Some aspects of the tropical viral disease Chikungunya are unknown, in particular the long-term persistence of symptoms in more than half of the cases.

Although many of those infected (around 3 million per year worldwide) make a full recovery after a week or so, others can still suffer from intense joint-pains months or even years later.

It's not known whether the ongoing symptoms are due to neurological damage done by the virus at the time of infection, or whether the virus remains in the body, continually causing the symptoms.

Currently, the cause of these chronic symptoms is not fully known. Markers of autoimmune or rheumatoid disease have not been found in people reporting chronic symptoms. However, some evidence from humans and animal models suggests chikungunya may be able to establish chronic infections within the host. Viral antigen was detected in a muscle biopsy of a person suffering a recurrent episode of disease three months after initial onset.

Source : Wikipedia