scholarly journals Discrepant Results of Hepatitis B Virus Genotype Determination by PCR and DNA Sequencing

2021 ◽  
Author(s):  
Yihan Xiao ◽  
Lan Ni ◽  
Zhigang Cui ◽  
Long Sun ◽  
Xiaojun Zhou ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Dna Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Full Length ◽  
Whole Genome ◽  
Hbv Genotype ◽  
Specific Primers ◽  
B Virus

Abstract Currently, multiplex-PCR with genotype-specific primers is widely used for preliminary screening of hepatitis B virus (HBV) genotyping, despite its relatively lower accuracy compared with whole genome sequencing. Here, we present the discrepant results of HBV genotyping by PCR and full-length sequencing. HBV DNA was isolated from chronic hepatitis B serum and the HBV genotype was detected by PCR using genotype-specific primers and full-length genome sequencing. As a result, the determination of genotype B by the PCR method was consistent with the DNA sequencing results; however, PCR revealed that genotype C exhibited a mixed genotype of B and C in the current study. In conclusion, the PCR-based genotyping method may not provide accurate information of the HBV genotype and whole genome sequencing remains the “gold standard” method for HBV genotyping.

scholarly journals Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Anna L. McNaughton ◽  
Hannah E. Roberts ◽  
David Bonsall ◽  
Mariateresa de Cesare ◽  
Jolynne Mokaya ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
B Virus

scholarly journals Genotyping Hepatitis B virus from whole- and sub-genomic fragments using position-specific scoring matrices in hbv star

2006 ◽  
Vol 87 (6) ◽  
pp. 1459-1464 ◽  
Author(s):  
Richard Myers ◽  
Caroline Clark ◽  
Arshad Khan ◽  
Paul Kellam ◽  
Richard Tedder
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Core Promoter ◽  
Full Length ◽  
Basal Core Promoter ◽  
Hbv Genotype ◽  
Promoter Sequences ◽  
Hbv Genotypes ◽  
Scoring Matrices ◽  
B Virus

Hepatitis B virus (HBV) genomes have been classified into eight genotypes based on phylogenetic analysis of sequence variation. Identifying and tracking the movement of HBV genotypes is important in terms of both monitoring infection rates and predicting disease and treatment. An HBV genotyping tool has been developed that compares query sequences with position-specific scoring matrices representing the eight HBV genotypes. This tool (hbv star) is rapid, robust and accurate and assigns genotype based on a statistically defined scoring model. hbv star confidently assigned 90 % of 590 full-length HBV genomes to an HBV genotype (Z score >2.0). Thirty-two of the residual 48 sequences were identified as non-human primate viruses and 16 sequences were identified as recombinant or putative recombinants. Receiver-Operated Characteristic (ROC) analysis was used to compare the accuracy of genotype prediction using basal core promoter sequences and surface and core genes with the accuracy achieved by using full-length sequences. A web interface to hbv star is available at http://www.vgb.ucl.ac.uk/starn.shtml.

scholarly journals Genotype C of hepatitis B virus can be classified into at least two subgroups

2004 ◽  
Vol 85 (2) ◽  
pp. 283-292 ◽  
Author(s):  
Tran Thien-Tuan Huy ◽  
Hiroshi Ushijima ◽  
Vo Xuan Quang ◽  
Khin Maung Win ◽  
Pairoj Luengrojanakul ◽  
...  
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Far East ◽  
Full Length ◽  
Hbv Genotype ◽  
B Virus ◽  
Protein Amino Acids ◽  
Genotype C

A genomic characterization of hepatitis B virus (HBV) was done for 56 pre-S1/pre-S2 genes and 10 full-length HBV genotype C isolates from five Asian countries. Phylogenetic analysis of the pre-S1/pre-S2 genes revealed two major groups within genotype C: one for isolates from southeast Asia including Vietnam, Myanmar and Thailand (named HBV/C1) and the other for isolates from Far East Asia including Japan, Korea and China (named HBV/C2). This finding was confirmed by phylogenetic analysis based on the full-length sequence of 32 HBV genotype C isolates, including 22 from database entries. Two isolates from Okinawa, the island off the southern end of Japan, formed a different branch. Specific amino acid sequence changes were identified in the large S protein (amino acids 51, 54, 60, 62 and 73) and P protein (amino acids 231, 233, 236, 248, 252 and 304). Our results indicate that genotype C of HBV can be classified into at least two subgroups.

474 Hepatitis B virus genomic markers for hepatocellular carcinoma on full-genome sequencing of 332 patients

2006 ◽  
Vol 44 ◽  
pp. S176-S177
Author(s):  
J.J.Y. Sung ◽  
S.K.W. Tsui ◽  
C.H. Tse ◽  
E.Y.T. Ng ◽  
K.S. Leung ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Genome Sequencing ◽  
Full Genome ◽  
Full Genome Sequencing ◽  
B Virus ◽  
Genomic Markers

scholarly journals Pyrosequencing Technology for Short DNA Sequencing and Whole Genome Sequencing

2007 ◽  
Vol 47 (2) ◽  
pp. 129-132 ◽  
Author(s):  
Baback GHARIZADEH ◽  
Mehran GHADERI ◽  
Pål NYRÉN
Keyword(s):  
Dna Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Pyrosequencing Technology

scholarly journals Deletion and Functional Analysis of Hepatitis B Virus X Protein: Evidence for an Effect on Cell Cycle Regulators

2018 ◽  
Vol 49 (5) ◽  
pp. 1987-1998 ◽  
Author(s):  
Mashael R. Al-Anazi ◽  
Nyla Nazir ◽  
Dilek Colak ◽  
Mohammed N. Al-Ahdal ◽  
Ahmed A. Al-Qahtani
Keyword(s):  
Cell Cycle ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Cyclin D1 ◽  
Full Length ◽  
Deletion Mutants ◽  
X Protein ◽  
P53 Expression ◽  
Huh7 Cells ◽  
B Virus

Background/Aims: The hepatitis B virus X protein (HBx) is a viral trans-activator that plays a crucial role in pathogenesis of hepatocellular carcinoma (HCC) via an unknown mechanism. The role of HBx in modulating cell proliferation and programmed cell death is replete with controversies. Thus, the goal of this study was to elucidate the effect of HBx and its deletion mutants on cell cycle progression in human hepatoma cells. Methods: Huh7 cells transfected with either full-length or truncated HBx were tested for their mitogenic potential based on their effect on the expression of key cell cycle-related proteins (p27, cyclin D1, p21, and p53) and pro-apoptotic proteins such as cleaved poly (ADP-ribose) polymerase (PARP) and Bax. Western blotting and immunofluorescence techniques were applied to detect changes in the expression levels and intracellular localization, respectively, of the investigated proteins. Also, Quantitative real-time PCR (qRT-PCR) was used to detect changes in RNA levels. Results: An increased anchorage-independent growth of cells transfected with HBx-WT and its deletion mutants was observed. The cell cycle regulatory molecules were differentially modulated by full-length HBx (1-154) and its different N- and C-terminal truncated forms (HBx (31-154), HBx (61-154), HBx (1-94), and HBx (61-124)). An enhanced modulation of p27, p21, and cyclin D1 was associated with HBx (1-154), whereas p53 expression was significantly inhibited by HBx (61-124). Similarly, the expression of cleaved PARP and Bax was efficiently suppressed by HBx (1-94) and HBx (61-154). Conclusion: The HBx-WT and its mutants play a critical role in the pathogenesis and progression of HCC by modulating cell cycle regulatory proteins.

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