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Breeding Back Viruses
By: Jay Evans
Spring! Great food coming in, bees that are becalmed by the mild temperatures, more daylight after work, a great time to be alive. For your beehives that survived the Winter, it is also a time where the itches of varroa mites are lessened and the viruses transmitted by these mites are at a low point (partly because the sisters with high virus loads have perished). I belong to the growing band of people who believe that bee viruses, while not the only problem faced by bees in the environment, are a leading problem. Virus levels in bees are exacerbated by mite levels, chemical stress, temperatures, and bland diets. The link between varroa mites and bee viruses was documented over 40 years ago (shoutout to UK researchers Brenda Ball and Stephen Martin who nailed it) and the evidence has piled on over the years. As mites move into a new area, their impacts on bee health seem lower at first, arguably because hitchhiking viruses are rare or absent. In Australia, mite-infested colonies were robust while viruses remained low, as shown by John Roberts and colleagues in 2020 (Roberts, J. M. K., Simbiken, N., Dale, C., Armstrong, J., & Anderson, D. L. (2020). Tolerance of Honey Bees to Varroa Mite in the Absence of Deformed Wing Virus. Viruses, 12(5), 575. https://doi.org/10.3390/v12050575). With foresight, they note for one villain, deformed wing virus that “…remaining free of this serious viral pathogen can have important implications for bee health outcomes in the face of Varroa”.
Unfortunately, for the U.S. and most of the beekeeping world, “remaining free” of mite-transmitted viruses is no longer on the table. Much work has been devoted to breeding efforts to diminish varroa mites, and now the same efforts are making headway against the viruses that define varroa disease. Specifically, thanks to both controlled selection regimes and passive disease monitoring, it is evident that resistance to bee viruses has a genetic component. To what extent can genes for resistance be captured through controlled breeding? Dirk de Graaf and colleagues in Belgium came upon one tool that seems useful for identifying virus-resistant stock, by quickly assessing viral loads of eggs across different queens. This tool minimizes some of the environmental causes of viral infection since it targets bees before they have a chance to face mites and other environmental challenges. Selection programs require first identifying variation in a target population and then showing that desired variants can be given a leg up within our lifetimes. Selection does not require knowing the exact genes behind a desired trait, but it helps to know if those genes behave in a predictable way. Father Gregor Mendel did not have a fancy lab but with gardening skills and decent notes he showed that some of the physical traits of peas were defined by a simple genetic trait. Simple genetic stories, especially for things like behavior and immunity, are the exception. Nevertheless, recent studies have shown that simply measuring traits in a careful way can shed light on which of those traits are available to breeders for selection programs.
Work in de Graaf’s group started by identifying ample variation in egg virus levels and showing that a decent fraction of this variation was driven by queen genetics (de Graaf, D.C., Laget, D., De Smet, L. et al. (2020) Heritability estimates of the novel trait ‘suppressed in ovo virus infection’ in honey bees (Apis mellifera). Sci Rep 10, 14310 https://doi.org/10.1038/s41598-020-71388-x). On top of the novelty of measuring egg viral loads, they had the insight to focus on drones, whose genes are truer to their mom’s since they are born from unfertilized eggs. With standard heritability stats, they predicted that around one third of the variation across eggs in viral loads can be attributed to genes, a good wedge for selecting this trait. More importantly, they showed a connection between the ‘ovo’ score and colony viral loads, and indeed confirmed that drone-egg ovo scores from one queen were more matched than worker-egg scores, strengthening the claim for genes versus queen health as a driver of egg viruses. In 2026 and led by team member Emma Bossuyt, the Ghent group published a re-cap of ten years of breeding for the ‘ovo’ trait (Bossuyt, E., Brunain, M., De Smet, L., Danneels, E., & de Graaf, D. C. (2026). Evaluation of 10-Year Selection for Virus Resistance in a Mass Breeding Program. Insects, 17(2), 137. https://doi.org/10.3390/insects17020137). The results are promising but also show how hard it is to maintain specific desired traits over time. They were able to enlist a majority of regional breeders into the program, hinting at broad acceptance of the importance of viruses for bee health. By breeding from queens whose eggs were virus-free, queen producers did increase that trait over time…at first. A reversal of sorts occurred toward the end of the project, perhaps reflecting new viral dynamics, human distractions including those caused by our own SARSCov2 viral dilemma, unmeasured environmental effects on queens, or the whack-a-mole tendency of viruses to test the limits of their hosts’ defenses. Regardless, this large effort seemed to tilt bee health in a positive way and increased awareness among bee breeders for a subtle but important immune trait.
While not necessary, breeding for immunity benefits from knowing a bit about the genetic mechanisms. A joint US-Canadian effort has tried this by ‘mapping’ genetic regions to find hot spots correlated with desired traits. Led by masters student Robert Lu in the Alberta laboratory of Olav Rueppell, this study focused on responses to experimental infection by Israeli acute paralysis virus, a mite-transmitted virus that can have strong effects on bee colonies (Lu, R. X., S. Bhatia, M. Simone-Finstrom, and O. Rueppell (2023) Quantitative Trait Loci Mapping for Survival of Virus Infection and Virus Levels in Honey Bees. Infection, Genetics and Evolution 116. https://doi.org/10.1016/j.meegid.2023.105534.). Several regions of the bee genome were linked with levels of IAPV, across sets of both ‘non-susceptible’ and ‘susceptible’ offspring. These regions were not always overlapping, suggesting that the ability to deal with viruses is a complex story involving multiple genes and their variants. Further, susceptibility to IAPV was not mirrored by susceptibility to a battery of other tested viruses. On the plus side, the study design allowed the identification of regions tied to levels of deformed wing viruses and others that, while not tested experimentally, are important. These additional threats now have an expanded set of genetic traits to target for selection. The study describes dozens of genes in the indicated regions, lots more work for science but a shopping list to compare with results from other groups. Team member Michael Simone-Finstrom is expanding the hunt for resistance genes in US bees from his USDA perch at the Honey Bee Breeding, Genetics, and Physiology Research Laboratory in Baton Rouge.
One thing that is clear from these studies is the immense value of stable, ambitious, long-term studies. In the case of the decade of work in Belgium, insights were gained from a Europe-wide database of bee breeding traits (https://www2.hu-berlin.de/beebreed/ZWS/), housed in Germany’s Institute for Bee Research in Hohen Neuendorf. This database is not unlike those available in the U.S. for everything from dairy cows (https://aipl.arsusda.gov/) to the soybeans that cows and humans consume (https://www.soybase.org/). It’s comforting to know that USDA scientists in Baton Rouge, including Simone-Finstrom, are joining an ambitious nationwide effort to document and benefit from bee breeding traits as part of the “plants-to-fishes” Breeding Insight program (https://breedinginsight.org/honey-bee2/). More evidence that, while science is often incremental, working as a colony can lead to lasting changes.
