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Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
Inferring epidemic contact structure from phylogenetic trees.
Gabriel E Leventhal1, Roger Kouyos, Tanja Stadler
1Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland. gabriel.leventhal@env.ethz.ch
Plos Computational Biology
|March 14, 2012
Summary
Epidemic contact networks leave a genetic fingerprint in pathogen populations. Analyzing phylogenetic tree imbalance reveals deviations from random mixing, as seen in the Swiss HIV epidemic.
Area of Science:
- Epidemiology
- Phylogenetics
- Computational Biology
Background:
- Contact structure significantly influences epidemic spread.
- Modeling contact networks is crucial in epidemiology.
- Detailed contact structures of real epidemics are often unknown.
Purpose of the Study:
- To determine if contact network structure leaves a detectable genetic fingerprint in pathogen populations.
- To investigate the relationship between contact network topology and pathogen phylogeny.
- To quantify deviations from random mixing using phylogenetic analysis.
Main Methods:
- Simulating disease outbreaks on various contact networks.
- Comparing generated phylogenies to assess the impact of network structure.
- Utilizing measures of phylogenetic tree imbalance.
- Analyzing the Swiss HIV epidemic phylogeny.
Main Results:
- Phylogenetic tree shape is strongly dependent on contact network structure.
- Tree imbalance measures effectively quantify deviations from random mixing.
- The Swiss HIV epidemic exhibits a significantly more unbalanced phylogeny than predicted by random mixing.
Conclusions:
- Contact network structure leaves a detectable genetic signature in pathogen phylogenies.
- Phylogenetic tree imbalance serves as a valuable tool to infer underlying contact structures.
- The Swiss HIV epidemic's contact structure deviates significantly from random mixing.
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