I think they used whirling disease as an excuse to drain the lake and get rid of the non-natives (ie. brookies) in johnson lake. Might as well try and kill 2 birds with one stone right?
Hopefully it works to get rid of whirling there, but as others have stated, it wouldn't take much for an eagle to swipe an infected fish from the nearby bow and transfer the disease back to the lake. I'm not a biologist but that seems plausible.
Next question is, how long can the spores survive without water? From what I gather, the spores are activated by water
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