Evolving pathogen phylogenies: a two-level branching approach

对于许多RNA病毒，病毒的RNA聚合酶缺乏校对机制导致频繁突变。高病毒突变率、大病毒群体大小和短复制期产生了丰富的病毒变异性，这是导致免疫逃逸或耐药性的原因。详细了解维持这种多样性的力量可以帮助对抗病毒感染。病原体的模式--特别是病原体的形状--会受到不同水平的交叉免疫所产生的选择压力的影响。我们专注于与持续性病毒相关的病毒基因的时间结构。我们提出了一个两个层次的分支模型（宿主-病原体），在不同的缩放制度的两个层次上的突变和竞争，其中宿主可以是被感染的病人或被感染的细胞在一个单一的病人。我们将进一步依赖于测量值（中性）多级分支动力学和两级多类型的分支动力学与突变和竞争的技术。

For many RNA viruses the lack of a proofreading mechanism in the virus' RNA polymerase results in frequent mutation. The high viral mutation rates, the large virus population size, and the short replication periods produce abundance of viral variability which is responsible for immune escape or drug resistance Understanding in detail the forces which maintain this diversity can assist in the struggle against viral infections. Pathogen patterns - and in particular the shapes of the phylogenies - are affected by the strength of selective pressure due to various levels of cross-immunity. We focus on the temporal structure of phylogenies associated with a persistent virus. We propose a two-level (host-pathogen) branching model with mutation and competition on both levels in different scaling regimes, where hosts can be either the infected patients or the infected cells within a single patient.We thereby extend our recent work on a panmitic virus population. We will further rely on techniques developed for measure-valued (neutral) multilevel branching dynamics and two-level multi-type branching dynamics with mutation and competition.