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

Hepatitis B virus genotype distribution and mutation patterns: Insights and clinical implications for hepatitis B virus positive patients

Hepatitis B virus (HBV) infection is still a major worldwide health concern, contributing to chronic liver disorders like hepatocellular carcinoma (HCC). This review comprehensively analyzes HBV genotype distribution, mutation patterns, and their clinical implications, focusing on diagnostic and therapeutic strategies for HBV-positive patients. The discussion begins with HBV virology, emphasizing its capacity for chronic hepatitis and its association with severe liver complications, notably HCC. Understanding HBV genotypes (A-J) and their distinct geographic distributions is crucial, as genotype variations influence disease progression and treatment responses. Genotypes like C are particularly linked to heightened HCC risk, highlighting the need for genotype-specific management strategies. The genomic structure of HBV, consisting of four open reading frames (ORFs) encoding essential viral proteins, is detailed, with emphasis on mutations within these ORFs influenced by host immune responses and antiviral therapies. These mutations contribute to viral resistance and virulence, impacting treatment outcomes through alterations in viral replication dynamics. Clinical implications are explored through genotype-specific impacts on disease outcomes and treatment approaches. Genotype and mutation analysis guide personalized treatment regimens, optimizing therapeutic efficacy while minimizing adverse effects and preventing drug resistance. Diagnostic molecular techniques such as polymerase chain reaction and sequencing are pivotal in genotype and mutation detection, facilitating tailored treatment decisions.

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data

The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numerous datasets and showed that the consensus genome of samples could be obtained reliably without further manual data curation. Our pipeline can be a valuable tool for fast identifying viral samples. The pipeline is publicly available on the project’s GitHub page (https://github.com/laczkol/QVG).

Genotyping and Molecular Diagnosis of Hepatitis A Virus in Human Clinical Samples Using Multiplex PCR-Based Next-Generation Sequencing

Hepatitis A virus (HAV) is a serious threat to public health worldwide. We used multiplex polymerase chain reaction (PCR)-based next-generation sequencing (NGS) to derive information on viral genetic diversity and conduct precise phylogenetic analysis. Four HAV genome sequences were obtained using multiplex PCR-based NGS. HAV whole-genome sequence of one sample was obtained by conventional Sanger sequencing. The HAV strains demonstrated a geographic cluster with sub-genotype IA strains in the Republic of Korea. The phylogenetic pattern of HAV viral protein (VP) 3 region showed no phylogenetic conflict between the whole-genome and partial-genome sequences. The VP3 region in serum and stool samples showed sensitive detection of HAV with differences of quantification that did not exceed <10 copies/μL than the consensus VP4 region using quantitative PCR (qPCR). In conclusion, multiplex PCR-based NGS was implemented to define HAV genotypes using nearly whole-genome sequences obtained directly from hepatitis A patients. The VP3 region might be a potential candidate for tracking the genotypic origin of emerging HAV outbreaks. VP3-specific qPCR was developed for the molecular diagnosis of HAV infection. This study may be useful to predict for the disease management and subsequent development of hepatitis A infection at high risk of severe illness.

Deep sequencing of hepatitis B virus using Ion Torrent fusion primer method

BACKGROUND

Hepatitis B virus (HBV) infection is worldwide a major cause of liver cirrhosis and hepatocellular carcinoma. Thousands of years ago, several HBV genotypes (A-I) evolved and have, as a result of human migration, become globally disseminated. Sequencing of HBV is used for genotyping, and investigation of outbreaks or of antiviral resistance. The present study describes a simplified deep sequencing of the whole HBV genome.

METHODS

Sequencing by Ion Torrent was evaluated and its performance compared with Sanger sequencing on clinical samples.

RESULTS

Amplification of overlapping segments spanning the entire HBV genome was successful at HBV DNA levels in serum as low as 100 IU/mL. The use of primers carrying adapter tags generated libraries without the need for fragmentation and ligation steps, and inclusion of barcode sequences allowed parallel analysis of multiple samples. A streamlined bioinformatic platform generated consensus sequences and superior mutation assessment as compared with Sanger sequencing, with which there was a 99.8 % average agreement.

CONCLUSION

Deep sequencing of the whole HBV genome by using PCR primers tagged with adapters that prepare overlapping amplicons for Ion Torrent analysis was efficient and accurate.

Next-generation sequencing for the diagnosis of hepatitis B: current status and future prospects

INTRODUCTION

Hepatitis B virus (HBV) causes a complex and persistent infection with a major impact on patients health. Viral-genome sequencing can provide valuable information for characterizing virus genotype, infection dynamics and drug and vaccine resistance.

AREAS COVERED

This article reviews the current literature to describe the next-generation sequencing progress that facilitated a more comprehensive study of HBV quasispecies in diagnosis and clinical monitoring.

EXPERT OPINION

HBV variability plays a key role in liver disease progression and treatment efficacy. Second-generation sequencing improved the sensitivity for detecting and quantifying mutations, mixed genotypes and viral recombination. Third-generation sequencing enables the analysis of the entire HBV genome, although the high error rate limits its use in clinical practice.