if all oxygen in the air was suddenly (by magic) replaced by carbon dioxide it would put extraordinary selective pressure on humans to evolve something other than oxygen-depending lungs. the most likely outcome would be that we'd all die instantly though.
I like the metaphor! I'd suggest two points, if humans evolved as fast as viruses and we couldn't replace all the oxygen on earth at once (and likely not at all in some places just as we can't get vaccine everywhere at once and not in some places at all) I would think it far more likely for human evolution to figure it out. Unlikely still, but maybe not outside the realm of possibility?
In keeping with the metaphor though and as others have pointed out in the thread - non oxygen lungs wouldn't make humans super humans, just different and if anything more likely to be weaker than their oxygen breathing counterparts as they adapt to a new environment? I think that is the running idea I'm getting at least.