So, in recently perusing Parazoology 2, I was struck the entry for nanoplasmosis, the Awakened form of toxoplasmosis. This particular microorganism eats soft nanites and emits a jamming field that interferes with nanite functioning. As far as I could tell toxoplasmosis wasn't mentioned in Stolen Souls or elsewhere in talking about its potential interaction with CFD.
It seems to me that this would be a tailor-made solution for CFD. While CFD does provide disease resistance, an Awakened microorganism could conceivably weather this resistance in the short term. Once able to get a toehold in the system, it would find plenty of food in the soft nanites, and could disable the hard nanites with the jamming field. Within a few weeks the hard nanites would be disposed of by natural elimination. And as far as damage to the host goes, according to the entry in Parazoology 2, the only damage was that to nanite systems.
While I realize Parazoology 2, didn't sell as much as the core releases, this is a very recent release. It isn't some obscure bit of SR lore from a 90s fiction piece. Heck the PDF was released after the release of the Storm Front and Fifth Edition PDFs. I know lore sometimes gets dropped between editions but this feels far too recent to not be currently canonical. Is this an intentional backdoor out of the CFD storyline? Or just something no one managed to correlate? Or just something we are supposed to ignore because, "Bwahaha super incurable disease ongoing metaplot," is going on here?