Wasn't there actually some famous Roman who taught that most diseases were caused by parasitic animals much too small to see? I don't know that this helped much.
That would be Marcus Terentius Varro but that was still around a thousand years after question in the OP. Nonetheless, with considerably more background in the subject I might have more ability to make my case.
Is there any reason you couldn't try to give them microscopes (and telescopes and eyeglasses while you were at it)? They already had glass working in most of the options given, although China was a bit slow in this area. It was mostly used for colorful decorative beads, but you could try to get the artisans to make them clearer and flatter until you had functional lenses.
I suppose you could try to make a microscope, but it would still be difficult considering clear crystal glass didn't appear until much later (and I have no idea how that is made) and you need a lot of light to be able to see through a microscope well anyways. Regardless, even if you managed to create a well functioning optical microscope you could only show bacteria, not viruses since they require an electron variant.