Murphy injured his ankle in Round 10 against Geelong, in what initially seen as a four to five week injury.
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However, his injury has taken longer than expected to recover.
The club was hopeful Murphy would be able to make a return for the final two weeks of the season, but Bolton confirmed on Friday morning that the skipper will not be risked in the final two rounds after failing yet another fitness test at training.
“It’s been really frustrating for Murph and us, it’s one of those injuries that’s just niggled and stayed around and we tested him this week and he’s still just not quite right,” Bolton said.
“So it’s probably the end for Murph this year so he can go and have a really strong pre-season.”
Marc Murphy is done for the year. Blues coach Brendon Bolton defended the rehab program. Focus now on 2017 #afl
— Drew Jones (@DrewJonesFOX) August 19, 2016
Marc Murphy "probably" done for the season, Bolton admits, after "frustrating" injury. pic.twitter.com/KwC6cnsUL4
— Lauren Wood (@LaurenA_Wood) August 19, 2016