Guardiola is one of fourteen members of staff self-isolating after testing positive for the virus, with his assistant juanma Lillo also out of aciton.
In addition, seven players will be unavailbe die to the outbreak.
That has left Rodolfo Borrell in charge of the game, but he confirmed they do not currently plan on requesting a postponement.
"At the moment we have seven players unavailable and up to 14 staff, so it's quite a big outbreak," Borrell said.
"We will play with the ones we have available, we don't have much more, but our aim is to keep playing as much as we can, trying to respect all competitions.
"At this moment we can fill the team. I don't know what will happen in the following days but right now it's an easy line-up to decide.
"We will play with what we've got, we have some first team players and some others that will come from our second team.
"We have to prepare for the game to happen. If then tomorrow for whatever reason it is not possible because of more news, this is out of our reach to know now.
"But right now, we are prepared to play the game and we have been preparing all days and we are mentally ready for it."
If tha game does, as expected, go ahead then Borrell insists he will not allow anyone to be using COVID as an excuse on the day.
"To fill in the whole squad and travel with at least five, six subs, we had to bring in some players from the second team," he added.
"But also the outbreak involves players from the second team so the situation is not that easy.
"The second team also had plenty of Covid cases, staff as well, but there's no excuse.
"We travel with the team, it will be a mixture of both (senior and Elite Development Squad), and we will obviously go for the win and try to get the best out of the game."
Burnley have also been affected by a COVID outbreak, meaning manager Sean Dyche will not be with his side when they face Huddersfield at Turf Moor.
A club statement read: "Burnley Football Club can confirm manager Sean Dyche will miss this weekend's FA Cup third-round tie at home to Huddersfield, after testing positive for Covid-19 on Tuesday.
"Sean will now follow the mandatory self-isolation protocols."
Assistant boss Ian Woan will take charge of the game for the Premier League side.