I was just discussing prions. Other pathogens do seem to present a bigger risk. I don't think anything would have 100% kill rate. Even weaponized microbes have like 99.8% or something. That still leaves about 16 million people. Plus there's all those preppers with their bunkers, some uncontacted tribes, people who live in isolated areas. Then it becomes more of a matter of how to organize, do they have the knowledge to survive in those types of conditions, etc. The species will survive, but it will be a very different world.
