I don't know if much is actually said on colds, viruses, or diseases. However, there is a bunch of what SpM calls, external diseases. Sort of a form of biological warfare, the use of poisoned arrows (Faramir and Gwaihir), the morgul blades, the Wraiths' "black breath," all have some sort of power to inflict sickness on people.
We can tell from the use of herbs (Athelas), Elrond and Gandalf both heal people, the Houses of Healing, that their could be some sort of internal disease(s) in Middle-earth. However, anytime we see these circumstances of the HoH, Elrond, Gandalf...athelas, it is used to heal an external disease caused by a poisoned dart, or magical sword.
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