We know something about the origin of the first cell. But what do we know about prions? How did they originate?
The computational study by Ehsani et al., 2011, argues that an ancestor metal-ion transporter gene ZIP served as the initial template for the prion founder gene, where the same author produced a 2012 paper that said this was probably a product of a spliced LIV-1 ZIP transcript that became reverse transcribed and inserted into the host genome. Thus, evidence in part points to a retrogene origin for prions (mediated by a retrovirus, especially since the gene is integrated into the host w/ no introns). They go on to state that two genomic rearrangements spanning hundreds of millions of years serve as the basis for the prion founder gene: A cysteine flanked core element inserted into the ZIP ectodomain, and then the insertion of a spliced, C-truncated ZIP transcript.
I don't think the evolutionary origin of prions are very well understood, yet, but I will try to find more recent data on the subject.