Alastair Cook has indicated Ben Stokes is likely to miss the third Test against Pakistan due to a calf injury and defended his decision not to enforce the follow-on as England won comfortably in Manchester on Monday.

Stokes went off injured on day four, pulling up in obvious discomfort after bowling a delivery at Old Trafford.

According to the captain, the 25-year-old all-rounder is in doubt for the next instalment of the four-match series at Edgbaston, England having levelled the contest at 1-1 with a 330-run victory.

"Jimmy [Anderson] is fine, your first game back you are a bit sore, but Stokesy looks in a bit of trouble with his leg," Cook said during the post-match presentation.

"Luckily Mark Wood is coming back - he bowled really well for the Lions, and we have got Steven Finn and Jake Ball."

Having posted 589-8 declared before bowling Pakistan out for just 198, Cook was criticised heavily in some quarters for opting not to make the tourists bat again immediately.

"I thought [it] would be bit of time off for the bowlers, it wasn't a minefield so I thought 'rest up and come in hard today'," he said.

"I didn't think it would cause quite the stir it has, but we got the result, it is a brilliant win for the lads and we're happy."

Root, having been moved up the order to number three, made 48 and nine as England surprisingly lost the opening Test at Lord's.

And the 25-year-old Yorkshireman was relieved to respond with a career-high 254 in the first innings in Manchester, followed by a handy unbeaten 71 in England's brief second spell at the crease as Cook declared again on 173-1.

"Everything we talked about before the game, was nice to go out there and do it," Root said.

"You put the hard yards in and work hard, and I had a good think to myself, and it's nice to turn it around quite quickly. 

"I don't look to [batting at] number three any differently to number four, but taking some risk out will help. Both sides have played some strong cricket but we are confident going into Edgbaston."