Pathogen and Hemocyte Dynamics in Three Apiaries Across a Bee Season

Honey bees 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 honey bee hemolymph samples using third-generation sequencing and flow cytometry in three apiaries over a honey bee season. Using nanopore sequencing, several viruses and bacteria were identified, including the first reported presence in European honey bees of La Jolla virus 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 transgenerational 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 transgenerational immunity. Additionally, dynamics in total hemocyte counts (THCs) 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.