In my opinion the queens are disappearing for one of several reasons. Of course there may be others.
1. Nosema infection in the mating nuc, from the attendant bees in the shipping cage or from Nosema in the colonies that lost the queens. (See comments about the use of pollen in fondant).
2. Viral infections from Varroa, the attendant bees in the shipping cage.
3. Queens being pulled too early from mating nucs, as has been mentioned they need to mature at least 3 weeks before being sold.
4. Chilling during shipping.
5. Queens reared in colonies containing coumaphos residues, resulting in queens that have part worker/part queen characteristics. You usually cannot see the differences unless examined under a microscope. These queens are poor performers and are superceded quickly.
In Greece there is a widespread use of fondant, often made by the beekeepers themselves and they often use pollen from Spain. Actually this is probably of Chinese origin and baptised as being Spanish once inside the EU. Research has shown that pollen often contains Nosema spores, yes both species AND viral RNA all of which have been show to be infective.
Chinese royal jelly used for grafting has been found to contain viral RNA which can then infect the queen and then be transferred to eggs laid and infect the workers and drones of the colony. Even the drones can pass these viruses on when mating. Greece is full of Chinese royal jelly.
Greece and Cyprus, as far as I know, are the only EU countries that have checkmite + as a registered treatment for Varroa. The active ingredient is the organic phosphate coumaphos. As mentioned above it can cause intercaste syndrome in queens. Checkmite is used widely in Greece and most of the wax used to manufacture foundation is contaminated.
Most chemicals used for Varroa control have some effect on the fertility of both queens and drones. They are very toxic substances that while not exhibiting any visual effects on the bees themselves, they do affect the sex cells negatively.
In our operation we have realised how harmful these chemicals are and now only use certified residue free foundation from Germany or when conditions are right we just give the bees a couple of frames with starter strips and they build them just fine.
