Career highlight: Olympic gold medallist with Australia's 4x100m medley relay team in 2008
Recent performance: 100m backstroke winner at Santa Clara meeting in 59.77 seconds - the fifth fastest time of 2011
"I was swimming absolutely terribly," she says. "My 200-metre backstroke was shocking. I was just passing the 15 metres-to-go rope and I saw the board and the names of the people who were already finished and I started crying."
Within a few days the teenager was diagnosed with Swine Flu. Seebohm was hospitalised and kept in an isolation ward to prevent contaminating anyone else.
"I was scared," she recalls. "I was in hospital for four days. It was very boring. Getting back into training after that was really hard. I was struggling all the time. I was fatigued. I couldn't keep up with everyone else.
"I knew national trials were coming up and I wasn't anywhere near where I wanted to be."
This, though, was just the beginning.
'Not right to race'
Over the coming months the multiple world record breaking swimmer endured several bouts of tonsillitis, bronchitis and pancreatitis.
Her mother Karen, herself a successful swimmer, was watching in the stands.
"It was very worrying. I knew something was wrong," says Karen.
"I couldn't see her coming past after a race. Then I saw her coach go down. I knew there was trouble and he waved for me to come down.
"In some ways it wasn't surprising because for the first time ever Emily had told me she felt she was not right to race. To her credit she gave it everything she could and that was the outcome of pushing herself to the limit."
The remainder of 2011 saw the Australian spend nearly as much time with doctors as swimming coaches.
I want to go back and do something I haven't done yet and get my own individual medal. Hopefully it's gold and hopefully I'll be singing my national anthem again
At the World Championships in Shanghai last summer she failed to podium, rounding off a torrid six months. While she admits she considered quitting the pool altogether as a result, she says the time in hospital motivated her to keep swimming.
"I kept saying every time I got sick: 'This is it, I'm going to pull out,'" says Seebohm.
"But every time I was in hospital I'd get so bored of being there I'd think: 'I'm going insane, I've got to go back to training.' So it actually kept pushing me back to the pool."
Doctors are still trying to get to the bottom of what caused the illnesses. Their most recent theory is that it may all be linked to some form of extreme allergy.
Whatever the cause, Emily is now looking forwards again, hoping the worst of her ill health is behind her.
'Hopefully it's gold'
While the huge impact on her training is not in doubt, Seebohm's coach Matt Brown thinks the whole saga may yet make her stronger.
"I think it's probably made her hungry," he says.
"I think it's kept her under the radar a bit as well. It's made her less of a target for her opponents. And I think that's been good.
"There is still a lot of work to do. She's got to get on the Australian team first. But we're not in this to come second or third. I think her dream is to be on that number one spot. But it's tough.
"As we saw in Shanghai, the difference between first and fourth is about 0.16 seconds. She knows what it's like to win and she knows what it's like to miss out."
The next stage for the teenager is arguably one of the toughest swimming competitions in the world - the Australian Olympic trials in Adelaide in March.
Only then can she be sure her dream of making it to London and adding more Olympic success to the relay gold from Beijing is still alive.
"I want to go back and do something I haven't done yet and get my own individual medal," says the swimmer.
"Hopefully it's gold and hopefully I'll be singing my national anthem again."
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