Pain from running, perhaps — affected after covering run (5)
I believe the answer is:
cramp
'pain from running perhaps' is the definition.
'affected after covering run' is the wordplay.
'affected' becomes 'camp' (I've seen this before).
'after covering' indicates putting letters inside.
'run' becomes 'r' (cricket abbreviation).
'camp' placed around 'r' is 'CRAMP'.
(Other definitions for cramp that I've seen before include "Sudden painful tightening of a muscle" , "development of vice" , "hamper" , "Involuntary muscular contraction" , "writers may be familiar with" .)