Pompey’s central defender missed last night’s 2-0 victory at Hull after feeling unwell on Friday morning.
He was part of the Blues squad that travelled to Humberside on Thursday and stayed overnight in the team hotel ahead of the game at the KCOM Stadium.
Rasmus Nicolaisen took his place as the Blues claimed a 2-0 win to take them to the top of League One.
Whatmough has since undergone a test and found to have the virus.
He will now self-isolate in accordance with government guidelines.
Pompey insist no other members of the squad are currently displaying symptoms.
But it’s understood those players who sat near the defender on the team bus on Thursday will now also be tested for Covid-19.
In a club statement, Pompey said: ‘Portsmouth Football Club can confirm that Jack Whatmough has tested positive for Covid-19.
‘The defender was feeling ill on the morning of Friday night’s win at Hull and is self-isolating in accordance with government guidelines.
‘The club will now implement our internal Covid procedures, although there are no other members of the squad currently displaying symptoms.
‘We would like to wish Jack a quick recovery and urge everyone to continue following government advice to help limit the spread of the virus.’
On Friday, it was announced that Peterborough’s next three league games would be postponed after a member of their playing squad tested positive, while another three squad members are displaying symptoms.
This week, Sunderland also announced that they would have to postpone games due to an outbreak of coronavirus.
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