In the comment section of Endogenous retroviruses (ERVs) as evidence for common ancestry. (Part 1) telic-meme asks:
"Question: Does anybody know what the current accepted explanation is for the origins of exogenous retroviruses?"
Origins of Viruses may not furnish the answer, which is probably unknowable however, possibilities are suggested. The author suggests that viruses have evolved together with their hosts. While there is evidence for viral adaptation, changes in viral genomes do not explain viral origins. Questions about viruses seem to parallel those of cellular organisms. While there is much knowledge about viruses and much data used to support evolutionary concepts related to them, there is little in the way of firm evidence to explain how they originated.
The parasitic nature of viruses confounds origin theories. Although viral genomes are small they nevertheless are not explained as resulting from prebiotic chemical reactions. Like their cellular hosts viruses contain nucleic acids whose nucleotides are sequenced as symbolic representations of specified amino acids composing proteins needed to sustain and replicate the viruses. No chemical process could generate this type of symbolic meaning. Not for viral or cellular genomes.
One would be tempted to seek an explanation based on natural selection. However although genomic viral changes are well documented and easily understood, citing a host organism to explain viral origins only creates more answers than questions. Evolutionary concepts presuppose the existence of mechanisms that allow for adaptive change. Viruses are dependent on two distinct genomes. Incremental pathways to minimal function are, at this point in time, the stuff of imaginative speculation. The core problem with viral and cellular origin theories lies with the causal options we have been restricted to. All are bottoms-up or emergent in nature. It is assumed that the symbolic complexity, evidenced by genomes, arises from underlying but unknown forces of nature. Unknown forces are manifested by equally indescribable pathways to cells and viruses.
Alternatives entail a lateral origin for viruses; the origin being the hosts themselves. Add this to the possible but unknown category. Downward causation is a third paradigm and a very ID friendly one.