Infect certain territories partially (5)
I believe the answer is:
taint
'infect' is the definition.
(synonyms)
'certain territories partially' is the wordplay.
'partially' indicates a hidden word.
'TAINT' is hidden within 'certain territories'.
(Other definitions for taint that I've seen before include "Evidence of pollution" , "Rot, spoil, define" , "Blemish" , "It isn't commonly" , "(Trace of) corruption" .)