One possibility is that you have the flu. Influenza is a viral infection which is treated with symptomatic relief e.g. pain medications, fluids and rest. It may take 1-2 weeks to completely resolve. Antibiotics are of no use in the flu.
On the other hand, The severe headache, cough and sore throat could also be from a sinus infection. In this case antibiotics are VERY important and may need to be taken for several weeks depending on how long the infection has been there. Doxycycline is not the best choice for a sinus infection.
My suggestion is this. If you have any fever, you should call your doctor and tell him what the temperature is and how severe the headache is.
If you do not have fever, but still feel no better in the next 1-2 days, you should definitely call the doctor and probably have a CAT scan or MRI of the brain/sinuses. Some sinus infections need to be drained by a surgical doctor especially if there is a blockage in the sinuses.
You might also ask him what is he treating you for, in other words what is his diagnosis about your illness?
Did they check your blood pressure since that can also cause headaches if it is very high.
Naproxen is a non-steroidal anti-inflammatory medication. Perhaps a different one may work better for you. Ibuprofen/Advil may help more than Naproxen and is available over the counter without a prescription. You should not take both at the same time.
Hope this has been helpful and that you feel better real soon.
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Dr. F.
I hope you feel better
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