The 31-year-old Astle had been in India with New Zealand's 'A' team and was elevated to the full squad earlier this week for a series that includes three ODIs and three T20Is. He is replaced by Ish Sodhi.
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"Todd was really impressive in the recent New Zealand 'A' tour over here and had done everything he possibly could to get himself ready for this series," said coach Mike Hesson said in a statement. "He deserved this opportunity and everyone in the team is certainly feeling for Todd. He'll return to New Zealand and get himself ready for a big summer."
Astle was first named in the New Zealand side in 2012 and has played just two Tests, the second of which was last year, and two T20Is, but is yet to represent Black Caps in ODI.
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His performances in domestic cricket, where he is also a handy lower-middle order batsmen, however, have kept him on the selectors' radar.
He had performed well on the 'A' tour to nudge Sodhi out of the one-day squad but managed to bowl just three deliveries before he was injured in New Zealand's warmup match against an Indian Board President's XI in Mumbai on Tuesday.
The first one-day international against India is on October 22.
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