He is the second senior player to be sidelined for the Wellington clash after Ross Taylor suffered a calf tear in the drawn first Test in Dunedin.
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Although the New Zealand line-up has not been finalised, Boult's long-time new-ball partner Tim Southee confirmed he was back in the side.
"I'll come in for Boulty, a straight swap for Trent, who will unfortunately miss this one," said Southee.
Boult pulled up during South Africa's second innings in the first Test with soreness at the top of his left leg.
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Southee said Boult has not recovered enough "to go again with another heavy workload possible here", indicating the balance of the side was still being debated despite the green Basin Reserve wicket looking seamer friendly.
This leaves open the prospect of New Zealand again playing two spinners, as they did in Dunedin at the expense of a fast bowler.
Southee said the side would not be finalised until just before the start on Thursday.
"There's a couple of question marks round a couple of players but I can confirm I come in for Trent and Neil Broom comes in for Rosco [Taylor]. But they'll finalise the side tomorrow."
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