Bioinformatics Seminar
Time:
Venue: Na
26 March 2019
NaThe phylogenetics of infectious diseases: from genome surveillance to ancient genomics
Sebastian DucheneMelbourne University
Genome sequence data are increasingly available for infectious pathogens across a range of timescales. For example ; genome surveillance studies routinely sample and sequence bacteria and viruses of public health interest ; whereas ancient DNA techniques have recovered pathogen genomes from mummified remains that are hundreds of years old. Phylogenetic methods take advantage of the mutational information in genomic data to infer the evolutionary history of an organism. These inferences range from estimating the time of origin of an infectious disease to untangling its epidemiological dynamics ; a field known as 'phylodynamics'. In principle ; phylodynamic methods should be applicable to genome surveillance studies to obtain near real-time inferences about the underlying epidemiological process. However ; in spite of the ease with which sequence data can be obtained ; recent outbreaks typically consist of very closely related pathogens ; which means that their genomes have low information content. I will present recent developments to combine notifications (i.e. confirmed cases that have not been sequenced) with genome data to improve phylodynamic inferences. These approaches consist of birth-death and coalescent branching processes ; where notifications inform the epidemiological dynamics but their phylogenetic position is treated as a nuisance parameter. Analyses of sequence data from different respiratory viruses demonstrate that notification data can improve the precision and accuracy of key parameters ; such as the basic reproductive number ; R0 ; and the time of origin of the outbreak. Beyond inferring recent pathogen dynamics ; phylogenetic methods can incorporate ancient DNA to improve our understanding of long-term pathogen evolution. To illustrate such inferences ; I will present case studies of ancient DNA from bacteria and viruses that have changed our understanding of their emergence and spread in humans.;;;