Virus phylogeography at the wild/domestic animal interface

With the recent advances in sequencing technology it is increasingly common to find freely available large genomic datasets composed of thousands of genetic samples of viral or bacterial origin. Because Bayesian approaches possess multiple advantages against more traditional phylogenetic methods, such methods are considered as a standard tool to study the evolution and circulation of fast-evolving pathogens such as viruses. With those Bayesian phylogenetic approaches, the evolutionary and transmission parameters of fast evolving infectious diseases can be estimated to inform their control of in both epidemic and endemic contexts. Zoonoses are diseases that have passed from a non-human animal to a human population. The emergence of such diseases in human populations can be caused by environmental changes bringing wild and domestic animals closer to each other facilitating the transmission to humans. Phylogenetic approaches can help us to understand how disease can be transmitted between wild and domestic animal populations. Using recently developed Bayesian phylogenetic methods the first aim of this thesis was to understand and study the transmission of infectious disease amongst wild and domestic animal populations. Therefore, I performed those epidemiological analysis in an endemic context, using both Eurasian avian influenza sequences and African foot-and-mouth disease virus (FMDV). The second aim was to develop a software capable of reducing potential sampling bias between multiple populations while analysing large genetic datasets in a short running time compared to currently available phylogenetic methods. I first studied the transmission and reassortment pattern of avian influenza within Europe and Asia using internal segments sequences (PB2) originated from wild and domestic birds. Using both a non-structured and structured coalescent approach I determined that the two continents constitute distinct demes that are sporadically connected. Most of the reassortment pattern observed occurred within western Europe and Eastern China. I also determined that while wild Anseriformes are responsible for most of the of the virus circulation in Europe, domestic Anseriformes birds are responsible for the virus movements in Asia. The circulation of the virus between Asia and Europe being mostly done by both domestic and wild Anseriformes birds. Secondly, to understand the patterns of FMDV, I compared the transmission patterns of four FMDV (FMDO, FMDA, FMD SAT1, FMD SAT2) serotypes and estimated the factors influencing the circulation of these viruses in Africa using a discrete and a continuous phylogeographic approach. One conclusion of this chapter is that FMDV strains currently circulating in African livestock were probably introduced in the early 18th century trough livestock movements for the serotype A/O and reintroduced from wild Buffalo population after the African rinderpest epidemic for the SAT serotypes. I also show that movements of domestic cattle were responsible of the FMDV propagation and circulation in Africa with a small role played by wild animal populations. Thirdly, using advanced Bayesian structured coalescent model approximations, I studied the role played by antelope in the transmission of FMDV SAT1 and SAT2 in Africa. I found that for both serotypes antelopes seem to act as an intermediate host between buffalo and cattle. In the last part of the thesis I present a new software “Epitree-sim” that allows the fast estimation of phylogenetic trees and transmission patterns between demes using a fast dating algorithm and repeated subsampling of the sequence analysed.