Pompey moved to the top of League One with an excellent 2-0 win at the KCOM Stadium, bizarrely despite not having a shot on target themselves after two own goals from the home side.
Kenny Jackett’s side did so, however, without defensive lynchpin Whatmough who was left out of the team after feeling unwell ahead of the game.
The Gosport lad was sent home from the team hotel ahead of the game on his own, with Danish defender Rasmus Nicolaisen coming into the middle of defence.
Jackett explained Whatmough was not showing any Covid-19 symptoms but Pompey erred on the side of caution over the development.
And the 24-year-old will now be tested for the disease to give certainty over whether he can rejoin the first-team setup.
Jackett said: ‘Jack was ill this morning and he felt better as the day went on, but we felt it wasn’t worth the risk.
‘He didn’t feel up to it so it was an opportunity for Nicolaisen and I thought he did very well.
‘The physio didn’t think he had any Covid symptoms but we sent him home anyway on his own so we can cover all bases.
‘Hopefully tomorrow or the next day he feels better.
‘He’ll get a Covid test anyway tomorrow but as it stands there were no symptoms and he was just a bit under the weather.’
Pompey were at the centre of the coronavirus narrative in March when Arsenal boss Mikel Arteta tested positive after his side faced Jackett’s men in the FA Cup.
James Bolton, Haji Mnoga, Andy Cannon, Harry Kavanagh and Sean Raggett have all since tested positive for Covid-19, along with former loanee Ross McCrorie, but there has not been any positive tests this season at Fratton Park.
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