Thompson was a late withdrawal from his regular Tuesday morning press conference after experiencing flu and gastro-like symptoms.
Several players including Bomber utility David Myers, who pulled out of Sunday's loss to Fremantle at the last minute, have fallen ill over the past 10 days.
"He's (Thompson) a little bit crook," senior assistant coach Simon Goodwin said after stepping in for Thompson.
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"There's been a virus going through the club over the last 10 days. He's got it, so he's missing today, but I'm sure he'll be back to his joking best over the next couple of days."He's keeping away from the team. We've pretty much said to anyone that gets crook, stay away from the club, stay away from the team so we can get rid of this bug."
Goodwin said the virus didn't have a major impact on the side heading into the clash against Fremantle and he was confident all players would be healthy for Saturday night's match against St Kilda.
Midfielder Brendon Goddard is "highly doubtful" to play against his former side after sustaining a groin injury against Fremantle but the Bombers will be buoyed by the returns of four key players.
Myers, ruckman Patrick Ryder and veterans Dustin Fletcher and Paul Chapman will return to the senior side this week, while Tom Bellchambers will play in the VFL.
The Bombers have two six-day breaks leading into their round five and six clashes against St Kilda and Collingwood, an issue now being compounded by illness and the sweltering conditions in Perth last Sunday.
Goodwin confirmed the players would have a lighter training load over the next fortnight to maximise recovery.Goodwin says Goddard is doubtful to play this weekend with a slight groin strain.
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"It's (the draw) what we've been given and it's a challenge for any club," he said.
"I think there is anomalies within the draw for any club and this is one for us. It was hot, we've got two six-day breaks, but our group is going to freshen up. We'll get the training we need to get in."