With this ability, the basic building blocks of resistance to disease, poison, and illness become linked to conscious thought. Normally fatal infections and diseases are instead quickly overcome and the body builds up a near instant resistance to further infection. Poisons are metabolized with few, if any, negative effects. While this is personally useful, there is another application.
The anti-bodies generated when exposed to various agents can reverse-engineer their immunity and produce the previously defeated disease, allowing it to be transferred to another person or group. The medium of distribution varies depending on the type of infection it's self. The Alternate couldn't make an airborne version of a blood-transmuted disease for example. It also seems to have somewhat of a localized range of control. Those infected with flu, for example, could take days to feel any effects. However because of their control of this ability, the Alternate could instantly accelerate it to it's worst.
However there are documented cases of skilled virogenetics who could combine and mutate strains of disease within their own body to form a new strain. Combined with a remote capacity to control the pathogens they produce, it's possible they could tailor design a new plague. A small side effect is a moderately increased healing capacity within their own body, allowing the Alternate to recover from almost any damage within a time frame between hours and days. It could not continue body function under massive trauma like a true regenerator, but it would mean a gunshot wound wouldn't bleed out over the course of a few minutes (even if the wound doesn't heal for the better part of a day).