CpG islands of hepatitis B virus genome isolated from Chinese patients

Hou, Zhuoni; Huang, Jihua; Zhong, Chengyao; Li, Lianbing; Xie, Qiang; Ma, Mingfu; Han, Tae-Ho; Wang, Degang; Maldonado, Martín; Xu, Lan; Huang, Tian-Hua; Zhong, Ying

doi:10.1016/j.gene.2015.02.036

Cited by 4 publications

(15 citation statements)

References 18 publications

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“…Consistent with the previous studies (Zhang et al 2013 ; Zhong et al 2015 ; Hou et al 2015 ), CGI and split CGII were much more common in HBV genotype B compared to genotype C. Nevertheless, 30 clones in genotype C from two patients (one CHB patient and one ACLF patient) contained CGI, while among the 16 clones in genotype B from a CHB patient, only three clones contained CGI.…”

Section: Resultssupporting

confidence: 89%

“…Although the function of CGI remains unclear, its absence might induce less methylation of the first CpG-rich region in HBV genotype C (Zhang et al 2013 ), and likely to be associated with the progressive liver diseases caused by HBV genotype C. To note, as shown in the present study, 30 clones in genotype C from two patients (one CHB patient and one ACLF patient) contained CGI, while among the 16 clones in genotype B from a CHB patient, only three clones contained CGI. Different from the previous studies (Hou et al 2015 ; Zhang et al 2013 ; Zhong et al 2015 ), data from HBV quasispecies emphasize that, distribution of CpG islands does not abide by genotypes strictly.…”

Section: Discussioncontrasting

confidence: 82%

“…Different distribution of CpG islands which can affect their methylation status and HBV gene expression, might further lead to different clinical outcomes of HBV infection. Previous studies have shown that distribution of CpG islands differed across HBV genotypes (Hou et al 2015 ; Zhang et al 2013 ; Zhong et al 2015 ). However, all of the nucleotide sequences mentioned in those studies were searched from Genbank at the National Center for Biotechnology Information.…”

Section: Introductionmentioning

confidence: 98%

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Characteristics of CpG Islands and their quasispecies of full-length hepatitis B virus genomes from patients at different phases of infection

et al. 2016

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BackgroundCpG islands in hepatitis B virus (HBV) genome are potential targets for methylation mediated gene silencing, and may be involved in the pathogenesis of HBV infection. To date, their characteristics in HBV quasispecies (QS) remain largely unknown. The purpose of this study was to investigate the characteristics of CpG islands in HBV QS. MethodsForty patients diagnosed as acute hepatitis B (AHB, n = 10), immune-tolerant HBV carriers (IT, n = 9), chronic hepatitis B (CHB, n = 11), or acute on chronic liver failure (ACLF, n = 10), were enrolled in this case–control study. A total of 599 clones were isolated, and full-length HBV genomes were sequenced.ResultsCpG island II (CGII) in AHB group was shorter in length and its QS heterogeneity was lower than that in the chronic infection group. Among the chronic infection subgroups, CGII and CpG island III (CGIII) in IT group were longer and their heterogeneity was lower compared to CHB and ACLF groups. Length of CGII correlated with HBV DNA levels positively while the complexity and diversity of CGII correlated with HBV DNA levels negatively. Moreover, CGII and CGIII were shorter in genotype B than those in genotype C, while QS complexity and diversity of either CGII or CGIII had no significant difference between genotype B and C.ConclusionsOverall, our results suggest that the distribution, length and QS heterogeneity of CpG islands in full-length HBV genome differ across clinical phases of infection, of which the mechanism warrants further study.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-3192-3) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 89%

Section: Discussioncontrasting

confidence: 82%

Section: Introductionmentioning

confidence: 98%

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Characteristics of CpG Islands and their quasispecies of full-length hepatitis B virus genomes from patients at different phases of infection

et al. 2016

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“…HBV persistence in liver cells increases the risk of HCC [24,25]. DNA methylation has been shown to occur in CpG dinucleotide contexts grouped together in clusters called CpG islands [26]. PreC/C and PreS/S genes of HBV have been associated with CpG islands [23,26].…”

Section: Introductionmentioning

confidence: 99%

“…DNA methylation has been shown to occur in CpG dinucleotide contexts grouped together in clusters called CpG islands [26]. PreC/C and PreS/S genes of HBV have been associated with CpG islands [23,26]. The occurrence and distribution of these islands in these HBV E genotypes remain unknown.…”

Section: Introductionmentioning

confidence: 99%

Profiles of mutations in hepatitis B virus surface and polymerase genes isolated from treatment-naïve Nigerians infected with genotype E

Olusola

Faneye

Oluwasemowo

et al. 2021

Journal of Medical Microbiology

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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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Hepatitis B virus DNA methylation and its potential role in chronic hepatitis B

Low

Ngeow

Chook

et al. 2022

Expert Rev. Mol. Med.

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Hepatitis B virus (HBV) infection led to 66% liver deaths world-wide in year 2015. Thirty-seven per cent of these deaths were the result of chronic hepatitis B (CHB)-associated hepatocellular carcinoma (HCC). Although early diagnosis of HCC improves survival, early detection is rare. Methylation of HBV DNA including covalently closed circular DNA (cccDNA) is more often encountered in HCC cases than those in CHB and cirrhosis. Three typical CpG islands within the HBV genome are the common sites for methylation. The HBV cccDNA methylation affects the viral replication and protein expression in the course of infection and may associate with the disease pathogenesis and HCC development. We review the current findings in HBV DNA methylation that provide insights into its role in HCC diagnosis.

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CpG islands of hepatitis B virus genome isolated from Chinese patients

Cited by 4 publications

References 18 publications

Characteristics of CpG Islands and their quasispecies of full-length hepatitis B virus genomes from patients at different phases of infection

Characteristics of CpG Islands and their quasispecies of full-length hepatitis B virus genomes from patients at different phases of infection

Profiles of mutations in hepatitis B virus surface and polymerase genes isolated from treatment-naïve Nigerians infected with genotype E

Hepatitis B virus DNA methylation and its potential role in chronic hepatitis B

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