It's been a rough year so far for Ionis Pharmaceuticals (IONS 1.46%). Its shares have plunged more than 20%. None of the positive developments achieved by the biotech have been enough to get investors excited.

Ionis announced its third-quarter results before the market opened on Wednesday. And investors probably still aren't too excited. Here are the highlights from the company's Q3 update.

Scientist holding a vial of solution while using a dropper. Strands of genetic material are overlaid on top.

Image source: Getty Images.

By the numbers

Ionis reported revenue of $160 million in the third quarter, a year-over-year decline of 4.7%. This result was also well below the average analysts' revenue estimate of $182.1 million.

The company announced a net loss of $43 million, or $0.22 per share, based on generally accepted accounting principles (GAAP). Ionis posted GAAP earnings of $18 million, or $0.18 per share, in the prior-year period. The consensus Wall Street estimate projected a net loss of $0.09 per share.

Ionis recorded non-GAAP earnings of $5 million in Q3. This reflected a sharp decline from non-GAAP earnings of $39 million delivered in the same quarter of 2019.

The biotech ended the third quarter with cash, cash equivalents, and short-term investments of $2.3 billion. Ionis' cash position stood at $2.5 billion on hand as of Dec. 31, 2019.

Behind the numbers

Biogen paid Ionis $74 million in royalties for spinal muscular atrophy (SMA) drug Spinraza in the third quarter. This total was in line with Ionis' royalties in Q2 but a big drop from royalties of $82 million received in the prior-year period. Spinraza generated $495 million in worldwide sales in Q3, with more than 11,000 patients on the therapy at the end of the quarter.

Ionis reported that its product sales from its other two approved drugs, Tegsedi and Waylivra, totaled $19 million in Q3, up 15% from the previous quarter and 58% year over year. Tegsedi is now available in 15 countries as a treatment for hereditary transthyretin amyloidosis (hATTR) with polyneuropathy, a rare genetic disease. Waylivra was approved by the European Medicines Agency for treating adults with genetically confirmed familial chylomicronemia syndrome (FCS) at high risk for pancreatitis, another rare genetic disease. It's currently available commercially in four European countries.

The company also reported research and development revenue of $65 million, up 15% sequentially but down nearly 10% year over year. Of this total R&D revenue, $44 million came from milestone payments from partners.

Ionis' biggest story of the third quarter, though, was its acquisition of Akcea. CEO Brett Monia stated, "This transaction supports our commercial strategy, further enabling us to maximize the value of our Ionis-owned pipeline."

Looking ahead

For now, at least, Ionis' fortunes depend mainly on Spinraza. Although the SMA drug isn't the fantastic growth driver it once was, Biogen CEO Michel Vounatsos stated in his company's Q3 conference call last week, "Despite increased competition, we believe Spinraza can continue to grow and serve as a foundation of care."

Even with some challenges for Spinraza, Ionis said that it remains on track to be "meaningfully profitable this year." As seen in Q3, a significant amount of the company's revenue will come from its R&D partnerships. The company expects to report results from several clinical studies in the near future.

Probably the most important things to watch with the biotech stock, though, relate to its two other commercial-stage programs. Ionis hopes to expand commercial availability of both Tegsedi and Waylivra in the European Union and Latin America. It also hopes to refile for U.S. approval of Waylivra next year.