This discussion may contain spoilers!
A horrible thought occurred to me yesterday: What if Sam was actually rabid? This could be how Telltale intends to axe Clementine (assuming they'd do such a ghastly thing), by having her gradually succumb to the virus over the course of the season. Carlos has already proven he's a staggeringly incompetent doctor, so it goes without saying ANY member of the group could die from a poorly-monitored infection, let alone Clementine. Everyone's become so paranoid about zombie bites, they're dangerously absent-minded about the more mundane, day-to-day bacterial/viral threats out there.
Think Telltale couldn't believably pull off something like that? Think again:
*The incubation period for rabies is typically 1–3 months, but may vary from <1 week to >1 year. *