Latest Publications
Xavier Didelot publications
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance
Xavier Didelot, Vinicius Franceschi, Simon D W Frost, Ann Dennis, Erik M Volz
The methodology for nonparametric inference of effective population size is well-developed in the Bayesian setting, but here we develop a frequentist approach based on nonparametric latent process models of population size dynamics. We appeal to statistical principles based on out-of-sample prediction accuracy in order to optimize parameters that control shape and smoothness of the population size over time. Our methodology is implemented in a new R package entitled mlesky. We demonstrate the flexibility and speed of this approach in a series of simulation experiments and apply the methodology to a dataset of HIV-1 in the USA. We also estimate the impact of non-pharmaceutical interventions for COVID-19 in England using thousands of SARS-CoV-2 sequences. By incorporating a measure of the strength of these interventions over time within the phylodynamic model, we estimate the impact of the first national lockdown in the UK on the epidemic reproduction number.
Phylogenetic analysis of the origin and spread of plague in Madagascar
Luis Roger Esquivel Gomez, Cyril Savin, Voahangy Andrianaivoarimanana, Soloandry Rahajandraibe, Lovasoa Nomena Randriantseheno, Zhemin Zhou, Arthur Kocher, Xavier Didelot, Minoarisoa Rajerison, Denise Kühnert
After a plague-free period of over 60 years in the northwestern coast city of Mahajanga, the disease reappeared in 1991 and caused several outbreaks until 1999. Previous research indicates that the disease was reintroduced to the city of Mahajanga from the Central Highlands instead of reemerging from a local reservoir. In this study we applied a Bayesian phylogeographic model to detect and date migrations of Y. pestis between the two locations that could be linked to the re-emergence of plague in Mahajanga. Our results indicate that two independent migrations from the Central Highlands caused the plague outbreaks in Mahajanga during the 1990s, with both introductions occurring during the early 1980s. They happened over a decade before the detection of human cases, thus the pathogen likely survived in wild reservoirs until the spillover to humans was possible diseases.