Plum pox virus (PPV), a potyvirus, is the most devastating threat to production of stone fruit worldwide. Strains have shown the ability to generate and maintain new variants that display differential pathologies. To further investigate PPV variant dynamics, we analyzed high-resolution sequence data generated from ribosome-associated PPV genomes (‘Translatome’) isolated from leaves of infected plum trees (Prunus domestica) over two growth periods (GP). During each GP, leaf samples were collected at 2, 4, 6, and 12 weeks leaf emergence. Bud samples were also collected pre- and post- vernalization. Translatome associated viral genomes are likely being translated and thus actively contributing to the infection process. Sequences were processed and variants called against the PPV Penn7 genome (EF640935). PPV translation levels were consistent with expected viral infection levels. Results show within GPs, translatome PPV variants occur at proportionately higher levels in newly developing plum tissues with low levels of infection while more mature tissues showing high infection levels display proportionately lower number of variants. Analysis of individual variants revealed distinct groups as some variants were maintained at either high or low levels at all sample times while other variants showed dynamic changes in their levels. Combined, these results suggest that PPV populations undergo cyclical transitions during seasonal bud break and leaf development.