Gundogan is now in a period of isolation after City confirmed the German international had contracted Covid-19.
He missed Monday’s 3-1 win against Wolves along with Aymeric Laporte, who has only just returned to training following a positive test.
Riyad Mahrez, who also contracted the virus, was on the bench, but Guardiola revealed his growing fears.
“I’m concerned for the society, not Man City,” he said. “The cases are increasing, they’re still there. It’s less aggressive, but it’s still there.
“Aymeric and Riyad passed it and now we have Ilkay. I think he feels quite well now, but he has to stay at home.
“We tried to be prudent, be alert in our private lives, but it is there. We are no different to any human being in society.
“We don’t want injuries, but we got three important injuries from the internationals. Unfortunately Ilkay got Covid. It’s important to stay at home.”
Bernardo Silva, Joao Cancelo and Aleks Zinchenko all picked up injuries on international duty, leaving City desperately short at the start of the season.
Sergio Aguero could also be out for another two months with a knee injury.
After a gruelling win against Wolves, Guardiola said he would have to turn to the academy for Thursday’s Carabao Cup tie against Bournemouth.
“We want the seven players out to come back,” he said. “We cannot expend the energy we did today on Thursday against Bournemouth because of Sunday [against Leicester]. A lack of preparation, seven players out, and not coming back soon.
“We will see how many players are available. We would like to continue in the Carabao Cup, but we don’t have players after this period to play every three or four days. It was so difficult. It is a good victory for us.
“We cannot pretend we can recover in three days and then another three days play again.”