The "Manhattan" virus (MV), "God Bug", "RapCer" "Softball" or spore is an engineered virus created by the Ceph.
The exact vector of the disease is unclear, however it is likely caused by exposure to nanite spores which are prevalent on Manhattan Island during the time of Crysis 2's main story line. The disease progresses in stages, as evidenced by containment personnel denying containment access to a man trying to reach his healthy wife on the basis that he was showing signs of being infected with "stage 1" of the virus during the evacuation mission at Central Station. Accurate laboratory testing does exist to verify MV infection. Medical professionals state that Tamoxifen and other antiviral drugs were of limited effect in treating MV. While treatment with antivirals did slow the disease process, the process inevitably resumed. Being an engineered and likely dynamically reprogrammable nano-virus, treatment for such an adaptable disease would be largely ineffective in the long term.
Later stage victims can be seen throughout the game in near-comatose states, often with strange organic growths (mycelia; see below) erupting from the lower abdomen and pelvis. In one of his first communications with Alcatraz, Jacob Hargreave asserts that the virus is but a part of a sophisticated organic recycling strategy employed by the Ceph to re-purpose human biomass. Tiny insectoid Ceph drones called "Ticks" can be seen harvesting Manhattan Virus infected tissue from dead or severely infected virus victims throughout the game. The re-purposed tissue is used by the Ceph directly, something which Alcatraz and Nathan Gould both discover when Alcatraz is sent to investigate a downed Ceph ship in search of alien tissue samples, only to find that supplemental tissue from the ship was in fact of human origin. The potential applications of MV-infected biomass are largely unexplored within the main story line. In Legion, however, it is speculated that the aliens' interest in Earth is on a purely scientific level; that is, they could be looking for unique, surprising proteins that evolved in Earth biota. If this is the case, the transported human tissue could be used as research material.
Whether the Manhattan virus and the nanospore-based bio weapon deployed by the Ceph Spires are essentially the same or not is a matter of conjecture. It is possible that both effects are caused by the same nanite agent and that the near instant fatality of spire exposure to unprotected humans is due to the greatly increased concentration immediately surrounding the spires. It is also possible that the same nanite spore is capable of being programmed to behave in many different ways perhaps even in response to changing conditions. Since the Manhattan Virus appears before any Ceph bioweapon spires were deployed, a second vector must exist for the initial infections prior to the first stages of the Ceph invasion. Little direct information about the Manhattan virus is given during the game and what is known is mostly assembled from small snatches of dialogue and direct observation.
In Crysis: Legion, the information available about the MV is slightly increased. It is described as an "Engineered agenetic bioweapon" and a "monogenerational saprophyte". MV infection appears to not be transmissible between humans, as the only people to display symptoms are those who came into direct contact with the viral spores (an instance is described where a little girl remained unaffected despite spending several hours in the presence of her infected mother). It can also not be contracted by most animal species, with the only vulnerable hosts being humans and higher apes. The virus prefers the wet parts of the body, such as the mouth, eyes, and open wounds. The infection usually consists of the spreading of fleshy tumoral "mycelia" throughout the body (starting in the aforementioned areas), which eventually cause death by organ constriction or blockage of the airways. It is revealed that in the middle stages of the infection, the virus also attacks the human brain and "re-wires" in it a compulsive desire for the host to move towards locations controlled by the Ceph (likely to ease the process of extermination). People affected by this "wanderlust" are in a state of deep religious reverie, although their other cognitive functions are not actually impaired (they can talk at length about what they see and feel). It is also commented that, given its lack of contagiousness, as well as the relatively short range of the dispersal spears, the virus might be a sort of "beta" version, undergoing a controlled trial-run in New York in preparation for a worldwide dispersion of the perfected, fully contagious product (which could be what the Central Park tower was meant to do).
It is speculated that, since practically all of the recovered Ceph technology (including the Nanosuits, which are based on stolen alien technology) has some sort of receptor or interaction with the viral spores, the MV might not be so much a bioweapon as a programmable terraforming agent (a "portable ecosystem", or perhaps an "external immune system") which the aliens have programmed to infect and kill humans.