I doubt the virus is still around 2-3 months later in their bodies. These effects are likely due to the hyperinflammation triggered later on during the course of the disease, if I am to follow the mechanism described in the well-detailed paper in Cell from a few weeks ago.

The virus is still a coronavirus (neural invasion, also noted for SARS-CoV-2, is also a feature of regular coronaviruses). These effects, although possibly severe and worthy of concern, are second-order effects.