Bayesian Estimates of the Evolutionary Rate and Age of Hepatitis B Virus

@article{Zhou2007BayesianEO,
  title={Bayesian Estimates of the Evolutionary Rate and Age of Hepatitis B Virus},
  author={Yang Zhou and Edward C. Holmes},
  journal={Journal of Molecular Evolution},
  year={2007},
  volume={65},
  pages={197-205}
}
Accurately estimating the evolutionary rate and age of hepatitis B virus (HBV) has proven to be one of the most difficult problems in studies of viral evolution. To help resolve these issues we employed a recently developed Bayesian coalescent approach to globally sampled human and avian hepadnavirus genome sequences, accounting for lineage-specific rate variation, the presence of overlapping reading frames, and the potential impact of recombination. Our analysis revealed an unexpectedly high… 
New Insights into the Evolutionary Rate of Hepatitis B Virus at Different Biological Scales
TLDR
By studying the HBV quasispecies dynamics for a chain of sequentially infected transmissions within a family, it is hypothesized that owing to the small genome size of HBV, transmission between hosts and adaptation within hosts must exhibit high levels of fitness trade-offs for the virus.
New perspectives on the evolutionary history of hepatitis B virus genotype F.
Bayesian Inference of the Evolution of HBV/E
TLDR
The results confirm that the hyperendemicity of HBV(E) in today's Africa is a recent phenomenon and likely the result of dramatic changes in the routes of viral transmission in a relatively recent past.
Origin of HBV and Its Arrival in the Americas – the Importance of Natural Selection on Time Estimates
TLDR
Estimating the divergence times of genotypes F and H and discussing how evolutionary rates estimated from recent samples may underestimate the divergence time of more ancient nodes in HBV phylogenies suggest that rates estimated based on recent samples will overestimate the evolutionary rate and underestimate the coalescence times forAncient nodes inHBV phylogeny.
An analysis of the molecular evolution of Hepatitis B viral genotypes A/B/D using a Bayesian evolutionary method
TLDR
Using a bayesian evolutionary method to predict the outbreak trends ofHBV through evolutionary trees of HBV, and provide theoretical foundations for clinical prevention and treatment of HBv are provided.
Analysis of the Molecular Evolution of Hepatitis B Virus Genotypes in Symptomatic Acute Infections in Argentina
TLDR
Since the acute infections could be an expression of the genotypes currently being transmitted to new hosts, the predominance of subgenotype F1b might have epidemiological, as well as, clinical relevance due to its potential adverse disease outcome among the chronic cases.
Dating the origin and dispersal of hepatitis B virus infection in humans and primates
TLDR
This study provides, for the first time, an estimated timescale for the HBV epidemic that closely coincides with dates of human dispersals, supporting the hypothesis that HBV has been co‐expanding and co‐migrating with human populations for the last 40,000 years.
Origin and dissemination of hepatitis B virus genotype C in East Asia revealed by phylodynamic analysis and historical correlates
TLDR
Evidence is provided to suggest this bottleneck was the result of limited human movement from/to China during the SARS outbreak in 2003, the first extensive evolutionary study of HBV/C in East Asia as well as the first to assess more realistic spatial ecological influences between co‐circulating infectious diseases.
...
...

References

SHOWING 1-10 OF 33 REFERENCES
A Revised Evolutionary History of Hepatitis B Virus (HBV)
TLDR
The phylogenetic distribution of recombination events among human HBV genotypes was examined and it was found that genotypes A plus D, and genotypes B plus C, had distinct patterns of recombinations suggesting differing epidemiological relationships among them, suggesting divergence in humans and apes has occurred only in the last 6000 years.
Reconstructing the Complex Evolutionary History of Hepatitis B Virus
TLDR
Both the pattern and the rate of nucleotide substitution are therefore complex phenomena in HBV and hinder any attempt to reconstruct the past spread of this virus.
Molecular Evolution of Hepatitis B Virus over 25 Years
TLDR
The results of this study suggest that HBV sequence divergence may occur more rapidly than previously estimated, in a host immune phase-dependent manner.
Recombination in the Genesis and Evolution of Hepatitis B Virus Genotypes
TLDR
Findings provide evidence for the occurrence of past, extensive recombination events in the evolutionary history of the currently classified genotypes of HBV and potentially in changes in its global epidemiology and associations with human disease.
Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences.
TLDR
It is suggested that the hepadnavirus family evolved independently of host-species divergence, because the divergence times of the viruses are much more recent than those of the host species.
Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis
TLDR
A comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method revealed a significant relationship between genetic divergence and isolation time for an extensive array of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock.
Reconstructing the origins of human hepatitis viruses.
  • P. Simmonds
  • Biology
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences
  • 2001
TLDR
The apparent conservatism of viruses over long periods implied by their epidemiological distributions instead suggests that nucleotide sequence change may be subject to constraints peculiar to viruses with single-stranded genomes, or with overlapping reading frames that defy attempts to reconstruct evolution according to the principles of the 'molecular clock'.
Constrained evolution with respect to gene overlap of hepatitis B virus
With the aim of elucidating the evolution of a hepadnavirus family, we constructed molecular phylogenetic trees for 27 strains of hepatitis B virus (HBV) using both the unweighted pair-grouping and
Genomic heterogeneity of hepatitis B virus in a 54-year-old woman who contracted the infection through materno-fetal transmission.
From the plasma of a 54-year-old woman, who acquired the persistent carrier state of hepatitis B virus through materno-fetal transmission, 49 clones of viral genomes were propagated. They did not
Long-term mutation rates in the hepatitis B virus genome.
TLDR
It was found that the entire HBV genome is extremely stable over long periods of time during the HBeAg-positive phase if the immune response (inflammation) is weak, whereas an average of 20 mutations emerged after development of hepatitis and/or loss of H beAg without association with clinical outcome.
...
...