What is the origin of viruses?

In a sense, viruses may predate life itself. They depend on life to reproduce, but bare RNA existed before it could reproduce.  When early RNA chanced on the mechanisms for its own reproduction, it was as if a virus infected something that wasn't otherwise alive. Some RNA took up permanent residence, while others gradually developed protein coats to make modern recognizeable viruses.  That first proto-life proto-virus was incredibly slow to reproduce, so it may even still be around us without being recognized: full cells (and the viruses that use them) fill the earth vastly more effectively. That proto-virus may not be directly related to modern viruses. Viruses may instead be stripped-down forms of cells, DNA/RNA ejected into the void and waiting for somebody else to infect. Alternatively, it could be cells that have gradually lost most of their cellular machinery, leaving only the genetic material and protein coat. Life is vicious at all levels, and will take advantage of any mechanisms it can. It may even be that all three mechanisms played a part. Since viruses don't leave fossils, we have little direct evidence. We get indirect evidence in the form of the genetic sequence, and there are genetic indications of all three theories. Viruses are so diverse that there's no reason to believe they evolved only once.  You share more common features with a plant or a bacterium than a cold virus shares with an HIV virus.