Biogen (BIIB -0.92%) announced its third-quarter results on Wednesday. Most of the headlines covering this update focused on the company's better-than-expected revenue and earnings.

It's certainly true that Biogen did top analysts' estimates on both the top and bottom lines. However, the bar for doing so wasn't high. Even with its "positive" results, Biogen's revenue fell 18% year over year while its earnings were more than halved from the prior-year period.

Put into context, the biotech's quarterly update actually wasn't anything for investors to cheer. Instead, there were three big problems with Biogen's Q3 results. 

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1. Multiple sclerosis franchise sales sinking 

Biogen's multiple sclerosis (MS) franchise remains the cornerstone for the company despite its efforts to expand into other indications. Its MS drugs contributed nearly two-thirds of total revenue in the third quarter.

The challenge for Biogen is its MS franchise sales continue to sink. In the second quarter, the company's MS drugs generated $1.8 billion, down 18% year over year. 

Unsurprisingly, the primary reason behind this decline is generic competition for Tecfidera. Sales for the drug in the third quarter plunged nearly 48% year over year. Although newer drug Vumerity, which is similar to Tecfidera, picked up some momentum, it wasn't nearly enough to offset these lower sales.

And Tecfidera wasn't the only weak spot. Sales for interferon drugs Avonex and Plegridy tumbled 21% and 49% year over year, respectively. 

2. Dismal launch for Aduhelm

Biogen CEO Michael Vounatsos said in the company's Q3 conference call, "We are obviously disappointed with the delayed uptake of ADUHELM in the U.S." There's good reason for that disappointment.

The commercial launch for the Alzheimer's disease drug has been a dismal one so far. Biogen reported sales for Aduhelm totaled only $0.3 million in the third quarter, down from $1.6 million in the previous quarter. This decrease resulted from wholesalers drawing down their inventory of the drug that was purchased in Q2.

Vounatsos especially blamed "the lack of clarity on reimbursement" as a factor in delaying patient access to Aduhelm. However, Biogen also faces significant challenges in convincing physicians that the drug is effective after the controversy over its U.S. approval. Reports of potential safety issues with Aduhelm haven't helped those efforts.

3. Potential catalysts still months away

The good news is that there are some upcoming potential catalysts for the biotech stock. The bad news is that those catalysts are still months away.

In particular, Biogen thinks that a Medicare National Coverage Determination (NCD) will boost sales of Aduhelm. This NCD will cover the entire class of monoclonal antibodies that target amyloid plaques in treating Alzheimer's disease. A draft decision is expected in January 2022 with a final decision roughly three months later.

Biogen's partner, Eisai, initiated a rolling submission for U.S. approval of lecanemab in September. Lecanemab is similar to Aduhelm but could have a more attractive safety profile. However, Alfred Sandrock, Biogen's head of research and development, doesn't expect Eisai's rolling submission to be completed until "sometime in 2022." 

The company also has another pipeline candidate that could be relatively close to the finish line. Biogen teamed up with Sage Therapeutics last year to develop and commercialize zuranolone. The two companies plan to file for approval of the drug in treating major depressive disorder in the second half of next year. A follow-up filing for approval in treating postpartum depression is expected in the first half of 2023.

In the meantime, Biogen could get a little help from Vumerity and Byooviz, its newly approved Lucentis biosimilar. But it seems likely that the stock could muddle along for a while.