Hi Welcome in H.C.M. I have gone through your query regarding persistent cough for last six weeks though you are having hypothyroidism and taking synthroid. Initially you were facing severe sore throat with blocked nose and clogged ears. After getting treatment with antibiotics you are now free from pain and clogged ears but cough is still there. You are being given treatment for acid reflux also but cough is still there. You are in doubt that this may be due to thyroid problem. Here I would like to tell you that hypothyroid is not responsible for your cough secondarily your hormone levels are now at normal level. Most likely in your case it appears to be due to- (a)- Post nasal drip due to sinusitis. (b)- Sub mucosal lymphadenitis in pharynx giving grannular appearance of pharyngeal wall which is well known for chronic irritation in throat. you are now advice for- 1- Culture and sensitivity of throat swab. 2- X- Ray of paranasal sinuses. 3- X- Ray of chest. 4- Blood - CBC, ESR, blood sugar (F & PP). after this much a thorough examination of chest and throat along with co-relation of inferences of investigation will help in reaching to final diagnosis that may be accordingly manage. Regards.