Abstract:
Bee viral ecology is a fascinating emerging area of research: viruses exert a range of efects on their
hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across
multiple bee species in a community. However, our understanding of bee viral communities is limited,
as it is primarily derived from studies of North American and European Apis mellifera populations. Here,
we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across
4 continents and Oceania. We developed a novel pipeline to rapidly and inexpensively screen for bee
viruses. This pipeline includes purifcation of encapsulated RNA/DNA viruses, sequence-independent
amplifcation, high throughput sequencing, integrated assembly of contigs, and fltering to identify
contigs specifcally corresponding to viral sequences. We identifed sequences for (+)ssRNA, (−)
ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e.
previously not observed in bees), with 27 represented by >0.1% of the reads in a given sample, and 7
contained an RdRp or replicase sequence which could be used for robust phylogenetic analysis. This
study provides a sequence-independent pipeline for viral metagenomics analysis, and greatly expands
our understanding of the diversity of viruses found in bee communities.
