The Asian Football Confederation praised China for the "difficult choice" to withdraw as the country battles to stamp out the virus with rapid lockdowns and mass testing.
A recent missile attack on the northern city of Erbil prompted the switch to Saudi Arabia for Thursday's game, FIFA and the Asian Football Confederation have announced.
Wuhan was supposed to host China, Taiwan, Thailand and Australia for the Group B qualifiers February 3-9, but they will now be held on the same dates in the eastern city of Nanjing.
Khalifa will extend his reign as president until at least 2023, by which time he will have completed a 10-year spell in charge of the 47-member body.
Malaysia has contended that its players will not be safe in Pyongyang, but it took statements from South Korea's president for the AFC to agree.
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