Prior endured a miserable Ashes in the 5-0 whitewash by Australia and his international future remains in doubt after undertaking major surgery on his injured Achilles.
His fellow South Africa-born team mate Trott has been in the international wilderness since pulling out of the Ashes after the first test in Brisbane due to a stress-related illness.
New Zealand-born Stokes was dismissed for three consecutive ducks and dropped after the second test against India, but is among six new faces centrally contracted for the 2014-15 season.
All rounder Moeen Ali, batsman Gary Ballance, wicketkeeper Jos Buttler, and pacemen Chris Jordan and Chris Woakes have all been contracted for the first time, reflecting the team's regeneration under coach Peter Moores, who replaced team director Andy Flower after the Ashes.
Seamer Steven Finn has retained his central contract, despite not playing a test for more than a year.
Another five players have been given incremental contracts, which are awarded to players who may feature in shorter format teams but may not have cemented their place in tests.
After a shock test series loss at home to Sri Lanka, Alastair Cook's England recovered from a heavy defeat at Lord's to beat India 3-1.
They round off their year with one-day series against Sri Lanka and a triangular one-day tournament against Australia and India before the Cricket World Cup next year.
England central contracts: Moeen Ali, James Anderson, Gary Balance, Ian Bell, Stuart Broad, Jos Buttler, Alastair Cook, Steven Finn, Chris Jordan, Joe Root, Ben Stokes, Chris Woakes.

Increment contracts: Ravi Bopara, Alex Hales, Eoin Morgan, Liam Plunkett, James Tredwell.

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