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Zhang C, An S, Lv R, Li K, Liu H, Li J, Tang Y, Cai Z, Huang T, Long L, Deng W. The dynamic variation position and predominant quasispecies of hepatitis B virus: Novel predictors of early hepatocarcinoma. Virus Res 2024; 341:199317. [PMID: 38242020 PMCID: PMC10831745 DOI: 10.1016/j.virusres.2024.199317] [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: 11/13/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
To find the predictors of early HCC based on the dynamic changes of HBV quasispecies, this study utilizing the second-generation sequencing (NGS) and high-order multiplex droplet digital PCR (ddPCR) technology to examine the HBV quasispecies in serum of total 247 subjects recruited from high-incidence area of HCC. In the discovery stage, 15 non-synonymous Single Nucleotide Polymorphisms (SNPs) with higher variant proportion in HCC case group were founded (all P<0.05). Furthermore, the variant proportions in some of these SNPs were observed changing regularly within 5 years before the onset of HCC, and 5 of them located in HBX, 2 in HBS and 2 in HBC. The HBV predominant quasispecies and their consensus sequences were identified by genetic evolution analysis, in which the high HBS and HBC quasispecies heterogeneity were found associated with the forming of multifarious quasispecies clones, and the HBX gene had the highest proportion of predominant quasispecies (46.7 % in HBX vs 12.7 % and 13.8 % in HBS and HBC respectively) with the key variations (G1512A, A1630G, T1753C/G/A, A1762T and G1764A) determined. In the validation stage, we confirmed that the combined double mutations of G1512A+A1630G, A1762T+G1764A, and the combined triple mutations of T1753C/G/A + A1762T+G1764A, all expressed higher in early HCC cases when comparing with control group (all P<0.05). We also demonstrated the advantages of ddPCR using in multi-variations detection in large-sample for early HCC surveillance and screening. So we think that the dynamic of key HBV variation positions and their different combinations determined by quasispecies anlysis in this study can act as the novel predictors of early hepatocarcinoma and suitable to popularize and apply in HCC screening.
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Affiliation(s)
- Chaojun Zhang
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Sanchun An
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Ruibo Lv
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Kezhi Li
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China; Guangxi Cancer Molecular Medicine Engineering Research Center, China
| | - Haizhou Liu
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China; Guangxi Cancer Molecular Medicine Engineering Research Center, China
| | - Jilin Li
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China; Guangxi Cancer Molecular Medicine Engineering Research Center, China
| | - Yanping Tang
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China; Guangxi Cancer Molecular Medicine Engineering Research Center, China
| | - Zhengmin Cai
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China; Guangxi Cancer Molecular Medicine Engineering Research Center, China
| | - Tianren Huang
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China; Guangxi Cancer Molecular Medicine Engineering Research Center, China.
| | - Long Long
- Big data College of Nanning normal University, Nanning, Guangxi 530100, China.
| | - Wei Deng
- Department of experimental research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China; Guangxi Cancer Molecular Medicine Engineering Research Center, China.
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Jia JA, Zhang S, Bai X, Fang M, Chen S, Liang X, Zhu S, Wong DKH, Zhang A, Feng J, Sun F, Gao C. Sparse logistic regression revealed the associations between HBV PreS quasispecies and hepatocellular carcinoma. Virol J 2022; 19:114. [PMID: 35765099 PMCID: PMC9238101 DOI: 10.1186/s12985-022-01836-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chronic infection with hepatitis B virus (HBV) has been proved highly associated with the development of hepatocellular carcinoma (HCC). AIMS The purpose of the study is to investigate the association between HBV preS region quasispecies and HCC development, as well as to develop HCC diagnosis model using HBV preS region quasispecies. METHODS A total of 104 chronic hepatitis B (CHB) patients and 117 HBV-related HCC patients were enrolled. HBV preS region was sequenced using next generation sequencing (NGS) and the nucleotide entropy was calculated for quasispecies evaluation. Sparse logistic regression (SLR) was used to predict HCC development and prediction performances were evaluated using receiver operating characteristic curves. RESULTS Entropy of HBV preS1, preS2 regions and several nucleotide points showed significant divergence between CHB and HCC patients. Using SLR, the classification of HCC/CHB groups achieved a mean area under the receiver operating characteristic curve (AUC) of 0.883 in the training data and 0.795 in the test data. The prediction model was also validated by a completely independent dataset from Hong Kong. The 10 selected nucleotide positions showed significantly different entropy between CHB and HCC patients. The HBV quasispecies also classified three clinical parameters, including HBeAg, HBVDNA, and Alkaline phosphatase (ALP) with the AUC value greater than 0.6 in the test data. CONCLUSIONS Using NGS and SLR, the association between HBV preS region nucleotide entropy and HCC development was validated in our study and this could promote the understanding of HCC progression mechanism.
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Affiliation(s)
- Jian-an Jia
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438 China
- Department of Laboratory Medicine, The 901th Hospital of Joint Logistics Support Force of Chinese People’s Liberation Army, Hefei, 230031 China
| | - Shuqin Zhang
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, 200433 China
| | - Xin Bai
- Molecular and Computational Program, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, 90089 USA
| | - Meng Fang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438 China
| | - Shipeng Chen
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438 China
| | - Xiaotao Liang
- Department of Computer Science, Fudan University, Shanghai, 200433 China
| | - Shanfeng Zhu
- Department of Computer Science, Fudan University, Shanghai, 200433 China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China
| | - Danny Ka-Ho Wong
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR, China
| | - Anye Zhang
- Department of Medicine, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033 China
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL UK
| | - Fengzhu Sun
- Molecular and Computational Program, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, 90089 USA
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438 China
- Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437 China
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3
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Wang Y, Xiao X, Chen S, Huang C, Zhou J, Dai E, Li Y, Liu L, Huang X, Gao Z, Wu C, Fang M, Gao C. The Impact of HBV Quasispecies Features on Immune Status in HBsAg+/HBsAb+ Patients With HBV Genotype C Using Next-Generation Sequencing. Front Immunol 2021; 12:775461. [PMID: 34899733 PMCID: PMC8656693 DOI: 10.3389/fimmu.2021.775461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022] Open
Abstract
Background This study aimed to explore the molecular mechanism of the coexistence of hepatitis B surface antigen (HBsAg) and hepatitis B surface antibody (HBsAb) serological pattern via intensive characterization of HBV s gene in both chronic hepatitis B (CHB) and hepatocellular carcinoma (HCC) patients. Method A total of 73 HBsAg+/HBsAb+ patients (CHB = 36, HCC = 37) and 96 HBsAg+/HBsAb− patients (CHB = 47, HCC = 49) were enrolled from 13 medical centers in China. The sequence features were elaborated based on the combination of next-generation sequencing (NGS) and multidimensional bioinformatics analysis. Results The 16 high-frequency missense mutations, changes of stop codon mutation, clustering, and random forest models based on quasispecies features demonstrated the significant discrepancy power between HBsAg+/HBsAb+ and HBsAg+/HBsAb− in CHB and HCC, respectively. The immunogenicity for cytotoxic T lymphocyte (CTL) epitope Se and antigenicity for the major hydrophilic region (MHR) were both reduced in HBsAg+/HBsAb+ patients (CTL Se: p < 0.0001; MHR: p = 0.0216). Different mutation patterns were observed between HBsAg+/HBsAb+ patients with CHB and with HCC. Especially, mutations in antigenic epitopes, such as I126S in CHB and I126T in HCC, could impact the conformational structure and alter the antigenicity/immunogenicity of HBsAg. Conclusion Based on NGS and bioinformatics analysis, this study indicates for the first time that point mutations and quasispecies diversities of HBV s gene could alter the MHR antigenicity and CTL Se immunogenicity and could contribute to the concurrent HBsAg+/HBsAb+ with different features in HCC and CHB. Our findings might renew the understanding of this special serological profile and benefit the clinical management in HBV-related diseases.
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Affiliation(s)
- Ying Wang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Xiao Xiao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China.,Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shipeng Chen
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Chenjun Huang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Jun Zhou
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Ya Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lijuan Liu
- Department of Laboratory Medicine, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Xianzhang Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhiyuan Gao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China.,Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chuanyong Wu
- Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Meng Fang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Chunfang Gao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China.,Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Enriquez-Navarro K, Maldonado-Rodriguez A, Rojas-Montes O, Torres-Ibarra R, Bucio-Ortiz L, De la Cruz MA, Torres-Flores J, Xoconostle-Cazares B, Lira R. Identification of mutations in the S gene of hepatitis B virus in HIV positive Mexican patients with occult hepatitis B virus infection. Ann Hepatol 2021; 19:507-515. [PMID: 32592870 DOI: 10.1016/j.aohep.2020.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND AIM Occult hepatitis B virus infection (OBI) is characterized by the presence of replication-competent hepatitis B virus (HBV) DNA in the liver and/or serum of patients with undetectable levels of the HBV surface antigen (HBsAg). Due to the shared infection routes HIV positive patients are at higher risk of developing OBI, thus, the aim of this study was to determine the frequency of OBI in Mexican HIV-infected patients and to identify mutations in the HBV S gene that could be associated to the development of OBI. MATERIALS AND METHODS Plasma samples from 50 HIV-infected patients with undetectable levels of the HBsAg were obtained and analyzed. The Core, PreS and S genes were amplified by nested PCR and sequenced by the Sanger method. To analyze HBV diversity in the OBI-positive patients, ten sequences of 762bp from the HBV S gene were selected, cloned, and subsequently sequenced for mutational analyses. RESULTS OBI infection was found with a frequency of 36% (18/50). All the HBV sequences corresponded to the H genotype. The most common mutations were: C19Y, Q129H, E164D, and I195M, with a frequency of 44%, 36%, 39% and 48% respectively. CONCLUSIONS In this study, we report the presence of OBI in a cohort of Mexican HIV-infected patients with an overall prevalence of 36%. Mutational analyses revealed that four non-silent mutations were frequent in different regions of the HBsAg gene, suggesting that they might be associated to the development of OBI in this population, nevertheless, further studies are required to determine their role in the pathogenesis of OBI.
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Affiliation(s)
- Karina Enriquez-Navarro
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, UMAE Hospital de Pediatría, CMN Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico; Posgrado en Biología Experimental, DCBS, Universidad Autónoma Metropolitana Iztapalapa, Mexico City, Mexico.
| | - Angelica Maldonado-Rodriguez
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, UMAE Hospital de Pediatría, CMN Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico.
| | - Othon Rojas-Montes
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, UMAE Hospital de Pediatría, CMN Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico.
| | - Rocio Torres-Ibarra
- Clinica de Hepatitis, Hospital de Infectologia Centro Médico Nacional La Raza, IMSS, Mexico City, Mexico.
| | - Leticia Bucio-Ortiz
- Laboratorio de Fisiología Celular, Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana Iztapalapa, Mexico City, Mexico.
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, UMAE Hospital de Pediatría, CMN Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico.
| | - Jesus Torres-Flores
- Laboratorio de Virología, Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico.
| | - Beatriz Xoconostle-Cazares
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Mexico City, Mexico.
| | - Rosalia Lira
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, UMAE Hospital de Pediatría, CMN Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico.
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High Prevalence of Preexisting HBV Polymerase Mutations in Pregnant Women Does Not Limit the Antiviral Therapy Efficacy. ACTA ACUST UNITED AC 2021; 2021:6653546. [PMID: 33986897 PMCID: PMC8079218 DOI: 10.1155/2021/6653546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/05/2021] [Accepted: 03/15/2021] [Indexed: 11/18/2022]
Abstract
Background HBV-resistant mutants in treatment-naïve patients may lead to antiviral treatment failure. It is not clear if HBV mutants are present in pregnant women and about the influence of the preexisting mutants on the short-term antiviral therapy during pregnancy. Method We enrolled 73 pregnant women with high HBV DNA load and telbivudine (TBV) treatment during pregnancy in this retrospective study. The UDPS was used to detect the HBV mutations before and after the TBV treatment. Results Before TBV treatment, the complexity of HBV quasispecies of all subjects was 0.40 ± 0.09; 41.1% (30/73) and 53.4% (39/73) subjects had rtM204I/V and rtN236 T/A detected, respectively; and 9.6% (7/73) patients had more than 20% frequency mutation of rtM204I/V, which was also similar with high frequency of rtN236 T/A mutation (41.1% vs. 53.4%, P=0.136; frequencies >20%: 9.6% vs. 5.5%, P=0.347). After TBV treatment, 71.2% (52/73) subjects had HBV DNA load ≥ 103 IU/mL at delivery. Among them, 75.0% of patients with rtM204I positive had HBV DNA load ≥103 IU/mL at delivery, which was comparable with the subjects without rtM204I (75.0% vs. 70.8%, P=0.710). No changes were found in the frequencies and the complexity of HBV quasispecies of rtM204I mutation after the TVB treatment. Conclusion The prevalence of preexisting drug-resistant mutations among pregnant women was high using UPDS. However, the preexisting HBV mutation had limited influence on the efficacy of short-term TBV treatment, and TBV treatment during late pregnancy seemed not to increase the risk of emerging HBV-resistant mutants.
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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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Chen S, Zhang Z, Wang Y, Fang M, Zhou J, Li Y, Dai E, Feng Z, Wang H, Yang Z, Li Y, Huang X, Jia J, Li S, Huang C, Tong L, Xiao X, He Y, Duan Y, Zhu S, Gao C. Using Quasispecies Patterns of Hepatitis B Virus to Predict Hepatocellular Carcinoma With Deep Sequencing and Machine Learning. J Infect Dis 2020; 223:1887-1896. [PMID: 33049037 DOI: 10.1093/infdis/jiaa647] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is one of the main leading causes of hepatocellular carcinoma (HCC) worldwide. However, it remains uncertain how the reverse-transcriptase (rt) gene contributes to HCC progression. METHODS We enrolled a total of 307 patients with chronic hepatitis B (CHB) and 237 with HBV-related HCC from 13 medical centers. Sequence features comprised multidimensional attributes of rt nucleic acid and rt/s amino acid sequences. Machine-learning models were used to establish HCC predictive algorithms. Model performances were tested in the training and independent validation cohorts using receiver operating characteristic curves and calibration plots. RESULTS A random forest (RF) model based on combined metrics (10 features) demonstrated the best predictive performances in both cross and independent validation (AUC, 0.96; accuracy, 0.90), irrespective of HBV genotypes and sequencing depth. Moreover, HCC risk scores for individuals obtained from the RF model (AUC, 0.966; 95% confidence interval, .922-.989) outperformed α-fetoprotein (0.713; .632-.784) in distinguishing between patients with HCC and those with CHB. CONCLUSIONS Our study provides evidence for the first time that HBV rt sequences contain vital HBV quasispecies features in predicting HCC. Integrating deep sequencing with feature extraction and machine-learning models benefits the longitudinal surveillance of CHB and HCC risk assessment.
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Affiliation(s)
- Shipeng Chen
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Zihan Zhang
- ISTBI and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.,School of Computer Science, Fudan University, Shanghai, China
| | - Ying Wang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Meng Fang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Jun Zhou
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Ya Li
- Department of Laboratory Medicine, the First Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Erhei Dai
- Department of Laboratory Medicine, Fifth Hospital of Shijiazhuang, Hebei Medical University, Hebei, China
| | - Zhaolei Feng
- Department of Laboratory Medicine, Jinan Infectious Disease Hospital, Shandong, China
| | - Hao Wang
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Shanghai, China
| | - Zaixing Yang
- Department of Laboratory Medicine, Taizhou First People's Hospital, Zhejiang, China
| | - Yongwei Li
- Department of Laboratory Medicine, Henan Province Hospital of Traditional Chinese Medicine, Henan, China
| | - Xianzhang Huang
- Department of Laboratory Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong, China
| | - Jian'an Jia
- Department of Laboratory Medicine, 901 Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army, Anhui, China
| | - Shuang Li
- Department of Infectious Diseases, First Affiliated Hospital of Nanjing Medical University, Jiangsu, China
| | - Chenjun Huang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Lin Tong
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Xiao Xiao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Yutong He
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Yong Duan
- School of Computer Science, Fudan University, Shanghai, China
| | - Shanfeng Zhu
- ISTBI and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China
| | - Chunfang Gao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
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8
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Duraisamy GS, Bhosale D, Lipenská I, Huvarova I, Růžek D, Windisch MP, Miller AD. Advanced Therapeutics, Vaccinations, and Precision Medicine in the Treatment and Management of Chronic Hepatitis B Viral Infections; Where Are We and Where Are We Going? Viruses 2020; 12:v12090998. [PMID: 32906840 PMCID: PMC7552065 DOI: 10.3390/v12090998] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
The management of chronic hepatitis B virus (CHB) infection is an area of massive unmet clinical need worldwide. In spite of the development of powerful nucleoside/nucleotide analogue (NUC) drugs, and the widespread use of immune stimulators such as interferon-alpha (IFNα) or PEGylated interferon-alpha (PEG-IFNα), substantial improvements in CHB standards of care are still required. We believe that the future for CHB treatment now rests with advanced therapeutics, vaccination, and precision medicine, if all are to bring under control this most resilient of virus infections. In spite of a plethora of active drug treatments, anti-viral vaccinations and diagnostic techniques, the management of CHB infection remains unresolved. The reason for this is the very complexity of the virus replication cycle itself, giving rise to multiple potential targets for therapeutic intervention some of which remain very intractable indeed. Our review is focused on discussing the potential impact that advanced therapeutics, vaccinations and precision medicine could have on the future management of CHB infection. We demonstrate that advanced therapeutic approaches for the treatment of CHB, in the form of gene and immune therapies, together with modern vaccination strategies, are now emerging rapidly to tackle the limitations of current therapeutic approaches to CHB treatment in clinic. In addition, precision medicine approaches are now gathering pace too, starting with personalized medicine. On the basis of this, we argue that the time has now come to accelerate the design and creation of precision therapeutic approaches (PTAs) for CHB treatment that are based on advanced diagnostic tools and nanomedicine, and which could maximize CHB disease detection, treatment, and monitoring in ways that could genuinely eliminate CHB infection altogether.
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Affiliation(s)
- Ganesh Selvaraj Duraisamy
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
| | - Dattatry Bhosale
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
| | - Ivana Lipenská
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
| | - Ivana Huvarova
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
| | - Daniel Růžek
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 České Budějovice, Czech Republic
| | - Marc P. Windisch
- Applied Molecular Virology Laboratory, Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463-400, Korea;
- Division of Bio-Medical Science and Technology, University of Science and Technology, Daejeon 305-350, Korea
| | - Andrew D. Miller
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, Černá Pole, CZ-61300 Brno, Czech Republic
- KP Therapeutics (Europe) s.r.o., Purkyňova 649/127, CZ-61200 Brno, Czech Republic
- Correspondence:
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9
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Comparison of Serum Hepatitis B Virus RNA Levels and Quasispecies Evolution Patterns between Entecavir and Pegylated-Interferon Mono-treatment in Chronic Hepatitis B Patients. J Clin Microbiol 2020; 58:JCM.00075-20. [PMID: 32554476 PMCID: PMC7448659 DOI: 10.1128/jcm.00075-20] [Citation(s) in RCA: 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: 01/14/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) RNA may independently predict virological and serological response. This study aimed to compare dynamic changes in serum HBV RNA levels and HBV quasispecies evolution patterns between entecavir and pegylated-interferon mono-treatment in chronic hepatitis B patients and to determine the clinical significance during treatment. TaqMan real-time PCR was used for quantitative analysis. HBV RNA levels were retrospectively determined in serial serum samples from 178 chronic hepatitis B patients who received either entecavir or pegylated-interferon treatment. Hepatitis B virus (HBV) RNA may independently predict virological and serological response. This study aimed to compare dynamic changes in serum HBV RNA levels and HBV quasispecies evolution patterns between entecavir and pegylated-interferon mono-treatment in chronic hepatitis B patients and to determine the clinical significance during treatment. TaqMan real-time PCR was used for quantitative analysis. HBV RNA levels were retrospectively determined in serial serum samples from 178 chronic hepatitis B patients who received either entecavir or pegylated-interferon treatment. Both serum HBV DNA and RNA quasispecies were analyzed via next-generation sequencing. Receiver operating characteristics (ROC) analysis was performed to evaluate the prediction value of individual biomarkers for hepatitis B e antigen (HBeAg) seroconversion. Patients who received pegylated-interferon treatment showed stronger declines in HBV RNA levels than did those who received entecavir treatment. Serum HBV RNA levels were lower in patients with subsequent HBeAg seroconversion. At baseline, the level of HBV RNA was better than other indicators in predicting HBeAg seroconversion. Moreover, the predictive value of serum HBV RNA levels was better in the entecavir group. Baseline HBV RNA exhibited a significantly higher genetic diversity than HBV DNA and had a significant decline after 4 weeks of entecavir treatment. Higher baseline genetic diversity may result in a better outcome in pegylated-interferon-treated patients. Serum HBV RNA levels showed different decline kinetics, and HBV RNA quasispecies showed different evolution patterns in entecavir and pegylated-interferon mono-treatment. Taken together, serum HBV RNA may serve as a promising biomarker of HBeAg seroconversion in patients during antiviral treatment.
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10
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Ko HY, Salem GM, Chang GJJ, Chao DY. Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology. Front Microbiol 2020; 11:1371. [PMID: 32636827 PMCID: PMC7318875 DOI: 10.3389/fmicb.2020.01371] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Dengue viral (DENV) infection results in a wide spectrum of clinical manifestations from asymptomatic, mild fever to severe hemorrhage diseases upon infection. Severe dengue is the leading cause of pediatric deaths and/or hospitalizations, which are a major public health burden in dengue-endemic or hyperendemic countries. Like other RNA viruses, DENV continues to evolve. Adaptive mutations are obscured by the major consensus sequence (so-called wild-type sequences) and can only be identified once they become the dominant viruses in the virus population, a process that can take months or years. Traditional surveillance systems still rely on Sanger consensus sequencing. However, with the recent advancement of high-throughput next-generation sequencing (NGS) technologies, the genome-wide investigation of virus population within-host and between-hosts becomes achievable. Thus, viral population sequencing by NGS can increase our understanding of the changing epidemiology and evolution of viral genomics at the molecular level. This review focuses on the studies within the recent decade utilizing NGS in different experimental and epidemiological settings to understand how the adaptive evolution of dengue variants shapes the dengue epidemic and disease severity through its transmission. We propose three types of studies that can be pursued in the future to enhance our surveillance for epidemic prediction and better medical management.
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Affiliation(s)
- Hui-Ying Ko
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gielenny M Salem
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gwong-Jen J Chang
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, United States
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
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11
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Mandary MB, Masomian M, Ong SK, Poh CL. Characterization of Plaque Variants and the Involvement of Quasi-Species in a Population of EV-A71. Viruses 2020; 12:E651. [PMID: 32560288 PMCID: PMC7354493 DOI: 10.3390/v12060651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 12/13/2022] Open
Abstract
Viral plaque morphologies in human cell lines are markers for growth capability and they have been used to assess the viral fitness and selection of attenuated mutants for live-attenuated vaccine development. In this study, we investigate whether the naturally occurring plaque size variation reflects the virulence of the variants of EV-A71. Variants of two different plaque sizes (big and small) from EV-A71 sub-genotype B4 strain 41 were characterized. The plaque variants displayed different in vitro growth kinetics compared to the parental wild type. The plaque variants showed specific mutations being present in each variant strain. The big plaque variants showed four mutations I97L, N104S, S246P and N282D in the VP1 while the small plaque variants showed I97T, N237T and T292A in the VP1. No other mutations were detected in the whole genome of the two variants. The variants showed stable homogenous small plaques and big plaques, respectively, when re-infected in rhabdomyosarcoma (RD) and Vero cells. The parental strain showed faster growth kinetics and had higher viral RNA copy number than both the big and small plaque variants. Homology modelling shows that both plaque variants have differences in the structure of the VP1 protein due to the presence of unique spontaneous mutations found in each plaque variant This study suggests that the EV-A71 sub-genotype B4 strain 41 has at least two variants with different plaque morphologies. These differences were likely due to the presence of spontaneous mutations that are unique to each of the plaque variants. The ability to maintain the respective plaque morphology upon passaging indicates the presence of quasi-species in the parental population.
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Affiliation(s)
- Madiiha Bibi Mandary
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia; (M.B.M.); (M.M.)
| | - Malihe Masomian
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia; (M.B.M.); (M.M.)
| | - Seng-Kai Ong
- Department of Biological Science, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia;
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia; (M.B.M.); (M.M.)
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12
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Wang M, Li J, Zhang X, Han Y, Yu D, Zhang D, Yuan Z, Yang Z, Huang J, Zhang X. An integrated software for virus community sequencing data analysis. BMC Genomics 2020; 21:363. [PMID: 32414327 PMCID: PMC7227348 DOI: 10.1186/s12864-020-6744-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND A virus community is the spectrum of viral strains populating an infected host, which plays a key role in pathogenesis and therapy response in viral infectious diseases. However automatic and dedicated pipeline for interpreting virus community sequencing data has not been developed yet. RESULTS We developed Quasispecies Analysis Package (QAP), an integrated software platform to address the problems associated with making biological interpretations from massive viral population sequencing data. QAP provides quantitative insight into virus ecology by first introducing the definition "virus OTU" and supports a wide range of viral community analyses and results visualizations. Various forms of QAP were developed in consideration of broader users, including a command line, a graphical user interface and a web server. Utilities of QAP were thoroughly evaluated with high-throughput sequencing data from hepatitis B virus, hepatitis C virus, influenza virus and human immunodeficiency virus, and the results showed highly accurate viral quasispecies characteristics related to biological phenotypes. CONCLUSIONS QAP provides a complete solution for virus community high throughput sequencing data analysis, and it would facilitate the easy analysis of virus quasispecies in clinical applications.
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Affiliation(s)
- Mingjie Wang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China
| | - Jianfeng Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xiaonan Zhang
- Key Lab of Medicine Molecular Virology of MOE/MOH, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Yue Han
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China
| | - Demin Yu
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China
| | - Donghua Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China
| | - Zhenghong Yuan
- Key Lab of Medicine Molecular Virology of MOE/MOH, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Zhitao Yang
- Emergency Department, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China.
| | - Jinyan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
| | - Xinxin Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China. .,Clinical Research Center, Ruijin Hospital North, Shanghai Jiaotong University, School of Medicine, Shanghai, 201821, China.
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13
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Xiao Y, Sun K, Duan Z, Liu Z, Li Y, Yan L, Song Y, Zou H, Zhuang H, Wang J, Li J. Quasispecies characteristic in "a" determinant region is a potential predictor for the risk of immunoprophylaxis failure of mother-to-child-transmission of sub-genotype C2 hepatitis B virus: a prospective nested case-control study. Gut 2020; 69:933-941. [PMID: 31446427 PMCID: PMC7229894 DOI: 10.1136/gutjnl-2019-318278] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 08/05/2019] [Accepted: 08/17/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE This study was performed to explore the correlation between the characteristics of hepatitis B virus (HBV) quasispecies in HBV-infected pregnant women and the risk of immunoprophylaxis failure for their infants. DESIGN In this prospective nested case-control study, the characteristics of HBV quasispecies in mothers whose infants were immunoprophylaxis success (control group) and those whose infants were immunoprophylaxis failure (case group) were analysed by the clone-based sequencing of full-length HBV genome and next-generation sequencing (NGS) of "a" determinant region, and were compared between the two groups. RESULTS The quasispecies characteristics including mutant frequency, Shannon entropy and mean genetic distance at amino acid level of "a" determinant region were significantly lower in case group than that in control group, using the full-length HBV genome clone-based sequencing assay. These results were confirmed by NGS assay. Notably, we discovered that the differences were also significant at nucleotide level by NGS assay. Furthermore, the risk of immunoprophylaxis failure could be predicted by analysing the three HBV quasispecies characteristics either at nucleotide level or at amino acid level of "a" determinant region, and the corresponding predictive values were tentatively set up. CONCLUSIONS HBV quasispecies with a more complex mutant spectrum in "a" determinant region might be more vulnerable to extinct through mother-to-child-transmission (MTCT). More importantly, analysing HBV quasispecies characteristics in pregnant women with high HBV DNA load might be helpful to predict the high-risk population of immunoprophylaxis failure, and consequently provide accurate intervention against MTCT of HBV.
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Affiliation(s)
- Yiwei Xiao
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Kuixia Sun
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China,Department of Clinical Laboratory, Peking University First Hospital, Beijing, 100034, P.R. China
| | - Zhongping Duan
- Artificial Liver Center, Beijing Youan Hospital, Capital Medical University, Beijing, 100054, P.R. China
| | - Zhixiu Liu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Yi Li
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Ling Yan
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Yarong Song
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Huaibin Zou
- Artificial Liver Center, Beijing Youan Hospital, Capital Medical University, Beijing, 100054, P.R. China
| | - Hui Zhuang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Jie Wang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
| | - Jie Li
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, P.R. China
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14
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Mei F, Ren J, Long L, Li J, Li K, Liu H, Tang Y, Fang X, Wu H, Xiao C, Huang T, Deng W. Analysis of HBV X gene quasispecies characteristics by next-generation sequencing and cloning-based sequencing and its association with hepatocellular carcinoma progression. J Med Virol 2019; 91:1087-1096. [PMID: 30712269 DOI: 10.1002/jmv.25421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVES This study aimed to describe the differences between next-generation sequencing (NGS) and cloning-based sequencing (CBS) in HBX quasispecies research and primitively investigate the relationship between the dominant HBX quasispecies and hepatocellular carcinoma (HCC). METHODS A total of 12 serum samples were collected. Serum hepatitis B virus (HBV) DNA was extracted, and the HBV X-region (HBX) was amplified by nested polymerase chain reaction (PCR). The PCR products were simultaneously tested with NGS and CBS to detect quasispecies of the HBX. RESULTS A total of 9348 eligible quasispecies sequences were obtained by NGS, which were much larger than the 98 of that by CBS. By the phylogenetic tree, the dominant quasispecies sequence of each sample could be found, although they had several nucleotides differences between the dominant quasispecies sequences found by CBS and NGS. By comparing the quasispecies heterogeneity, it was found that the quasispecies complexity value of HBV X-region obtained by NGS was higher than CBS (P < 0.05). The diversity values, including d, dS, dN, an d d N/ dS obtained by NGS were lower than by CBS (all of P < 0.01). The relativity of Spearman(rs) in d, dS, and dN were statistically significant (rs_ d = 0.865, P = 0.001; rs_ dS = 0.722, P = 0.014; and rs_ dN = 0.738, P = 0.011, respectively). There were 21 different bases between the HBX quasispecies of case A and control B. CONCLUSION The results of this can be used as guidance when researchers plan to choose a suitable method to study quasispecies, especially the HBV X gene quasispecies. Some high-risk mutations of HBX quasispecies were also found in this study and their relationship with HCC need deeper exploration.
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Affiliation(s)
- Fanbiao Mei
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jingjing Ren
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Long Long
- The Faculty of Big Data, Guangxi Teachers Education University, Nanning, Guangxi, China
| | - Jilin Li
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Kezhi Li
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Haizhou Liu
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yanping Tang
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiang Fang
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hanghang Wu
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Chanchan Xiao
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Tianren Huang
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wei Deng
- Experimental Research Department, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
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15
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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.
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16
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Sopena S, Godoy C, Tabernero D, Homs M, Gregori J, Riveiro-Barciela M, Ruiz A, Esteban R, Buti M, Rodríguez-Frías F. Quantitative characterization of hepatitis delta virus genome edition by next-generation sequencing. Virus Res 2018; 243:52-59. [PMID: 28988126 DOI: 10.1016/j.virusres.2017.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 10/02/2017] [Accepted: 10/02/2017] [Indexed: 02/07/2023]
Abstract
AIM To determine the capacity of next-generation sequencing (NGS) for quantifying edited and unedited HDV populations, and to confirm if edition is a general phenomenon taking place along the entire HDV region analyzed, as we previously reported (Homs M et al. PLoS One 2016, 11, e0158557). METHODS Four serum samples from 4 patients with chronic HDV/HBV infection were included in the study. The region selected for analysis covered 360 nucleotides (nt), positions 910-1270 of the HDV genome, which included the HDAg ORF editing site (nt 1014 within codon 196). Quantification of edited and unedited genomes was performed by molecular cloning and Sanger sequencing and by NGS. To evaluate the reliability of the NGS values obtained, we combined a clone with an edited codon and one with an unedited codon in known percentages in a series of artificial mixtures, which were then analyzed by NGS. In addition, we determined the nt changes occurring over the complete amplified region after excluding the editing codon (196) to evaluate edition along it. RESULTS In total, 11,208 quality-filtered sequences were obtained in the 4 samples. The 95% confidence intervals for the proportions of unedited populations by molecular cloning and NGS were overlapping, and those of cloning were wider, indicating that they are comparable and that NGS is more precise than cloning. Unedited genomes predominated over edited ones in all 4 samples analyzed by NGS and in 3 of the 4 samples analyzed by molecular cloning. In total, 83,276 quality-filtered sequences were obtained from the artificial mixtures. Percentages of the two viral populations detected by NGS in these mixtures were comparable to the expected percentages. Evaluation of edition along the HDV coding region showed that transitions were more frequent than transversions, accounting for 63.09% and 36.91%, respectively. Interestingly, among the 4 possible transition-type changes, G:A and A:G accounted for 73.86% of the total. CONCLUSION Next-generation sequencing proved useful to quantify edited and unedited HDV genomes, and provided relevant information on the HDV quasispecies.
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Affiliation(s)
- Sara Sopena
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
| | - Cristina Godoy
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
| | - Maria Homs
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Roche Diagnostics SL, 08174 Sant Cugat del Vallès, Spain.
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
| | - Alicia Ruiz
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
| | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
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A comparative study on the characterization of hepatitis B virus quasispecies by clone-based sequencing and third-generation sequencing. Emerg Microbes Infect 2017; 6:e100. [PMID: 29116219 PMCID: PMC5717089 DOI: 10.1038/emi.2017.88] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/12/2017] [Accepted: 09/17/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) has a high mutation rate due to the extremely high replication rate and the proofreading deficiency during reverse transcription. The generated variants with genetic heterogeneity are described as viral quasispecies (QS). Clone-based sequencing (CBS) is thought to be the ‘gold standard’ for assessing QS complexity and diversity of HBV, but an important issue about CBS is cost-effectiveness and laborious. In this study, we investigated the utility of the third-generation sequencing (TGS) DNA sequencing to characterize genetic heterogeneity of HBV QS and assessed the possible contribution of TGS technology in HBV QS studies. Parallel experiments including 3 control samples, which consisted of HBV full gene genotype B and genotype C plasmids, and 10 patients samples were performed by using CBS and TGS to analyze HBV whole-genome QS. Characterization of QS heterogeneity was conducted by using comprehensive statistical analysis. The results showed that TGS had a high consistency with CBS when measuring the complexity and diversity of QS. In addition, to detect rare variants, there were strong advantages conferred by TGS. In summary, TGS was considered to be practicable in HBV QS studies and it might have a relevant role in the clinical management of HBV infection in the future.
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Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing. Sci Rep 2017; 7:10168. [PMID: 28860476 PMCID: PMC5578979 DOI: 10.1038/s41598-017-10591-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 08/11/2017] [Indexed: 02/07/2023] Open
Abstract
Despite full immunoprophylaxis, mother-to-child transmission (MTCT) of Hepatitis B Virus still occurs in approximately 2–5% of HBsAg positive mothers. Little is known about the bottleneck of HBV transmission and the evolution of viral quasispecies in the context of MTCT. Here we adopted a newly developed tag linkage deep sequencing method and analyzed the quasispecies of four MTCT pairs that broke through immunoprophylaxis. By assigning unique tags to individual viral sequences, we accurately reconstructed HBV haplotypes in a region of 836 bp, which contains the major immune epitopes and drug resistance mutations. The detection limit of minor viral haplotypes reached 0.1% for individual patient sample. Dominance of “a determinant” polymorphisms were observed in two children, which pre-existed as minor quasispecies in maternal samples. In all four pairs of MTCT samples, we consistently observed a significant overlap of viral haplotypes shared between mother and child. We also demonstrate that the data can be potentially useful to estimate the bottleneck effect during HBV MTCT, which provides information to optimize treatment for reducing the frequency of MTCT.
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19
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F221Y mutation in hepatitis B virus reverse transcriptase is associated with hepatocellular carcinoma prognosis following liver resection. Mol Med Rep 2017; 15:3292-3300. [PMID: 28339094 DOI: 10.3892/mmr.2017.6362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 02/09/2017] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) reverse transcriptase (RT) is encoded by the polymerase gene in the reverse transcriptase region, which overlaps with the S gene. The association between mutations of HBV RT and the pathobiological features of hepatocellular carcinoma (HCC) remain to be elucidated. The present study aimed to examine mutations in this region of the HBV genome and its clinical significance. Briefly, HBV total DNA was extracted from 84 pairs of HCC tumor tissue and corresponding adjacent non‑tumor tissue samples. The RT/S regions (nt130‑1161) were amplified and sequenced using the Sanger method, and associations between RT mutations and the clinical characteristics of patients with HCC were analyzed. Finally, 27 and 29 mutations with frequencies >5% were identified in the RT and S regions, respectively. The rtF221Y variation and a tumor size >8 cm were found to be independent risk factors for the postoperative recurrence of HCC, with hazard ratios of 2.345 (95% CI, 1.391‑3.953; P=0.001) and 1.838 (95% CI, 1.069‑3.161; P=0.028), respectively. rtF221Y was also an independent risk factor for poor overall survival rates (HR=2.557; 95% CI, 1.344‑4.866; P=0.004). The mutation of R122 K in the HBV S protein was closely associated with tumor recurrence (P<0.001). As a result, rtF221Y was identified as a risk factor for poor prognosis and may be a potential viral marker for predicting prognosis in HCC.
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20
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Yu F, Lu Z, Cai J, Huang K, Chen B, Li G, Dong P, Zheng J. MALAT1 functions as a competing endogenous RNA to mediate Rac1 expression by sequestering miR-101b in liver fibrosis. Cell Cycle 2016; 14:3885-96. [PMID: 26697839 DOI: 10.1080/15384101.2015.1120917] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Emerging evidence shows that Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) plays a pivotal role in cell proliferation, migration, and invasion in tumors. However, the biological role and underlying mechanism of MALAT1 in liver fibrosis remains undefined. In this study, up-regulation of MALAT1 was observed in fibrotic liver tissues and in activated hepatic stellate cells (HSCs). In addition, depletion of MALAT1 inhibited the activation of HSCs in vitro and attenuated collagen deposits in vivo. Our results demonstrated that MALAT1 expression is negatively correlated with microRNA-101b (miR-101b) expression. Furthermore, there was a negative feedback loop between the levels of MALAT1 and miR-101b. Luciferase reporter assay indicated that MALAT1 and RAS-related C3 botulinum substrate 1 (Rac1) are targets of miR-101b. We uncovered that MALAT1 regulates Rac1 expression through miR-101b as a competing endogenous RNA (ceRNA), thereby influencing the proliferation, cell cycle and activation of primary HSCs. Collectively, The ceRNA regulatory network may prompt a better understanding of liver fibrogenesis and contribute to a novel therapeutic strategy for liver fibrosis.
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Affiliation(s)
- Fujun Yu
- a Department of Infectious Diseases ; The First Affiliated Hospital of Wenzhou Medical University ; Wenzhou , China
| | - Zhongqiu Lu
- b Department of Emergency ; The First Affiliated Hospital of Wenzhou Medical University ; Wenzhou , China
| | - Jing Cai
- c Department of Gastroenterology ; Wenzhou central Hospital ; Wenzhou , China
| | - Kate Huang
- d Department of Pathology ; The First Affiliated Hospital of Wenzhou Medical University ; Wenzhou , China
| | - Bicheng Chen
- e Wenzhou Key Laboratory of Surgery; The First Affiliated Hospital of Wenzhou Medical University ; Wenzhou , China
| | - Guojun Li
- f Department of Hepatology ; Ningbo Yinzhou Second Hospital ; Ningbo , China
| | - Peihong Dong
- a Department of Infectious Diseases ; The First Affiliated Hospital of Wenzhou Medical University ; Wenzhou , China
| | - Jianjian Zheng
- e Wenzhou Key Laboratory of Surgery; The First Affiliated Hospital of Wenzhou Medical University ; Wenzhou , China
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21
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Hepatitis B virus resistance substitutions: long-term analysis by next-generation sequencing. Arch Virol 2016; 161:2885-91. [PMID: 27447462 DOI: 10.1007/s00705-016-2959-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/28/2016] [Indexed: 01/07/2023]
Abstract
HBV phylogenetics and resistance-associated mutations (RAMs) were surveyed by next-generation sequencing of 21 longitudinal samples from seven patients entering antiviral therapy. The virus populations were dominated by a few abundant lineages that coexisted with substantial numbers of low-frequency variants. A few low-frequency RAMs were observed before treatment, but new ones emerged, and their frequencies increased during therapy. Together, these results support the idea that chronic HBV infection is dominated by a few virus lineages and that an accompanying plethora of diverse, low-frequency variants may function as a reservoir that potentially contribute to viral genetic plasticity, potentially affecting patient outcome.
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Soverini S, de Benedittis C, Mancini M, Martinelli G. Mutations in the BCR-ABL1 Kinase Domain and Elsewhere in Chronic Myeloid Leukemia. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2016; 15 Suppl:S120-8. [PMID: 26297264 DOI: 10.1016/j.clml.2015.02.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 01/14/2015] [Accepted: 02/26/2015] [Indexed: 12/21/2022]
Abstract
Chronic myeloid leukemia (CML) has been the first human malignancy to be associated, more than 50 years ago, with a consistent chromosomal abnormality--the t(9;22)(q34;q11) chromosomal translocation. The resulting BCR-ABL1 fusion gene, encoding a tyrosine kinase with deregulated activity, has a central role in the pathogenesis of CML. Ancestral or additional genetic events necessary for CML to develop have long been hypothesized but never really demonstrated. CML can successfully be treated with tyrosine kinase inhibitors (TKIs). Mutations in the BCR-ABL1 kinase domain might arise, however, that confer resistance to 1 or more of the currently available TKIs. Hence, the critical role of BCR-ABL1 mutation screening for optimal therapeutic management, with the current gold standard technique, conventional sequencing, likely to be replaced soon by ultra-deep sequencing. Mutations in genes other than BCR-ABL1 include ASXL1, TET2, RUNX1, DNMT3A, EZH2, and TP53 in chronic phase patients and RUNX1, ASXL1, IKZF1, WT1, TET2, NPM1, IDH1, IDH2, NRAS, KRAS, CBL, TP53, CDKN2A, RB1, and GATA-2 mutations in advanced phase patients. The latter also display additional cytogenetic abnormalities, including submicroscopic regions of gain or loss that only single nucleotide polymorphism arrays or array comparative genomic hybridization can detect. Whether whole genome/exome sequencing studies will uncover novel mutations relevant for pathogenesis, progression, and risk-adapted therapy is still unclear.
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Affiliation(s)
- Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology "L. e A. Seràgnoli," University of Bologna, Bologna, Italy.
| | - Caterina de Benedittis
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology "L. e A. Seràgnoli," University of Bologna, Bologna, Italy
| | - Manuela Mancini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology "L. e A. Seràgnoli," University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology "L. e A. Seràgnoli," University of Bologna, Bologna, Italy
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23
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Pérez PS, Di Lello FA, Mullen EG, Galdame OA, Livellara BI, Gadano AC, Campos RH, Flichman DM. Compartmentalization of hepatitis C virus variants in patients with hepatocellular carcinoma. Mol Carcinog 2016; 56:371-380. [PMID: 27163636 DOI: 10.1002/mc.22500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 04/03/2016] [Accepted: 05/02/2016] [Indexed: 12/24/2022]
Abstract
Chronic Hepatitis C Virus (HCV) infection is a major risk for hepatocellular carcinoma (HCC) development. HCV Core protein has been associated with the modulation of potentially oncogenic cellular processes and E2 protein has been useful in evolutive studies to analyze the diversity of HCV. Thus, the aim of this study was to evaluate HCV compartmentalization in tumoral, non-tumoral liver tissue and serum and to identify viral mutations potentially involved in carcinogenesis. Samples were obtained from four patients with HCC who underwent liver transplantation. Core and E2 were amplified, cloned and sequenced. Phylogenies and BaTS Test were performed to analyze viral compartmentalization and a signature sequence analysis was conducted by VESPA. The likelihood and Bayesian phylogenies showed a wide degree of compartmentalization in the different patients, ranging from total clustering to a more scattered pattern with small groups. Nevertheless, the association test showed compartmentalization for the three compartments and both viral regions tested in all the patients. Signature amino acid pattern supported the compartmentalization in three of the cases for E2 protein and in two of them for Core. Changes observed in Core included polymorphism R70Q/H previously associated with HCC. In conclusion, evidence of HCV compartmentalization in the liver of HCC patients was provided and further biological characterization of these variants may contribute to the understanding of carcinogenesis mediated by HCV infection. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Paula S Pérez
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico A Di Lello
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Omar A Galdame
- Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Rodolfo H Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego M Flichman
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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24
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Soverini S, De Benedittis C, Mancini M, Martinelli G. Present and future of molecular monitoring in chronic myeloid leukaemia. Br J Haematol 2016; 173:337-49. [PMID: 26947577 DOI: 10.1111/bjh.13966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Currently, physicians treating chronic myeloid leukaemia (CML) patients can rely on a wide spectrum of therapeutic options: the best use of such options is essential to achieve excellent clinical outcomes and, possibly, treatment-free remission (TFR). To accomplish this, proper integration of expert clinical and laboratory monitoring of CML patients is fundamental. Molecular response (MR) monitoring of patients at defined time points has emerged as an important success factor for optimal disease management and BCR-ABL1 kinase domain mutation screening is useful to guide therapeutic reassessment in patients who do not achieve optimal responses to tyrosine kinase inhibitor therapy. Deeper MRs might be associated with improved long-term survival outcomes. More importantly, they are considered a gateway to TFR. In molecular biology, novel procedures and technologies are continually being developed. More sophisticated molecular tools and automated analytical solutions are emerging as CML treatment endpoints and expectations become more and more ambitious. Here we provide a critical overview of current and novel methodologies, present their strengths and pitfalls and discuss what their present and future role might be.
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Affiliation(s)
- Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Caterina De Benedittis
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Manuela Mancini
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
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25
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Zhang ZH, Wu CC, Chen XW, Li X, Li J, Lu MJ. Genetic variation of hepatitis B virus and its significance for pathogenesis. World J Gastroenterol 2016; 22:126-144. [PMID: 26755865 PMCID: PMC4698480 DOI: 10.3748/wjg.v22.i1.126] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) has a worldwide distribution and is endemic in many populations. Due to its unique life cycle which requires an error-prone reverse transcriptase for replication, it constantly evolves, resulting in tremendous genetic variation in the form of genotypes, sub-genotypes, and mutations. In recent years, there has been considerable research on the relationship between HBV genetic variation and HBV-related pathogenesis, which has profound implications in the natural history of HBV infection, viral detection, immune prevention, drug treatment and prognosis. In this review, we attempted to provide a brief account of the influence of HBV genotype on the pathogenesis of HBV infection and summarize our current knowledge on the effects of HBV mutations in different regions on HBV-associated pathogenesis, with an emphasis on mutations in the preS/S proteins in immune evasion, occult HBV infection and hepatocellular carcinoma (HCC), mutations in polymerase in relation to drug resistance, mutations in HBV core and e antigen in immune evasion, chronicalization of infection and hepatitis B-related acute-on-chronic liver failure, and finally mutations in HBV x proteins in HCC.
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26
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Molecular Detection and Characterization of Hepatitis B Virus. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chen S, Wu J, Gu E, Shen Y, Wang F, Zhang W. Evaluation of the dynamic pattern of viral evolution in patients with virological breakthrough during treatment with nucleoside/nucleotide analogs by ultra‑deep pyrosequencing. Mol Med Rep 2015; 13:651-60. [PMID: 26648309 PMCID: PMC4686096 DOI: 10.3892/mmr.2015.4577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 09/14/2015] [Indexed: 12/23/2022] Open
Abstract
Virological breakthrough is a clinical manifestation in patients infected with chronic hepatitis B (CHB), who undergo treatment with nucleoside/nucleotide analogs (NUCs). The current understanding of the underlying mechanism of virological breakthrough is limited. Ultra‑deep pyrosequencing (UDPS) is a novel and powerful tool used to investigate minor viral variants and viral evolution. The present study used UDPS to investigate the viral evolution pattern during virological breakthrough in patients with CHB treated with NUCs. A total of 12 patients who experienced virological breakthrough were recruited in the present study. During the treatment with lamivudine, adefovir was added as a rescue therapy when virological breakthrough emerged, and the therapy was continued until week 96. Serum samples from each patient were collected at different time points for UDPS analysis. Treatment with lamivudine resulted in an increased rate of the viral mutations, rtM204V/I, rtL180M and rtL80I. Virological breakthrough was accompanied by significant rtM204I/V substitutions in eight of the patients. A total of three types of rt204 mutation, associated with virological breakthrough, were observed, including YIDD variant‑dominated, YVDD variant‑dominated and YMDD wild‑type‑dominated virological breakthrough. YVDD variants reverted to the wild‑type following the adefovir add‑on rescue therapy, although the YIDD variants remained dominant following the combination therapy. The mechanism underlying virological breakthrough was revealed to be complex and associated with the rapid replication of mutated variants. UDPS analysis, therefore, provided a useful tool to investigate the dynamic evolution pattern of hepatitis B virus.
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Affiliation(s)
- Shaolong Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jing Wu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Erli Gu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Yaojie Shen
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Feifei Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
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28
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Han Y, Gong L, Sheng J, Liu F, Li XH, Chen L, Yu DM, Gong QM, Hao P, Zhang XX. Prediction of virological response by pretreatment hepatitis B virus reverse transcriptase quasispecies heterogeneity: the advantage of using next-generation sequencing. Clin Microbiol Infect 2015; 21:797.e1-8. [PMID: 25882357 DOI: 10.1016/j.cmi.2015.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/18/2015] [Accepted: 03/28/2015] [Indexed: 02/07/2023]
Abstract
Prediction of antiviral efficacy prior to treatment remains largely unavailable. We have previously demonstrated the clinical value of on-treatment hepatitis B virus (HBV) reverse transcriptase (RT) quasispecies (QS) evolution patterns. In this study, we aimed to elucidate the relevance for prediction of pretreatment HBV RT QS characteristics by comparing the performance of next-generation sequencing (NGS) and clone-based Sanger sequencing (CBS). Thirty-six lamivudine-treated patients were retrospectively studied, including 18 responders and 18 non-responders. CBS and NGS data of pretreatment serum HBV were used to generate RT QS genetic complexity and diversity scores, according to our previous studies. The ability of both methods to predict responsiveness was evaluated with receiver operating characteristic (ROC) curves. A cut-off value was generated on the basis of prediction ability. Responders had significantly higher pretreatment RT QS genetic complexity and diversity (in the first two parts, which overlapped with the S gene, at both the nucleotide and amino acid levels) than non-responders by NGS-based testing. NGS-based algorithms predicted response better than CBS in the ROC curve analysis. The mean distance of the second contig had the highest area under the curve (AUC) value. When the cut-off value was set to 0.007186, the difference between survival curves was significant (p 0.0090). Pretreatment HBV RT QS heterogeneity in the overlapping region of the RT and S genes could be a predictor of antiviral efficacy. NGS improves the predictions of virological outcomes relative to CBS algorithms. This may have important implications for the clinical management of subjects chronically infected with HBV.
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Affiliation(s)
- Y Han
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - L Gong
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Department of Liver Diseases, the Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - J Sheng
- Shanghai Centre for Bioinformation Technology, China
| | - F Liu
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - X-H Li
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - L Chen
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - D-M Yu
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Q-M Gong
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - P Hao
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, China
| | - X-X Zhang
- Department of Infectious Diseases, Institute of Infectious and Respiratory Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Translational Medicine Research Centre, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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29
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Montoya V, Olmstead AD, Janjua NZ, Tang P, Grebely J, Cook D, Richard Harrigan P, Krajden M. Differentiation of acute from chronic hepatitis C virus infection by nonstructural 5B deep sequencing: a population-level tool for incidence estimation. Hepatology 2015; 61:1842-50. [PMID: 25645961 DOI: 10.1002/hep.27734] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/28/2015] [Indexed: 01/19/2023]
Abstract
UNLABELLED The ability to classify acute versus chronic hepatitis C virus (HCV) infections at the time of diagnosis is desirable to improve the quality of surveillance information. The aim of this study was to differentiate acute from chronic HCV infections utilizing deep sequencing. HCV nonstructural 5B (NS5B) amplicons (n = 94) were generated from 77 individuals (13 acute and 64 chronic HCV infections) in British Columbia, Canada, with documented seroconversion time frames. Amplicons were deep sequenced and HCV genomic diversity was measured by Shannon entropy (SE) and a single nucleotide variant (SNV) analysis. The relationship between each diversity measure and the estimated days since infection was assessed using linear mixed models, and the ability of each diversity measure to differentiate acute from chronic infections was assessed using generalized estimating equations. Both SE and the SNV diversity measures were significantly different for acute versus chronic infections (P < 0.009). NS5B nucleotide diversity continued to increase for at least 3 years postinfection. Among individuals with the least uncertainty with regard to duration of infection (n = 39), the area under the receiver operating characteristic curve (AUROC) was high (0.96 for SE; 0.98 for SNV). Although the AUROCs were lower (0.86 for SE; 0.80 for SNV) when data for all individuals were included, they remain sufficiently high for epidemiological purposes. Synonymous mutations were the primary discriminatory variable accounting for over 78% of the measured genetic diversity. CONCLUSIONS NS5B sequence diversity assessed by deep sequencing can differentiate acute from chronic HCV infections and, with further validation, could become a powerful population-level surveillance tool for incidence estimation.
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Affiliation(s)
- Vincent Montoya
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea D Olmstead
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Naveed Z Janjua
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick Tang
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Jason Grebely
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Darrel Cook
- BC Center for Disease Control, Vancouver, British Columbia, Canada
| | - P Richard Harrigan
- BC Center for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Mel Krajden
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
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30
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Wang YW, Shan X, Huang Y, Deng H, Huang WX, Zhang DZ, Chen J, Tang N, Shan YL, Guo JJ, Huang A. A novel baseline hepatitis B virus sequencing-based strategy for predicting adefovir antiviral response. INFECTION GENETICS AND EVOLUTION 2015; 33:269-76. [PMID: 25983054 DOI: 10.1016/j.meegid.2015.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/25/2015] [Accepted: 05/14/2015] [Indexed: 02/07/2023]
Abstract
Adefovir dipivoxil (ADV) is used as first-line monotherapy or rescue therapy in chronic hepatitis B (CHB) patients. In this study, we sought to identify nucleotide changes in the reverse transcriptase (RT) of hepatitis B virus (HBV) at baseline and explore their predictive value for ADV antiviral response. Ultra-deep pyrosequencing (UDPS) was utilized to determine HBV genetic variability within the RT region at baseline and during a 48-week ADV therapy. According to the viral load at the end of ADV treatment, all patients were classified into responders (HBV DNA level reduction of ⩾ 3 log 10 IU/mL) and suboptimal responders (HBV DNA level reduction of <3 log 10 IU/mL). Based on UDPS data at baseline, we identified 11 nucleotide substitutions whose combination frequency was significantly associated with the antiviral response among 36 CHB patients in the study group. However, the baseline distribution and frequency of rt181 and rt236 substitutions known to confer ADV resistance was a poor predictor for the antiviral response. Compared with baseline serum HBeAg, HBV-DNA and ALT levels, the baseline HBV sequence-based model showed higher predictive accuracy for ADV response. In an independent cohort of 31 validation patients with CHB, the sequence-based model provided greater predictive potency than the HBeAg/HBV-DNA/ALT and the HBeAg/HBV-DNA/ALT/sequence combinations. Taken together, we confirm the presence of ADV resistance variants in treatment-naïve patients and firstly unravel the predictive value of the baseline mutations in the HBV RT region for ADV antiviral response.
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Affiliation(s)
- Yu-Wei Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China; Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Xuefeng Shan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China; Department of Pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yao Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Haijun Deng
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Wen-Xiang Huang
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Da-Zhi Zhang
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Chen
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ni Tang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - You-Lan Shan
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jin-Jun Guo
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Ailong Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
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Characterization of Full-Length Genomes of Hepatitis B Virus Quasispecies in Sera of Patients at Different Phases of Infection. J Clin Microbiol 2015; 53:2203-14. [PMID: 25926495 DOI: 10.1128/jcm.00068-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/24/2015] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B virus (HBV) infection results in different clinical presentation due to different levels of immune response. Our study aimed to characterize HBV full-length genome quasispecies (QS) in patients with different phases of infection to better understand its pathogenesis. Forty treatment-naive HBV-infected patients were enrolled, including 10 cases of acute hepatitis B (AHB), 9 cases of immunotolerant (IT) HBV carriers, 11 cases of chronic hepatitis B (CHB), and 10 cases of acute-on-chronic liver failure (ACLF). The present study was conducted by clone-based sequencing. QS heterogeneity within each open reading frame was calculated. The mutation frequency index (MFI) and amino acid variations within the large HBsAg, HBcAg, and HBxAg regions were analyzed based on the different infection phases. In total, 606 HBV full-length sequences were obtained. HBV QS had higher heterogeneity in ACLF and CHB than that in IT among chronically infected individuals. AHB patients had the lower QS heterogeneity at onset than those with chronic infection. ACLF patients had the highest frequency of mutations in the core promoter and precore region. A triple mutation (A1762T/G1764A/G1896A) was observed more frequently in genotype C than in genotype B. The MFI indicated that specific peptides of the studied regions had more frequent mutations in ACLF. Furthermore, several amino acid variations, known as T- and B-cell epitopes, were potentially associated with the immunoactive phase of infection. More HBV genome mutations and deletions were observed in patients with more severe diseases, particularly in specific regions of the core and preS regions, the clinical significance and mechanism of which need to be further investigated.
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Yano Y, Azuma T, Hayashi Y. Variations and mutations in the hepatitis B virus genome and their associations with clinical characteristics. World J Hepatol 2015; 7:583-92. [PMID: 25848482 PMCID: PMC4381181 DOI: 10.4254/wjh.v7.i3.583] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/27/2014] [Accepted: 12/29/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) infection is major global issue, because chronic HBV infection is strongly associated with liver cancer. HBV spread worldwide with various mutations and variations. This variability, called quasispecies, is derived from no proof-reading capacity of viral reverse transcriptase. So far, thousands of studies reported that the variety of genome is closely related to the geographic distribution and clinical characteristics. Recent technological advances including capillary sequencer and next generation sequencer have made in easier to analyze mutations. The variety of HBV genome is related to not only antigenicity of HBs-antigen but also resistance to antiviral therapies. Understanding of these variations is important for the development of diagnostic tools and the appropriate therapy for chronic hepatitis B. In this review, recent publications in relation to HBV mutations and variations are updated and summarized.
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Affiliation(s)
- Yoshihiko Yano
- Yoshihiko Yano, Takeshi Azuma, Department of Gastroenterology, Kobe University Graduate School of Medicine, Kusunoki-cho, Kobe 650-0017, Japan
| | - Takeshi Azuma
- Yoshihiko Yano, Takeshi Azuma, Department of Gastroenterology, Kobe University Graduate School of Medicine, Kusunoki-cho, Kobe 650-0017, Japan
| | - Yoshitake Hayashi
- Yoshihiko Yano, Takeshi Azuma, Department of Gastroenterology, Kobe University Graduate School of Medicine, Kusunoki-cho, Kobe 650-0017, Japan
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Datta S, Chatterjee S, Veer V. Recent advances in molecular diagnostics of hepatitis B virus. World J Gastroenterol 2014; 20:14615-14625. [PMID: 25356025 PMCID: PMC4209528 DOI: 10.3748/wjg.v20.i40.14615] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/13/2014] [Accepted: 06/05/2014] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) is one of the important global health problems today. Infection with HBV can lead to a variety of clinical manifestations including severe hepatic complications like liver cirrhosis and hepatocellular carcinoma. Presently, routine HBV screening and diagnosis is primarily based on the immuno-detection of HBV surface antigen (HBsAg). However, identification of HBV DNA positive cases, who do not have detectable HBsAg has greatly encouraged the use of nucleic acid amplification based assays, that are highly sensitive, specific and are to some extent tolerant to sequence variation. In the last few years, the field of HBV molecular diagnostics has evolved rapidly with advancements in the molecular biology tools, such as polymerase chain reaction (PCR) and real-time PCR. Recently, apart of PCR based amplification methods, a number of isothermal amplification assays, such as loop mediated isothermal amplification, transcription mediated amplification, ligase chain reaction, and rolling circle amplification have been utilized for HBV diagnosis. These assays also offer options for real time detection and integration into biosensing devices. In this manuscript, we review the molecular technologies that are presently available for HBV diagnostics, with special emphasis on isothermal amplification based technologies. We have also included the recent trends in the development of biosensors and use of next generation sequencing technologies for HBV.
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Di Lello FA, Culasso ACA, Parodi C, Baré P, Campos RH, García G. New evidence of replication of hepatitis C virus in short-term peripheral blood mononuclear cell cultures. Virus Res 2014; 191:1-9. [PMID: 25087877 DOI: 10.1016/j.virusres.2014.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND Even though hepatocytes are the main site for hepatitis C virus (HCV) replication, peripheral blood mononuclear cells (PBMC) have also been proposed as a suitable site for HCV replication. However, this issue still remains under discussion. We have previously developed an innovative system where HCV-RNA can be recovered during PBMC culture from HCV infected patients. Thus, the aim of this work was to use this novel approach in order to observe the evolution and replication of HCV genotype 1b in the PBMC of an HIV-HCV coinfected patient. METHODS HCV-RNA was extracted from serum, uncultured PBMC and PBMC culture at day 6, 20 and 33. The evolutionary analysis was performed using the direct sequences of three viral regions: 5'UTR, E2 and NS5A. Additionally, E2 region was cloned in order to extend the evolutive analysis. RESULTS In the present work, the molecular characterization of HCV along the culture showed a clear dynamic evolving process with the appearance of several nucleotide or amino acid changes in the three regions analyzed. Furthermore, the population analysis of E2 clones showed emerging and loss of lineages which indicate the fast evolutive dynamics of this system. CONCLUSIONS Since evolution can take place only if the virus is replicating in the culture, this finding constitutes an important evidence of viral replication in PBMC. Moreover, this extrahepatic compartment could be very important due to the presence of distinctive variants that could be responsible for resistance to treatment, viral pathogenesis and other clinical implications.
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Affiliation(s)
- Federico Alejandro Di Lello
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | | | - Cecilia Parodi
- Instituto de Investigaciones Hematológicas "Mariano R. Castex", Instituto de Medicina Experimental (IMEx), Academia Nacional de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Patricia Baré
- Instituto de Investigaciones Hematológicas "Mariano R. Castex", Instituto de Medicina Experimental (IMEx), Academia Nacional de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rodolfo Héctor Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gabriel García
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
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Clinical implications of evolutionary patterns of homologous, full-length hepatitis B virus quasispecies in different hosts after perinatal infection. J Clin Microbiol 2014; 52:1556-65. [PMID: 24574300 DOI: 10.1128/jcm.03338-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection via perinatal transmission is common in the Asia-Pacific region, but related quasispecies (QS) characteristics are not yet defined. To investigate the homologous, full-length HBV QS after perinatal infection and their clinical implications, five pairs of mother-daughter patients with chronic HBV infection (one patient with liver cirrhosis, one with immune tolerance, and eight with chronic hepatitis) were included. Full-length HBV were amplified by PCR from serum samples before antiviral treatment and cloned; an average of 17 clones per sample were sequenced, and the QS complexities, diversities, and evolution patterns were analyzed. Full-length HBV sequence similarities within mother-daughter pairs were 91.3 to 98.3%. The QS complexities of full-length HBV were similar between mothers and daughters (median of 0.9734 compared to 0.9688, P>0.05), as were the diversities (median of 3.396×10(-3) compared to 4.617×10(-3) substitutions/site, P>0.05). However, the distribution patterns of QS complexities and diversities within specific genes were different, and QS genetic distances of the mothers were higher than those of daughters, both more evident in pairs with different antiviral responses and different immune phases or stages. The nucleotide substitution rate of full-length HBV was 14.388×10(-5) substitutions/site/year, whereas the preC/C gene rate was the highest. Mutations and indels were more common in clones from the mothers, which decreased the affinity of epitopes by 6- to 89-fold. The various genes from homologous HBV genomes evolved in different patterns despite numerically comparable full-length QS complexities and diversities. The different patterns may correlate with the immune stages of chronic HBV infection, which warrants further study.
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