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Degenek, who plays his club football with Red Star in Serbia, returned a positive test prior to his Doha-bound flight, despite being asymptomatic.
The defender joins Seattle Sounders left-back Brad Smith on the list of players who won’t feature against Oman and Japan respectively, as Australia aim to continue their winning run towards World Cup qualification.
With Arnold in need of a replacement to fill his 25-man squad, Bailey Wright will now deputise in Degenek's absence, with the final 10 members due to arrive in Qatar on Tuesday.
Australia have won their opening two games in Group B and will be considered the 'home' team at the Khalifa International Stadium on Friday morning (AEDT).
Oman, meanwhile, beat Japan 1-0 in their first match - before falling 1-0 at home to Saudi Arabia - and will hope for another surprise result against the Socceroos.
