HBVdb: a knowledge database for Hepatitis B Virus

Hayer, Juliette; Jadeau, Fanny; Deléage, Gilbert; Kay, Alan; Zoulim, Fabien; Combet, Christophe

doi:10.1093/nar/gks1022

Cited by 187 publications

(185 citation statements)

References 40 publications

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“…Thus, HBV and several other viruses can currently be genotyped using the NCBI web-based HBV genotyping tool [25] . To further facilitate HBV genotype determination, several experts in the field have introduced different online HBV genotyping tools, such as the hepatitis B virus database (HBVdb) [26] , HBV STAR [27] , BioAfrica-Oxford HBV Automated Subtyping Tool [28] , HepSEQ Genotyper [29,30] and the jumping profile Hidden Markov Model (jpHMM) [31] .…”

Section: Online Methods To Genotype Hbvmentioning

confidence: 99%

Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions

Pourkarim¹

2014

WJG

163

177

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The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term "recombino-subgenotype". Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term "immigro-subgenotype" to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.

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Section: Online Methods To Genotype Hbvmentioning

confidence: 99%

Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions

Pourkarim¹

2014

WJG

163

177

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“…The unmapped tags extracted from the mapping results were aligned to 16 representative HBV genomes downloaded from HBVdb (25). Because the HBV genome is circular, each genome was tandemly repeated for mapping all genome sequences.…”

Section: Methodsmentioning

confidence: 99%

Single-Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma

Altinel¹,

Hashimoto²,

et al. 2016

J Virol

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Hepatitis B virus (HBV) is a major cause of liver diseases, including hepatocellular carcinoma (HCC), and more than 650,000 people die annually due to HBV-associated liver failure. Extensive studies of individual promoters have revealed that heterogeneous RNA 5′ ends contribute to the complexity of HBV transcriptome and proteome. Here, we provide a comprehensive map of HBV transcription start sites (TSSs) in human liver, HCC, and blood, as well as several experimental replication systems, at a single-nucleotide resolution. Using CAGE (cap analysis of gene expression) analysis of 16 HCC/nontumor liver pairs, we identify 17 robust TSSs, including a novel promoter for the X gene located in the middle of the gene body, which potentially produces a shorter X protein translated from the conserved second start codon, and two minor antisense transcripts that might represent viral noncoding RNAs. Interestingly, transcription profiles were similar in HCC and nontumor livers, although quantitative analysis revealed highly variable patterns of TSS usage among clinical samples, reflecting precise regulation of HBV transcription initiation at each promoter. Unlike the variety of TSSs found in liver and HCC, the vast majority of transcripts detected in HBV-positive blood samples are pregenomic RNA, most likely generated and released from liver. Our quantitative TSS mapping using the CAGE technology will allow better understanding of HBV transcriptional responses in further studies aimed at eradicating HBV in chronic carriers.IMPORTANCE Despite the availability of a safe and effective vaccine, HBV infection remains a global health problem, and current antiviral protocols are not able to eliminate the virus in chronic carriers. Previous studies of the regulation of HBV transcription have described four major promoters and two enhancers, but little is known about their activity in human livers and HCC. We deeply sequenced the HBV RNA 5′ ends in clinical human samples and experimental models by using a new, sensitive and quantitative method termed cap analysis of gene expression (CAGE). Our data provide the first comprehensive map of global TSS distribution over the entire HBV genome in the human liver, validating already known promoters and identifying novel locations. Better knowledge of HBV transcriptional activity in the clinical setting has critical implications in the evaluation of therapeutic approaches that target HBV replication.

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“…To systematically identify potential sgRNAs targeting HBV DNA, we used the CRISPR DESIGN tool (http:// crispr.mit.edu) to design potential sgRNAs. To achieve a broad-spectrum antiviral activity, we selected 9 sgRNAs that target regions with the highest levels of conservation among HBV strains (Supplementary information, Figure S1E) [13]. We tested the sgRNAs using an in vitro transfection assay in HepAD38 cells, a hepatocyte line with an integrated HBV genome.…”

Section: Dear Editormentioning

confidence: 99%

A non-viral CRISPR/Cas9 delivery system for therapeutically targeting HBV DNA and pcsk9 in vivo

et al. 2017

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HBVdb: a knowledge database for Hepatitis B Virus

Cited by 187 publications

References 40 publications

Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions

Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions

Single-Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma

A non-viral CRISPR/Cas9 delivery system for therapeutically targeting HBV DNA and pcsk9 in vivo

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