Plot hole: The director of CDC informs the cabinet that the biological weapon at hand is a "prion variant indigenous to the East Congo" and refers to it as a "strain". A prion is a protein, not a bacterium, so it cannot be indigenous to a certain place and cannot belong to any strain. More importantly, prion diseases are not known to be transmissible in an airborne fashion (Mad Cow and Kuru, also prion diseases, are transmitted by ingestion), which kinda takes the air out of the threat. However, the description of prion disease symptoms and the example of Creutzfeldt-Jakob disease as being caused by prions are accurate.
Plot hole: Jack is informed that experimental treatment using stem cells from a genetically compatible donor is being developed that might be able to cure his condition. Stem cells are used to treat diseases where a cell type in the patient's body malfunctions, such as insulin-producing beta cells in diabetes, or where injury has killed cells that do not regenerate, such as in spinal cord injury. In these cases stem cells can replace the damaged cells and make sense as therapy (bone marrow transplant as leukemia treatment is one real such treatment). Prions (which is what the show calls the bioagent) and bacteria (which is how the show describes the bioagent) cannot be cured by stem cells, since the cause of the disease is not damaged or defective cells. Even if the disease damaged brain cells and stem cells cured that, it would resume later since the causative agent is still there.
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.
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