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Roy suffered a hamstring tear in Friday's win over West Indies and James Vince, who had a lengthy net session at Old Trafford on Monday, will replace the opener.
The England and Wales Cricket Board has suspended all professional cricket until May 28 but is looking at the possibility of playing internationals behind closed doors.
England have suspended professional cricket until at least May 28 due to the global health crisis, which also looms over their home series against the West Indies, Pakistan, Australia and Ireland.
Twelve months ago on this day, England had claimed the 50 over World Cup title after beating New Zealand by virtue of a contentious boundary count-back rule as scores were tied even after the Super Over.
Karthik handed over the reins to his deputy Morgan hours before their IPL match against Mumbai Indians.
Karthik told the KKR management that he wants to "focus on his batting and contributing more to the team's cause."
Chasing a modest target of 149, Mumbai were home and dry with 19 balls to spare.
The result also meant defending champions Mumbai Indians qualified for the play-offs.
"Genuinely feel Eoin Morgan should lead the side, surely not DK. World Cup-winning captain should surely lead IPL side," Sreesanth tweeted after KKR suffered an 18-run defeat to Delhi Capitals on Saturday night.
After the bowlers restricted KKR to 148/5, opener Quinton de Kock blazed his way to an unbeaten 78 off 44 balls to complete the task for Mumbai.
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