Abstract
We sequenced small (s) RNAs from field collected honeybees (Apis mellifera) and bumblebees ( Bombus pascuorum ) using the Illumina technology. The sRNA reads were assembled and resulting contigs were used to search for virus homologues in GenBank. Matches with Varroa destructor virus-1 (VDV1) and Deformed wing virus (DWV) genomic sequences were obtained for A. mellifera but not B . pascuorum . Further analyses suggested that the prevalent virus population was composed of VDV-1 and a chimera of 5’-DWV-VDV1-DWV-3’. The recombination junctions in the chimera genomes were confirmed by using RT-PCR, cDNA cloning and Sanger sequencing. We then focused on conserved short fragments (CSF, size > 25 nt) in the virus genomes by using GenBank sequences and the deep sequencing data obtained in this study. The majority of CSF sites confirmed conservation at both between-species (GenBank sequences) and within-population (dataset of this study) levels. However, conserved nucleotide positions in the GenBank sequences might be variable at the within-population level. High mutation rates (Pi>10%) were observed at a number of sites using the deep sequencing data, suggesting that sequence conservation might not always be maintained at the population level. Virus-host interactions and strategies for developing RNAi treatments against VDV1/DWV infections are discussed.
Highlights
Virus infections are closely associated with colony collapse in the European honeybee Apis mellifera
When small RNA (sRNA) reads were mapped against the reference sequences, 31,192 unique reads could be perfectly matched to either the VDV-1, WDV or Kakugo virus (KV) genomes (Figure 2, Table S2 and Figure S3)
These viral derived small interfering RNAs (vsiRNA) were dominated by 22-nt long species (Figure S1), distributed throughout the genomes with hotspots, and originated from both plus and minus RNA strands (Figure 2)
Summary
Virus infections are closely associated with colony collapse in the European honeybee Apis mellifera (reviewed by [1,2]). Colonisation of hives by V. destructor in areas previously mite free has resulted in the selection of certain Deformed wing virus (DWV) strains [3,4,5,6] The emergence of these selected strains appears to disturb the balance between the virus and honeybee populations, initiating collapse of honeybee colonies [3,4,5,6,7]. There is a Kakugo virus (KV, genus Iflavirus) [44,45,46], which is very closely related to DWV genetically but is associated with aggressive behaviour in guard bees These viruses have positive-sense, single-stranded RNA (+ssRNA) genomes of approximately 10 Kb, containing a single open reading frame flanked by 5’ and 3’ untranslated regions (UTR). Rapid viral evolution represents an elevated challenge for developing treatments and/or controlling measures against the virus infections
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