Roy suffered a hamstring tear in Friday’s win over West Indies and Morgan confirmed James Vince, who had a lengthy net session at Old Trafford on Monday (June 17), will replace the opener on Tuesday.
Roy made a superb 153 against Bangladesh in Cardiff but his replacement as opener Joe Root impressed with an unbeaten century which sealed an eight-wicket win for the hosts.
The 26-year-old Roy will miss the matches against Afghanistan and Sri Lanka but Morgan is confident he will be back before the June 30 game against India.
Morgan said that he had not spoken to selector Ed Smith about possibly recalling Alex Hales, who was withdrawn from the squad on the eve of the tournament for recreational drug use.
Morgan had better news about his own health after suffering the back spasm in the match against West Indies after which he delivered his news conference standing up, saying he has improved and is hopeful of playing on Tuesday.
England is fourth in the table with six points from four matches and will be overwhelming favorites against bottom-placed Afghanistan who have lost all four games.
Afghanistan captain Gulbadin Naib said he was hoping for a spin-friendly wicket which would suit the likes of Rashid Khan.
Despite not winning any games so far, Naib said the tournament had been a good learning experience for his players.
(Production: Andy Ragg)