So far, this is what I have come up with ... EBOLA and Swine Flu and possibly SARS

I will try to update here when I find more info on the other patents.

I imagine that a company like Merck would pay a royalty to the CDC if they produce the vaccine that a patent is held on.

http://www.globalresearch.ca/why-does-the-cdc-own-a-patent-on-ebola-invention/5395727
http://www.nbcnews.com/id/3076748/ns/health-infectious_diseases/t/scientists-race-patent-sars-virus/#.WHByD1P_rb0