There are plenty of organisms in the real world that look like plants, but aren't too. Pokemon are able to be explained biologically because the setting has put them in their own species of creature.
Humans are one species, Pokemon are several different species. This is why viruses don't work. This is also ignoring all of the other points I made. Even if we were to assume they made this miracle virus it wouldn't explain the fact that trainer Pokemon remain unaffiliated. We can't argue that the virus is sentient because that would mean an even more impossible disease.
To say that there is so much we don't know about viruses therefore it's fine to make it up is a flawed way of thinking. If it hasn't been observed in reality, and your story is based in reality, then you should stick with the information that is known.
The fact of the matter is that we do know a lot about viruses, but we know little of certain specific strains. Is there stuff we don't know? Certainly, but I'd argue we still know a lot considering no one has died of Smallpox in a while.
Honestly though you could have humans with laser vision if you wanted in your RP because it's your RP. It doesn't mean I can't say that humans having laser vision in a Pokemon RP doesn't make sense though.
My question has not gotten an answer yet though. Why is it that my solution to this is not viable? Point to me where the virus being a drug would change anything at all for what you have planned, and what has happened so far.