So, before a large nuclear war engulfed the earth, the USA government ordered two private contractors, Gene-Tek and Atlas Biotech, to create a disease called Hyper Necrosis. It is supposed to make a person decompose while they are still alive and conscious, at least until the early black putrefaction stage. It is transmitted by a modified bacteriophage. It can be transmitted by injection, or through the airborne version. It is also transmitted by contaminated water. So my question is, how could you make a disease that does this in real life?
You are basically looking for how to make wet gangrene: (skip below description if your stomach is weak)
Wet, or infected, gangrene is characterized by thriving bacteria and has a poor prognosis (compared to dry gangrene) due to sepsis resulting from the free communication between infected fluid and circulatory fluid. In wet gangrene, the tissue is infected by saprogenic microorganisms (Clostridium perfringens or Bacillus fusiformis, for example), which causes tissue to swell and emit a fetid smell. Wet gangrene usually develops rapidly due to blockage of venous (mainly) or arterial blood flow. The affected part is saturated with stagnant blood, which promotes the rapid growth of bacteria. The toxic products formed by bacteria are absorbed, causing systemic manifestation of sepsis and finally death. The affected part is edematous, soft, putrid, rotten, and dark.
Lucky you, in the quoted text it is already said it caused by infection of some type of bacteria.
MRSA is an antibiotic resistant form of staph infection. In extreme cases it becomes a flesh eating disease that causes hideous sores and necrosis in it's victims. It is transmitted via skin to skin contact, or contact with items recently in contact with an infected individual. I think you need to dial down your expectations for what a disease can do though. The idea that something is crazy virulent enough to be transmitted via water, air, touch and bodily fluid AND linger as a lethal strain outside of its host within the surrounding environment for decades is basically a planetary extinction level event. Its also not very possible due to some factors I will detail here.
Diseases actually trend towards evolving to become less lethal rather than more lethal. The longer a disease can exist within a host while contagious without killing them the more it can reproduce, in addition organisms develop immunity to the disease over time. It is a dance between natural selection factors, every so often a new strain emerges from a mutation and causes periodic outbreaks that are less severe than the original but still dangerous. Decades after the war symptom-less carriers exist within the human and animal populations. People are by and large immune by this point but children, the elderly, and people with poor immune systems still occasionally catch it and die. Every once in a blue moon a more virulent strain might mutate and cause localized outbreaks within regions.
The ultimate pinnacle of bacterial and viral evolution is not to kill as many hosts as quickly as possible, but to hit a point of equilibrium within its host population. You can brew up very virulent plagues, but keeping them that way long term is not possible, nor is it prudent to use such organisms as a weapon.
I initially thought that a bacteriophage did not make sense as they target bacteria, not humans. But there might be a way. Bacteriophages can code for toxins that increase the virulence of the bacteria they infect.
Staphylococcal toxins that act on cell membranes include alpha toxin, beta toxin, delta toxin, and several bicomponent toxins. Strains of S. aureus can host phages, such as the prophage Φ-PVL that produces Panton-Valentine leukocidin (PVL), to increase virulence. The bicomponent toxin PVL is associated with severe necrotizing pneumonia in children. The genes encoding the components of PVL are encoded on a bacteriophage found in community-associated MRSA strains.
Your phage could infect normal skin bacteria and contain the gene for toxins that produce the effects you want in the skin. The normal bacteria begin to express this toxin and sicken the host. The infected bacteria might actually be crippled by the phage infection and so no longer be able to reproduce - thus infection with toxin-expressing skin bacteria would not be an issue.
That reminds me a lot of Necrotising fasciitis. Some kind of weaponized version of this could do what you need as mentioned below it kills the cells and muscle tissue around the affected area.
Necrotising fasciitis is a rare but serious bacterial infection that affects the tissue beneath the skin, and surrounding muscles and organs (fascia).
It's sometimes called the "flesh-eating disease", although the bacteria that cause it don't "eat" flesh – they release toxins that damage nearby tissue.
Necrotising fasciitis can start from a relatively minor injury, such as a small cut, but gets worse very quickly and can be life threatening if it's not recognised and treated early on.