More than 30 viruses infecting Apis mellifera have been described. Among them, five viruses are widely spread in the colonies all around the world, and the Deformed wing virus and the Sacbrood virus have been shown to contribute to colony losses. Most of them are transmitted by the vector Varroa destructor, but they can be transmitted both horizontally and vertically, i.e. from the queen and/or drones to their progeny. Thus, the queen management practices and especially the requeening practices of the beekeepers may impact the virus loads in the colonies. In order to assess the impacts of an annual requeening compared to natural supersedure, we monitored a three-year experiment comparing these two strategies. Within each of these two strategies, two honeybee strains are compared in two different apiaries (120 colonies in total): a “requeening strain” from a beekeeper who annually requeens his colonies, and a “natural replacement strain” from a beekeeper who lets his colonies naturally replace their queens. Thus, this experiment allows to consider the effects of both queen management practices and honeybee strain on the health status of the colonies. Since the beginning of the experiment in 2016, the viral loads of the colonies were followed annually in spring and autumn by quantitative PCR and varroa pressure was assessed at the end of each summer, after the honey harvest. Through this experiment, we investigate the possible impacts of two contrasted queen management strategies on the evolution of the colony viral loads over three years. The possible consequences of requeening on the colony health status are also considered through the comparison of the queen viral load to the mean viral load of the colony workers.