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Sai Sudharsan, Jitesh Sharma and Harshit Rana have been named as replacements.
A makeshift senior Indian team led by Shubman Gill will play Zimbabwe in a five-match T20I series in Harare, starting from July 6.
The Chennai Super King player's tally of 148 runs from four matches places him among the top 10 batters this season, and only two other players in that group boast a better strike rate than Dube's 160.86.
Dube's fifty headlined India's facile six-wicket win on Thursday, and the knock also earned him the player-of-the-match award.
Only England pacer Stuart Broad has gone for more runs than Dube in a single over in a T20I.
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