I think I have a virus. Terrible knee pain, fever and dizziness. Then 3 days later cold symptoms. My joints ache but knees worst. Had flu shot.

Likely flu. That sounds like a flu, however reactive arthritis may happen with other viral infections. Check with your doctor to exclude strep as well since it could also effect joints, cause fever, but even more dangerously, cause heart and kidney problems.
Having a flu. Shot isn't a total guarantee that you won't catch influenza. If your symptoms aren't resolving please seek evaluation.

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