Final answer:
The flagellated parasite that causes the majority of subacute encephalitis cases is Trypanosoma, specifically Trypanosoma brucei, which is responsible for African sleeping sickness.
Step-by-step explanation:
The protozoan Trypanosoma is a flagellated parasite that causes the majority of subacute encephalitis cases, specifically African sleeping sickness. Members of the genus Trypanosoma are notorious for causing diseases like sleeping sickness and Chagas disease, both are transmitted through insect vectors. Trypanosoma brucei, specifically, is transmitted by the bite of tsetse flies in Africa, causing African sleeping sickness, which can be fatal without proper medical treatment. This protozoan is known for its ability to evade the human immune system through antigenic variation, which allows it to continue to infect the host by changing its surface glycoproteins with each infectious cycle, thus avoiding detection. The symptoms include confusion, difficulty sleeping, lack of coordination, and if left untreated, it can cause the patient to lapse into a coma and eventually die.