Ashwin, who suffered a side strain at Green Park in Kanpur, could only bowl 4.4 overs in the opening game and veteran off-spinner Harbhajan Singh played the next two matches after being selected as back-up in the squad.
On being pointed out that Ashwin's name was missing from the Test list, Thakur clarified that the in-form bowler was very much part of both the squads and chief selector Sandeep Patil said that his medical assessment report is expected after the fourth ODI.
Delhi pacer Ishant Sharma, who sat out the third day's play in his side's Ranji game against Haryana, will miss the first Test in Mohali due a one-match ban he has to serve after his on-field actions during the final Test in Sri Lanka.
The pacer has been deemed fit and is expected to feature in the second Test in Bangalore.
After losing the three-match T20 rubber 0-2, India are trailing the five-game ODI series 1-2.