Williams Kadie-Ann, Pennings Pleuni
Department of Biology, San Francisco State University, California, 94132.
Department of Biology, San Francisco State University, California, 94132
G3 (Bethesda). 2020 Apr 9;10(4):1213-1223. doi: 10.1534/g3.119.400772.
The evolution of drug resistance in pathogens such as HIV is an important and widely known example in the field of evolutionary medicine. Here, we focus on a unique data set from the late 1990s with multiple viral sequences from multiple time points in 118 patients. We study patterns of evolutionary dynamics in the viral populations in these patients who were treated with Reverse Transcriptase Inhibitors and Protease Inhibitors in the late 1990s. Specifically, we aim to visualize and analyze examples of population genetic processes such as selective sweeps and clonal interference. The figures and descriptions in this paper can be used in evolution and population genetics classes. We show and analyze a wide variety of patterns, specifically: soft sweeps, hard sweeps, softening sweeps and hardening sweeps, simultaneous sweeps, accumulation of mutations and clonal interference.
病原体（如艾滋病毒）耐药性的演变是进化医学领域一个重要且广为人知的例子。在此，我们聚焦于20世纪90年代末的一个独特数据集，该数据集包含118名患者在多个时间点的多条病毒序列。我们研究了这些在20世纪90年代末接受逆转录酶抑制剂和蛋白酶抑制剂治疗的患者体内病毒群体的进化动力学模式。具体而言，我们旨在可视化并分析群体遗传过程的实例，如选择性清除和克隆干扰。本文中的图表和描述可用于进化与群体遗传学课程。我们展示并分析了各种各样的模式，具体包括：软清除、硬清除、软化清除和硬化清除、同时清除、突变积累和克隆干扰。
