Sharka, caused by Plum pox virus (PPV), is a severe disease of trees belonging to the Prunus family. In various countries the management of sharka epidemics relies on the removal of symptomatic trees. However, this strategy supposes that the infectious trees are symptomatic and vice versa. This assumption implies a synchrony between the date when an infected tree expresses symptoms (i.e., at the end of the incubation period) and the date when it becomes infectious (i.e., at the end of the latency period). However, few experiments directly estimate the mismatch between the end of incubation and latency. Our aim is to test the synchrony hypothesis in an experiment based on aphid-mediated transmission from PPV-infected plants at various times around the date of symptom expression. Because of the associated logistical constraints, we numerically optimized a protocol designed to estimate (with a 1-day precision) a mismatch between incubation and latency. The distribution of the dates of symptom expression after inoculation of peach plantlets was experimentally characterized to define relevant dates for the transmission experiments. Then, through numerical experiments based on different scenarios, we demonstrated that the estimated mismatch between incubation and latency was unbiased, and we optimized the number of plant-to-plant transmissions under realistic experimental conditions.