Temporal dynamics of intrahost molecular evolution for Tobacco etch virus

Populations of plant RNA viruses are highly polymorphic, which may allow rapid within-host evolution. In this study we used Tobacco etch virus (TEV) as a model organism to experimentally test the origin and evolutionary fate of genetic variability both in space (different plant tissues) and in time (both as the plant grows and along experimental passages) in terms of molecular adaptation dynamics. Longitudinal samples from experimentally evolved populations in the natural host, Nicotiana tabacum, and in an alternative host, Capsicum annuum, were phenotypically characterized and genetically analyzed. Two phenotypic viral traits have been tracked along the evolution experiment, the number of TEV genomes produced per a fixed amount of total RNA (i.e., viral load) and the negative effect of infection in plant weight and size (i.e., virulence). These two traits depend on the interaction between the virus and multiple cell factors. Mutant swarms from different tissues and evolutionary time points have been characterized using ultra-deep sequencing. Finally, these experiments were complemented with a computational approach that simulates the evolution experiments and allows relevant population genetic parameters to be inferred.