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Why did it take Dr. Abrams so long to realize that isopod parasites were causing the outbreak? He'd been performing surgery and amputating limbs from infected patients, so wouldn't he have noticed larvae and adult isopods inside their tissues?
well, he was an doctor (and I don't know if he was an amputee surgeon either, meaning he probably wasn't experienced at amputating multiple limbs in a short space of time) overwhelmed with patients with a mysterious disease, maybe it honestly took him some time to realize that the isopods were a source and not a symptom because of that.
Donna at one point notes that he treated over three hundred people over the course of the day. Simple answer is, he's just completely rushed off his feet going from one patient to another trying to keep them alive and trying to get some answers from the C.D.C. He announces what he's discovered late in the day when everyone's dead and, for better or worse, he's had time to collect his thoughts.
In fish, tongue-eating louse infestation doesn't cause lesions on the skin. Why are infected humans developing lesions? Are the lesions the result of a bacterial infection from pathogens carried by the isopods? Do the isopods release some kind of chemical that induces an allergic reaction in their human hosts?
it could actually be any number of those things. Since the isopods are a parasite so foreign to human hosts, I suppose getting infected by one could cause all sorts of weird side effects.
Donna mentions that the government gave Claridge money in exchange for its silence. Who could the government give the money to? Nearly all of Claridge's residents succumbed to the isopods, the mayor and police chief died, and no survivors would dream of going anywhere near the town. How could the government make an arrangement with the town if there is no town left?
My guess would be that Donna is just collectively lumping in whoever survived as 'the town'; presumably some town official or councillor who happened to survive took over as Acting Mayor on behalf of the people who didn't die horribly. As for an arrangement, my guess would be something as simple as "Keep your mouth shut and we'll give you plenty of money to move somewhere nice very very far away from the place where nearly all your friends and loved ones died horribly" would probably suffice for most people.