I assume you are referring to JCV leading to progressive multifocal leukoencephalopathy (PML). Some patients have been treated effectively with highly active antiretroviral therapy (HAART).
Here is a fairly recent article about it, in the context of HIV.
Our brains are our most important organs so I understand your fear of an intellectual decline. I think you would do well to seek out an expert on the disease for a second opinion.