Stokes had taken an indefinite break from the game last month after leading England to a 3-0 ODI series win over Pakistan.
Calling Stokes the heartbeat of the team, Root said he will be badly missed in the India series beginning Wednesday but considering the phase that he is in, cricket is secondary.
Stokes will be replaced by Craig Overton for the India Test series.
Stokes had missed the two-Test series against New Zealand due to the finger injury he sustained during this year's Indian Premier League (IPL).
Stokes was not scheduled to take part in white-ball matches till seven COVID-19 cases in the regular team forced the entire squad into self-isolation.
The second-string side has done quite well as it comfortably won the first two ODIs against Pakistan, surprising stand-in skipper Ben Stokes with the way they have adapted to the situation.
An entirely new England squad was scrambled together on Tuesday, a day after the main squad recorded seven positive tests for the coronavirus.
Stokes was originally left out of the squad to focus on his recovery from a finger operation.
Stokes was announced as the captain for the three ODIs against Pakistan after the first-choice squad reported seven Covid-19 cases.
Stokes marked his return to cricket after a surgery to his left index finger on Sunday, striking an 18-ball 29 and taking one wicket, as his county side Durham defeated Birmingham Bears by 22 runs in the Vitality Blast T20 tournament
The 30-year-old Stokes had to pull out of the Indian Premier League (IPL) before its suspension after a fracture to his left index finger. He underwent a surgery for it.
The 30-year-old Stokes had to pull out of Indian Premier League (IPL) before its suspension after a fracture to his left index finger. He underwent surgery for it.
Stokes sustained a fractured finger during Rajasthan Royals' opening game against Punjab Kings and was subsequently ruled out of the league last month.
Hit by foreign pull-outs, the Rajashthan outfit was left with just four overseas players -- Jos Buttler, Chris Morris, Mustafizur Rahman, and David Miller -- in their camp.
Till Friday, Chennai has hosted nine IPL games and only twice has the team batting first scored in excess of 170.
The injury occurred while Stokes was fielding during Royals' opening match against Punjab Kings on Monday.
Royals put up a stiff fight in their first match against Punjab Kings with skipper Samson's ton taking them to within four runs of Punjab's 221-run total.
Stokes sustained the injury while taking a catch to get the wicket of Chris Gayle in his side's fixture against Punjab Kings on Monday.
KKR's Eoin Morgan has revealed the two names who will open the batting for Rajasthan Royals in the upcoming edition of the IPL.
India is set to host the T20 World Cup later this year and Stokes feels it is the perfect opportunity for English players.
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