Little is known specifically about the agent of FSE. Indeed the nature of the infectious agents causing infectious spongiform encephalopathies in other species (e.g. scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, and Creutzfeld-Jacob disease and kuru in man) is also not well understood.

Theories as to their structure include either a protein ('prion') or a protein-nucleic acid (‘virino’) combination. Scrapie infectivity is associated with protein fibrils (scrapie associated fibrils (SAF)), in which it has not been possible to detect a scrapie-specific nucleic acid.

The spongiform encephalopathy agents are extremely hardy: they will survive high temperatures and UV-irradiation which would normally destroy nucleic acids. However, it is possible that the protein component is in some way able to protect a very small nucleic acid (possibly RNA) genome, and small pieces of protected cellular RNA have been found bound up in SAF. In addition, no other replicating 'lifeform' is known which does not contain nucleic acid, and it is difficult to conceive how a protein could transmit so much strain-specific variation (strains can be typed by comparison of their pathogenicity in laboratory mice) as is found among different scrapie strains. On the other hand, the protein fibrils associated with the spongiform encephalopathies are encoded by genes found in normal tissues, and the fibrils themselves appear to consist of a host cell which has been abnormally processed (modified PrP) during infection. One suggestion is that the infectious agent is simply abnormally folded protein (prion) which somehow catalyses (crystallises?) the abnormal folding of otherwise normal protein produced in CNS and other tissues, thereby giving the impression of replication.

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