The want-away United striker had flown out to Thailand with the rest of the squad where he was expected to feature in David Moyes' first game in charge against Singha All-Star XI.
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However, the 27-year-old has become the latest injury concern to hit the Premier League winners following a back problem picked up by Nemanja Vidic, and Rooney will now fly back to England for treatment.
“Following a scan this evening on a hamstring injury sustained in training, it has been decided that Wayne Rooney should return home immediately for further assessment and rehabilitation,” read a statement on the club's website.
United's medical team expect Rooney to be unavailable for selection for a month, which puts his participation in the club's opening game of the Premier League season in do