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Iyer has had recurring troubles with his back and had also undergone a surgery last year.
The 29-year-old made 35, 13, 27, 29 in the opening two Tests and was guilty of not capitalising on starts.
“He has complained of stiffness and back issue,” a BCCI source told PTI.
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The selectors are yet to announce the squad for the last three Tests but they could do that on Friday.
On Monday, India bounced back to level the five-match series with a 106-run victory in Visakhapatnam. England, who have flown back to Abu Dhabi before the third Test in Rajkot beginning February 15, won the series opener by 28 runs.
India will assemble in Rajkot on February 11 and England are expected to reach there a day after.