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Eoin Morgan, Joe Root and Joe Root were both part of England's first squad.
After four players and four staff members were tested positive for Covid-19, England will select a new team for the ODI series against Pakistan.
The series was to start with an ODI in Cardiff.
However, tests on Monday showed seven positive results. The rest of England's party will have to self-isolate as a result.
According to the ECB, Ben Stokes will once again be captain of a squad that will be announced in the coming hours.
After breaking his finger during the IPL earlier in the year, Stokes was unable to play for England.
According to an ECB statement, those affected by positive tests will now be subject to self-isolation starting on 4 July in accordance with the UK Government protocol.
"The remaining members have been deemed close contact and will also isolate."
Tom Harrison, chief executive officer of the ECB, said: "We were mindful that the emergence and enforcement of bio-secure environments could increase the likelihood of an outbreak.
"We have been working quickly to identify a new squad over the night, and we are grateful for Ben Stokes who will be returning to England duties as captain."
The 10 day isolation period that the squad will be subject to will cover all three ODIs against Pakistan.
Thursday's fixture in Sophia Gardens will be followed by games at Lord's 10 July and Edgbaston 3 days later.
England will then be facing three Twenty20 fixtures against Pakistan, on 16-18 and 20 July.
"A chaotic situation"
Jonathan Agnew, BBC Sport cricket correspondent
Ben Stokes is just getting back into cricket. He's just started to get back into cricket after playing a few games with Durham.
It's quite chaotic.
It'll be a great opportunity for some, and England already had a large squad for cover, including coronavirus.
England is happy that this series isn't the most prominent. The Twenty20 Series is very important, and it's not too late for them to organize for the World Cup.
Although the 50-overs stuff is not important, it will cause disappointment in the England camp if they miss the Twenty20 series.