Pain at Base of the Skull, Neck Stiffness, AccompanIed by Flu-Like Symptoms

Patient : Hello, Yesterday I visited the doctor after having a fever, cough, congestion, and body aches for 3 days, getting progressively worse each day. I tested negative for the flu (I had a flu shot 3 weeks ago), but the doctor said if she were to make a "gestalt estimate", although I'm technically testing negative, all symptoms point to the flu so I should treat it like that. She prescribed a cough medicine (cheratussin with codeine) and an anti-biotic "just in case" (azithromycin). Anyway, on to my question - since returning from the doctor (about 18 hours ago) I've had a persistent pain, starting at the base of my skull, descending down my neck and rising up through my head to the back of my eyes and top of my skull (especially when I cough). My neck feels stiff and it's painful to move my head from side to side, but the most pain is coming from the very base of my skull and its very sensitive to the touch. Initially I thought maybe I just slept in an awkward position, but the pain has increased over night and I'm beginning to worry a bit, since I've never experienced this feeling before. Is this a pain that comes with the territory of flu-like symptoms, or is there actual cause for concern? Thank you for your help.
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