Metagenomic analysis reveals recombinant Deformed Wing Viruses in winter-collapsed colonies

Abstract Honey bee ( Apis mellifera ) colonies frequently collapse in winter, and multifactorial causes are being discussed, such as infestation with the Varroa destructor mite and infection with bee-associated viruses, including the Deformed Wing Virus (DWV). DWV is one of the important bee pathogens, and in addition to the two widespread main variants DWV-A and DWV-B, the occurrence of DWV-A/DWV-B recombinants is increasingly reported. In some regions, DWV-A was described as being replaced by recombinants. While recombinants are recognized, their diversity at the level of individual bees remains poorly understood. In the present study, the diversity of DWV in adult honey bees in three apiaries with several winter-collapsed colonies (S1, S2, and S3) was investigated using metatranscriptomics of dead honey bees. Nanopore technology was used for metagenomic sequencing to detect 24 bee-associated viruses as well as Vairimorpha ceranae . Additionally, the sequence data were used to analyze the bacterial community of the bees. The long reads from Nanopore sequencing allowed the reconstruction of predominant DWV genomes and the detection of occurring recombinants. Targeted Nanopore-based amplicon sequencing of individual bees was conducted to qualitatively and quantitatively characterize DWV recombinants at the level of individual bees. Five recombinant DWV variants based on the DWV-B backbone were identified, which all contained a DWV-A-derived fragment in the 5’ region that encompassed the entire partial leader protein (LP) sequence. Although the recombinants were mostly associated with the presence of DWV-B, in some individual bees recombinant variants were detected without DWV-B. Apart from the DWV-A fragment detected in the recombinants, DWV-A was not found. The study showed that individual honey bees can harbour a single recombinant or multiple recombinants.