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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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Wong DKH, Kopaniszen M, Omagari K, Tanaka Y, Fong DYT, Seto WK, Fung J, Huang FY, Zhang AY, Hung IFN, Lai CL, Yuen MF. Effect of hepatitis B virus reverse transcriptase variations on entecavir treatment response. J Infect Dis 2014; 210:701-707. [PMID: 24610871 DOI: 10.1093/infdis/jiu133] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Entecavir therapy often reduces hepatitis B virus (HBV) DNA to an undetectable level, but HBV DNA remain detectable in some patients. We investigated whether baseline HBV reverse transcriptase (rt) polymorphism and quasispecies complexity and diversity were associated with treatment response. METHODS Pretreatment HBV DNA levels, HBV rt sequence, serology, and quasispecies complexity and diversity from 305 entecavir-treated patients were determined. These data were tested for their association with year 1 virological outcome, defined by optimal response (undetectable HBV DNA; lower limit of detection, ≤12 IU/mL) or partial response (detectable HBV DNA). RESULTS Four rt variants were more frequently detected in the 64 partial responders than in the 241 optimal responders (all P < .05). Multivariate analysis revealed that high baseline HBV DNA level (P < .0001; odds ratio [OR], 2.32), HBV e antigen (HBeAg) positivity (P < .001; OR, 3.70), and rt124N (P = .002; OR, 3.06) were associated with a partial entecavir response. Compared with the optimal responders, the partial responders had a lower quasispecies complexity and diversity. CONCLUSIONS Apart from the known factors (high baseline HBV DNA level and HBeAg positivity), a novel single nucleotide polymorphism (rt124N) and lower quasispecies complexity and diversity were associated with partial entecavir response at year 1.
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Affiliation(s)
| | | | - Katsumi Omagari
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Japan
| | | | | | - James Fung
- Department of Medicine State Key Laboratory for Liver Research
| | | | | | | | - Ching-Lung Lai
- Department of Medicine State Key Laboratory for Liver Research
| | - Man-Fung Yuen
- Department of Medicine State Key Laboratory for Liver Research
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Tuma P, Pineda JA, Labarga P, Vidal F, Rodriguez C, Poveda E, Santos J, Gonzalez-García J, Sobrino P, Tural C, Soriano V. HBV primary drug resistance in newly diagnosed HIV-HBV-coinfected individuals in Spain. Antivir Ther 2011; 16:585-9. [PMID: 21685546 DOI: 10.3851/imp1778] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND The wide use of lamivudine (3TC) as oral therapy for chronic HBV infection has favoured the selection and circulation of 3TC-resistant HBV strains worldwide. Although transmission of 3TC-resistant HBV variants has been reported only sporadically, few studies have been conducted in the HIV population where exposure to 3TC has been greater forming part of antiretroviral therapy (ART) regimens. METHODS All individuals positive for serum hepatitis B surface antigen (HBsAg), newly diagnosed with HIV-1 infection, naive to ART and enrolled in the Spanish HIV cohort (CoRIS) since 2004 were identified. The HBV polymerase gene was sequenced and drug resistance mutations were characterized retrospectively in stored frozen plasma specimens. RESULTS From 4,419 ART-naive HIV-1-infected individuals, 223 (5.1%) were positive for serum HBsAg. Baseline stored sera were available for 84 patients, of whom 73 could be characterized virologically. This population was mainly represented by men who had sex with men (52.1%), native Spaniards (65.7%) and Latin Americans (16.4%). The mean age was 36 years, mean CD4(+) T-cell count 375 cells/mm(3) and mean plasma HIV RNA 4.5 log(10) copies/ml. The HBV genotype distribution was 64% A, 20% F, 12% D and 4% others. Drug-resistant mutations in the HBV polymerase were found in four (5.5%) patients: two harboured rtL180M, one rtL80V and one rtV173L. CONCLUSIONS The rate of primary drug resistance in HBV among newly diagnosed HIV-HBV-coinfected patients in Spain is currently low (5.5%) and restricted to 3TC. Thus, HBV drug resistance testing before prescription of oral antiviral therapy is not warranted, although periodic surveillance might be recommended.
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Affiliation(s)
- Paula Tuma
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain
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Fan X, Fang D, Bin D, Xueyong L, Jun C, Hongshan W. Serum levels of surface large envelope proteins: prognostic markers for hepatitis B e antigen-negative patients with adefovir dipivoxil treatment. Antivir Ther 2009; 14:1149-56. [PMID: 20032544 DOI: 10.3851/imp1456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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