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Sorry to hear that, and hope the treatment will vanquish the demon again.
As far as vaccination, one friend of mine lost almost every young bird she had 2 years in a row before she started vaccinating. In an ideal world, where you have an unlimited amount of space to raise many birds, not vaccinating birds may eventually lead to resistance. In her case, she would never be able to keep a laying flock again if she does not vaccinate. Since all birds stay at her place until they pass on I do not think vaccinating them is affecting the virus in any significant way. It is very hard to see each of your hatchlings die just as they approach laying age and you have become attached to them.
I also think it unlikely that vaccinations alone make the virus stronger. It a virus that readily mutates on its own without the help of vaccination, and would, like the Flu virus, be constantly challenging resistance. Chickens are just unfortunately more susceptible than many other birds species.
I had never heard it stated like this article did. Poultry World is geared to the commercial industry, if I recall. Why they'd much care about this, I'm not sure, though I guess pastured poultry operations might.
Honestly, I think there are Mareks diagnoses when it is not Mareks by labs that just "assume" when they see a tumor that it is MD and don't actually test. Bacterial infections that rage in the body can send bacteria through the bloodstream and form little tumors all over the place, I was told emphatically by my "long-distance vet" who mainly treats thoroughbreds in Kentucky, though he doctored Ladyhawk's chickens as well when he was out for her Arabian mare, stitched up Lancelot after a fox brawl, etc. He said labs are getting very lazy, especially ones where the testing is free, one of those "you get what you pay for" kind of things. Plus, state labs as a whole really don't give a crap about backyard flocks since they are here for the benefit of commercial flocks anyway. In absence of any signs of the disease other than some tumors they don't even test, a lab report that says MD is just a paper towel, IMO.
On the other hand, and this is just me, if I couldn't keep chickens alive because of MD and had to vaccinate for it just to keep them (and the consumer vaccine is useless, according to folks in the know anyway-it MUST be the hatchery one that is kept at -170* or something like that) I'd not keep them. I know Karen has done a remarkable job with hers, but I don't want to do that. I'd quit, let them all die out, and eventually, get guineas or some other less susceptible species. They say Egyptian Fayoumis are highly resistant to Marek's, which is interesting. Flighty, yes, but very hardy.