A patient taking Novartis’ multiple sclerosis pill Gilenya (fingolimod) has been diagnosed with a rare brain disease, the drug giant has said.

However, the company is emphasising that the patient had previously been treated with Biogen Idec/Elan’s MS drug Tysabri, which has already been associated with the rare disease progressive multifocal leukoencephalopathy.

According to Novartis, “the current assessment is that Tysabri is the drug most likely associated with this case of PML. However, a contribution of Gilenya to the evolution of this case can’t be excluded.”

This is a setback for Novartis, which had been pinning its hopes on Gilenya, the world’s first oral treatment for multiple sclerosis. Analysts have estimated sales of the drug could be in the realm of the billion dollar mark while the National Institute for Health and Clinical Excellence recently reversed an initial decision and is now recommending the drug for use on the NHS.

However, Gilenya has been marred with safety problems – one person has already died in the USA just 24 hours after starting treatment, and there have been other unexplained deaths and reports of heart issues associated with the drug.

The European Medicines Agency is currently reviewing the drug’s safety profile and is due to make a ruling on 20 April.   

“The development has to be taken seriously, but the question is more whether this is a trend, with a second or even third case coming up in the next few weeks,” analyst Andrew Weiss, of Vontobel in Zurich, told the Wall Street Journal. “The timing is unfortunate, with the pill’s risk-profile under investigation and certainly, there was no need for a second problem.”

Novartis said it was not aware of any confirmed PML cases associated with taking Gilenya in patients who had not also been treated with Tysabri.

Tysabri’s manufacturers have denied commenting on the role either drug has played in the case.