We can assume it is not airbone, because in one of the safehouses a safety checklist is crossed out with 'NOT AIRBORNE'.
I also don't think it's some kind of alien meteor, as I cannot think of a way for the survivors to already have an immunity to an off-world virus/pathogen/etc.
The simplest answer, virus spread through bites is probably it. Think a very evovled strain of rabies. Terrorist attack?
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