So the breakthroughs in "nanomachines" are actually coming in biology. Cell and gene therapy is absolutely exploding right now with methods of reprogramming cells and viruses to do things like deliver payloads, rewrite the genome, kill or replace diseased cells, etc. Turns out the real nanomachines were the friends we made on the way. Viruses are absolutely self assembling and self replicating nanomachines with a programmable instruction set that we are learning how to re-write. It's not how we conceived it in the sci-fi of the past because progress in physics and computing seemed much faster than the glacial pace of biology, but biology is absolutely nanotechnology and the tools for manipulating it have come into their own in the last 20 years.

It's also worth mentioning that the human immune system is an insane rube goldberg machine where almost every pathway has multiple mechanisms of negative feedback regulation. It's almost universal that when your cells sense a cytokine produced by a viral infection, like interferon gamma, they respond to it (inflammation, fever, antiviral gene transcription, etc), but they also up-regulate genes that serve to dampen the cell's response to interferon. If you put a cell in a steady state amount of cytokine, it will usually have a strong initial response, followed by a damping of the signal. There are a lot of mechanisms by which this happens (down-regulating the receptor, up-regulating the inhibitors of the receptor, etc.)

People are regularly exposed, every season we have X million exposed, and 5% or whatever are severe. Due to the pandemic we basically skipped 2X exposures that would have happened, so now we are having 2-3x all at once. Even if the same 5% were severe, it would be bad. That also ignores two other factors, viruses spread better in populations with fewer immune individuals to act like fire breaks, and we also probably put selection pressure on flu and rsv to be more contagious (to allow survival during covid measures). All of that together is probably a perfect storm of infection. We are probably infecting a lot more people per day than a normal year due to all these factors.