Wow - what an interesting one. I went through this issue years ago and this is the way that it was explained to me -- code to the highest degree of specificity. Since the doc says that the cough, fever, and runny nose are due to the URI then you have to code the URI -- The only time that this wouldn't be the case is if the signs and symptoms can be related to something else. If the doctor states that the patient has a URI, but is a smoker or inhaled chemicals a few days ago then it leaves the cough with a differential and the cough would have to be coded as well. Instructors will tell you that you can code the cough even if you have a definitive dx of URI - and you can, just not as the primary.
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