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Lymphocytic encephalitis is a viral infectious disease caused by the Lymphocytic Choriomeningitis Virus (LCMV). Originally carried by rodents, primarily rats, LCMV is no longer lethal to humans, who have developed an immunity to the virus several hundred years ago.
A beacon, believed to have been left by the Thirteenth Tribe on their way to Earth, was contaminated by LCMV. When a basestar discovers the beacon while exploring the Lion's Head Nebula, the Cylons bring the device on board and unleash the virus. Some time later, a team of Colonial marines discovers the drifting basestar and boards the vessel, finding everything save for a small group of humanoids dead. They take the ill Cylons (a Two, a Four, a Five, a Six, and an Eight) prisoner and return to Galactica just as the basestar's self-destruct mechanism activates and destroys the ship.
Though humans are immune, the virus is highly lethal to Cylons because of a bio-electric component that causes a fatal system error within the host. It is theorized that this system error disrupts the management of a humanoid Cylon's immune system, progressively weakening and eventually killing the infected individual. Furthermore, the Cylons speculate that if an infected host is resurrected, the system error will follow, potentially afflicting the Resurrection Ship and eventually the entire Cylon fleet.
This theory forms the basis of a plan devised by Lee Adama to eradicate the Cylon race. By killing the infected Cylons prisoners near a Resurrection Ship, the aforementioned bio-electrical effect would be spread to all Cylons upon download. Ultimately, the plan is thwarted when Karl Agathon kills the prisoners before Galactica can penetrate the Resurrection Ship's upload radius. Agathon does this despite the risk of being executed for treason, as he feels that the genocide of the Cylon race, despite the fact that they had tried to do the same to mankind, is morally wrong.
During the time that the infected Cylons are held captive aboard Galactica, Dr. Cottle creates a simple vaccine that dramatically reverses the effect of the virus on said Cylons. However, an antibody in their blood breaks down the vaccine's RNA backbone, rendering the treatment useless. Because of that, the Cylons require regular close interval injections of the vaccine, or their condition significantly worsens. If regular injections are provided, an infected Cylon could be kept alive indefinitely.
Unlike the other Cylons Sharon Agathon displays immunity to the virus—although she is exposed to LCMV, the pathogen does not adversely affect her. Cottle postulates that human antibodies were transferred over to Sharon during her pregnancy with her half-human daughter Hera, and that these antibodies are subduing the virus (Torn).