Silurian plague

The Silurian plague, (AUDIO: Hosts of the Wirrn) or the Nightmare, (PROSE: Blood Heat) was a disease caused by a strain of deadly bacteria (TV: Doctor Who and the Silurians) or, by another account, a virus. It was used by the Silurians as a biological weapon against primates. (PROSE: The Scales of Injustice)

Origins
The plague was created by the Silurian scientist Bokka K'to (PROSE: The Scales of Injustice) when the Silurians ruled the Earth. They would use the bacteria on the proto-human apes that raided their crop fields and killed millions of them. When the Silurians retreated into hibernation they kept samples of the bacteria. (TV: Doctor Who and the Silurians, AUDIO: Lost in Time)

Uses against modern humans
When the Silurians attempted to reclaim Earth, Morka had K'to infect Major Baker with the bacteria. Baker in turn infected Edward Masters, who later travelled to London, infecting several people at Marylebone station. The outbreak quickly escalated into epidemic across England, with it even reaching France. The Third Doctor later created a cure for the disease from a sample given to him by Okdel L'da. The cure was mass produced and sent out over England, making humanity immune to the bacteria. (TV: Doctor Who and the Silurians) In an alternate universe manipulated into existence by, the plague instead successfully decimated humanity and allowed the Silurians to reclaim Earth. To the humans that survived it, the virus was known as "the Nightmare". (PROSE: Blood Heat)

Later from the Doctor's perspective, but earlier in the total time-scale, a Triad of Silurians awakened from a hibernation facility under Hyde Park in the 1890s planned to use the plague to decimate the human "infestation" of London. They captured three men whom they intended to use as carriers, including a Mr Doyle. However, Vastra took out the Triad before they could send out the prisoners, and the Twelfth Doctor used the antidote he'd developed in his third incarnation on the three prisoners before releasing them. (GAME: Lost in Time)

Other information
C19's vault contained a sample of the virus. (PROSE: The Scales of Injustice)