The Pandemrix vaccine likely "fooled" the brain to attack cells in the brains that regulate sleeping patterns. The cells in question produce a protein called hypocretin, which regulates whether a person is awake or asleep.
Sweden offered its citizens the vaccine against swine flu during the epidemic in 2009-2010, which claimed between nine to 31 Swedes' lives. Experts at the time said they feared the disease would be as big a killer as the Spanish flu in the late 1910s when an estimated three to five percent of the world's population succumbed.
Since the inoculation drive, however, more than a hundred Swedes – many of them teenagers – have developed narcolepsy.
The Swedish Medical Products Agency (Läkemedelsverket) ordered a massive study to determine if the vaccine had any connection to narcolepsy. It compared 3.3 million vaccinated Swedes with 2.5 million who were not vaccinated.
"We can see that over the whole study period we have 126 cases of those vaccinated getting narcolepsy," Ingemar Person, professor behind the study, said in a statement on Tuesday. "There were 20 cases among those not vaccinated. We're talking about a threefold increase in risk."
The scientists at the Stanford School of Medicine have now said that a part of vaccine had some similarities to parts of hypocretin that trigger the immune system. The scientist said that the ensuing reaction meant the body's own immune system could not see the difference between the hypocretin and the parts of the flu virus that the body was meant to attack.
The end result: The body attacked the part of the brain that regulates sleeping patterns.
"We have long thought that auto-immune diseases don't afflict the brain, but that is obviously not correct," Stanford researcher Emmanuel Mignot commented the study.
Narcolepsy is a chronic nervous system disorder that causes excessive drowsiness, often causing people to fall asleep uncontrollably, and in more severe cases to suffer hallucinations or paralysing physical collapses called cataplexy.
Sweden was not alone in facing narcolepsy cases after the jab drive. In Finland, 79 children aged four to 19 developed narcolepsy after receiving the Pandemrix vaccine in 2009 and 2010, while in Sweden the number was close to 200, according to figures in the two countries released last year. Sweden has more than nine million citizens, while Finland has some five million – making the cases approximately proportionate to population size.
In the past years, the Finnish and Swedish governments have both agreed to provide financial compensation for the affected children after their own national research showed a link between the inoculation and narcolepsy.