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The Lancashire legspinner has sustained a stress fracture in his back and has been replaced in the squad by Sussex's Danny Briggs
Matt Parkinson has been ruled out of England Lions' winter tour through injury.
It remains to be seen whether his time in Australia's domestic T20 tournament will be affected by the issue, though given he is not joining the franchise until January 4 the 22-year-old will have a little extra time to recover.
"It's a real shame for Matt that he's forced to miss the tour. He had a fine summer for Lancashire and his selection was just reward for the ability that he's shown," the ECB's technical director of elite coaching Andy Flower said.
Matt Parkinson has suffered a stress fracture in his back
"He's been shut down from bowling and he'll see a spinal specialist this week as we try to determine the full extent of his injury."
Parkinson is not the first young England spinner to suffer from a stress fracture in his back.
Mason Crane, the Hampshire leggy who made his Test debut in last winter's Ashes series in Australia, has struggled with a similar problem for much of 2018.
England face Pakistan A in one four-day 'Test', five 50-over games and two T20s in the UAE, starting on November 18.