Brief Answer: Virus infection with secondary bacterial infection Detailed Answer: Hi. Noted your Medical history of hypothyroidism and grain dust allergy but no cold or flu for several years. Also noted the present complaints. I hope your thyroid status at the moment is normal, please check for FT3, FT4 and TSH if not done in recent times. Hypothyroidism does cause a problem in early recovery and healing process. The very color of the phlegm - green indicates secondary bacterial infection , (some of them may not give rise to fever). This has given you fatigue, weakness. The passage of infected to the intestines can give loose stools. Coughing can cause the chest pain. Coughing increases in lying down position as the phlegm shifts to irritate the respiratory system or a post-nasal drip ( if you have) irritates the throat. Your Doctor may be right in her thought- It was started as a virus infection , getting worst. Now you need to take an antibiotic, mucolytic and anti-inflammatory medicines as per your Doctor,s advise. Steam inhalation with a plain water helps as a great mucolytic- although increases coughing initially , the removal of phlegm helps a lot. If there is no response with such a therapy, I would advise blood tests , X-ray chest, and Sputum test- routine , microscopic and culture sensitivity. I hope this answers your query; feel free to ask for more if you feel or need.

---