1. I doubt the air circulation system for the tunnel was working or even had worked for a long time. The oxygen content of the air was probably pretty low even before the cave-in. So I can buy that scenario, with only a little suspension of disbelief.

The real problem with the influenza story-line is that almost everyone in the house should have become ill. It was an extremely virulent outbreak. 80-90% of the household should have gotten sick and 1/4 to 1/2 of them should have died. I suspect that would have been a bit much for what the show is, though.