Pathogen Population Genomics and Evolution

导言：随着病原体遗传数据，特别是全基因组序列数据的日益可用， 迫切需要分析工具和创新办法来加以利用。特别是， 使用基因组数据推断下的传播链和病原体进化的方法 通过宿主免疫力、疫苗和抗生素进行的选择仍处于起步阶段。这些问题都是 与一次检查一个序列时所问的问题类型根本不同， 阐明了感染和发病机制的保守方面的生物学。种群基因组研究 了解病原体的种群异质性及其后果和原因。这些推论自然 适用于传输动态模型的参数估计， 从根本上说，确定这些模型应该如何构建，以及测试它们的 预测。迄今为止，使用MIDAS和非MIDAS资金进行分析工作，非MIDAS资金用于 在过去的五年里，我们利用病原体， 人口基因组学和遗传学，我们已经确定了许多机会，以改善和扩大方法 在未来五年内，以及将现有的方法应用于生物学的重大问题， 流行病学

Introduction: With increasing availability of pathogen genetic and especially whole-genome sequence data, there is a pressing need for analytical tools and innovative approaches to make use of them. In particular, methods for using genomic data to make inferences about transmission chains and pathogen evolution under selection by host immunity, vaccines, and antibiotics, are still in their infancy. These questions are fundamentally different from the types of questions asked when examining one sequence at a time, which illuminate the biology of conserved aspects of infection and pathogenesis. Population genomic studies shed light on population heterogeneity in the pathogen, its consequences and causes. These inferences naturally lend themselves to the estimation of parameters for transmission-dynamic models and, even more fundamentally, to the determination of how such models should be structured, and the testing of their predictions. To date, using MIDAS and non-MIDAS funding for analytic efforts, and non-MIDAS funding for the costs of sequencing, we have made a number of significant discoveries over the last five years using pathogen population genomics and genetics, and we have identified many opportunities to improve and expand methods over the next five years, as well as to apply existing methods to significant questions of biology and epidemiology.