Development of a novel DNA sequencing method not only for hepatitis B virus genotyping but also for drug resistant mutation detection

Abstract

Background In HBV-infected patients, different genotypes of the hepatitis B virus influence liver disease progression and response to antiviral therapy. Moreover, long-term antiviral therapy will eventually select for drug-resistant mutants. Detection of mutations associated to antiviral therapy and HBV genotyping are essential for monitoring treatment of chronic hepatitis B patients. Results In this study, a simple method of partial-S gene sequencing using a common PCR amplification was established for genotyping clinical HBV isolates sensitively, which could detect the drug-resistant mutations successfully at the same time. Conclusions The partial S gene sequencing assay developed in this study has potential for application in HBV genotyping and drug resistant mutation detection. It is simpler and more convenient than traditional S gene sequencing, but has nearly the same sensitivity and specificity when compared to S gene sequencing.

Nucleic Acid-Based Approaches for Detection of Viral Hepatitis

“…LCR is categorized as a probe amplification method in which two pairs of probes hybridized to the adjacent single stranded target DNA. The specificity and sensitivity of LCR assay are high; however, they depends on the type of microorganisms ( Table 1 ) ( 5 , 25 , 31 , 32 ).…”

“…LCR is a rapid, sensitive and specific technology for simultaneous genotyping and mutants viral agents. The use of this method is limited and is applied for detecting resistant viral hepatitis agents of HBV, HCV, HEV, and HDV in human serum samples ( 5 , 31 , 32 ).…”

Molecular epidemiology of hepatitis B virus isolated from Bangladesh

“…Sequencing part of surface gene from 370 to 861 nt (491 bp) can be termed as partial S gene sequencing that can reveal genotyping, subtyping and common mutations as efficiently as total S gene sequencing (Wang et al 2013 ). This small part of the S gene is conserved and contains ‘a’ determinant region as well as many drug resistant and vaccine mutant sites (Wang et al 2013 ).…”

“…Sequencing part of surface gene from 370 to 861 nt (491 bp) can be termed as partial S gene sequencing that can reveal genotyping, subtyping and common mutations as efficiently as total S gene sequencing (Wang et al 2013 ). This small part of the S gene is conserved and contains ‘a’ determinant region as well as many drug resistant and vaccine mutant sites (Wang et al 2013 ). Recent reports in different areas of the world, showing the anti-viral drugs resistant strains of HBV, strongly alert the need for monitoring drug resistant and vaccine mutant sites along with mutations in other genes of the genome of HBV (Sayan et al 2010 ; Pastor et al 2009 ; Han et al 2009 ).…”

Functional Genomics, Genetics, and Bioinformatics

“…Each of these “-omics” generates a huge amount of high-throughput data, and it is a challenge both to analyze these data and to further investigate the function of specific molecules. Though more genomes have been completed due to the rapid development of sequencing technology [ 9 ], we cannot understand the information contained within a genome until we mine out its implicated functions including downstream transcription, translation, epigenetics modulation, and metabolic pathways. In this special issue, we mainly focus on functional “-omics” and bioinformatics.…”