It looks as if Gilead Sciences Inc. will have to roll the dice on trial next month if it wants to protect the patent rights to its blockbuster hepatitis C treatment. It wouldn’t be the first time.

U.S. District Judge Beth Labson Freeman of the Northern District of California on Tuesday rejected Gilead’s summary-judgment motion of patent invalidity against Merck & Co. Inc., saying there’s a genuine dispute over whether compounds patented by Merck in 2002 were recognizable as potential treatments for liver disease.

That leaves the parties headed for a March 7 trial.

“The evidence presented by Merck demonstrates that a skilled artisan could have accepted without … question the alleged utility of the asserted patents,” Freeman wrote, rendering summary judgment inappropriate “at this juncture.”

Freeman also granted summary judgment to Merck on infringement based on Gilead’s concession.

The dispute is over Gilead’s sofosbuvir compound, acquired with the company’s $11 billion purchase of Pharmasset Inc. in 2011. Sofosbuvir is a key ingredient in Gilead’s Sovaldi and Harvoni medications, which together generate some $20 billion a year in sales.

Roche Pharmaceuticals previously challenged Gilead’s rights to sofosbuvir, but Gilead beat back the claims in a trial before private arbitrators. Gilead has also defeated patent attacks on sofosbuvir by Merck and its subsidiaries in Europe and Canada.

But so far the company has faced a bumpier road in U.S. litigation with Merck. The companies are thrashing out patents before Freeman and U.S. District Judge Leonard Stark in Delaware. In December, Stark issued a claim-construction order adopting all of the positions advanced by Merck subsidiary Idenix.

The issue before Freeman was whether Merck’s 7,105,499 and 8,481,712 patents are invalid for failing to establish practical utility under Section 112. Gilead and its Fish & Richardson attorneys argue that Merck and partners patented only a vague procedure without any biological activity data, then updated the application once Pharmasset discovered the specific nucleoside compound that remedies hepatitis.

Merck countered that given the state of hepatitis treatment in 2002, the claim specification did not require hard data to establish utility. Merck and its hepatitis treatment partner Ionis Pharmaceuticals Inc. are represented on the motion by Hughes Hubbard & Reed; Fried, Frank, Harris, Shriver & Jacobson; and Durie Tangri.

Freeman was sympathetic to Gilead’s arguments at a December hearing, according to a published report, but only to a point. “I think you’re giving me a strong case on summary judgment,” she reportedly told Fish & Richardson partner Jonathan Singer, “but I’m not sure it’s strong enough to succeed.”

Freeman continued that theme in Tuesday’s order. “According to Merck’s expert, the specifications of the asserted patents contained enough information for one of ordinary skill to understand the utility of the claimed methods and compounds,” she wrote, “and there was ample data at the time suggesting nucleoside analogs could treat HCV.”

That is enough to put the issue before a jury, she concluded in Gilead Sciences v. Merck. In granting summary judgment of infringement, she emphasized that ultimate liability remains unproven “because of Gilead’s outstanding invalidity defenses.”

Hughes Hubbard partner Stephen Rabinowitz argued the motion for Merck.

Contact the reporter at sgraham@alm.com.