Inferring the Clonal Structure of Viral Populations from Time Series Sequencing

@article{Chedom2015InferringTC,
  title={Inferring the Clonal Structure of Viral Populations from Time Series Sequencing},
  author={Donatien F. Chedom and Pablo Ramiro Murcia and Chris D. Greenman},
  journal={PLoS Computational Biology},
  year={2015},
  volume={11}
}
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We would like to identify the underlying evolutionary structures. We utilize two sources of information to attempt this; within segment linkage information, and mutation prevalence. We demonstrate that clone haplotypes, their prevalence, and maximum parsimony… Expand

References

SHOWING 1-10 OF 54 REFERENCES
Probabilistic Inference of Viral Quasispecies Subject to Recombination
TLDR
A jumping hidden Markov model is presented that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data and an implementation of the EM algorithm to find maximum likelihood estimates of the model parameters is presented. Expand
Ultra-deep sequencing for the analysis of viral populations.
TLDR
Analysis of ultra-deep sequencing data obtained from diverse virus populations is challenging because of PCR and sequencing errors and short read lengths, such that the experiment provides only indirect evidence of the underlying viral population structure. Expand
Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows
TLDR
The problem of viral population reconstruction from amplicon or shotgun NGS reads was solved using the MCF formulation, and two new methods, AmpMCF and ShotMCF, for reconstruction of the whole-genome intra-host viral variants and estimation of their frequencies were developed, based on Multicommodity Flows. Expand
Viral Population Estimation Using Pyrosequencing
TLDR
It is demonstrated that pyrosequencing reads allow for effective population reconstruction by extensive simulations and by comparison to 165 sequences obtained directly from clonal sequencing of four independent, diverse HIV populations. Expand
Guidelines for Identifying Homologous Recombination Events in Influenza A Virus
TLDR
It is concluded that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses. Expand
Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data
TLDR
The entire process of inferring viral diversity from sample collection to computing measures of genetic diversity is reviewed, including sample preparation, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination is discussed. Expand
Evolutionary analysis of the dynamics of viral infectious disease
TLDR
This Review outlines the questions that can be answered using viral evolutionary analysis across a wide range of biological scales and describes the current state of the art in such analysis. Expand
Why do RNA viruses recombine?
TLDR
There is little evidence that recombination is favoured by natural selection to create advantageous genotypes or purge deleterious mutations, as predicted if recombination functions as a form of sexual reproduction, and recombination may be a mechanistic by-product of the evolutionary pressures acting on other aspects of virus biology. Expand
Viral Mutation Rates
TLDR
There appears to be a negative correlation between mutation rate and genome size among RNA viruses, and nucleotide substitutions are on average four times more common than insertions/deletions (indels) in retroviruses. Expand
Rates of evolutionary change in viruses: patterns and determinants
TLDR
It is shown that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity. Expand
...
1
2
3
4
5
...