scholarly journals Molecular Epidemiology of Hepatitis B Virus (HBV) Genotypes Prevalent in KP

2021 ◽  
Vol 17 (4) ◽  
pp. 727-734
Author(s):  
Farzana Farzana ◽  
Ayaz Ahmad ◽  
Ijaz Ali
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Nucleotide Sequences ◽  
Phylogenetic Study ◽  
S Gene ◽  
Hbv Genotypes ◽  
Specific Pcr ◽  
B Virus ◽  
Qualitative Pcr

Hepatitis B virus (HBV) infection is a major public health dilemma affecting about 2 billion of world population and more than 350 million people are chronic HBV carriers including Pakistan with an estimated prevalence rate of 3%. HBV can be categorized into 10 genotypes (A-H) clarified by more than 8% of sequence divergence based on the whole genome. Although Pakistan is highly endemic to HBV no large scale study of HBV genotypes based on sequence analysis has been reported yet so the ongoing research study was aimed to explore the existing patterns of HBV genotypes based on sequencing method and phylogenetic analysis of HBV S gene distributed in Khyber Pakhtukhwa (KP)which isone of the third most populated province of Pakistan. A total of 3000 chronically HBV positive samples were collected from 7 most populous districts of KP and were analyzed by ICT followed by qualitative PCR for confirmation. Type-specific PCR or restriction fragment length polymorphism (RFLP) and random sequencing of the partial Sgene were carried out for HBV genotypes characterization. We obtained a 100 of, S gene nucleotide sequences out of which 28 nucleotide sequences demonstrating the whole diversity of the sequenced types were further used for phylogenetic study using Mega 6 software. Active infection of HBV was confirmed in all patients through qualitative PCR and three genotypes A, C, and D were confirmed by type specific PCR and RFLP. The most prevalent genotype detected was genotype D 68.3% followed by genotype A 22.6% and genotype C 8.53%. Phylogenetic analysis of the obtained sequences based on HBV S gene revealed that some of our HBV sequences clustered with some local isolates showing close homology with them while other clustered together with some foreign isolates with a high bootstrap value. However, one isolate didn’t match or show any similarity with any of HBV strain available in online repositories that point towards a great divergence and a distinctive origin of the strain.

scholarly journals Hepatitis B Virus Pre-S Gene Deletions and Pre-S Deleted Proteins: Clinical and Molecular Implications in Hepatocellular Carcinoma

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 862
Author(s):  
Yueh-Te Lin ◽  
Long-Bin Jeng ◽  
Wen-Ling Chan ◽  
Ih-Jen Su ◽  
Chiao-Fang Teng
Keyword(s):  
Hepatocellular Carcinoma ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Molecular Mechanisms ◽  
Incidence Rates ◽  
Gene Deletions ◽  
S Gene ◽  
B Virus ◽  
Potential Applications ◽  
Prevention And Therapy

Hepatocellular carcinoma (HCC) is one of the most frequent and fatal human cancers worldwide and its development and prognosis are intimately associated with chronic infection with hepatitis B virus (HBV). The identification of genetic mutations and molecular mechanisms that mediate HBV-induced tumorigenesis therefore holds promise for the development of potential biomarkers and targets for HCC prevention and therapy. The presence of HBV pre-S gene deletions in the blood and the expression of pre-S deleted proteins in the liver tissues of patients with chronic hepatitis B and HBV-related HCC have emerged as valuable biomarkers for higher incidence rates of HCC development and a higher risk of HCC recurrence after curative surgical resection, respectively. Moreover, pre-S deleted proteins are regarded as important oncoproteins that activate multiple signaling pathways to induce DNA damage and promote growth and proliferation in hepatocytes, leading to HCC development. The signaling molecules dysregulated by pre-S deleted proteins have also been validated as potential targets for the prevention of HCC development. In this review, we summarize the clinical and molecular implications of HBV pre-S gene deletions and pre-S deleted proteins in HCC development and recurrence and highlight their potential applications in HCC prevention and therapy.

scholarly journals Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6142
Author(s):  
Therese A. Catanach ◽  
Andrew D. Sweet ◽  
Nam-phuong D. Nguyen ◽  
Rhiannon M. Peery ◽  
Andrew H. Debevec ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Sequence Alignment ◽  
Sequence Data ◽  
Large Data ◽  
Large Data Sets ◽  
Data Sets ◽  
Hbv Genotypes ◽  
B Virus ◽  
Automated Algorithms

Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.

scholarly journals Utility of oral fluid samples to determine hepatitis B virus genotypes, mutations and phylogenetic analysis

2021 ◽  
Author(s):  
Livia Villar ◽  
Barbara Lago ◽  
Cristianne Bezerra ◽  
Ana Mendonça ◽  
Leticia Nabuco ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Oral Fluid ◽  
B Virus ◽  
Virus Genotypes

scholarly journals Antiviral effects of hepatitis B virus S gene-specific anti-gene locked nucleic acid in transgenic mice

2018 ◽  
Vol 6 (8) ◽  
pp. 183-191
Author(s):  
Shu-Rong Xiao ◽  
Gui-Dan Xu ◽  
Wu-Jun Wei ◽  
Bin Peng ◽  
Yi-Bin Deng
Keyword(s):  
Hepatitis B Virus ◽  
Nucleic Acid ◽  
Hepatitis B ◽  
Transgenic Mice ◽  
Locked Nucleic Acid ◽  
S Gene ◽  
Antiviral Effects ◽  
B Virus

scholarly journals Application of Hepatitis B Virus Genotyping and Phylogenetic Analysis in Intrafamilial Transmission of Hepatitis B Virus

2005 ◽  
Vol 41 (11) ◽  
pp. 1576-1581 ◽  
Author(s):  
C.-L. Lin ◽  
J.-H. Kao ◽  
B.-F. Chen ◽  
P.-J. Chen ◽  
M.-Y. Lai ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Intrafamilial Transmission ◽  
B Virus
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