scholarly journals Genotyping hepatitis B virus dual infections using population-based sequence data

2012 ◽  
Vol 93 (9) ◽  
pp. 1899-1907 ◽  
Author(s):  
Bastian Beggel ◽  
Maria Neumann-Fraune ◽  
Matthias Döring ◽  
Glenn Lawyer ◽  
Rolf Kaiser ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Sequence Data ◽  
Synthetic Data ◽  
Dual Infection ◽  
Population Based ◽  
Model Verification ◽  
Sequencing Data ◽  
B Virus ◽  
Dual Infections

The hepatitis B virus (HBV) is classified into distinct genotypes A–H that are characterized by different progression of hepatitis B and sensitivity to interferon treatment. Previous computational genotyping methods are not robust enough regarding HBV dual infections with different genotypes. The correct classification of HBV sequences into the present genotypes is impaired due to multiple ambiguous sequence positions. We present a computational model that is able to identify and genotype inter- and intragenotype dual infections using population-based sequencing data. Model verification on synthetic data showed 100 % accuracy for intergenotype dual infections and 36.4 % sensitivity in intragenotype dual infections. Screening patient sera (n = 241) revealed eight putative cases of intergenotype dual infection (one A–D, six A–G and one D–G) and four putative cases of intragenotype dual infection (one A–A, two D–D and one E–E). Clonal experiments from the original patient material confirmed three out of three of our predictions. The method has been integrated into geno2pheno[hbv], an established web-service in clinical use for analysing HBV sequence data. It offers exact and detailed identification of HBV genotypes in patients with dual infections that helps to optimize antiviral therapy regimens. geno2pheno[hbv] is available under http://www.genafor.org/g2p_hbv/index.php.

scholarly journals Universal infant immunization and occult hepatitis B virus infection in children and adolescents: A population-based study

Hepatology ◽  
2015 ◽  
Vol 61 (4) ◽  
pp. 1183-1191 ◽  
Author(s):  
Hong-Yuan Hsu ◽  
Mei-Hwei Chang ◽  
Yen-Hsuan Ni ◽  
Cheng-Lun Chiang ◽  
Jia-Feng Wu ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Virus Infection ◽  
Hepatitis B ◽  
Population Based ◽  
Hepatitis B Virus Infection ◽  
Population Based Study ◽  
Occult Hepatitis ◽  
B Virus ◽  
Occult Hepatitis B ◽  
Universal Infant

scholarly journals Prevalence of anti-HBc total positivity in an impoverished Urban Community in Banglades

2018 ◽  
Vol 43 (2) ◽  
pp. 63-70
Author(s):  
Dilip Kumar Ghosh ◽  
Chanchal Kumar Ghosh ◽  
Mukta Nath ◽  
Syed Alamgir Safwath ◽  
Santosh Kumar Saha ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Urban Community ◽  
Total Positivity ◽  
Population Based ◽  
Hepatitis B Vaccination ◽  
Systematic Sampling ◽  
Cross Sectional ◽  
The Core ◽  
B Virus

The infection with the Hepatitis B virus (HBV) is a global health problem. Hepatitis B virus (HBV) infections are rapidly spreading in developing countries due to the lack of health education, poverty, illiteracy and Hepatitis B vaccination. No widespread population based data of HBV is available in the country's aspect. So, a population-based serological survey was done to determine the prevalence of the Hepatitis B core antibody total (IgM+IgG) in an impoverished Urban Community in Dhaka, Bangladesh. A descriptive cross-sectional study was conducted among 384 healthy individuals and age between 18-60 years from the urban slum in Dhaka city. The study was implemented through collaboration with Shaheed Suhrawardy Medical College, Dhaka from January 2013 to June 2013. The study participants were selected through systematic sampling procedure and blood tested for anti-HBc. Anti-HBc estimations were carried out by VITROS Immune diagnostic assay. The study was pertained Ethical permission from Bangladesh Medical Research Council (BMRC) and every participant was informed regarding their written informed consent. Among the 384 respondents, 183(47.6%) individuals were positive for the core antibody of hepatitis B virus (anti-HBc). The anti HBc positive group consisted almost of equal number of male 93, (24.2%) and female 90 (23.4%). There was a significantly increasing prevalence of the core antibody among young adults and middle age of the respondents (28.7%). Major risk factors for exposure to Hepatitis B appeared to be Ear-nose-body piercing, Circumcision by Hajam, unsafe blood transfusion and unsterile dental intervention. High prevalence of hepatitis B Core antibody (47.6%) indicates that the members of this urban community are highly exposed to hepatitis B virus.

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 Hepatitis B virus infection in Nigeria: a systematic review and meta-analysis of data published between 2010 and 2019

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Busayo I. Ajuwon ◽  
Isabelle Yujuico ◽  
Katrina Roper ◽  
Alice Richardson ◽  
Meru Sheel ◽  
...  
Keyword(s):  
Systematic Review ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Disease Surveillance ◽  
Control Strategies ◽  
Meta Analysis ◽  
Population Based ◽  
North West ◽  
B Virus ◽  
The Impact

Abstract Background Hepatitis B virus (HBV) is an infectious disease of global significance, causing a significant health burden in Africa due to complications associated with infection, such as cirrhosis and liver cancer. In Nigeria, which is considered a high prevalence country, estimates of HBV cases are inconsistent, and therefore additional clarity is required to manage HBV-associated public health challenges. Methods A systematic review of the literature (via PubMed, Advanced Google Scholar, African Index Medicus) was conducted to retrieve primary studies published between 1 January 2010 and 31 December 2019, with a random-effects model based on proportions used to estimate the population-based prevalence of HBV in the Nigerian population. Results The final analyses included 47 studies with 21,702 participants that revealed a pooled prevalence of 9.5%. A prevalence estimate above 8% in a population is classified as high. Sub-group analyses revealed the highest HBV prevalence in rural settings (10.7%). The North West region had the highest prevalence (12.1%) among Nigeria’s six geopolitical zones/regions. The estimate of total variation between studies indicated substantial heterogeneity. These variations could be explained by setting and geographical region. The statistical test for Egger’s regression showed no evidence of publication bias (p = 0.879). Conclusions We present an up-to-date review on the prevalence of HBV in Nigeria, which will provide critical data to optimise and assess the impact of current prevention and control strategies, including disease surveillance and diagnoses, vaccination policies and management for those infected.

scholarly journals Ethnic differences in viral dominance patterns in patients with hepatitis B virus and hepatitis C virus dual infection

Hepatology ◽  
2012 ◽  
Vol 55 (5) ◽  
pp. 1640-1640 ◽  
Author(s):  
Gabriele Rockenbach ◽  
Alexandre JosÉ De Melo Neto ◽  
Nêmora Tregnago Barcellos ◽  
Fernando Herz Wolff
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Ethnic Differences ◽  
Dual Infection ◽  
B Virus

scholarly journals Molecular Sequence Data of Hepatitis B Virus and Genetic Diversity After Vaccination

2009 ◽  
Vol 170 (12) ◽  
pp. 1455-1463 ◽  
Author(s):  
W. M. van Ballegooijen ◽  
R. van Houdt ◽  
S. M. Bruisten ◽  
H. J. Boot ◽  
R. A. Coutinho ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Sequence Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
B Virus

Effect of Acute Self-Limited Hepatitis C Virus (HCV) Superinfection on Hepatitis B Virus (HBV)-Related Cirrhosis. Virological Features of HBV–HCV Dual Infection

2004 ◽  
Vol 49 (2) ◽  
pp. 281-288 ◽  
Author(s):  
Norio Akuta ◽  
Fumitaka Suzuki ◽  
Mariko Kobayashi ◽  
Akihito Tsubota ◽  
Yoshiyuki Suzuki ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Dual Infection ◽  
B Virus

scholarly journals Maternal Hepatitis B Virus or Hepatitis C Virus Carrier Status and Long-Term Endocrine Morbidity of the Offspring—A Population-Based Cohort Study

2020 ◽  
Vol 9 (3) ◽  
pp. 796 ◽  
Author(s):  
Naim Abu Freha ◽  
Tamar Wainstock ◽  
Tzvi Najman Menachem ◽  
Eyal Sheiner
Keyword(s):  
Cohort Study ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Cox Regression ◽  
Population Based ◽  
Carrier Status ◽  
B Virus

This study aimed to investigate the long-term effect of maternal hepatitis B virus (HBV) or hepatitis C virus (HCV) carrier status on offspring endocrine morbidity. A population-based cohort study included all singleton deliveries between the years 1991–2014 at the Soroka University Medical Center, Beer-Sheva, Southern Israel. The mothers were subdivided into three groups, HBV carriers, HCV carriers and non-carriers. Data regarding the long-term endocrine morbidity of their offspring were compared between the groups. The study included 242,905 (99.7%) non-carrying mothers, 591 (0.2%) mothers who were carriers for HBV and 186 (0.1%) mothers who were carriers for HCV. The Kaplan–Meier’s survival curve demonstrated a significantly higher cumulative endocrine morbidity in children born to mothers with HCV (log-rank test, p = 0.002). Specifically, higher rates of hypoglycemia were noted among the offspring born to mothers who were carriers of HCV (1.1%; p = 0.001) compared with the offspring of mothers who were either carriers of HBV (0.2%) or non-carriers (0.1%). A Cox regression model controlled for maternal age, gestational age, maternal diabetes, hypertensive disorders of pregnancy, found maternal HCV carrier status to be independently associated with pediatric endocrine morbidity in the offspring (adjusted hazard ratio = 5.05, 95% CI: 1.625–15.695, p = 0.005). Maternal HCV carrier status is an independent risk factor for long-term endocrine morbidity.

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