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Title: Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing

item Cornman, Robert
item DAINAT, BENJAMIN - Non ARS Employee
item Chen, Yanping - Judy
item VANENGELSDORP, DENNIS - University Of Maryland
item WEAVER, DANIEL - Bee Weaver, Llc
item Evans, Jay

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/10/2013
Publication Date: 8/8/2013
Citation: Cornman, R.S., Boncristiani, H., Dainat, B., Chen, Y., Vanengelsdorp, D., Weaver, D., Evans, J.D. 2013. Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencin. Biomed Central (BMC) Genomics. 14:154.

Interpretive Summary: Viral disease has been implicated in many cases of bee losses worldwide. One puzzle for scientists and regulators involves determining whether known bee viruses have specific strains that are especially harmful to bees. Here we use a modern genomic technique to investigate the occurrence of such damaging strains. We found variation across the genomes of all bee viruses, and a possible difference in Israel acute paralysis virus that is associated with virulence. These results can help in the improvement of management advice and the regulation of bees and hive products, by indicating which virus types present the highest risks to bees.

Technical Abstract: Deep sequencing of viruses isolated from infected hosts is an efficient way to measure population-genetic variation and can reveal patterns of dispersal and natural selection. In this study, we mined existing Illumina sequence reads to investigate single-nucleotide polymorphisms (SNPs) within two RNA viruses of the Western honey bee (Apis mellifera), deformed wing virus (DWV) and Israel acute paralysis virus (IAPV). All viral RNA was extracted from North American samples of honey bees or, in one case, the ectoparasitic mite Varroa destructor. Consensus sequences of DWV for each sample showed little phylogenetic divergence, low nucleotide diversity, and strongly negative values of Fu and Li’s D statistic, suggesting a recent population bottleneck and/or purifying selection. The Kakugo strain of DWV fell outside of all other DWV sequences at 100% bootstrap support. IAPV consensus sequences supported the existence of multiple clades as had been previously reported, and Fu and Li’s D was closer to neutral expectation overall, although a sliding-window analysis identified a significantly positive D within the protease region, suggesting selection maintains diversity in that region. Within-sample mean diversity was comparable between the two viruses on average, although for both viruses there was substantial variation among samples in mean diversity at third codon positions and in the number of high-diversity sites. FST values were bimodal for DWV, likely reflecting neutral divergence in two low-diversity populations, whereas IAPV had several sites that were strong outliers with very low FST. This initial survey of genetic variation within honey bee RNA viruses suggests future directions for studies examining the underlying causes of population-genetic structure in these economically important pathogens.