I'm not enough of a virologist to say "Retroviruses accidentally reverse transcribe human mRNAs often when we get a retroviral infection," but I'm willing to bet money they do.
It's quite possible, but largely irrelevant - you would first have to prove that a specific cDNA under question did actually occur naturally. And in any case, a controlled process that produces large amounts of a cDNA is very different from a freak accident like this. Technically speaking, it's also possible that many patented synthetic molecules do actually occur in nature due to biological or spontaneous chemical processes. That doesn't make them unpatentable.
Either way, the sequences of cDNA are fundamentally natural. All of the cDNA sequence is found in the genomic sequence. I can't retype a popular book on a typewriter, exclude a boring chapter or two, and claim it's novel and claim exclusive rights to it based on the fact that no one had previously typed it out on a typewriter. Transcribing and editing is all cDNA is.
cDNA is a chemically synthesized product. So is (for instance) an impotence drug. To a chemist there is very little distinction, other than you're using polymerases for the first product, and probably some sort of weird metal catalyst for the second.
If some biotech company comes up with a completely novel protein designed by a computer, they should be able to COPYRIGHT it. That's creating something, not simply copying something that's natural.
I'm confused, what does copyright have to do with this?
nor should you be able to modify an existing virus and patent that
Why not? If I take a naturally occurring biological entity and modify it to do something completely different and unnatural, how is that not a patentable invention? You are basically demanding that everyone performing any kind of molecular bioengineering start completely from scratch and completely avoid anything that vaguely resembles something natural. We'd also have to avoid using traditional amino acids or nucleic acids, because those are naturally synthesized, which means we couldn't use existing biological systems to replicate our products. This is just insane; it may be an interesting research question but everything we do builds upon prior knowledge, and you are asking that we throw all that out.