Lymphocytic Virus
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The Lymphocytic virus is an ancient pathogen which induces Lymphocytic encephalitis in susceptible individuals/species. A beacon, believed to have been left by the Thirteenth Tribe on their way to Earth, was contaminated by the virus. A Cylon Baseship discovered the beacon, and agents, upon examining it, unknowingly unleashed the virus infecting all of the Cylons aboard.
A bio-electrical feedback effect caused by the virus disrupts regulation of the Cylon immune system, thus the effects of the virus can potentially propagate to other Cylons via the downloading process. This fact formed the basis of a plan devised by Lee Adama to eradicate the Cylon Race. The plan proposed that by killing Cylon prisoners infected with the virus within the vicinity of a resurrection ship, the aforementioned bio-electrical feedback effect would be spread to all Cylons upon download of the infected Cylons consciousnesses.
The plan was ultimately thwarted by Helo, who felt that the genocide of his wife's race, despite the fact that they were Cylons and had tried to do the same, was morally wrong. However, the plan was ill-conceived as there was nothing to stop the Cylon's from destroying the Resurrection ship the moment they realised it was infected. Also, there was a strong possibility that a cure or treatment would have been found reasonably quickly, given the fact that Baltar was immune to the virus and therefore must have been carrying relevant antibodies.
Dr. Cottle exactly matched the virus to one identified 3000 years before, and commented that Humans had developed full immunity to it two centuries ago. This information further consolidated the theory that the beacon was left by the Thirteenth Tribe, as the Scrolls of Pythia imply that their journey to Earth occurred at about the same time.