I thought about posting this in S&T, but there's too much speculation, I think. I'm still formulating ideas anyway. Plus, I don't know half of what I'm talking about is.
I was thinking about infections and viruses in BIONICLE. For the most part, the word "virus" is used in BIONICLE to refer to something the Brotherhood of Makuta used in experiments. "Infection" and the only real mention of illness (in MNOG) involves infected Kanohi.
My idea is that viruses in BIONICLE are similar to computer viruses, that infiltrate a computer and can pretty much take over. Given that much of BIONICLE now is compared to computer programs and so forth, this makes sense.
Viruses, when used by Makuta, "program" the Rahi they are making. One virus will give them a more aggressive program, one will give them a more domesticated program, and so forth, but they can also be used to alter the program of other creatures, as shown when Teridax used viruses to put Mata Nui into "sleep mode", and essentially shut him down, much like a computer virus.
Makuta viruses could also be used to add tissue to whatever Rahi they are creating, much like a biological cancer virus reprograms cells to make a new type of tissue (even though in the Real World, tumors are dangerous rather than beneficial--and given the failed experiments some Makuta had, it's probably accurate to describe them that way) A Makuta would start with a base, and then use both "biologic-style" viruses and "computer-style" viruses to shape and program the animal, respectively.
Infection, on the other hand, I think is not an illness at all, but rather something the Great Beings had in mind from the very start. Given the importance of the Makuta's mission, particularly in Teridax's case, it makes sense that somewhere along the line, they would need help from some of the Great Being's creations. So the Great Beings allowed the Makuta to take a portion of their "program" (antidermis) and give it physical form (kraata), separate from the Makuta. Like a biological virus, this would be essentially a packet of information that would reprogram a being when they infected their Kanohi, which contains a copy of that being's "program" (and without which many of them cannot continue to operate). Once infected, that virus' program would take over the system, and that infected being now serves the Makuta for as long as they wear that mask.
Kraata could also infect other devices intended for infection, like the "Comet" brand Kohlii balls and they also could control Rahkshi armor using that same basic "Servant of Makuta" program, but until inside Rahkshi armor, their primary purpose was to spread the program.