S.K.
Well I can't tell you what it is exactly for your son , only your doctor can tell that.
But my son went through something similar. He started with a bad cold and then a cough which wouldn't go away. He wouldn't sleep well in the night because of the stuffy nose and cough. Took him to the doctor and they told M. it could be viral since he had fever too for 3-4 days(I had thought fever was because of teething). He stopped eating anything much , so took him in again and they told M. he had developed a ear infection. So he was on amox, didn't clear up. He was on antibiotics again since it didn't work first time. His fever was long gone and his cold and cough didn't go away for another week or two.So he was sick for about a month or so.My son had just started daycare , so I was told he fell sick because he was exposed to so many germs there.
Has anything changed for your son - environment wise? Have you started taking him to a new playarea or a friend's place or started daycare? I have no idea about allergies. Can you call your nurse advisor and discuss this with them? I hope your son feels better soon!