ArticleJournal of clinical microbiology2013
Comparison of next-generation sequencing and clone-based sequencing in analysis of hepatitis B virus reverse transcriptase quasispecies heterogeneity.
Article in Journal of clinical microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Article
- Sparse logistic regression revealed the associations between HBV PreS quasispecies and hepatocellular carcinoma.Virology journal · 2022Article
- The Impact of HBV Quasispecies Features on Immune Status in HBsAg+/HBsAb+ Patients With HBV Genotype C Using Next-Generation Sequencing.Frontiers in immunology · 2021Article
- High Prevalence of Preexisting HBV Polymerase Mutations in Pregnant Women Does Not Limit the Antiviral Therapy Efficacy.The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2021Article
- Review
- Comparison of Serum Hepatitis B Virus RNA Levels and Quasispecies Evolution Patterns between Entecavir and Pegylated-Interferon Mono-treatment in Chronic Hepatitis B Patients.Journal of clinical microbiology · 2020Article
- Characterization of Plaque Variants and the Involvement of Quasi-Species in a Population of EV-A71.Viruses · 2020Article
- An integrated software for virus community sequencing data analysis.BMC genomics · 2020Article
- Article
- Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology.Frontiers in microbiology · 2020Review
- Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC.PLoS genetics · 2018Article
- A comparative study on the characterization of hepatitis B virus quasispecies by clone-based sequencing and third-generation sequencing.Emerging microbes & infections · 2017Article
- Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing.Scientific reports · 2017Article
- Genetic variation of hepatitis B virus and its significance for pathogenesis.World journal of gastroenterology · 2016Review
- Evaluation of the dynamic pattern of viral evolution in patients with virological breakthrough during treatment with nucleoside/nucleotide analogs by ultra‑deep pyrosequencing.Molecular medicine reports · 2016Article
- Characterization of Full-Length Genomes of Hepatitis B Virus Quasispecies in Sera of Patients at Different Phases of Infection.Journal of clinical microbiology · 2015Article
- Variations and mutations in the hepatitis B virus genome and their associations with clinical characteristics.World journal of hepatology · 2015Review
- MALAT1 functions as a competing endogenous RNA to mediate Rac1 expression by sequestering miR-101b in liver fibrosis.Cell cycle (Georgetown, Tex.) · 2015Article
- Recent advances in molecular diagnostics of hepatitis B virus.World journal of gastroenterology · 2014Review
- Hepatitis B virus genetic mutations and evolution in liver diseases.World journal of gastroenterology · 2014Review
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We previously reported that, based on clone-based sequencing (CBS), hepatitis B virus (HBV) heterogeneity within the reverse transcriptase (RT) region was a predictor of antiviral efficacy. Here, by comparing ultradeep pyrosequencing (UDPS), i.e., next-generation sequencing (NGS), with CBS in characterizing the genetic heterogeneity of HBV quasispecies within the RT region, we evaluated the performance of UDPS in the analysis of HBV viral populations. HBV genomic DNA was extracted from serum samples from 31 antiviral treatment-naive patients with chronic hepatitis B. The RT region quasispecies were analyzed in parallel using CBS and UDPS. Characterization of quasispecies heterogeneity was conducted using bioinformatics analysis. Quasispecies complexity values were calculated with the formula Sn = -Σi(pilnpi)/lnN. The number of qualified strains obtained by UDPS was much larger than that obtained by CBS (P < 0.001). Pearson analysis showed that there was a positive correlation of quasispecies complexity values at the nucleotide level for the two methods (P < 0.05), while the complexity value derived from UDPS data was higher than that derived from CBS data (P < 0.001). Study of the prevalences of variations within the RT region showed that CBS detected an average of 9.7 ± 1.1 amino acid substitutions/sample and UDPS detected an average of 16.2 ± 1.4 amino acid substitutions/sample. The phylogenetic analysis based on UDPS data showed more genetic entities than did that based on CBS data. Viral heterogeneity determination by the UDPS technique is more sensitive and efficient in terms of low-abundance variation detection and quasispecies simulation than that by the CBS method, although imperfect, and thus sheds light on the future clinical application of NGS in HBV quasispecies studies.
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