Patents can be obtained for things that are not legal. A patent does not mean you can do it. It means you can keep others from doing it. Also, something occurring in nature cannot be patented in its natural state. All of these claims start off with "A method of treating diseases . . . ". That is not at all claiming a natural substance.
Is it legal for a government/company to own a patent?
In the U.S., it is absolutely legal for a company to own and enforce a patent. Every invention must, of course, have inventors (which must be real persons).
According to the following page, the U.S. government owned 47,220 patents between 1969 and 2008, most assigned to the U.S. Navy: