Lymphocytic encephalitis is viral disease that is highly lethal to Cylons. It is an ancient human disease that originally was carried by rodents, primarily rats. A couple hundred years ago, humans developed an immunity to the virus. 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.
The virus is especially virulent in Cylons because there is a bio-electric feedback component to the pathogen. It corrupts how the brain of a Cylon agent manages their immune system. If a Cylon who is infected dies and is resurrected, the disease will follow, infecting the Resurrection Ship and eventually the entire Cylon fleet.
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 believes he can create a simple vaccine that can dramatically reverse to effect on the Cylons. However, they have an antibody in their blood which breaks down the RNA of the vaccine. Because of that, they will need regular close interval injections of the vaccine or they will die.
The strain of the virus that infected a baseship via the Lion's Head beacon is an exact match to one reported over 3,000 years ago, right around the time that the Thirteenth Colony left Kobol (A Measure of Salvation), as the Scrolls of Pythia imply.