Well, you were over-complicating again there.
"This virus works on a similar principle. The virus is a true virus. It is biological. It uses the Matrix as a delivery system. Those that go near the Carrier become infected inside the Matrix. But the virus has been designed so that it is very mentally... strong? Very real. So real, in fact, that within mere minutes of the infection in the Matrix, the real world body becomes infected. And that is in fact the killer. The more the real world body falls sick, the worse you feel inside the Matrix, and the more infected the real world body becomes. In a short amount of time, the real world body dies.
"And that is how it kills. It is entirely harmless to Artificial Intelligences."