Almost any material is eligible for submitting an application. In fact, government-sponsored commercial research (through the federal SBIR programs) carries a mandate as part of the terms of funding that novel inventions created under the research be patented. As part of this mandate, the government retains certain rights to the invention (this prevents a commercial researcher from re-licensing back to the government something that the government had already paid to produce). That is where many of those clauses come from. This patent, however, has the U.S. government as the sole assignee, which is an indication that the work was likely performed entirely by federal employees at a federal laboratory.
Examiners at the USPTO decide what is allowable in the claims of a grant, according to the MPEP. After a lengthy period of prosecution (nearly four years), the examiner issued a Final Rejection of all claims in this application on February 12, 2015. There were several reasons for the rejection, but the reason pertinent to your question is described by the examiner as follows (emphasis is mine):
Claims 1, 3, and 20 are rejected under 35 U.S.C. 101 because the claimed invention is not directed to patent eligible subject matter. Based upon an analysis with respect to the claim as a whole, claim(s) 1, 3, and 20 do not recite something significantly different than a judicial exception. The rationale for this determination is explained below: The hEbola virus of claim 1 is a natural product, and is judicially excepted from patent eligible subject matter, regardless of its isolation by applicants. Since killed viruses exist in nature, claim 3 also involves ineligible subject matter. The composition of claim 20, containing the virus or a protein extract therefrom in combination with a pharmaceutically acceptable carrier, does not markedly change the structure of the naturally occurring products, and therefore is also ineligible. This is a new grounds of rejection.