Assessing the accuracy of Approximate Bayesian Computation approaches to infer epidemiological parameters from phylogenies

Abstract

Phylodynamics typically rely on likelihood-based methods to infer epidemiological parameters from dated phylogenies. These methods are essentially based on simple epidemiological models because of the difficulty in expressing the likelihood function analytically. Computing this function numerically raises additional challenges, especially for large phylogenies. Here, we use Approximate Bayesian Computation (ABC) to circumvent these problems. ABC is a likelihood-free method of parameter inference, based on simulation and comparison between target data and simulated data, using summary statistics. We simulated target trees under several epidemiological scenarios in order to assess the accuracy of ABC methods for inferring epidemiological parameter such as the basic reproduction number (R0), the mean duration of infection, and the effective host population size. We designed many summary statistics to capture the information in a phylogeny and its corresponding lineage-through-time plot. We then used the simplest ABC method, called rejection, and its modern derivative complemented with adjustment of the posterior distribution by regression. The availability of machine learning techniques including variable selection, motivated us to compute many summary statistics on the phylogeny. We found that ABC-based inference reaches an accuracy comparable to that of likelihood-based methods for birth-death models and can even outperform existing methods for more refined models and large trees. By re-analysing data from the early stages of the recent Ebola epidemic in Sierra Leone, we also found that ABC provides more realistic estimates than the likelihood-based methods, for some parameters. This work shows that the combination of ABC-based inference using many summary statistics and sophisticated machine learning methods able to perform variable selection is a promising approach to analyse large phylogenies and non-trivial models.