Nanoprobe virus

The nanoprobe virus was a technology developed by the Borg Queen in 2375, as a way to gradually assimilate the Human race after the failure of two direct attempts. The plan involved detonating a biogenic charge in Earth's atmosphere, upon which the virus would then begin to infect all lifeforms, primarily species 5618: Humans. The process of assimilation would be so gradual, that half the planet's population would be turned into drones by the time anyone realized what was happening.

The Borg Queen revealed the plan to an abducted Seven of Nine and ordered her to program the nanoprobes, due to her knowledge of humans. However, Seven refused. 

In 2376, The Doctor's daydream program included a scenario where a Borg sphere deployed an "assimilation virus" against the USS Voyager. It infected Harry Kim, Chakotay, and Tuvok, rapidly turning them into drones. With the bridge crew incapacitated, the Emergency Command Hologram sprang into action and saved the day. 

Apocrypha

 * In the novelizations of the events immediately following, it is revealed that the nanoprobe virus was brought to Earth and rapidly infecting the population.