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Zhu C, Tang M, Fu Y, Xun Z, Lin C, Wu S, Chen T, Zeng Y, Yang B, Ou Q, Liu C. Characterization of BCP/PreC/C region quasispecies in treatment-naive patients with different phases of HBV infection using next-generation sequencing. Int J Med Microbiol 2024; 315:151619. [PMID: 38564936 DOI: 10.1016/j.ijmm.2024.151619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND To analysis of quasispecies (QS) changes and high-frequency mutations in the BCP/PreC/C region of patients at different phases of hepatitis B virus (HBV) infection and provides novel biomarkers for the diagnosis of chronic hepatitis B (CHB) patients. METHODS With the application of next-generation sequencing technology, we were able to sequence the HBV BCP/PreC/C regions in 40 patients, each at different phases of the HBV infection. The heterogeneity of QS and the frequency of mutations were calculated using MEGA 7 software. RESULTS Our results show that the complexity and diversity of the BCP/PreC/C QS in HBeAg-positive CHB patients are significantly higher than those in HBeAg-positive chronic infection patients, while HBeAg-negative chronic infection patients had significantly higher QS complexity and diversity than HBeAg-negative CHB patients. In addition, HBeAg-negative patients showed reduced complexity but increased diversity compared with HBeAg-positive patients. Receiver operating characteristic curves showed that G1764A, C2102T, dN and complexity of QS could be used as potential biomarkers for diagnosing HBeAg-positive CHB, while the A2189C, dS and complexity of QS could be used as potential biomarkers for diagnosing HBeAg-negative chronic hepatitis. Finally, our study also found that G1896A and A2159G may be hotspot mutations affecting HBeAg seroconversion. CONCLUSION Our research elucidates the evolution of HBV by analyzing QS heterogeneity and mutation patterns, offering novel serum biomarkers for enhancing clinical diagnosis and disease prognosis. This comprehensive approach sheds light on the intricate dynamics of HBV progression and paves the way for more precise medical interventions.
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Affiliation(s)
- Chenggong Zhu
- Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Minjie Tang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ya Fu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhen Xun
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Caorui Lin
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Songhang Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yongbin Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
| | - Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
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Kim K, Choi YM, Kim DH, Jang J, Choe WH, Kim BJ. Locked nucleic acid real-time polymerase chain reaction method identifying two polymorphisms of hepatitis B virus genotype C2 infections, rt269L and rt269I. World J Gastroenterol 2023; 29:1721-1734. [PMID: 37077521 PMCID: PMC10107212 DOI: 10.3748/wjg.v29.i11.1721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/13/2023] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND The presence of two distinct hepatitis B virus (HBV) Pol RT polymorphisms, rt269L and rt269I, could contribute to the unique clinical or virological phenotype of HBV genotype C2. Therefore, a simple and sensitive method capable of identifying both types in chronic hepatitis B (CHB) patients infected with genotype C2 should be developed.
AIM To develop a novel simple and sensitive locked nucleic acid (LNA)-real time-polymerase chain reaction (RT-PCR) method capable of identifying two rt269 types in CHB genotype C2 patients.
METHODS We designed proper primer and probe sets for LNA-RT-PCR for the separation of rt269 types. Using synthesized DNAs of the wild type and variant forms, melting temperature analysis, detection sensitivity, and endpoint genotyping for LNA-RT-PCR were performed. The developed LNA-RT-PCR method was applied to a total of 94 CHB patients of genotype C2 for the identification of two rt269 polymorphisms, and these results were compared with those obtained by a direct sequencing protocol.
RESULTS The LNA-RT-PCR method could identify two rt269L and rt269I polymorphisms of three genotypes, two rt269L types [‘L1’ (WT) and ‘L2’] and one rt269I type (‘I’) in single (63 samples, 72.4%) or mixed forms (24 samples, 27.6%) in 87 (92.6% sensitivity) of 94 samples from Korean CHB patients. When the results were compared with those obtained by the direct sequencing protocol, the LNA-RT-PCR method showed the same results in all but one of 87 positive detected samples (98.9% specificity).
CONCLUSION The newly developed LNA-RT-PCR method could identify two rt269 polymorphisms, rt269L and rt269I, in CHB patients with genotype C2 infections. This method could be effectively used for the understanding of disease progression in genotype C2 endemic areas.
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Affiliation(s)
- Kijeong Kim
- Department of Microbiology, College of Medicine, Chung-Ang University, Seoul 06974, South Korea
| | - Yu-Min Choi
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Dong Hyun Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Junghwa Jang
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Won Hyeok Choe
- Department of Internal Medicine, Konkuk University School of Medicine, Seoul 05030, South Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, South Korea
- Liver Research Institute, College of Medicine, Seoul National University, Seoul 03080, South Korea
- Seoul National University Medical Research Center, Seoul 03080, South Korea
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Kim DH, Choi YM, Jang J, Kim BJ. Global prevalence and molecular characteristics of three clades within hepatitis B virus subgenotype C2: Predominance of the C2(3) clade in South Korea. Front Microbiol 2023; 14:1137084. [PMID: 36970691 PMCID: PMC10033913 DOI: 10.3389/fmicb.2023.1137084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
Hepatitis B Virus (HBV) genotypes reflect geographic, ethical or clinical traits and are currently divided into 10 genotypes (A–J). Of these, genotype C is mainly distributed in Asia, is the largest group and comprises more than seven subgenotypes (C1–C7). Subgenotype C2 is divided into three phylogenetically distinct clades, C2(1), C2(2), and C2(3), and is responsible for most genotype C infections in three East Asian nations, including China, Japan, and South Korea, which are major HBV endemic areas. However, despite the significance of subgenotype C2 with regard to clinical or epidemiologic aspects, its global distribution and molecular characteristics remain largely unknown. Here, we analyze the global prevalence and molecular characteristics between 3 clades within subgenotype C2 using 1,315 full genome sequences of HBV genotype C retrieved from public databases. Our data show that almost all HBV strains from South Korean patients infected with genotype C belong to clade C2(3) within subgenotype C2 [96.3%] but that HBV strains from Chinese or Japanese patients belong to diverse subgenotypes or clades within genotype C, suggesting clonal expansion of a specific HBV type, C2(3), among the Korean population. Our genome sequence analysis indicated a total of 21 signature sequences specific to the respective clades C2(1), C2(2), and C2(3). Of note, two types of four nonsynonymous C2(3) signature sequences, sV184A in HBsAg and xT36P in the X region, were detected in 78.9 and 82.9% of HBV C2(3) strains, respectively. In particular, HBV strains C2(3) versus C2(1) and C2(2) show a higher frequency of reverse transcriptase mutations related to nucleot(s)ide analog (NA) resistance, including rtM204I and rtL180M, suggesting an increased possibility of C2(3) infection in those with NA treatment failure. In conclusion, our data show that HBV subgenotype C2(3) is extremely prevalent in Korean patients with chronic HBV infection, which is distinct from two other East Asian nations, China and Japan, where diverse subgenotypes or clades within genotype C coexist. This epidemiologic trait might affect distinct virological and clinical traits in chronic HBV patients in Korea, where exclusively C2(3) infection is predominant.
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Affiliation(s)
- Dong Hyun Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Yu-Min Choi
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Junghwa Jang
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Liver Research Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Seoul National University Medical Research Center (SNUMRC), Seoul, Republic of Korea
- *Correspondence: Bum-Joon Kim,
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Belaiba Z, Ayouni K, Gdoura M, Kammoun Rebai W, Touzi H, Sadraoui A, Hammemi W, Yacoubi L, Abdelati S, Hamzaoui L, Msaddak Azzouz M, Chouikha A, Triki H. Whole genome analysis of hepatitis B virus before and during long-term therapy in chronic infected patients: Molecular characterization, impact on treatment and liver disease progression. Front Microbiol 2022; 13:1020147. [PMID: 36325017 PMCID: PMC9618822 DOI: 10.3389/fmicb.2022.1020147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/15/2022] [Indexed: 07/23/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains a serious public health concern worldwide despite the availability of an efficient vaccine and the major improvements in antiviral treatments. The aim of the present study is to analyze the mutational profile of the HBV whole genome in ETV non-responder chronic HBV patients, in order to investigate antiviral drug resistance, immune escape, and liver disease progression to Liver Cirrhosis (LC) or Hepatocellular Carcinoma (HCC). Blood samples were collected from five chronic hepatitis B patients. For each patient, two plasma samples were collected, before and during the treatment. Whole genome sequencing was performed using Sanger technology. Phylogenetic analysis comparing the studied sequences with reference ones was used for genotyping. The mutational profile was analyzed by comparison with the reference sequence M32138. Genotyping showed that the studied strains belong to subgenotypes D1, D7, and D8. The mutational analysis showed high genetic variability. In the RT region of the polymerase gene, 28 amino acid (aa) mutations were detected. The most significant mutations were the pattern rtL180M + rtS202G + rtM204V, which confer treatment resistance. In the S gene, 35 mutations were detected namely sP120T, sT126S, sG130R, sY134F, sS193L, sI195M, and sL216stop were previously described to lead to vaccine, immunotherapy, and/or diagnosis escape. In the C gene, 34 mutations were found. In particular, cG1764A, cC1766G/T, cT1768A, and cC1773T in the BCP; cG1896A and cG1899A in the precore region and cT12S, cE64D, cA80T, and cP130Q in the core region were associated with disease progression to LC and/or HCC. Other mutations were associated with viral replication increase including cT1753V, cG1764A/T, cC1766G/T, cT1768A, and cC1788G in the BCP as well as cG1896A and cG1899A in the precore region. In the X gene, 30 aa substitutions were detected, of which substitutions xT36D, xP46S, xA47T, xI88F, xA102V, xI127T, xK130M, xV131I, and xF132Y were previously described to lead to LC and/or HCC disease progression. In conclusion, our results show high genetic variability in the long-term treatment of chronic HBV patients causing several effects. This could contribute to guiding national efforts to optimize relevant HBV treatment management in order to achieve the global hepatitis elimination goal by 2030.
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Affiliation(s)
- Zeineb Belaiba
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Kaouther Ayouni
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Wafa Kammoun Rebai
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Walid Hammemi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Lamia Yacoubi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Salwa Abdelati
- Department of Gastroenterology, Polyclinic of CNSS, Sousse, Tunisia
| | - Lamine Hamzaoui
- Department of Gastroenterology, Hospital of Tahar Maamouri, Nabeul, Tunisia
| | | | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
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Lai X, Chen W, Wu Y, Gao Y, Zhang Y, Xu X, Fu Y, Wang X, Yang Y, Zhang Y. Effect of mutations across reverse transcriptase region on HBV replication and progression of liver diseases in Chinese patients. J Clin Lab Anal 2022; 36:e24530. [PMID: 35657116 PMCID: PMC9279987 DOI: 10.1002/jcla.24530] [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: 11/21/2021] [Revised: 05/05/2022] [Accepted: 05/19/2022] [Indexed: 11/06/2022] Open
Abstract
It was known that mutations in the RT region were mainly related to nucleot(s)ide analogs resistance. Increasing studies indicated that RT mutations were related to advanced liver diseases (ALD) and had effects on HBV replication, but the distribution characteristics of mutations across RT region in the development of liver diseases and the effect of RT mutations on HBV replication were not fully clarified. HBV RT region was direct-sequenced in 1473 chronic HBV-infected patients. Mutation frequencies were analyzed to identify the specific mutations differing between groups classified by genotypes, loads of HBV DNA, or progression of liver diseases. In the range of rt145-rt290, rt145, rt221, rt222, rt267, and rt271 were the genotype-polymorphic sites, while rt238 was the genotype-specific sites. Mutations at rt163, rt173, rt180, rt181, rt184, rt191, rt199, and rt214 were more frequent among patients with C-genotype HBV, while those at rt220, rt225, rt226, rt269, and rt274 were more frequent among patients with B-genotype HBV. RtM204V/I could reduce the HBV DNA loads while rtQ/L267H/R could increase the HBV DNA loads. RtV214A/E/I (OR 3.94, 95% CI 1.09 to 14.26) was an independent risk factor for advanced liver diseases. In summary, the hotspots of mutations were different between B and C genotypes. Besides the effect on the S region, RT mutations had effects on HBV replication by other unknown ways. RtV214A/E/I was found to be an independent risk factor for ALD, suggesting that mutations at rt214 site could be used as a potential virological marker for the liver disease progression.
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Affiliation(s)
- Xiaoqin Lai
- Pharmacy DepartmentThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Wenfa Chen
- Pharmacy DepartmentThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Yuzhu Wu
- Pharmacy DepartmentThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Yali Gao
- Pharmacy DepartmentThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Yalan Zhang
- Pharmacy DepartmentThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Xuwei Xu
- Pharmacy DepartmentThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Ya Fu
- Department of Clinical LaboratoryThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Xinwen Wang
- Department of OrthopedicsSouthern Medical UniversityGuangzhouChina
| | - Yanbing Yang
- Department of ImagingMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhouChina
| | - Yin Zhang
- Pharmacy DepartmentThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
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Association of Pre-S/S and Polymerase Mutations with Acute and Chronic Hepatitis B Virus Infections in Patients from Rio de Janeiro, Brazil. Viruses 2022; 14:v14071375. [PMID: 35891356 PMCID: PMC9315576 DOI: 10.3390/v14071375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 02/01/2023] Open
Abstract
Several hepatitis B virus (HBV)-related factors, including the viral load, genotype, and genomic mutations, have been linked to the development of liver diseases. Therefore, in this study we aimed to investigate the influence of HBV genetic variability during acute and chronic infection phases. A real-time nested PCR was used to detect HBV DNA in all samples (acute, n = 22; chronic, n = 49). All samples were sequenced for phylogenetic and mutation analyses. Genotype A, sub-genotype A1, was the most common genotype in the study population. A total of 190 mutations were found in the pre-S/S gene area and the acute profile revealed a greater number of nucleotide mutations (p < 0.05). However, both profiles contained nucleotide mutations linked to immune escape and an increased risk of hepatocellular carcinomas (acute, A7T; chronic, A7Q). Furthermore, 17 amino acid substitutions were identified in the viral polymerase region, including the drug resistance mutations lamivudine and entecavir (rtL180M), with statistically significant differences between the mutant and wild type strains. Owing to the natural occurrence of these mutations, it is important to screen for resistance mutations before beginning therapy.
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Li H, Qian F, Zou W, Jin F, Li D, Zhang Y. OUP accepted manuscript. Trans R Soc Trop Med Hyg 2022; 116:874-880. [PMID: 35543271 DOI: 10.1093/trstmh/trac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 02/17/2022] [Accepted: 04/16/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Haiyan Li
- Department of Laboratory Medicine, Huzhou Maternity and Child Health Care Hospital, 2 East Street, Huzhou, Zhejiang Province, China
| | - Fuchu Qian
- Department of Precision Medicine, Affiliated Central Hospital Huzhou University, Huzhou Central Hospital, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
- Huzhou Key Laboratory of Molecular Medicine, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
| | - Weihua Zou
- Department of Laboratory Medicine, Affiliated Central Hospital Huzhou University, Huzhou Central Hospital, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
| | - Fang Jin
- Department of Precision Medicine, Affiliated Central Hospital Huzhou University, Huzhou Central Hospital, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
- Huzhou Key Laboratory of Molecular Medicine, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
| | - Dongli Li
- Department of Precision Medicine, Affiliated Central Hospital Huzhou University, Huzhou Central Hospital, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
- Huzhou Key Laboratory of Molecular Medicine, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
| | - Yaqin Zhang
- Department of Laboratory Medicine, Huzhou Maternity and Child Health Care Hospital, 2 East Street, Huzhou, Zhejiang Province, China
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Zou W, Qian F, Jin F, Li D, Chen J. Characterization of mutations in the reverse transcriptase region of hepatitis B virus in treated and untreated chronic hepatitis B patients. Trans R Soc Trop Med Hyg 2021; 115:870-877. [PMID: 33236067 DOI: 10.1093/trstmh/traa142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/19/2020] [Accepted: 11/06/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The reverse transcriptase (RT) region of the hepatitis B virus (HBV) is the target of antiviral treatment. However, the discrepancy in RT mutations between nucleos(t)ide analogue (NA)-treated and -untreated chronic hepatitis B (CHB) patients is un clear. METHODS Serum samples were collected from 119 NA-treated and 135 NA-untreated patients. The sampling time was decided by the clinician. Full-length HBV RT regions were amplified using nest polymerase chain reaction. The mutations within the RT region were analysed by direct sequencing. RESULTS The incidence of RT mutations in treated patients was higher than that in untreated patients (p<0.05). The classic drug-resistant mutations were detected in 44.5% (53/119) of treated patients, which was significantly higher than in untreated patients (6.7% [9/135]) (p<0.05). The non-classical mutations showed their complexity and diversity in both patient groups. Multiple mutations (three or more) were more frequent in treated patients than in untreated patients (p<0.05). Several novel mutations might be related to NA resistance. CONCLUSIONS The selection pressures of NAs accelerated the development of RT mutations, especially within the functional domain. Mutations in the RT region occurred not only at classical sites, but also at other non-classical sites, which might be related to drug resistance and/or viral replication. The biological function and fitness of HBV isolates harbouring these novel mutations need further in vitro and in vivo verification experiments.
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Affiliation(s)
- Weihua Zou
- Department of Laboratory Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
| | - Fuchu Qian
- Department of Precision Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China.,Huzhou Key Laboratory of Molecular Medicine, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
| | - Fang Jin
- Department of Precision Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China.,Huzhou Key Laboratory of Molecular Medicine, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
| | - Dongli Li
- Department of Precision Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China.,Huzhou Key Laboratory of Molecular Medicine, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
| | - Jing Chen
- Department of Precision Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China.,Huzhou Key Laboratory of Molecular Medicine, 1558 Sanhuan North Road, Huzhou, Zhejiang Province, China
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Fu Y, Wu S, Hu Y, Chen T, Zeng Y, Liu C, Ou Q. Mutational characterization of HBV reverse transcriptase gene and the genotype-phenotype correlation of antiviral resistance among Chinese chronic hepatitis B patients. Emerg Microbes Infect 2021; 9:2381-2393. [PMID: 33124952 PMCID: PMC7605321 DOI: 10.1080/22221751.2020.1835446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background and Aims: The drug resistance of hepatitis B virus (HBV) originates from mutations within HBV reverse transcriptase (RT) region during the prolonged antiviral therapy. So far, the characteristics of how these mutations distribute and evolve in the process of therapy have not been clarified yet. Thus we aimed to investigate these characteristics and discuss their contributing factors. Methods: HBV RT region was direct-sequenced in 285 treatment-naive and 214 post-treatment patients. Mutational frequency and Shannon entropy were calculated to identify the specific mutations differing between genotypes or treatment status. A typical putative resistance mutation rtL229V was further studied using in-vitro susceptibility assays and molecular modeling. Results: The classical resistance mutations were rarely detected among treatment-naive individuals, while the putative resistance mutations were observed at 8 AA sites. rtV191I and rtA181T/V were the only resistance mutations identified as genotype-specific mutation. Selective pressure of drug usage not only contributed to the classical resistance mutations, but also induced the changes at a putative resistance mutation site rt229. rtL229V was the major substitution at the site of rt229. It contributed to the most potent suppression of viral replication and reduced the in-vitro drug susceptibility to entecavir (ETV) when coexisting with rtM204V, consistent with the hypothesis based on the molecular modeling and clinical data analysis. Conclusions: The analysis of mutations in RT region under the different circumstances of genotypes and therapy status might pave the way for a better understanding of resistance evolution, thus providing the basis for a rational administration of antiviral therapy.
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Affiliation(s)
- Ya Fu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Songhang Wu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Yuhai Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Yongbin Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Clinical Laboratory Diagnostics, The First Clinical College, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Gene Diagnosis Research Center, Fujian Medical University, Fuzhou, China
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10
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Marino A, Cosentino F, Ceccarelli M, Moscatt V, Pampaloni A, Scuderi D, D'Andrea F, Rullo EV, Nunnari G, Benanti F, Celesia BM, Cacopardo B. Entecavir resistance in a patient with treatment-naïve HBV: A case report. Mol Clin Oncol 2021; 14:113. [PMID: 33903819 PMCID: PMC8060856 DOI: 10.3892/mco.2021.2275] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Among nucleos(t)ide analogue therapies for hepatitis B virus (HBV) treatment, entecavir (ETV) and tenofovir disoproxil fumarate (TDF)/tenofovir alafenamide are associated with the lowest rate of drug resistance. ETV is a drug requiring at least three substitutions in the reverse transcriptase (RT) domain to develop resistance, which is a rare occasion in treatment-naïve patients. However, pre-existing or acquired single mutations in the RT domain could lead to a virological breakthrough, after viral suppression. The present case report describes a 58-year-old female patient with hepatitis B virus (HBV) and high viral load who started HBV treatment with ETV. After 85 weeks of treatment, HBV-DNA declined to 0 IU/ml and remained undetectable for 3 years. However, after that period of time, the HBV-DNA rebounded, followed by the rise of liver enzymes (aspartate aminotransferase and alanine transaminase). Only the substitution M204I was detected in the HBV polymerase region. The patient was then switched to TDF treatment, achieving normalization of the liver enzymes and a decline in HBV-DNA levels. The present case report suggests that nucleoside-naïve patients should be cautiously monitored for resistance, even more than biochemically (transaminases, bilirubin) and virologically (HBV-DNA), even if complete HBV suppression is achieved.
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Affiliation(s)
- Andrea Marino
- Department of Clinical and Experimental Medicine, Division of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, I-95122 Catania, Italy
| | - Federica Cosentino
- Department of Clinical and Experimental Medicine, Division of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, I-95122 Catania, Italy
| | - Manuela Ceccarelli
- Department of Clinical and Experimental Medicine, Division of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, I-95122 Catania, Italy
| | - Vittoria Moscatt
- Department of Clinical and Experimental Medicine, Division of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, I-95122 Catania, Italy
| | - Alessio Pampaloni
- Department of Clinical and Experimental Medicine, Division of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, I-95122 Catania, Italy
| | - Daniele Scuderi
- Department of Clinical and Experimental Medicine, Division of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, I-95122 Catania, Italy
| | - Flavia D'Andrea
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, I-98124 Messina, Italy
| | - Emmanuele Venanzi Rullo
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, I-98124 Messina, Italy
| | - Giuseppe Nunnari
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, I-98124 Messina, Italy
| | - Francesco Benanti
- Department of Clinical and Experimental Medicine, Division of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, I-95122 Catania, Italy
| | - Benedetto Maurizio Celesia
- Department of Clinical and Experimental Medicine, Division of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, I-95122 Catania, Italy
| | - Bruno Cacopardo
- Department of Clinical and Experimental Medicine, Division of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, I-95122 Catania, Italy
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11
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rt269I Type of Hepatitis B Virus (HBV) Polymerase versus rt269L Is More Prone to Mutations within HBV Genome in Chronic Patients Infected with Genotype C2: Evidence from Analysis of Full HBV Genotype C2 Genome. Microorganisms 2021; 9:microorganisms9030601. [PMID: 33803998 PMCID: PMC7999911 DOI: 10.3390/microorganisms9030601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 12/03/2022] Open
Abstract
Recently, it has been reported that the rt269I type of hepatitis B virus (HBV) polymerase (Pol) versus the rt269L type is more significantly related to lower viral replication and HBeAg negative infections in chronic hepatitis B (CHB) patients of genotype C2. In this study, we compared mutation rates within HBV genomes between rt269L and rt269I using a total of 234 HBV genotype C2 full genome sequences randomly selected from the HBV database (115 of rt269L and 119 of rt269I type). When we applied the Benjamini and Hochberg procedure for multiple comparisons, two parameters, dN and d, at the amino acids level in the Pol region were significantly higher in the rt269I type than in the rt269L type. Although it could not reach statistical significance from the Benjamini and Hochberg procedure, nonsynonymous (NS) mutations in the major hydrophilic region (MHR) or “a” determinant in the surface antigens (HBsAg ORF) related to host immune escape or vaccine escape are more frequently generated in rt269I strains than in rt269L. We also found that there are a total of 19 signature single nucleotide polymorphisms (SNPs), of which 2 and 17 nonsynonymous mutation types were specific to rt269L and rt269I, respectively: Of these, most are HBeAg negative infections (preC-W28*, X-V5M and V131I), lowered HBV DNA or virion production (C-I97F/L, rtM204I/V) or preexisting nucleot(s)ide analog resistance (NAr) (rtN139K/H, rtM204I/V and rtI224V) or disease severity (preC-W28*, C-I97F/L, C-Q182K/*, preS2-F141L, S-L213I/S, V/L5M, T36P/S/A, V131I, rtN139K/H, rtM204I/V and rtI224V). In conclusion, our data showed that rt269I types versus rt269L types are more prone to overall genome mutations, particularly in the Pol region and in the MHR or “a” determinant in genotype C2 infections and are more prevalent in signature NS mutations related to lowered HBV DNA replication, HBsAg and HBeAg secretion and potential NAr variants and hepatocellular carcinoma (HCC), possibly via type I interferon (IFN-I)-mediated enhanced inflammation. Our data suggest that rt269L types could contribute to liver disease progression via the generation of immune escape or enhanced persistent infection in chronic patients of genotype C2.
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12
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Olusola BA, Faneye AO, Oluwasemowo OO, Motayo BO, Adebayo S, Oludiran-Ayoade AE, Aleru B, George UE, Oragwa AO. Profiles of mutations in hepatitis B virus surface and polymerase genes isolated from treatment-naïve Nigerians infected with genotype E. J Med Microbiol 2021; 70. [PMID: 33704041 DOI: 10.1099/jmm.0.001338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Introduction. Hepatitis B virus (HBV) infection is the leading cause of hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). HBV genotype E (HBV/E) is the predominant genotype in West Africa and has been linked epidemiologically with chronic and occult HBV infections as well as development of HCC. Mutations in the surface and polymerase genes of HBV have been associated with occult infection, drug resistance, vaccine escape, as well as HCC.Hypothesis/Gap Statement. There is limited data on the occurrence and patterns of mutations associated with occult infection, drug resistance, vaccine escape and HCC for HBV/E.Aim. This study characterized amino acid (aa) substitutions in the major hydrophilic (MHR) and reverse transcriptase (RT) regions of the surface and polymerase genes respectively of HBV sequences from a group of Nigerians with genotype E infection. The CpG islands of the PreC/C and PreS/S regions of these sequences were also described.Methodology. HBV surface and polymerase genes were detected using PCR techniques. Occurrence of new and previously described mutations in these genes were analysed using phylogenetic techniques.Results. Overall 13 HBV isolates were each sequenced for polymerase and surface genes mutations. Thirteen and nine PreS/S and PreC/C HBV genes respectively were analysed for CpG islands. Mutations in the MHR and a-determinants region of the S protein were discovered in eleven and nine of the 13 tested isolates respectively. These mutations were concomitant with aa changes in the RT functional domains of the isolates. Mutations associated with vaccine escape, occult infection and poor HCC prognosis were identified in HBV/E isolated in this study. Furthermore, all the isolates had at least one putative nucleotide analogue resistance mutations. Drug resistance mutations had the highest association with CpG islands.Conclusion. The results of this study contribute to further understanding of HBV variability in Nigeria and the West African region. This will aid the planning of adequate HBV immunization and treatment programmes for the countries in the region.
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Affiliation(s)
- Babatunde A Olusola
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adedayo O Faneye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Babatunde O Motayo
- Federal Medical Center, Abeokuta, Nigeria.,Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Sopeju Adebayo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ayomide E Oludiran-Ayoade
- Present address: Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.,Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Bisola Aleru
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Uwem E George
- Department of Biological Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Arthur O Oragwa
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Jos, Jos-Plateau State, Nigeria
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13
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Complex genetic encoding of the hepatitis B virus on-drug persistence. Sci Rep 2020; 10:15574. [PMID: 32968103 PMCID: PMC7511938 DOI: 10.1038/s41598-020-72467-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022] Open
Abstract
Tenofovir disoproxil fumarate (TDF) is one of the nucleotide analogs capable of inhibiting the reverse transcriptase (RT) activity of HIV and hepatitis B virus (HBV). There is no known HBV resistance to TDF. However, detectable variation in duration of HBV persistence in patients on TDF therapy suggests the existence of genetic mechanisms of on-drug persistence that reduce TDF efficacy for some HBV strains without affording actual resistance. Here, the whole genome of intra-host HBV variants (N = 1,288) was sequenced from patients with rapid (RR, N = 5) and slow response (SR, N = 5) to TDF. Association of HBV genomic and protein polymorphic sites to RR and SR was assessed using phylogenetic analysis and Bayesian network methods. We show that, in difference to resistance to nucleotide analogs, which is mainly associated with few specific mutations in RT, the HBV on-TDF persistence is defined by genetic variations across the entire HBV genome. Analysis of the inferred 3D-structures indicates no difference in affinity of TDF binding by RT encoded by intra-host HBV variants that rapidly decline or persist in presence of TDF. This finding suggests that effectiveness of TDF recognition and binding does not contribute significantly to on-drug persistence. Differences in patterns of genetic associations to TDF response between HBV genotypes B and C and lack of a single pattern of mutations among intra-host variants sensitive to TDF indicate a complex genetic encoding of the trait. We hypothesize that there are many genetic mechanisms of on-drug persistence, which are differentially available to HBV strains. These pervasive mechanisms are insufficient to prevent viral inhibition completely but may contribute significantly to robustness of actual resistance. On-drug persistence may reduce the overall effectiveness of therapy and should be considered for development of more potent drugs.
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14
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Qian F, Zou W, Jin F, Li D, Shen Y. Prevalence of Potential Resistance Related Variants Among Chinese Chronic Hepatitis B Patients Not Receiving Nucleos(T)ide Analogues. Infect Drug Resist 2020; 13:2407-2416. [PMID: 32765014 PMCID: PMC7381783 DOI: 10.2147/idr.s249476] [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: 02/14/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022] Open
Abstract
Background and Aims Potential drug resistance (DR) related variants in the hepatitis B virus (HBV) reverse transcriptase (RT) region may be associated with the effectiveness of antiviral drugs and disease progression. The aim of this study was to investigate the prevalence and clinical characteristics of potential DR-related variants in Chinese CHB patients not receiving nucleos(t)ide analogues (NAs). Patients and Methods Two hundred and six untreated CHB patients from Huzhou Central Hospital in eastern China were recruited for this study. The serum DNA was extracted and the HBV RT region was amplified using nest polymerase chain reaction (nest-PCR). The 42 potential DR-related variants were analyzed by direct sequencing. Results Among these CHB patients, HBV genotype B and genotype C were identified in 121 (58.7%) and 85 (41.3%) patients, respectively. Potential DR-related variants were detected in 42.7% (88/206) of patients. Primary and secondary DR variants were found in 7.3% (15/206) of patients, including rtL80I/V, rtI169T, rtV173L rtL180M, rtA181T/V, rtM204I/V, and rtN236T. The variants at rt53, rt82, rt221, rt233, rt237, and rt256 were specific for genotype B, and those at rt38, rt84, rt126, rt139, rt153, rt191, rt214, rt238, and rt242 were specific for genotype C. Moreover, the variation frequency in the A-B interdomain (3.96%) was significantly higher than that in the functional domains (1.17%) and non-A-B interdomains (1.11%). Multivariate logistic regression analysis showed that lower HBV-DNA load (<106 IU/mL) was an independent factor associated with potential DR-related variants in untreated CHB patients (P <0.05). Conclusion Potential DR-related variants were frequent and complex in untreated Chinese CHB patients. Furthermore, the variants may contribute to decreased serum HBV-DNA loads. However, the effects of potential DR-related variants on the antiviral therapy and liver disease progression require further study.
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Affiliation(s)
- Fuchu Qian
- Department of Precision Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, People's Republic of China.,Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, People's Republic of China
| | - Weihua Zou
- Department of Laboratory Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, People's Republic of China
| | - Fang Jin
- Department of Precision Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, People's Republic of China.,Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, People's Republic of China
| | - Dongli Li
- Department of Precision Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, People's Republic of China.,Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, People's Republic of China
| | - Yujuan Shen
- Department of Infectious Diseases, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, People's Republic of China
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15
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Wang S, Li H, Kou Z, Ren F, Jin Y, Yang L, Dong X, Yang M, Zhao J, Liu H, Dong N, Jia L, Chen X, Zhou Y, Qiu S, Hao R, Song H. Highly sensitive and specific detection of hepatitis B virus DNA and drug resistance mutations utilizing the PCR-based CRISPR-Cas13a system. Clin Microbiol Infect 2020; 27:443-450. [PMID: 32360447 DOI: 10.1016/j.cmi.2020.04.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Undetectable or low-level hepatitis B virus (HBV) DNA and drug resistance mutations in patients may increase the risk of HBV transmission or cause active viral replication and other clinical problems. Here, we established a highly sensitive and practical method for HBV and drug resistance detection using a polymerase chain reaction (PCR) -based CRISPR-Cas13a detection system (referred to as PCR-CRISPR) and evaluated its detection capability using clinical samples. METHODS Specific CRISPR RNAs (crRNAs) are designed for HBV DNA detection and YMDD (tyrosine-methionine-aspartate-aspartate) variant identification. The HBV DNA was detected in 312 serum samples for HBV diagnosis using quantification PCR (qPCR) and PCR-CRISPR. Additionally, 424 serum samples for YMDD testing were detected by qPCR, direct sequencing, and our assay. RESULTS Using PCR-CRISPR, one copy per test of HBV DNA was detected with HBV-1 crRNA in 15 min after PCR amplification. Consistent results with qPCR were observed for 302 samples, while the remaining 10 samples with low-level HBV DNA were detectable by PCR-CRISPR and droplet digital PCR but not by qPCR. PCR-CRISPR diagnosed all 412 drug-resistant samples detected by the YMDD detection qPCR kit and direct sequencing, as well as the other 12 drug-resistant samples with low-level HBV DNA undetectable by qPCR and direct sequencing. CONCLUSIONS We developed a novel PCR-CRISPR method for highly sensitive and specific detection of HBV DNA and drug resistance mutations. One copy per test for HBV DNA and YMDD drug resistance mutations could be detected. This method has wide application prospects for the early detection of HBV infection, drug resistance monitoring and treatment guidance.
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Affiliation(s)
- S Wang
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - H Li
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Z Kou
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - F Ren
- Beijing Artificial Liver Treatment and Training Centre, Beijing You An Hospital, Affiliated Hospital of Capital Medical University, Beijing, China
| | - Y Jin
- Beijing Artificial Liver Treatment and Training Centre, Beijing You An Hospital, Affiliated Hospital of Capital Medical University, Beijing, China
| | - L Yang
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - X Dong
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - M Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - J Zhao
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - H Liu
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - N Dong
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - L Jia
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - X Chen
- Beijing Artificial Liver Treatment and Training Centre, Beijing You An Hospital, Affiliated Hospital of Capital Medical University, Beijing, China
| | - Y Zhou
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - S Qiu
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - R Hao
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - H Song
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China.
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16
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Koyaweda GW, Ongus JR, Machuka E, Juma J, Macharia R, Komas NP, Pelle R. Detection of circulating hepatitis B virus immune escape and polymerase mutants among HBV-positive patients attending Institut Pasteur de Bangui, Central African Republic. Int J Infect Dis 2019; 90:138-144. [PMID: 31682960 PMCID: PMC6912157 DOI: 10.1016/j.ijid.2019.10.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 02/06/2023] Open
Abstract
Background Previous studies in the Central African Republic (CAR) have reported the presence of hepatitis B virus (HBV) recombinant genotype E/D and a suspicion of immune escape mutants (IEMs), without further investigation into their impact on prevention and diagnosis. Consequently, this study investigated HBV mutations among hepatitis B surface antigen (HBsAg)-positive patients attending Institut Pasteur de Bangui in the CAR. Methods Sera from a total of 118 HBsAg-positive patients with no previous history of HBV treatment or vaccination at the Institut Pasteur de Bangui, were sampled between 2017 and 2019. Subsequently, the region spanning the surface and polymerase genes of HBV was amplified by PCR and sequenced. HBV sequences were genotyped/subgenotyped by phylogenetic analysis and serotyped based on predicted amino acid residues at positions s122, s127, s140, s159, and s160. They were then analyzed for HBV IEMs and polymerase mutations. Results The region spanning the surface and polymerase genes was successfully amplified and sequenced for 51 samples. Of the HBV sequences, 49 were genotype E and two were genotype A subgenotype A1; these were serotyped as ayw4 and ayw1, respectively. Potential IEMs sY100C, sA128V, and sM133T, and several polymerase mutants were identified. Conclusions This study raises awareness of the need for further studies to be conducted on a large scale to better understand HBV mutations for improved disease control and prevention strategies in the country.
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Affiliation(s)
| | - Juliette Rose Ongus
- Jomo Kenyatta University of Agriculture and Technology, Medical Laboratory Sciences Department, Nairobi, Kenya
| | - Eunice Machuka
- Biosciences eastern and central Africa International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - John Juma
- Biosciences eastern and central Africa International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Rosaline Macharia
- Center for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Narcisse Patrice Komas
- Institut Pasteur de Bangui, Viral Hepatitis Laboratory, Bangui, Central African Republic
| | - Roger Pelle
- Jomo Kenyatta University of Agriculture and Technology, Medical Laboratory Sciences Department, Nairobi, Kenya.
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17
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Characterization and Clinical Significance of Natural Variability in Hepatitis B Virus Reverse Transcriptase in Treatment-Naive Chinese Patients by Sanger Sequencing and Next-Generation Sequencing. J Clin Microbiol 2019; 57:JCM.00119-19. [PMID: 31189581 PMCID: PMC6663897 DOI: 10.1128/jcm.00119-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/28/2019] [Indexed: 02/07/2023] Open
Abstract
Mutations in hepatitis B virus (HBV) reverse transcriptase (RT) are associated with nucleos(t)ide analogue (NA) resistance during long-term antiviral treatment. However, the characterization of mutations in HBV RT in untreated patients has not yet been well illustrated. The objective of this study was to investigate the characterization and clinical significance of natural variability in HBV RT in treatment-naive patients. HBV RT sequences were analyzed in 427 patients by Sanger sequencing and in 66 patients by next-generation sequencing. Primary or secondary NA resistance (NAr) mutations were not found, except A181T in RT (rtA181T) by Sanger sequencing, but they were detected by next-generation sequencing. Mutations were found in 56 RT amino acid (aa) sites by Sanger sequencing, 36 of which had mutations that could lead to changes in B or T cell epitopes in the RT or S protein. The distribution of mutations was diverse in different sections within the RT region. Multiple mutations showed significant association with HBV DNA, HBsAg, HBeAg, age, and severity of liver fibrosis. Mutations at rt251, rt266, rt274, rt280, rt283, rt284, and rt286 were found most in the advanced liver disease (ALD) group by next-generation sequencing. The present study demonstrates that next-generation sequencing (NGS) was more suitable than Sanger sequencing to monitor NAr mutations at a low rate in the treatment-naive patients, and that mutations in the RT region might be involved in the progression to ALD.
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Lee SY, Choi YM, Oh SJ, Yang SB, Lee J, Choe WH, Kook YH, Kim BJ. rt269I Type of Hepatitis B Virus (HBV) Leads to HBV e Antigen Negative Infections and Liver Disease Progression via Mitochondrial Stress Mediated Type I Interferon Production in Chronic Patients With Genotype C Infections. Front Immunol 2019; 10:1735. [PMID: 31402915 PMCID: PMC6677150 DOI: 10.3389/fimmu.2019.01735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/09/2019] [Indexed: 12/19/2022] Open
Abstract
Hepatitis B virus infection is a serious global health problem and causes life-threatening liver disease. In particular, genotype C shows high prevalence and severe liver disease compared with other genotypes. However, the underlying mechanisms regarding virological traits still remain unclear. This study investigated the clinical factors and capacity to modulate Type I interferon (IFN-I) between two HBV polymerase polymorphisms rt269L and rt269I in genotype C. This report compared clinical factors between rt269L and rt269I in 220 Korean chronic patients with genotype C infections. The prevalence of preC mutations between rt269L and rt269I was compared using this study's cohort and the GenBank database. For in vitro and in vivo experiments, transient transfection using HBV genome plasmid and HBV virion infection using HepG2-hNTCP-C4 and HepaRG systems and hydrodynamic injection of HBV genome into mice tails were conducted, respectively. This report's clinical data indicated that rt269I vs. rt269L was more significantly related to HBV e antigen (HBeAg) negative serostatus, lower levels of HBV DNA and HBsAg, and disease progression. Our epidemiological study showed HBeAg negative infections of rt269I infections were attributed to a higher frequency of preC mutations at 1896 (G to A). Our in vitro and in vivo studies also found that rt269I could lead to mitochondrial stress mediated STING dependent IFN-I production, resulting in decreasing HBV replication via the induction of heme-oxygenase-1. In addition, we also found that rt269I could lead to enhanced iNOS mediated NO production in an IFN-I dependent manner. These data demonstrated that rt269I can contribute to HBeAg negative infections and liver disease progression in chronic patients with genotype C infections via mitochondrial stress mediated IFN-I production.
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Affiliation(s)
- So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, College of Medicine, Seoul National University, Seoul, South Korea
| | - Yu-Min Choi
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, College of Medicine, Seoul National University, Seoul, South Korea
| | - Song-Ji Oh
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, College of Medicine, Seoul National University, Seoul, South Korea
| | - Soo-Bin Yang
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, College of Medicine, Seoul National University, Seoul, South Korea
| | - JunHyeok Lee
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, College of Medicine, Seoul National University, Seoul, South Korea
| | - Won-Hyeok Choe
- Department of Internal Medicine, Konkuk University School of Medicine, Seoul, South Korea
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, College of Medicine, Seoul National University, Seoul, South Korea
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, College of Medicine, Seoul National University, Seoul, South Korea
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Choi YM, Lee SY, Kim BJ. Naturally occurring hepatitis B virus reverse transcriptase mutations related to potential antiviral drug resistance and liver disease progression. World J Gastroenterol 2018; 24:1708-1724. [PMID: 29713126 PMCID: PMC5922991 DOI: 10.3748/wjg.v24.i16.1708] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/10/2018] [Accepted: 04/15/2018] [Indexed: 02/06/2023] Open
Abstract
The annual number of deaths caused by hepatitis B virus (HBV)-related disease, including cirrhosis and hepatocellular carcinoma (HCC), is estimated as 887000. The reported prevalence of HBV reverse transcriptase (RT) mutation prior to treatment is varied and the impact of preexisting mutations on the treatment of naïve patients remains controversial, and primarily depends on geographic factors, HBV genotypes, HBeAg serostatus, HBV viral loads, disease progression, intergenotypic recombination and co-infection with HIV. Different sensitivity of detection methodology used could also affect their prevalence results. Several genotype-dependent HBV RT positions that can affect the emergence of drug resistance have also been reported. Eight mutations in RT (rtL80I, rtD134N, rtN139K/T/H, rtY141F, rtM204I/V, rtF221Y, rtI224V, and rtM309K) are significantly associated with HCC progression. HBeAg-negative status, low viral load, and genotype C infection are significantly related to a higher frequency and prevalence of preexisting RT mutations. Preexisting mutations are most frequently found in the A-B interdomain of RT which overlaps with the HBsAg “a” determinant region, mutations of which can lead to simultaneous viral immune escape. In conclusion, the presence of baseline RT mutations can affect drug treatment outcomes and disease progression in HBV-infected populations via modulation of viral fitness and host-immune responses.
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Affiliation(s)
- Yu-Min Choi
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
| | - So-Young Lee
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
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