Day 7: 6:00 AM - 7:00 AM - S7-E23
Plot hole: The head scientist tells Tony that they need Jack's organs to reconstitute that pathogen since there is not enough of it in the sample. Assuming it's a virus, even a small sample could easily be grown in the lab to yield large amounts of the virus. Assuming it's a prion, they don't even need a sample since the could simply build it again from scratch so long as they knew the protein sequence (which is a likely assumption). In either case, Jack is unnecessary.
Chosen answer: Nobody knew, not even the writers, until at least halfway through the season when they were writing the end. They wanted to keep all options open.
Nick N.