New tools for the rapid analysis of Poliovirus genomic surveillance data

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This project aims to apply a range of phylogeographic models to quantify the geographic spread of poliovirus. This analysis aims to produce a protocol which can be implemented downstream of standard sanger sequencing and next generation sequencing methods being trialled within the vaccine epidemiology research group and will include tree construction and visualisation methods. -To improve on current phylogenetic methods used to infer phylogenies for wild poliovirus 10 in Pakistan and Afghanistan. - Analyses based on new epidemiological blocks of transmission with genetically related poliovirus and connected human demography. - Discrete trait analysis fitting to infer geographic location of internal nodes in the phylogeny and determine movement of virus between epidemiological blocks. - Extension of discrete trait methods to quantify the influence of incomplete sampling on the movement rates inferred. - Application of coalescent approximations to better understand the influence of incomplete sampling. This may not be possible on the full data set provided for endemic countries as the number of states and lineages to be considered is too large. - To provide visualisations of genetic data for poliovirus with more coherent and relevant information for policymakers. - Simple workflow from phylogenetic output to visualisation in R. - Inclusion of information deemed to be of importance by policymakers. - Form code in to an R package or code notebook to provide the visualisation functionality for use on other datasets.