Detection of hepatitis B virus genotypes using oligonucleotide chip among hepatitis B virus carriers in Eastern China

Tang, Xueyang; Zhang, Ji-Shen; Zhao, Hui; Yang, Gong; Wang, Yongzhong; Zhao, Jianjian

doi:10.3748/wjg.v13.i13.1975

Cited by 11 publications

(7 citation statements)

References 22 publications

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“…This method is rapid and inexpensive and widely used for large population studies; however, any mutation in the genome may alter the result of the assay due to primer-DNA hybridization mismatching [37] . Recently, the DNA Chip method [38] , invader assays [39] , real-time PCR [40][41][42] , hybridization and dot blot methods [43] have been employed for HBV genotype detection [38] . These techniques are highly sensitive; however, fidelity can be affected by any mutation within the HBV genome.…”

Section: Molecular-based 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: Molecular-based 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

View full text Add to dashboard Cite

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“…In addition, this technique does not allow a mutation frequency estimate, so it is not suitable for dynamic studies. Other sequence-specific genotypic resistance tests are available or are being developed, such as restriction fragment length/mass polymorphism (11,33,41), oligonucleotide microarray and gene chip technology (19,36), mutation-specific real-time PCR (39), matrix-assisted laser desorption ionization-time of flight mass spectrometry (17), and pyrosequencing (14,20). On the whole, all of the sequence-specific methods present the same drawbacks of reverse hybridization.…”

mentioning

confidence: 99%

Use of Massively Parallel Ultradeep Pyrosequencing To Characterize the Genetic Diversity of Hepatitis B Virus in Drug-Resistant and Drug-Naive Patients and To Detect Minor Variants in Reverse Transcriptase and Hepatitis B S Antigen

Solmone

Vincenti

Prosperi

et al. 2009

J Virol

145

152

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“…Point mutation assays can detect specific variants at as low as 5% of the virus population, but only if well-established mutations are present, whereas it may miss mutations that are not yet associated with resistance (2). Other sequence-specific genotypic resistance tests are available or under development, such as restriction fragment length/mass polymorphism, mutation-specific real-time PCR, oligonucleotide microarray, and gene chip technology (7,8). The use of novel technologies to sequence multiple genetic variants in a heterogeneous pool of amplified DNA molecules, such as those from a virus quasispecies, by massively parallelizing PCR amplification, represents the next-generation sequencing (NGS) that is able to quantitatively detect minority variants at levels as low as 1 to 2% (9, 10).…”

mentioning

confidence: 99%

Ultrasensitive Amplification Refractory Mutation System Real-Time PCR (ARMS RT-PCR) Assay for Detection of Minority Hepatitis B Virus-Resistant Strains in the Era of Personalized Medicine

et al. 2013

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Resistance to antiviral treatment for chronic hepatitis B virus (HBV) has been associated with mutations in the HBV polymerase region. This study aimed at developing an ultrasensitive method for quantifying viral populations with all major HBV resistance-associated mutations, combining the amplification refractory mutation system real-time PCR (ARMS RT-PCR) with a molecular beacon using a LightCycler. The discriminatory ability of this method, the ARMS RT-PCR with molecular beacon assay, was 0.01 to 0.25% for the different HBV resistance-associated mutations, as determined by laboratory-synthesized wild-type (WT) and mutant (Mut) target sequences. The assay showed 100% sensitivity for the detection of mutant variants A181V, T184A, and N236T in samples from 41 chronically HBV-infected patients under antiviral therapy who had developed resistance-associated mutations detected by direct PCR Sanger sequencing. The ratio of mutant to wild-type viral populations (the Mut/WT ratio) was >1% in 38 (63.3%) of 60 samples from chronically HBV-infected nucleos(t)ide analogue-naive patients; combinations of mutations were also detected in half of these samples. The ARMS RT-PCR with molecular beacon assay achieved high sensitivity and discriminatory ability compared to the gold standard of direct PCR Sanger sequencing in identifying resistant viral populations in chronically HBV-infected patients receiving antiviral therapy. Apart from the dominant clones, other quasispecies were also quantified. In samples from chronically HBV-infected nucleos(t)ide analogue-naive patients, the assay proved to be a useful tool in detecting minor variant populations before the initiation of the treatment. These observations need further evaluation with prospective studies before they can be implemented in daily practice. N ucleos(t)ide analogues are a fundamental tool for the treatment of hepatitis B virus (HBV)-associated liver disease because of their potent antiviral activity in the absence of remarkable side effects and major contraindications (1). Longterm nucleos(t)ide analog therapy among patients significantly improves survival and reduces the risk of liver-related major complications, such as death, hepatocellular carcinoma (HCC), and liver decompensation (2). A major concern with nucleos(t)ide analogue therapy is the risk for the development of viral populations with resistance-associated mutations (3, 4). Standard direct PCR Sanger sequencing and point mutation assays are able to detect viral populations with resistance-associated mutations only when they become dominant, leaving a gap in the understanding of the dynamics in the development of resistance. Direct PCR Sanger sequencing detects, on average, mutations present at ratios of Ͼ20% of the circulating virus population (5). Clonal sequencing has a higher sensitivity for detecting low-prevalence HBV mutations, but it is costly and labor-intensive (6). Point mutation assays can detect specific variants at as low as 5% of the virus population, but only if well-established mutatio...

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Detection of hepatitis B virus genotypes using oligonucleotide chip among hepatitis B virus carriers in Eastern China

Cited by 11 publications

References 22 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

Use of Massively Parallel Ultradeep Pyrosequencing To Characterize the Genetic Diversity of Hepatitis B Virus in Drug-Resistant and Drug-Naive Patients and To Detect Minor Variants in Reverse Transcriptase and Hepatitis B S Antigen

Ultrasensitive Amplification Refractory Mutation System Real-Time PCR (ARMS RT-PCR) Assay for Detection of Minority Hepatitis B Virus-Resistant Strains in the Era of Personalized Medicine

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