"Shadab's blood tests have revealed (a) virus and doctors have advised him a four week rest," it said in a statement.
"Shadab is out of the five-match one-day series against England and a Twenty20 match (also against England)," it added.
The Pakistan team will fly to England on Tuesday and play a five-match one-day series against the number one ranked home team, starting May 5.
Shadab has played 34 one-day internationals, 32 Twenty20 matches and five Test matches in a promising career that started in 2017.
Chief selector Inzamam-ul-Haq described Shadab's loss as "bad news", adding her hopes the spinner will be ready for the tournament.
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