Abstract
Hepatitis B virus (HBV) has a high mutation rate due to the extremely high replication rate and the proofreading deficiency during reverse transcription. The generated variants with genetic heterogeneity are described as viral quasispecies (QS). Clone-based sequencing (CBS) is thought to be the ‘gold standard’ for assessing QS complexity and diversity of HBV, but an important issue about CBS is cost-effectiveness and laborious. In this study, we investigated the utility of the third-generation sequencing (TGS) DNA sequencing to characterize genetic heterogeneity of HBV QS and assessed the possible contribution of TGS technology in HBV QS studies. Parallel experiments including 3 control samples, which consisted of HBV full gene genotype B and genotype C plasmids, and 10 patients samples were performed by using CBS and TGS to analyze HBV whole-genome QS. Characterization of QS heterogeneity was conducted by using comprehensive statistical analysis. The results showed that TGS had a high consistency with CBS when measuring the complexity and diversity of QS. In addition, to detect rare variants, there were strong advantages conferred by TGS. In summary, TGS was considered to be practicable in HBV QS studies and it might have a relevant role in the clinical management of HBV infection in the future.Emerging Microbes & Infections (2017) 6, e100; doi:10.1038/emi.2017.88; published online 8 November 2017
Highlights
Hepatitis B virus (HBV) is a hepatotropic virus and its infection is a leading cause of viral hepatitis
The application of one representative of third-generation sequencing (TGS) technology, single-molecule real-time sequencing in HBV QS research was investigated
To compare the genetic heterogeneity of HBV QS measured by clone-based sequencing (CBS) and TGS, 3 control samples and 10 clinical samples were collected and various statistical methods were applied for QS characterization
Summary
Hepatitis B virus (HBV) is a hepatotropic virus and its infection is a leading cause of viral hepatitis. HBV is non-cytopathic but can lead to chronic liver inflammation and fibrosis, result in liver cirrhosis and/or hepatocellular carcinoma.. Nucleoside/nucleotide analogs are the currently approved antivirals for patients with chronic HBV infection, which target HBV reverse transcriptase (RT) region, QS variations within HBV RT region was believed to have an impact on virological response of antiviral treatment.. As documented in several studies, the charcteristics or evolutionary patterns of HBV QS within RT region correlate with the antiviral response to nucleoside/nucleotide analogs and clinical outcomes, more comprehensive understanding of HBV full-length genome mutations and QS will be helpful to guide the treatment of patients with antiviral treatment The generated variants with genetic heterogeneity are described as viral quasispecies (QS). Nucleoside/nucleotide analogs are the currently approved antivirals for patients with chronic HBV infection, which target HBV reverse transcriptase (RT) region, QS variations within HBV RT region was believed to have an impact on virological response of antiviral treatment. As documented in several studies, the charcteristics or evolutionary patterns of HBV QS within RT region correlate with the antiviral response to nucleoside/nucleotide analogs and clinical outcomes, more comprehensive understanding of HBV full-length genome mutations and QS will be helpful to guide the treatment of patients with antiviral treatment
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