Oasis Retrovirus
A virus created by Ryu Kobolt, a mutant and the leader of the hidden city of Oasis.
The retrovirus was designed to wipe out all human life on Earth. Kobolt believed that the planet could not support ten billion people, especially with wars, pollution, and ecological devastation.
His "short-lived but lethal" virus would ravage the world while Kobolt and his chosen followers would remain safe hidden in suspended animation beneath the city of Oasis.
In several hundred years, after the virus had died off and the Earth had recovered, his people would leave their frozen sanctuary to a healed Earth.
X-Men 2099: Oasis

Osiris Plague
A viral infection developed by the Osiris Corporation to take down one of its competitors. Mentioned once briefly, no more is known.
Doom 2099 #8.

Passive Neurosis
Passive neurosis is more of a legal concept than a medical condition.
It is defined as a condition where a person shows significant mood swings — depression, anxiety, or violent behavior — to such a point that it negatively affects the people around them.
 
People judged to have this condition by a court of law can be involuntarily committed to a mental institution.
The diagnosis requires four different individuals submitting proof of a person's severe negative moods.
 
Paul-Phillip Ravage's sister uses this legal ploy to get him committed to a mental facility, so she can assume control of the family company.
Ravage 2099 #17, 18

Phone virus
Created by scientists at Macroware, a subsidiary of Alchemax, this software creates a mental virus that can be transmitted via videophone, telephone, or even a saved message.
Someone exposed to this virus can be compelled to follow simple instructions, even at the cost of their own life. The virus was only used twice, and it was destroyed with the deaths of its creators.
2099 Unlimited #2

Predator-Linked Neural Trauma
A cadre of the very rich in Transverse City have started their own competitive hunting club.
They genetically engineer monsters, known as "Predators," which look like a cross between creations of H.R. Geiger and H.P. Lovecraft.
The human hunters neurologically link to these Predators and use them to track and kill unwary victims, trying to rack up as high a score as possible.
 
If the Predator is killed while still neurologically linked to a player, that person suffers immediate neurological damage which causes amnesia, aphasia (in this case, the inability to form coherent words), and uncontrolled psychotic violence.
Ghost Rider 2099 #11

Surge
An illegal virtual reality program that is targeted against another person's avatar.
The program fries the victim's brain, destroying their avatar as well as killing them in the real world.
Spider-Man 2099 #25

Tailored virus
Used to introduce metagene factors into an individual"s genetics using DNA recoding in the 24th and 25th century.
People with these genetic factors gain superpowers and are considered "transhuman."
By 2399, the majority of the population has become transhuman.
2099: Manifest Destiny

Techno-Organic Virus
Quote: "It's a virus that turns regular, healthy cells into living circuitry!"
This techno-organic virus is used by the alien Phalanx to overwrite the genetics of other species and absorb them into the Phalanx's hive mind.
This is not like the Borg from Star Trek, where pieces of the individual are replaced with machinery, but instead the entire person becomes living circuity under the control of the Phlalanx.
 
The virus was first seen in the New Mutants (the character Warlock is composed of techno-organic living circuitry, but has escaped to our planet).
The Phalanx and their virus have returned to bedevil the X-Men repeatedly. 
In the world of 2099, a planetoid sent by the Phalanx orbits the Earth, waiting to unleash the virus upon what remains of the world's population.
A team of top scientists including Dr. Doom, Miguel O'Hara, and Xina Kwan work to prevent this from happening and protect the Earth.
 
This particular virus is called the "Transmode Virus" or the "T.O. Virus."
 
Kwan mentions that she's familiar with techno-organic viruses, but has not seen one as virulent as the Transmode Virus, suggesting there are other techno-organic viruses in 2099.
 
Special electronic dampening technology can — at least temporarily — protect against infection with the virus. Spider-Man 2099 has a costume equipped with this technology to protect himself when fighting the Phalanx.
World of 2099 #2, #4