The Nanoprobe virus was a new type of nanotechnology developed by the Borg Collective in order for it to serve as a new method of assimilation of highly resistant species.

It was developed in the year 2375 under the supervision of the Borg Queen and involved a unique programming of nanoprobes in order to accomplish this task. The Borg intended to use it against the resistant natives of Sector 001 who had thwarted previous attempts at assimilating their culture and technology. In order to get a better understanding for the role, the Borg Queen abducted Seven of Nine from the USS Voyager and intended to get the former Drone to program the nanoprobes though she ultimately refused and was later saved by her comrades. (VOY episode: "Dark Frontier")

Despite this being the case, an outbreak of assimilated beings occured on Earth in 2378 which was attributed to being the result of the return of the USS Voyager crew. However, the truth of the matter involved a conspiracy involving Starfleet Intelligence Director of Covert Ops Brenna Covington who intended to transform herself into a Borg Queen as well as numerous inhabitants on Earth. The process was flawed due to the Borg equipment involved and only turned random selection of people into Drones based on certain characteristics. Ultimately, Director Covington was defeated and killed with the crisis ending the threat posed by the nanovirus. (VOY novel: The Farther Shore)

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Later, during a renewed Borg offensive in 2409, the Collective began to deploy their assimilation nanovirus with the intention of transforming entire sectors into Borg drones. This proved to be a new and deadly threat to the United Federation of Planets who had a Starfleet team working on a counteragent at Kessik IV where they intended to get samples. Contact was lost with the research team which led to Admiral D'Vak of Battle Group Omega assigning missions in order to retrieve the scientists so that a cure could be used against the nanoprobe virus. (STO video game: Asset Recovery)

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