WHITEHOUSE STATION, NJ ( TheStreet) --In the race to market the first next-generation treatment for hepatitis C, Merck ( MRK) is out to an early lead.

Or, as my kids would so delicately put it: " Vertex Pharmaceuticals ( VRTX), you just got burned!!!"

The U.S. Food and Drug Administration accepted Merck's approval filing for its hepatitis C drug boceprevir, the company said Thursday. The news from Merck is a bit of a surprise since the company hadn't previously announced or confirmed that boceprevir had been filed with U.S. regulators.

It's also a tad embarrassing for Vertex, which is still waiting to hear back from FDA about the acceptance of the approval filing for telaprevir, its competing hepatitis C drug. That news should come by Jan. 24, based on Vertex's previous announcement that it filed the drug's application on Nov. 23.

Still, it seems as if Merck beat Vertex to the FDA by at least two weeks.

Merck's boceprevir, therefore, has a chance to grab bragging rights as the first, next-generation hepatitis C drug approved by FDA.

If both drugs are approved, boceprevir could be on the market by the second week of May, or approximately two to three weeks before Vertex has a chance to do the same with telaprevir.

In the grand scheme of things, a two-week head start is trivial. But given Vertex's reputation for supreme confidence (some would say cockiness), the fact that slothy Big Pharma giant Merck has taken the early lead in the hepatitis C drug race is a surprising comeuppance.

Vertex shares were down 19 cents to $36.68 in early Thursday trading.

A Merck spokesman would not confirm the exact FDA filing date for boceprevir. A Vertex spokesman said, "We expect to hear from the FDA this month regarding our request for priority review."

Cheer up, Vertex. The race to approval for a new hepatitis C drug is really just the starting point. What really matters is how each drug fares in the commercial market. Merck's early lead now may not matter much once doctors and patients have a choice of which drug to use.

"We believe this gap in timing could benefit Vertex as it will gain visibility on Merck's pricing of Boceprevir before announcing its own," said JMP Securities analyst Liisa Bayko in a note to clients Thursday morning. "Moreover, the three-week lead time in the marketplace is unlikely to translate into much of a competitive advantage as we believe Telaprevir's compound has a stronger profile with superior efficacy and a differentiated safety profile."

--Written by Adam Feuerstein in Boston.

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Adam Feuerstein writes regularly for TheStreet.com. In keeping with TSC's editorial policy, he doesn't own or short individual stocks, although he owns stock in TheStreet.com. He also doesn't invest in hedge funds or other private investment partnerships. Feuerstein appreciates your feedback; click here to send him an email.

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