individuals contained mixtures of genotypes B and C sequences. Second, multi-dimensional scaling (MDS) analysis of the data showed that the first principal coordinate was closely associated with the fraction of genotype B (or C) sequences and the second principal coordinate was highly associated with the probability of HCC. Third, we also designed K-nearest neighbors (KNN) and support vector machine (SVM) based classifiers for CHB and HCC with high prediction accuracy. The results were validated in an independent data set.
Collapse
|
9
|
Rajoriya N, Combet C, Zoulim F, Janssen HLA. How viral genetic variants and genotypes influence disease and treatment outcome of chronic hepatitis B. Time for an individualised approach? J Hepatol 2017; 67:1281-1297. [PMID: 28736138 DOI: 10.1016/j.jhep.2017.07.011] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 06/27/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022]
Abstract
Chronic hepatitis B virus (HBV) infection remains a global problem. Several HBV genotypes exist with different biology and geographical prevalence. Whilst the future aim of HBV treatment remains viral eradication, current treatment strategies aim to suppress the virus and prevent the progression of liver disease. Current strategies also involve identification of patients for treatment, namely those at risk of progressive liver disease. Identification of HBV genotype, HBV mutants and other predictive factors allow for tailoured treatments, and risk-surveillance pathways, such as hepatocellular cancer screening. In the future, these factors may enable stratification not only of treatment decisions, but also of patients at risk of higher relapse rates when current therapies are discontinued. Newer technologies, such as next-generation sequencing, to assess drug-resistant or immune escape variants and quasi-species heterogeneity in patients, may allow for more information-based treatment decisions between the clinician and the patient. This article serves to discuss how HBV genotypes and genetic variants impact not only upon the disease course and outcomes, but also current treatment strategies. Adopting a personalised genotypic approach may play a role in future strategies to combat the disease. Herein, we discuss new technologies that may allow more informed decision-making for response guided therapy in the battle against HBV.
Collapse
Affiliation(s)
- Neil Rajoriya
- Toronto Centre for Liver Diseases, Toronto General Hospital, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
| | - Christophe Combet
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69XXX, France
| | - Fabien Zoulim
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69XXX, France; Department of Hepatology, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Harry L A Janssen
- Toronto Centre for Liver Diseases, Toronto General Hospital, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada.
| |
Collapse
|
10
|
Jia J, Li H, Wang H, Chen S, Wang M, Feng H, Gao Y, Wang Y, Fang M, Gao C. Hepatitis B virus core antigen mutations predict post-operative prognosis of patients with primary hepatocellular carcinoma. J Gen Virol 2017; 98:1399-1409. [PMID: 28640739 PMCID: PMC5656792 DOI: 10.1099/jgv.0.000790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/26/2017] [Indexed: 12/11/2022] Open
Abstract
The aim of this study was to explore the relationship between hepatitis B virus (HBV) core antigen (HBc) mutations and the post-operative prognosis of HBV-related hepatocellular carcinoma (HCC). In total, 98 patients suffering from HBV-related HCC and treated with surgery were enrolled, with a 48 month follow-up. The preCore/Core region of the HBV genome from tumour tissue (TT) and paired adjacent non-tumour tissue (ANTT) of these patients was sequenced, and a phylogenetic tree was reconstructed. The correlations between the viral features and evolutionary divergence of preCore/Core amino acid sequences from 67 paired TTs and ANTTs were analysed. Cox proportional hazard model analysis was applied for post-operative hazard risk evaluation. Phylogenetic analysis revealed that all of the sequences were ascribed to genotype C. The evolutionary divergence of amino acid sequences from matched TTs and ANTTs was significantly negatively correlated with serum and intrahepatic HBV DNA levels. Multivariate analysis showed that the HBc E77 mutation was associated with shorter overall survival, and HBc S87 and P156 mutations were independent risk factors for relapse. Furthermore, in contrast to with patients without the S87 mutation, no correlation was observed between serum HBV DNA and intrahepatic HBV DNA in HCC patients with the S87 mutation. Analysis of the intrahepatic sequence may advance our understanding of viral status; thus, it is useful for prognosis prediction for HBV-related HCC.
Collapse
Affiliation(s)
- Jian’an Jia
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
- Department of Laboratory Medicine, 105th Hospital of PLA, Hefei 230031, PR China
| | - Huiming Li
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Hui Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
- Department of Clinical Laboratory, First Affiliated Hospital of Chinese PLA’s General Hospital, Beijing 100048, PR China
| | - Shipeng Chen
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Mengmeng Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Huijuan Feng
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Yuzhen Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Yunjiu Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Meng Fang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| |
Collapse
|
11
|
Clinical features and viral quasispecies characteristics associated with infection by the hepatitis B virus G145R immune escape mutant. Emerg Microbes Infect 2017; 6:e15. [PMID: 28325923 PMCID: PMC5378923 DOI: 10.1038/emi.2017.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 12/12/2022]
Abstract
Coexistence of the hepatitis B surface antigen (HBsAg) and hepatitis B surface antibody (anti-HBs) is an uncommon phenomenon, and the underlying mechanisms remain largely unknown. Amino-acid (aa) substitution from glycine to arginine at aa 145 (G145R), in the major hydrophilic region, has been reported in patients with HBsAg and anti-HBs coexistence. However, there is limited knowledge about the clinical features and viral quasispecies characteristics associated with G145R mutant hepatitis B virus (HBV) infection. We herein describe the dynamic changes in the serological and virological markers in a case of hepatitis B with coexisting HBsAg and anti-HBs, caused by a G145R immune escape mutant (genotype C). Entecavir was administered during the 4th week after admission. Alanine aminotransferase peaked in the 16th week, while both the HBsAg and HBeAg declined rapidly. HBsAg clearance and hepatitis B e antigen (HBeAg)/hepatitis B e antibody (anti-HBe) seroconversion were achieved in the 36th week, and then entecavir was withdrawn. A follow-up of 96 weeks showed that HBV DNA remained undetectable and that anti-HBs was maintained above 100 mIU/mL. The quasispecies characteristics of the G145R mutant HBV were investigated via ultra-deep sequencing. The complexity and genetic distance of the S and RT regions were much higher in the 8th week than at baseline or in the 4th week. Moreover, the frequencies of mutations (L173P, Q181R and A184V) in cytotoxic T lymphocyte epitopes increased before entecavir treatment. These findings extend understanding of the evolution of HBV under host immune pressure and of the clinical outcomes of affected patients.
Collapse
|