At least with heat recovery ventilators, the air streams do not mix at all. Unless the virus finds a way to penetrate the metal fins of the heat exchanger, it should be completely fine.
There are a few different types. One type blows air out "across rocks" to warm them up, and then reverses the fan pulling air in "across the same rocks" I simplified a lot in the above, but the idea should be clear - there is some mixing of streams in this style.
