I think some of them are likely to be extra-human in origin--Only because of the incredibly high amount of conservation between coding regions from species to species. And since prion proteins are coded proteins (though, we're not sure what they do yet), then it seems likely that at least some of the species of prion proteins may have origins that predate humans.
For the evidence available that would seem to make sense. Bovine Spongiform Encephalopathy (BSE) is transmissible to humans, though you don't actually get BSE. You get a variant of CJD (vCJD I believe those creative researchers named it

), from a protein almost identical to the CJD one. Which suggests then, that BSE protein responsible for BSE in cows, is also coded for and produced in people.
I think though, not all prion diseases have homologues in other species--Which may mean there has been unique gene duplication events and subsequent protein family radiations which produce unique prion proteins in species as well.
Really a lot more work needs done on prions, but I think because of their rarity in causing human morbidity, the funding (unfortunately) just isn't there. Sad to say, but that happens to a lot of rare diseases.
Certainly, any 'death by prion' would probably be up there with my top "least ways I would want to die". Especially considering there is literally no treatments for the cause of the disease. We can really only target symptoms and try to make a person comfortable as they lapse into dementia, insanity, neurodegeneration or in the case FFI--death from insomnia.
I don't know, that would be a pretty amazing feat of biology. But with all the new stuff we've learned about prions, I wouldn't put it past them.
I know some naturally occurring prions have been shown to have sensitivity to proteases, but I'm not sure if these are endogenous to the organism or if researchers are digesting them with exogenous (to the species) proteases.
Many of the synthetic model prion systems created in bacteria also show sensitivity to proteases, specifically eukaryotic ones. We're still working out what exactly creates that high protease resistance in disease causing prions.
You would think, from a functional and steric standpoint, that prions would be resistant to either exoproteases
or endoproteases, not both. But, it seems if they are one of those protein flukes of nature that get to have their cake and eat it too.
I'd agree, a species would probably need to evolve a new novel protease to deal with the disease. I suspect though, that historically (evolutionary speaking), prion mortality has "flown under the radar" so to say and not exerted enough selective pressure on a population for such a thing to occur. Who knows though? Maybe some proteases, yet to be discovered actually do protect us from prion diseases and we are just unawares, as of yet.
The scary thing, is how many different proteins we've discovered (and thinking of those yet to be discovered) which belong to the prion family. Maybe it will turn out, this has been an ongoing evolutionary battle for a long time and many of the prion "traps" are kept in check by such novel protreases. I'd suspect though, if that were the case, we'd see prion diseases more often when the genes for these proteases get's wrecked.
I'd counter that though (I'm debating myself here, must be my prion disease :)!) with, there maybe diseases which are prion diseases and we just don't know it. Alzheimer's and a few others (especially many of the "unknown cause dementias") spring to mind--As we still don't really know what causes them, and many of the symptoms (especially the plaque findings) ring suspiciously of prion disease to me.
I suspect you are right. Modern genetics has certainly taught us (polymorphisms and whatnot) the amount of variability between individuals at the molecular level. It would have been a very interesting study to look at the onset of disease, exposure amount and acidity of the GI tract in individuals who acquired Kuru before the practices which lead to transmission stopped.
Certainly, its something that could investigated in an animal model. Now if I can just find an unsuspecting herd of sheep, a pile of scrapie and someone to fund the research
Thanks