Examples of virus originated from a living system
Prion diseases are still very poorly understood, but one of the dominant theories is that they are misfolded proteins that cause disease by catalyzing the misfolding of more proteins of the same type.  If that is the case, then they arise from the organism that they affect simply by protein misfolding.  In the case of bovine spongiform encephalopathy (mad cow disease) being transmitted to humans and resulting in new variant Creutzfeldt-Jakob disease, it seems like it might be transmissible between species, but it probably needs to infect a closely related species so that the protein has a homolog it can act upon.

Can't say I know of any examples where people have shown the de novo creation of a virus from a living organism.  There are definitely virus protein homologs in the genomes of organisms, but directionality is hard to argue since its common for viruses to pick up host genes, or leave behind viruses genes.