actually this is a brilliant idea. The disease or plague could be healed by a medical ninja. This would add to the necessity for a village to have medical ninja. The knowledge to heal a specific disease would have to be passed down, the same could be done for poisons. Also these diseases could just weaken your character in some way like lowering your stamina, causing dizziness, making your chakra less efficient. The cures for these would be sought after, and cause a lot of tension among villages.
To implement it into the PvE world: Make it a random event that can show up in any village once every...few months, say 4-5. As our good friend here has said, make sure that it can only 'weaken' players. A temporary decrease across certain stats--depending on the disease--would affect different types of fights; again, depending on the disease. So--ex common slang for a medical term I'm not creative enough to come up with--"Bone-Eater" could be a disease that affects the strength of bones, decreasing stats points in strength and stamina, which would obviously hurt Taijutsu users the most -- and the accompanying animation effects could be slowing down your character's movement ability, perhaps (in severe cases) to almost nil.
Another could be a disease that weakens the flow of chakra by clogging up certain points of one's chakra flow, making the execution of jutsu 'Significantly' weaker and--again, in severe cases--causing minor damage to the player every time they attempt a jutsu.
In order to implement this into PvP...just make diseases able to be spread by being in contact--talking a maximum of 5 meters here, so it doesn't affect EVERYONE--with a contagious subject for...say -- 3 minutes, perhaps less depending on the average rate of combat. Having a max range of contagion would allow players to still talk too each other, just not get very close; with pretty much the same thing translating over to foes in combat. A disease spread around to enough villages could 'then' be classified--By The Players--as a 'plague' or an 'epidemic'.
Even though it might not cause death, it can definitely impact your character's ability to function, and having enough of a variety can make curing certain ones within certain villages...tricky, perhaps leading to temporary village cooperation. And of course, reinforcing the need for medical nin in EVERY village.
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