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Leicester Tigers' George Ford, son of England defence coach Mike, will start at 10 while the pacy midfield combination of Ryan Mills (Gloucester Rugby) and Elliot Daly (London Wasps) will take their places at 12 and 13, respectively.
Of the XV that will start the game against Wales, only Vunipola survives from England U20's last competitive match which was in the IRB Junior World Championship in Argentina last summer. Rob Buchanan (Harlequins), Charlie Matthews (Harlequins) and Gray also featured in the match, coming off the bench.
With a relatively new squad at his disposal, Hunter is excited to see what his players have to offer after a series of successful training camps.
He said: "We're excited about getting stuck into the 6 Nations, we've enjoyed good camps in Portugal and Surrey and it's time to put ourselves to the test. Starting off against Wales in Wales is as good as it gets and we'll be taking each game as it comes throughout the campaign.
"We've got our squad for Wales and that's our primary focus, and after that we'll focus on Italy. It will be a tough match in Llanelli for us, they will have the crowd behind them, they'll be physical, they have good runners and we'll be tested.
"I'm pleased with where we are. It is tough to whittle the squad down to 22, we have some outstanding players at this age grade and a lot of competition for places. It's vital to get the blend right and we want to give the lads the opportunity both to perform and develop."
England U20 starting XV:
15) Ben Ransom (Saracens)
14) Andy Short (Worcester Warriors)
13) Elliot Daly (London Wasps)
12) Ryan Mills (Gloucester Rugby)
11) Jamie Elliott (Northampton Saints)
10) George Ford (Leicester Tigers)
9) Dan Robson (Gloucester Rugby)
1) Mako Vunipola (Bristol Rugby)
2) Mike Haywood (Northampton Saints)
3) Henry Thomas (Sale Sharks)
4) Kieran Low (London Irish)
5) Charlie Matthews (Harlequins)
6) Matt Kvesic (Worcester Warriors)
7) Matt Everard (Leicester Tigers)
8) Alex Gray (Newcastle Falcons) (Captain)
16) Rob Buchanan (Harlequins)
17) Ryan Bower (Leicester Tigers)
18) Addison Lockley (Exeter Chiefs)
19) Ollie Stedman (Leeds Carnegie)
20) Chris Cook (Bath Rugby)
21) Guy Armitage (London Irish)
22) Christian Wade (London Wasps)