Pathogen and Hemocyte Dynamics in Three Apiaries across a bee season

Honeybees are dying due to a disease complex consisting of viruses, parasites, chemicals, nutritional deficiencies and management problems. In the present study, pathogens and hemocytes were analyzed in honeybee hemolymph samples using third-generation sequencing and flow cytometry in three apiaries over a honeybee season. Using nanopore sequencing, several viruses and bacteria were identified, including new detections in Belgian and European honeybees of Varroa orthomyxovirus-1, La Jolla virus, Hubei-partiti-like virus 34 and Apis rhabdovirus 5. Seasonal pathogen peaks were found, with spring and summer showing the highest loads which coincide with the main flowering periods. Notably, viral infections often did not persist after initial detection despite the continuous appearance of new bees, hinting at colony-wide trans-generational immunity. However, Hubei-partiti-like virus 34 remained endemic in one apiary and was found even in young bees, raising concerns about its ability to evade the trans-generational immunity. Additionally, dynamics in total hemocyte counts were identified. Understanding pathogen and immune factor dynamics throughout the bee season will help identify weak colonies and provide valuable insights into colony collapse and its prevention.