Opener Lokesh Rahul has also recovered from his shoulder surgery and has retained his place in the side as the selectors showed consistency, which has been the hallmark of this committee over the past one year.
The three-member selection committee decided on a 16- member squad via tele-conference with 15 members, who were a part of India's fourth Test against Australia in Dharamsala, being retained.
That Rohit will make a comeback was indicated by skipper Kohli in England and that was precisely the reason why he was rested for the limited overs series against West Indies.
Nair had gone off the boil after his triple century against England and could not even score a single half-century with scores of 26, 23 and 5 against Australia.
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The national selection committee has named Karun the captain of the India A 'Test' side to South Africa, where he is expected to play both formats.
The 16th member of the squad is third opener Abhinav Mukund, who made a comeback against Australia. The four pacers Ishant Sharma, Bhuvneshwar Kumar, Umesh Yadav and Mohammed Shami were automatic selections.
Squad: Virat Kohli (Captain), Murali Vijay, Lokesh Rahul, Cheteshwar Pujara, Ajinkya Rahane (vice-captain), Rohit Sharma, Ravichandran Ashwin, Ravindra Jadeja, Wriddhiman Saha (wk), Ishant Sharma, Umesh Yadav, Hardik Pandya, Bhuvneshwar Kumar, M Shami, Kuldeep Yadav, Abhinav Mukund.