Keep a close eye on the status of the troops and generals when a plague occurs on one of your cities.
Usually, the plague that sweeps the city ends after a few years, but in many cases the general is still carrying the diseases. When that happens, the plague will break out again.
So, when you see the skull icon gone on the city, check on your governer. If he is still carrying the disease, send him on a vacation on some remote corner of the earth - build a fort(I guess its a villa in this case) and keep your general there. In some cases he may recover, but many times, he will be sick until he dies. I guess one has no choice but to consider as an intervention from the Fates when a plague hits your general.
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