A flagellated parasite that can cause subacute encephalitis, and most likely affects the majority of the world's population at some time in their lives, is the protozoan .

The protozoan that fits the description you provided is Toxoplasma gondii. This parasite is indeed flagellated and can cause a form of encephalitis, particularly in individuals with weakened immune systems. It's also estimated that up to one third of the world's population has been infected with Toxoplasma gondii at some point in their lives, often without showing any symptoms.

The protozoan that fits the description given is Toxoplasma gondii. This parasite is indeed flagellated and can cause subacute encephalitis. It is also estimated that it affects a large portion of the world's population at some point in their lives, often without causing noticeable symptoms.