Hi caraway,

I would get out and start running again as soon as you feel comfortable, even if it is shorter distances or a varied route.  Of course, it is important to follow your doctor's advice and take note of any of the medications (and potential side-effects) that you may be taking.  Maybe start out again walking with some slow jogging for certain areas to see how that goes.  The best rule is to listen to your body and take things slow, but do not be discouraged. 

In general, minor infections usually do not prohibit moderate exercise, but again, it depends on your individual circumstance.  Pay closer attention to hydration because, although it is always important, it is more critical when your immune system is compromised, you are eating less, or taking certain pills that influence the absportion of nutrients and the balance of sodium. 

Again, walking or a slow pace should be fine, and should increase your energy levels.  (As long as your respiratory functions are not overly distressed, then getting back on track as soon as possible whould be a good idea.)

Wishing you a speedy recovery and happy miles!