The trio has been selected keeping in mind that India's tour of Pakistan looks unlikely at the moment and there is a one month window before the team travels to Australia in January for the limited-overs series.
In case the Pakistan series happens, three stand byes have also been announced.
However, the selection committee chaired by Vinay Lamba could not give a convincing answer as to why India's current Test captain and a prolific one-day player like Kohli was not named captain if he is available.
However, he clarified that the selectors are yet to speak to the India players confirming their availability.
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A similar case of miscommunication had happened when Ishant Sharma was not initially named in the four-day squad despite being available as he could not be contacted at the time of the meeting.
"Look we have not had any direct contact with the players but we did not want to take any chances in case they are available. But as a safety measure, we have kept three stand byes also," Lamba said.
For the record, veteran pacer Ashish Nehra, who has quit the longer format, has been selected in the one day side.
Squad: Gautam Gambhir (captain), Unmukt Chand, Shikhar Dhawan, Virat Kohli, Nitish Rana, Milind Kumar, Manan Sharma, Pawan Negi, Ashish Nehra, Pradeep Sangwan, Ishant Sharma, Navdeep Saini, Subodh Bhati, Shivam Sharma, Rahul Yadav (wk).
Stand byes: Dhruv Shorey (Shikhar Dhawan), Vaibhav Rawal (Virat Kohli), Vikas Tokas (Ishant Sharma).