Analysis of hepatitis B virus genotyping and drug resistance gene mutations based on massively parallel sequencing

Han, Yingxin; Zhang, Yinxin; Mei, Yanhua; Wang, Yuqi; Liu, Tao; Guan, Yanfang; Tan, Deming; Yu, Liang; Yang, Lei; Yi, Xin

doi:10.1016/j.jviromet.2013.06.015

Cited by 13 publications

(9 citation statements)

References 38 publications

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“…One should be careful about what threshold to use to define a clinically meaningful population. In recent studies, minority variants were defined as differences greater than 0.5 and 1.0% of mutations detected by deep sequencing [24,25]. In this study, the proportions of the total numbers of reads containing mutations I169L/M, S202R, M204I/L or N236S were >1.0%.…”

Section: Discussionmentioning

confidence: 68%

A Deep-Sequencing Method Detects Drug-Resistant Mutations in the Hepatitis B Virus in Indonesians

et al. 2014

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Objective: The long-term administration of a nucleos(t)ide analogue (NA) for the treatment of chronic hepatitis B may encourage the emergence of viral mutations associated with drug resistance. Minor populations of viruses may exist before treatment, but are difficult to detect because of technological limitations. Identifying minor viral quasispecies should be useful in the clinical management of hepatitis B virus (HBV) infection. Methods: Six treatment-naïve Indonesian patients with chronic HBV infection participated in this study. The polymerase region of the HBV genome, including regions with known drug-resistant mutations, was subjected to capillary sequencing and MiSeq sequencing (Illumina). Mutations were analyzed with Genomics Workbench software version 6.0.1 (CLC bio). Results: The mean mapping reads for the six samples was 745,654, and the mean number of amplified fragments ranged from 17,926 to 25,336 DNA reads. Several known drug-resistant mutations in the reverse transcriptase region were identified in all patients, although the frequencies were low (0.12-1.06%). The proportions of the total number of reads containing mutations I169L/M, S202R, M204I/L or N236S were >1.0%. Conclusion: Several known NA-resistant mutations were detected in treatment-naïve patients in Indonesia using deep sequencing. Careful management of such patients is essential to prevent drug-resistant mutations from spreading to other patients.

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Section: Discussionmentioning

confidence: 68%

A Deep-Sequencing Method Detects Drug-Resistant Mutations in the Hepatitis B Virus in Indonesians

et al. 2014

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“…This lack of association might be due to the short segment of reverse transcriptase (RT) gene overlapping the S gene fragment that we amplified. A more detailed study is needed to investigate the HBV RT gene, where most of the antiviral resistant mutations are reported [45].…”

Section: Discussionmentioning

confidence: 99%

Analysis of Hepatitis B virus (HBV) mutations in patients from Western Saudi Arabia with chronic disease

El‐Kafrawy

Jamjoom

Akbar

et al. 2018

J Infect Dev Ctries

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Introduction: Extensive research has provided a link between HBV variants and the clinical complications of liver diseases. This study was performed to further investigate the relationship between HBV variants in preS, S and BCP/PC regions and disease progression in chronic hepatitis B (CHB) cases in Jeddah, Saudi Arabia. Methodology: 182 CHB patients were recruited for this study. HBV DNA was amplified by PCR in the PreS, S, and BCP/PC regions. Sequences were generated from 31 and 26 treated cases in PreS and S regions respectively and from 72 cases in the BCP/PC region. Results: The majority of cases (86.7%) were genotype D. Mutations at preS1-A2922C, X-A1624C and PC-G1887A were detected only in cases with either a high fibrosis score or hepatocellular carcinoma (HCC), while mutations at positions PC-C1982A, PC-G1951T, X-C1628T and X-A1630G were detected more frequently in HCC cases, without reaching statistical significance. Seven deletions were detected in the PreS-region. No deletions were detected in the CCAAT box. The accumulation of mutations per sample in the preS1-2 and S regions were associated with elevated ALT (p < 0.001, 0.001 and 0.001; respectively) and increased fibrosis (p = 0.018, 0.02 and 0.013; respectively). The accumulation of mutations per sample in the BCP/PC region is associated with high viral load. Occult hepatitis B infection (OBI) was identified in 5 samples. Conclusion: Our results add to the knowledge about HBV genotype-D variants. The accumulation of mutations per sample and OBI seem to play a role in the progression of HBV infection. G1896A was associated with the HBeAg negativity. The preS deletions did not play a role in liver disease progression.

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“…These authors observed genotype changes in P/S genes in four patients during natural quasispecies dynamics and in two patients during treatment. The detection of HBV drug resistance mutations in P/S genes (preferably RT polymerase) using NGS has been extensively reported [ 11 , 15 , 16 , 17 ]. In all those studies, pyrosequencing or Illumina was carried out after gene PCR amplification.…”

Section: Introductionmentioning

confidence: 99%

A New Method for Next-Generation Sequencing of the Full Hepatitis B Virus Genome from A Clinical Specimen: Impact for Virus Genotyping

et al. 2020

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Hepatitis B virus (HBV) is an enveloped virus that induces chronic liver disease. HBV has been classified into eight genotypes (A–H) according to its genome sequence by using Sanger sequencing or reverse hybridization. Sanger sequencing is often restricted to analyzing the S gene and is inaccurate for detecting minority genetic variants, whereas reverse hybridization detects only known mutations. Next-generation sequencing (NGS) is a robust tool for clinical virology with different protocols available. The objective of this study was to develop a new method for the study of viral genetic polymorphisms or more accurate genotyping using genome amplification followed by NGS. Plasma obtained from five chronically infected HBV individuals was used for viral DNA isolation. HBV full-genome PCR amplification was the enrichment method for NGS. Primers were used to amplify all HBV genotypes in three overlapping amplicons, following a tagmentation step and Illumina NGS. For phylogenetic analysis, sequences were extracted from the HBVdb database. We were able to amplify a full HBV genome; further, NGS was shown to be a robust method and allowed better genotyping, mainly in patients carrying mixed genotypes, classified according to other techniques. This new method may be significant for whole genome analyses, including other viruses.

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Analysis of hepatitis B virus genotyping and drug resistance gene mutations based on massively parallel sequencing

Cited by 13 publications

References 38 publications

A Deep-Sequencing Method Detects Drug-Resistant Mutations in the Hepatitis B Virus in Indonesians

A Deep-Sequencing Method Detects Drug-Resistant Mutations in the Hepatitis B Virus in Indonesians

Analysis of Hepatitis B virus (HBV) mutations in patients from Western Saudi Arabia with chronic disease

A New Method for Next-Generation Sequencing of the Full Hepatitis B Virus Genome from A Clinical Specimen: Impact for Virus Genotyping

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