What Causes A Respiratory Infection Along With Coughing And Breathing Difficulty?

I have had a respiratory virus for two and half weeks it went from my throat to my chest to my ears and fever when I start to feel better the next day I feel worse and even more tired and coughing and having a hard time breathing. I have to get back to work but can not do antibiotics nor can I take anything for aces and pains all do to my allergies. I had a hooping cough shot on May 10th I have been told that my body thinks that it thinks it is infected with the hooping cough virus and my white cells are over acting and is making my body unable to fight what is happing. Please give me your answer.