A new save isn't buried in systems on run one. Each in-run mechanic unlocks for the whole save when any virus reaches its level (Hosts & Host Traits: 2 finished generations; the Cytokine Storm instead switches on from the fourth organ at any level), then is introduced on its own: a NEW MECHANIC UNLOCKED card that pauses the run the moment it first shows up (right as the organ starts for tumors, room tiers and immune learning), and except for the Cytokine Storm it's guaranteed to appear in that organ. Only one is introduced per run; the rest wait for later runs. Hosts & Host Traits is introduced on the host reveal before you land instead.
When Detection stays high, the host may take antivirals, a vaccine booster or interferon. Walk out of the room to escape the dose, or survive it for a reward.
From the Codex
The host feeling sick and taking medicine when Detection is 75 or more.
Fun fact: Walking out of the room escapes a dose; surviving it pays out.
From the fourth organ on, if your build gets too strong, the storm meter fills and the immune system sends crimson adapted cells that resist your build.
From the Codex
The immune system's answer to a runaway build: when you kill ordinary cells too easily, or barely get scratched, it starts sending cells built to resist you.
Fun fact: Kill the crimson ones first: they're the ones keeping the fight fair.