BioCryst Pharmaceuticals, which cut half its work force in December in a cost-cutting move, isn’t closing the books on its proposed intravenous flu treatment known as peramivir.

While the RTP-based drug firm said Monday that it had received a “stop-work order” from the federal government for portions of the federally funded ($235 million) peramivir project, it also said some work would be supported.

BioCryst (Nasdaq: BCRX) also is continuing to talk with the Food and Drug Administration about how peramivir might be advanced in testing. 

In November, BioCryst terminated a Phase 3 trial.

“We are encouraged by these recent communications, and we look forward to advancing our peramivir discussions with the FDA and [Health and Human Services],” BioCryst CEO Jon Stonehouse said in a statement.

“Our ultimate objective is the approval of peramivir as an intravenous treatment option that could benefit patients in the United States,” he added.

“The Stop–Work Order is understandable, as it focuses the scope of reimbursable activities to those that are essential and supportive to continuing regulatory communications, with the objective of preparing an NDA [new drug application with the FDA] submission. If the conversations with the FDA and [Biomedical Advanced Research and Development Authority]/HHS are successful, BioCryst stands ready to file an NDA for peramivir as soon as feasible.”

BioCryst said it expects to meet with the FDA in the second quarter. 

The news set BioCryst shares sharply higher Monday. After closing Friday at $1.19, shares opened up 35 cents at $1.54 and reached a high of $1.63. However, shares faded later to close at $1.38.

The 52-week high for BioCryst is $5; its low in that time frame has been $1.08.

The company recently reported that its cash reserves declined to $37 million even though it cut losses for 2012.

In its quarterly and annual earnings report, BioCryst reported a loss of $11.1 million, or 22 cents per share, in the fourth quarter. That was a decline of $2.1 million from a year earlier. Revenues dropped to $4.1 million from $5.2 million a year earlier. 

The company also took a $1.8 million charge as part of the layoffs and restructuring announced in December. 

For the year, BioCryst lost $39.1 million, down from $56.9 million in 2011.

Revenues increased to $26.3 million from $19.6 million. The company also cut its research and development spending to $51.5 million from $57.2 million. 

The company said in December that it was cutting 38 jobs. BioCryst also recently called off a proposed merger with a California firm.

BioCryst also is working on antiviral and hepatitis C programs.