Causing you pain isn’t an evolutionary advantage in and of itself. It’s an advantage only if it enables some other benefit–like, as you said, causing coughing to increase transmission.
In many cases, you get a sore throat specifically because that’s where the virus has infected you, so you’re literally feeling the virus destroying your body’s cells in order to create copies of itself. The virus does not know there is a human, does not know that what it does causes pain. The virus doesn’t “know” anything–indeed, it inarguably “knows” *even less* than what a bacteria would “know,” because viruses are literally nothing more than “How To Make More <X>virus” instructions and a capsin shell to hold those instructions together.
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