Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany.
Nucleic Acids Res. 2011 Jan;39(1):e4. doi: 10.1093/nar/gkq909. Epub 2010 Oct 18.
Phylodynamic techniques combine epidemiological and genetic information to analyze the evolutionary and spatiotemporal dynamics of rapidly evolving pathogens, such as influenza A or human immunodeficiency viruses. We introduce 'allele dynamics plots' (AD plots) as a method for visualizing the evolutionary dynamics of a gene in a population. Using AD plots, we propose how to identify the alleles that are likely to be subject to directional selection. We analyze the method's merits with a detailed study of the evolutionary dynamics of seasonal influenza A viruses. AD plots for the major surface protein of seasonal influenza A (H3N2) and the 2009 swine-origin influenza A (H1N1) viruses show the succession of substitutions that became fixed in the evolution of the two viral populations. They also allow the early identification of those viral strains that later rise to predominance, which is important for the problem of vaccine strain selection. In summary, we describe a technique that reveals the evolutionary dynamics of a rapidly evolving population and allows us to identify alleles and associated genetic changes that might be under directional selection. The method can be applied for the study of influenza A viruses and other rapidly evolving species or viruses.
系统发生动力学技术结合流行病学和遗传学信息，分析快速进化病原体（如甲型流感或人类免疫缺陷病毒）的进化和时空动态。我们引入“等位基因动态图（AD 图）”作为可视化群体中基因进化动态的方法。使用 AD 图，我们提出了如何识别可能受到定向选择的等位基因的方法。我们通过对季节性甲型流感病毒进化动态的详细研究来分析该方法的优点。季节性甲型流感（H3N2）的主要表面蛋白和 2009 年猪源甲型流感（H1N1）病毒的 AD 图显示了在两种病毒群体进化过程中固定下来的替代物的连续变化。它们还可以早期识别后来成为优势的那些病毒株，这对于疫苗株选择问题很重要。总之，我们描述了一种揭示快速进化群体进化动态的技术，并允许我们识别可能受到定向选择的等位基因和相关遗传变化。该方法可用于研究甲型流感病毒和其他快速进化的物种或病毒。
