Bacteria, Cloud Farm
The mega-corporation Synthia has developed genetically modified bacteria which thrive on ultraviolet radiation, and seeded the atmosphere under the ozone holes with them.
As the bacteria flourish in this environment, they coalesce into a foul-smelling sludge which is harvested to make protein-rich food.
 
Humans exposed to the bacteria are quickly and painfully dissolved.
Punisher 2099 #12

Cancer Flu Epidemic
According to Ghost Rider 2099, the cancer flu epidemic ran rampant through Neo-Chicago between 2021 and 2032.
Nothing else is mentioned about the epidemic, but the name hints at a widespread contagious infection with a flu-like virus that also caused cancer.
 
In the real world, we know that certain viruses can cause cancers, though the flu virus is not one of those.
The most common cancer-causing virus is the Human Papillomavirus (HPV), which can cause cervical cancer and throat cancer, among others.
Luckily, there is a vaccine against HPV available.
Ghost Rider 2099 #5

Cyber-Autism
This condition occurs when a person's avatar ("archetype" in 2099 slang) gets stuck or damaged while they are in cyberspace, leaving the physical body with permanent neurological damage.
Doom 2099 #7

Gamma Radiation
Just like in the regular Marvel Universe, exposure to high levels of Gamma Radiation in 2099 will cause an individual to mutate into a more powerful being, albeit one who is green.
The change may be permanent, or it may be intermittent, with the person changing back and forth between normal and mutated forms.
In 2099, this first occurred when studio agent John Eisenhart was exposed to high doses of gamma radiation at the Knights of Banner training facility and became Hulk 2099.
Later, during a major earthquake, a gamma bomb was detonated, exposing everyone in what was left of California to high doses of gamma radiation. This could have led to an interesting storyline, but was barely followed up on — only a few scattered panels in other books here and there.
 
In the real world, exposure to gamma radiation is quite dangerous. At lower doses, it raises the risk of developing cancer, and at higher doses, it causes radiation poisoning and direct tissue damage.
2099 Unlimited #1, Hulk 2099 #10

Identity Fragmentation Syndrome
Identity Fragmentation Syndrome (IFS) is a condition studied by the unethical Dr. Rudolf Menkell.
He believes that the condition is caused by exposure to modern environmental toxins, such as pollution.
Individuals with Identity Fragmentation Syndrome experience physical, temporal, and dimensional changes, including de-evolution to earlier forms of humanity.
To study the syndrome in depth, Dr. Menkell injects his unfortunate patients with highly concentrated toxins and monitors the results. 
Most people with this condition develop multiple personalities and show significantmutations, such as growing extra heads or limbs.
 
The condition is permanent and there is no known cure. Avoiding further toxin exposure can prevent the syndrome from worsening.
Ravage 2099 #16, 17

Induced Repetitive Menemonic Syndrome
In this rare neurological condition, the brain gets trapped in a memory loop.
One known cause is an overdose of the medication Mnemopromethylene, a highly potent sedative that works through the hippocampus (a part of the brain important to memories).
The syndrome can be treated by the drug Nootropine, though the drug is now considered illegal and is nearly impossible to find.
 
I suspect it was supposed to have been called Induced Repetitive Mnemonic Syndrome, but that is not how it is spelled in the comic.
Ghost Rider 2099 #6

Lessa-Six
Lessa-Six is a deadly infectious disease in the future world of Marvel's 2099. The disease is briefly mentioned, and no further information is given.
 
I suspect this is a typo for the Lassa virus, which causes an infection known as Lassa Fever or Lassa Hemorrhagic Fever.
This disease causes fever, weakness, headaches, and muscle aches.
Oral or gastrointestinal bleeding is common, and post-infection hearing loss can occur.
Luckily the disease is only found in certain parts of Africa, and the vast majority of people who become infected survive.
Ghost Rider 2099 #15

Machupo caixao Virus
While under attack by a psychic entity, Dr. Sandoz flashes back to his worst memory: when he was trapped in Bolivia battling a plague caused by the Machupo caixao virus.
This particular infection left its victims mindless, hungry, and in constant pain. Essentially, the Machupo caixao virus turned its victims into angry zombies.
 
The doctor at one point refers to the machupo virus as "Benway's doomsday virus," a reference to Doctor Benway from William Burroughs's book The Naked Lunch.
 
While Machup caixao is fictional, there is an infectious Machupo virus in the real world (no zombies, though).
Machupo mammarenavirus causes Bolivian Hemorrhagic Fever, sometimes called Black Typhus, and is spread to humans from a species of mouse found in parts of Bolivia.
Similar to many viral infections, symptoms start with fever, headaches, and muscle aches. After roughly a week, the infection progresses to what is known as the hemorrhagic phase, and bleeding symptoms such as petechiae (red spots on the skin caused by bleeding capillaries)and bloody noses occur.
Roughly a third of patients will go on to develop more severe bleeding or neurologic symptoms such as tremors or convulsions. The mortality rate is roughly 25 to 30%.
Ghost Rider 2099 #23

Mutt-Town Plague
This plague was a particularly devastating disease in Marvel's frequently apocalyptic world of 2099. The plague wiped out most of Aspen in 2090.
X-Man 2099 #22