Coalescent-based models for selection and superspreading in viral - - PowerPoint PPT Presentation

Coalescent-based models for selection and superspreading in viral phylogenies

Patrick Hoscheit October 12th, 2015

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Phylodynamics

Principle

The epidemiology of a virus is strongly linked to its evolution. We can use

• ne to understand the other.

Starting from a sample of viral genetic sequences, Estimate a phylogeny Write down a model relating the epidemic to the observed phylogeny (possibly including other data) Estimate model parameters through Bayesian or Maximum-Likelihood methods Usually, all three steps are performed together to take uncertainty in phylogenetic reconstruction into account (BEAST).

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Example : Gire et al. (2014)

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Superspreading and selection

Superspreading refers to non-heritable exceptional transmission events. Distorts phylogenies by creating many closely related lineages Many pathogens are concerned (Ebola, MERS-CoV, FMD,…) Strongly related to “environmental” conditions (contacts, breeding, sanitary measures,…) Selection acts on pathogens mostly through cross-immunity, but also through sanitary interventions (vaccination, antibiotics,…) Lineages with high fitness tend to replace other ones Creates highly imbalanced phylogenies

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Example : Inter-patient HIV vs. Influenza A

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Our project

We aim to find new methods to deal with superspreading and strong selection in viral phylogenies by using nonbinary coalescent models For now, only applicable to (RNA) viruses, but maybe in the future, bacteria or eukaryotes In collaboration with Prof. Oliver Pybus (Dept of Zoology, Univ. of Oxford) March 2015–March 2016 Come see my poster !

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