Michael, at least two of those bees look diseased to me! The two top ones with the shiny bodies. CBPV? Varroa is in SA, isn't it? (
See The Apiarist here. Scroll down the page to the photo of bees with CBPV.) The black bee looks healthy - but black!? I'm glad you're going to send some to be analysed.
And then all that sugary waste from the bio-digester ... I don't suppose you collect honey from colonies that have access to all that stuff, do you? Can't all that waste be covered up?
Waste processing site far away from my bees, waste bags are opened and processed immediately, however, when you're processing large amounts as we do small pieces fall, drips happen when unloading, sticky residue left on outside of bags and tractor tyres etc etc,,, It;s impossible to cover up everything, it is after all a processing unit to convert animal waste/Poo into energy,,, rather have a bit of chocolate laying around than the other stuff that we feed here...
As far as diseases go,
I have been very fortunate and have never had any varroa mites, thought I did once when inspecting a cutout in quarantine but turned out to be Braula...
Dont want to hijack the thread but will post a pic if I can find it... My heart sank when I first spotted it... Then it was gone???
Re harvesting Honey,,, well I did remove a wild colony less than a Km away a few months back and yes, I removed all the honey ( small hive beetles)
It was the second best I have ever had, very dark and very rich,,, the only way i could explain is it burnt the back of your throat it was so sweet...?? was it from the chocolate waste? Uncertain... Tasted great over pork rashers....