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Openside flanker Hooper, who has been fulltime captain of the Tahs for the past four seasons, still intends making himself available to be Wallabies skipper.
Test lock Rob Simmons will take over the reins, while utility back Kurtley Beale is the new vice-captain.
"The decision has been a long one and this has been something on my mind in this environment a good 18 months, so it hasn't been something on a whim." Hooper said.