More review problems for England
Root, in his second Test as captain, has experienced problems with the Decision Review System, seeing two referrals wasted on the first day after pressure from bowlers Stokes and Stuart Broad.
That was probably the explanation for his reluctance to use a review after Broad's muted appeal for an Amla edge behind was rejected. Subsequent replays showed the faintest nick.
In Broad's following over, Anderson, at gully, leapt high and thrust out his left hand, but failed to cling on to the chance offered by Elgar.
Later, Cook was correct to challenge when given out leg before to Morne Morkel, with the ball-tracker suggesting it was going over the top of the stumps,
Still, he and opening partner Keaton Jennings each had a further appeal to survive in a testing period before the close.
'We have two days to knock them off' - what they said
England bowling coach Ottis Gibson: "It is a great game to win from here. You have to give a lot of credit to South Africa. There was a lot of character shown not just by our bowling unit but the fielders.
"The captain said he wanted people to step up and Anderson came in and led really well this morning. Wood has not got any wickets but bowled really well in patches coming off the back of a long lay-off and Stokes was fantastic today.
"It has been a very tough couple of days but we have two days to make 474."
Ben Stokes went for just 34 runs in his 20 overs, also taking the key wickets of Dean Elgar and Faf du Plessis
Ex-England batsman Ed Smith: "The groundsman here at Trent Bridge reckons the pitch will get flatter the more the sun comes out. Let's hope for England's sake he is correct.
"There were some ominous signs late on with Vernon Philander swinging the ball round but England battled through a horrible period without loss."
Former England spinner Graeme Swann: "England should be thinking they can chase this. Joe Root is a positive lad and will think it's chaseable. I played in a game where India chased 380-4 against us in Chennai.
"Joe has very little captaincy experience but in a game where he led Yorkshire, Middlesex knocked off 480. I think Hampshire did something similar to him too. He'll be thinking if they can do it to my team, I'll do it to somebody else's."
