With the advent of affordable sequencing techniques, phylogenies are routinely gene- rated in epidemiological studies on viruses. The question is, can these really tell us more about epidemiological processes than classical incidence data? Recent works in the field of phylodynamics lead to the development of epidemiological parameter inference by maximum likelihood. But these methods are essentially based on simple epidemio- logical models like birth-death model. Indeed, they are limited by the difficulty to compute de likelihood function for more complex models.
Approximate Bayesian Computation (ABC) perform parameter inference and bypass the compu- tation of the likelihood function. ABC methods are based on simulation and comparison between target data and simulated data using summary statistics. We created a flexible simulation system implementing an event-driven approach of construction of phylogenies from epidemiological models. It is based on the assumption that phylogenies are similar to transmission trees. Then we designed summary statistics that summarize the epidemiolo- gical information of phylogenies. Inference precision by our method is really close to the precision obtained by a likelihood method implemented in BEAST. This work shows that phylogenies of viral sequences and ABC can inform us on epidemiological parameters and is a first step towards the analysis of more detailed epidemiological scenarios.
Saulnier E, Gascuel O, Alizon S (2017) Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study. PLoS Comput Biol 13(3):e1005416
Alizon S, Saulnier E (2017) Phylodynamique des infections virales. Virologie 21(3):119-129 (in French)
Alizon S., Lion S., Murall C. L. & Abbate J. L. (2014) Quantifying the epidemic spread of Ebola virus (EBOV) in Sierra Leone using phylodynamics. Virulence. 5(8): 825-827
Hartfield M., Bull R., White P. A., Lloyd A., Luciani F. & Alizon S. (2014) Evidence that hepatitis C virus genome partly controls infection outcome. Evol App 7(5): 533-47For further details, see our publications »