New tools for the rapid analysis of Poliovirus genomic surveillance data

该项目旨在应用一系列系统地理模型来量化脊髓灰质炎病毒的地理传播。这项分析旨在制定一种可在疫苗流行病学研究小组内试验的标准桑格测序和下一代测序方法的下游实施的方案，并将包括树构建和可视化方法。-改进目前用于推断巴基斯坦和阿富汗野生脊髓灰质炎病毒10的系统发育的方法。-基于与基因相关的脊髓灰质炎病毒的新的流行病学传播块和相关的人口统计学进行的分析。-离散特征分析适合推断内部节点在系统发展史中的地理位置，并确定病毒在流行病区之间的移动。-扩展离散特征方法，以量化不完全抽样对推断的移动率的影响。-应用合并近似，以更好地了解不完全抽样的影响。这在为流行国家提供的全部数据集上可能是不可能的，因为要考虑的国家和谱系的数量太多了。-为政策制定者提供脊髓灰质炎病毒遗传数据的可视化，提供更连贯和相关的信息。-从系统发育输出到R中可视化的简单工作流程-包括政策制定者认为重要的信息。-将代码形成R包或代码笔记本，以提供可视化功能，以便在其他数据集上使用。

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.