New insights into honey bee viral and bacterial seasonal infection patterns using third-generation nanopore sequencing on honeybee haemolymph

A honeybee apiary was followed to visualize pathogen circulation over time. We sampled honeybees of different ages (one-day-old and foragers) to decrease the risk of missing pathogens and to visualize pathogen evolution in certain age groups. We used, instead of PCR, third-generation nanopore metagenomic sequencing of honeybee hemolymph to identify all pathogens (viruses and bacteria) without contamination from the gut microbiome, compared to whole bees. To our knowledge, this is the first study in which bacterial and viral loads in the honeybee hemolymph are longitudinally followed up during almost a year.