Honey Bee Cases

(contributed by Kim Mogen and Brad Mogen, University of Wisconsin-River Falls)

Download the files for this case: Honey bee case files

These cases focus on honey bee health and issues associated with the role of bees in agriculture and the environment. Techniques used in these cases include PCR, gel electrophoresis, and sequence alignment/tree building.

The files for each case (DNA sequences, primers, etc.) can be downloaded as a zipped file (.zip). To unzip the folder containing the files, right-click on the .zip file and select “Extract all”.



Honey bees are keystone species that play an important part in everyone’s day-to-day life. Approximately one third of our agricultural crops depend on honey bee pollination, amounting to about $15 billion of the food supply nationwide. For example, 100% of almond crops are pollinated by honey bees, which requires over one million bee colonies to be trucked into California from other parts of the country each year.

Since about 2006 there has been a major decline in the number of honey bees and other pollinators, which so far has no definitive cause. One aspect of this decline in honey bees is called colony collapse disorder (CCD), where the bees have simply disappeared or abandoned their hives, almost overnight.  The cause of CCD is complicated; focus has been on pesticide use, mite levels, and virus levels, however global warming and habit loss are also thought to play a part. Researchers are investigating all aspects of honey bee health and hive management in order to determine the best strategies for ensuring that honey bee populations continue to thrive rather than decline.


Case A. Effect of pesticide exposure on virus infection

Honey bees are commonly exposed to pesticides as they forage for pollen and nectar. Some pesticides are known to disorient bees and thus affect their behavior. Sub-lethal exposures of some pesticides are considered possible contributing factors to Colony Collapse Disorder (CCD). Dr. Muskiver was curious if pesticide exposure was linked to virus infection, another possible contributing factor to CCD.

To test this question, Dr. Muskiver set up four test hives, and fed the honey bees either with untreated pollen or pollen treated with sub-lethal doses of the pesticide Imidocloprid, a neonicotinoid.  Samples of 20 bees from each hive were collected, RNA was extracted, and cDNA synthesized in order to run PCR. Multiplex PCR was performed using primers specific for 4 viruses, and also for the bee actin gene as a control. PCR products can be identified based on the size of the product:

Primers PCR product size
Actin 120 bp
Deformed wing virus (DWV) 203 bp
Black queen cell virus (BQCV) 322 bp
Sac brood virus (SBV) 487 bp
Israeli acute paralysis virus (IAPV) 719 bp

DNA samples for testing:

Negative control – bee sample with no viruses present
Positive control – bee sample containing all four viruses
Hive 1 – exposed to pesticides
Hive 2 – exposed to pesticides
Hive 3 – no pesticides exposure
Hive 4 – no pesticide exposure


  • What are the results for each experimental hive, in terms of viruses that are detected?
  • Do the control sample produce the results you expected?
  • Is there any correlation between pesticide exposure and viruses detected? How would you explain these results to Dr Muskiger?
  • What are some other tests that could be done to address this question? What would you suggest that these researcher do next?


Case BVarroa mites and virus diversity

Recent declines in honey bee populations have given rise to the syndrome named Colony Collapse Disorder (CCD). Several potential stressors have been identified. A team of research scientists, funded by the North American Honey Bee Council, decide to survey colonies from around North America for two of the notable stressors – Deformed Wing Virus (DWV), a virus that causes wing deformation, and Varroa destructor, a parasitic mite that feeds on the bee.

It has recently been reported that V. destructor  transmits certain strains of DWV more effectively, and that long-term mite infection reduces virus diversity and leads to the prevalence of more pathogenic viruses (Martin et al. 2012). The scientists are interested in testing the relationship between DWV strains and the Varroa mite in North America. Bees were sampled from the following locations, and the level of mite infestation was determined for each hive sampled:

Central Ontario – low mite levels
Northwestern Washington –  low mite levels
Southeast Florida – high mite levels
Northern Arizona –  moderate mite levels
Southern British Columbia – moderate mite levels


RNA was extracted from samples of 20 bees, and copied into cDNA for PCR amplification of the DWV pol gene.  All samples tested positive for DWV. PCR products were cloned and individual clones were sequenced.  Use sequence alignment and phylogenetic trees to compare virus sequences isolated from each region.


  • What can you observe about DWV diversity in the various regions by examining the trees?
  • What additional data would you want to collect in order to continue this study?