Thoughts from a few days ago about the nature of the infection and the US's response:
1) Coach, Ellis, Rochelle, and Nick are all immune. The military identifies them in different terms ("Are you equipped for carriers?"). From the messages left behind by others, carriers are immune to the infection but can still pass on the infection to other people. The survivors of L4D2 (and probably the classic survivors of L4D1 too) are carriers, and probably unintentionally infected many people around them.
2) It would appear the US military was more prepared for this than CEDA was, being aware of such things as the nature of immunity and implementing tighter and more effective quarantine strategies (They still retained use of their fighter jets, helicopters, and land vehicles). There are signs of military abandonment of positions and the like, but it looks orderly, they retreat when necessary and keep the fight going. All of the CEDA checkpoints you see in the game are disaster zones, you can see evidence of total ruin and regular, uninfected people rushing the barricades in panic and being gunned down. You can see the rows of orderly body bags CEDA was laying down (They probably ran out of time to retrieve the rest of the bodies). In fact, the only significant CEDA contribution to the war was the extraction and utilization of the infected bile.
3) The military rescued the survivors at the end of The Parish, which indicates that they waited for some reason. Not for the reason that Nick stated ("Or maybe they'll line us up against a wall and shoot us"), because if the Army had wanted that they could have done so at any point the survivors were running across the bridge. They had jets in the air, the bridge appears to have been already wired for demolition, etc. It appears to be a legitimate evacuation, but not because the Army was that desperate for people, they had a Chopper at the end of the bridge anyway and ten minutes allotted before departure.
4) It seems quite transparently clear that any humans born after this war will have a good chance of being immune. Carriers will be the overwhelming majority of the surviving population and their children will likely acquire their immunity. Non-immune survivors won't have as many children due to being simply outnumbered, and over time their vulnerability will be lost to future generations. Quite simply, the carrier is the "new" face of human civilization.
