Genetic Diversity in the SIR Model of Pathogen Evolution
Genetic Diversity in the SIR Model of Pathogen Evolution
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DOI：
10.1371/journal.pone.0004876
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发表时间：
2009-03-16
期刊：
影响因子：
3.7
通讯作者：
Campos, Paulo R. A.
中科院分区：
文献类型：
--
作者：
Gordo, Isabel;Gomes, M. Gabriela M.;Campos, Paulo R. A.
我们介绍了一个模型，用于评估病原体种群的遗传多样性的水平和模式，其流行病学遵循一个易感染的恢复模型（SIR）。我们将病原体的种群建模为由亚群（感染的宿主）组成的集合种群，病原体在其中复制和突变。宿主将病原体传播给未感染的宿主。我们表明，病原体的变化水平是很好的预测的解析表达式，病原体中性分子变异的感染水平的范围内，并随着感染的持续时间增加。然后，我们在模型中引入选择，并研究适应度（R-0（1+s））高于常驻菌株适应度（R 0）的新致病菌株的入侵概率。我们表明，这种入侵概率是由新病原体的R-0的相对增量给出的。通过分析该框架中的遗传多样性模式，我们确定了替换过程中的分子特征，并将其与甲型流感病毒序列中观察到的分子特征进行了比较。
We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR). We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts), where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R-0(1+s)) is higher than the fitness of the resident strain (R0). We show that this invasion probability is given by the relative increment in R-0 of the new pathogen (s). By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.