On the surface, it looks like Biogen Idec (Nasdaq: BIIB) is handling the entrance of Novartis' (NYSE: NVS) new oral multiple sclerosis drug, Gilenya, quite well. Fourth-quarter sales of Biogen's injected and infused competitors were quite robust. Avonex sales were up 10%, and sales of Tysabri, which Biogen sells with Elan (NYSE: ELN), increased 12% year over year.

The real picture is a little bleaker. While sales of Avonex were up 9% in the U.S., the revenue bump was entirely due to a price increase. The number of vials it sold actually decreased 4% year over year. Price increases can only last so long.

The number of patients taking Tysabri increased, but the growth has waned considerably. The slowdown seems to have little to do with Gilenya. Novartis estimates that only 5%-7% of patients starting on Gilenya switched from Tysabri. While it's certainly more convenient to take a pill than go into a doctor's office for an infusion, Tysabri has better efficacy data, which is keeping most patients on the drug.

The more likely reason for the slowdown in Tysabri sales growth is the increasing number of patients getting progressive multifocal leukoencephalopathy, a potentially deadly brain infection. To woo more patients away from Teva Pharmaceuticals' (Nasdaq: TEVA) Copaxone, Bayer's Betaseron, and Rebif sold by Merck KGaA and Pfizer (NYSE: PFE), Biogen and Elan need to stratify the risk and then attract the patients that are at the lowest risk for getting PML.

The launch of an assay to determine if a patient has the JC virus, which causes PML, should help considerably. Biogen and Elan still need clinical trial data from two trials -- aptly named Stratify-1 and Stratify-2 -- to confirm that a negative JC-virus status decreases the risk of getting PML, but they do have data suggesting that the corollary is true: All 22 patients that got PML for which the companies had pre-PML samples tested positive for the JC virus.

If Biogen can decrease patients' worries about getting PML and reaccelerate Tysabri sales growth, competition from Gilenya will be a minor dent in its revenue growth.

Interested in keeping track of Biogen Idec and Elan as they try to reaccelerate Tysabri sales? Click on their names to add them to My Watchlist, which will help you keep track of all our Foolish analysis on the companies.

Pfizer is a Motley Fool Inside Value pick. Elan is a Motley Fool Rule Breakers recommendation. Novartis is a Motley Fool Global Gains choice. The Fool owns shares of Teva Pharmaceutical Industries. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors.

Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Fool has a disclosure policy.