Years in the making, the hepatitis C battle can finally move from a battle of clinical-trial-laden press releases to a battle in the marketplace. Vertex Pharmaceuticals (Nasdaq: VRTX) announced today that the Food and Drug Administration approved Incivek. The thumbs-up comes on the heels of Merck's (NYSE: MRK) approval of Victrelis a little over a week ago.

The early winner will be the company that gets in front of doctors and makes it easy for patients to get reimbursement through their insurance. Merck has more experience in both areas than Vertex does, but Incivek means a lot more to the small biotech than Victrelis means to Merck. What it lacks in experience, Vertex may be able to make up for by throwing additional people at the problem. In Europe, once Incivek is approved there, the battle will be of equal-sized foes since Vertex licensed the EU rights to the drug to Johnson & Johnson (NYSE: JNJ).

The midterm battle will still be over data. And Incivek still has the upper hand here. It cured as much as 79% of patients new to treatment, compared to Victrelis' 66%. The trials aren't completely comparable since the placebo group in the Incivek trial fared better than the comparable group in the Victrelis trial, but doctors have been known to overlook that important fact. Both labels include information about response-guided therapy, which allows doctors to stop pegylated-interferon and ribavirin taken with them if the patient shows an early response. Incivek's data support stopping the drugs, which have nasty side effects, after 24 weeks, while patients taking Victrelis will have to stay on the drugs for 28 weeks if the doctor is following the label.

Who will win the long term? There won't be one -- at least not as single agents: Victrelis vs. Incivek. The drugs are the first of the next-generation hepatitis C treatments, but there are plenty of drugs from Gilead Sciences (Nasdaq: GILD), Bristol-Myers Squibb (NYSE: BMY), Pharmasset (Nasdaq: VRUS), and others coming up behind. They'll be combined with Victrelis and Incivek, first to remove pegylated-interferon and then to shoot for increased cure rates.

Investors need to keep one eye on sales data and the other on upcoming competitors and whether Merck and Vertex are forming partnerships with them.

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