I actually went to a presentation by Kristi Miller at UBC before the Christmas holidays. She didn't even bring this up. One driving force behind her research is to further understand why wild salmon stock population fluctuate. That way in the future it may be possible to predict collapses/booms before they happen so scientists can provide better management recommendations for the fishery. The discovery of the virus was actually a coincidence as she wasn't looking for one.
So, to me, it is not clear at all why the federal government "muzzled" her. Her research was very important and it seems like it would benefit everyone.
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