The clinical course and the prognosis vary from patient to patient, ranging from a mild form with complete recovery (10%) to a severe form with a high mortality (30%). Most of the survivors are left with neurological sequelae (e.g. motor deficits, epilepsy, developmental delay). Poor prognosis is associated with delayed diagnosis, involvement of brainstem (part of the brain that connects the brain with the spinal cord and controls the heart and lung functions) and recurrent episodes. Recurrent or familial ANE without the RANBP2 mutation has a more severe outcome and greater predilection for males than that with the RANBP2 mutation. This suggests that there are unknown gene mutations linked to ANE.ANE has the 2nd in the mortality rates and is another distinct neurological complication of influenza infection with reported mortality rates of 30%–40% second only to historical descriptions of encephalitis lethargica (60%) among neurologic complications of influenza.

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