The present disclosure relates to methods and compositions for the detection of infectious proteins or prions in samples, including the diagnosis of prion related diseases. One embodiment is an ultrasensitive method for detecting PrP-res (PrPSc) that allows the use of recombinant PrP-sen (rPrP-sen) as a substrate for seeded 
polymerization. A sample is mixed with purified rPrP-sen to make a reaction mix which is incubated to permit aggregation of the rPrP-sen with the PrP-res that may be present in the sample. Any aggregates are intermittently disaggregated by agitation (for example by 
sonication) and the reaction allowed to proceed to amplify target substrate. Any rPrP-res(Sc) in the reaction mix is detected to indicate the presence of PrP-res in the original sample. This 
assay, which is called rPrP-PMCA, is surprisingly much faster than existing PMCA methods, yet it still retains sufficient sensitivity to detect extremely low levels of PrP-res. An alternative of rPrP-PMCA is the 
QUIC method in which shaking of the reaction mixture is substituted for 
sonication. The surprising speed and efficiency of the method permits the 
rapid identification and diagnosis of prion 
disease, which can limit the transmission of prion diseases, particularly through the 
food supply.