Within-leaf homogeneity of a plant virus revealed by ultra-deep-sequencing

Viruses, and in particular RNA viruses, have a notoriously inaccurate replication, making around 10-4 errors per incorporated nucleotide. However, long-term population studies have shown that virus diversity builds up at a comparatively slow pace over years, a phenomenon that seems even more acute in plant virus populations. In order to understand how these seemingly contradictory observations might be explained, we used deep-sequencing technology as a way to access with unprecedented resolution virus diversity within tree leaves. From mutant frequency and assumptions relating to virus replication, we derived two estimates bracketing the actual mutation rate. We also derived dN/dS values indicating little selection within recently infected leaves but purifying selection within leaves of a chronically infected tree. These results inform us on the evolutionary processes that operate during virus replication and within-leaf selection. They provide elements about the proximal (mechanistic) and ultimate (evolutionary) causes of the high mutation rate of RNA viruses.

病毒，尤其是RNA病毒（RNA virus），以复制保真性极差而闻名，每掺入一个核苷酸便会产生约10^-4次复制错误。然而长期种群研究表明，病毒多样性在数年尺度上的积累速度相对缓慢，这一现象在植物病毒种群中表现得更为突出。为阐释这一看似矛盾的观测结果，我们借助深度测序技术（deep-sequencing technology），以空前的分辨率对林木叶片内的病毒多样性进行了表征。基于突变频率及病毒复制相关假设，我们推导出两组涵盖真实突变率的估算值。我们还计算得到了dN/dS值，该结果显示，在新近染病的叶片中几乎不存在选择压力，而在长期染病林木的叶片中则存在纯化选择（purifying selection）。上述研究结果揭示了病毒复制过程中以及叶片内选择作用下的演化进程，为阐释RNA病毒高突变率的近因（机制层面）与远因（演化层面）提供了理论依据。