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.