How serious is the Covid-19 threat to athletes at the Tokyo Olympics?

The decision to ban spectators from Olympic venues highlights the tightrope organisers are walking at these games.

Case numbers have been rising for the past three weeks in Tokyo and now average more than 600 a day, forcing the government, the International Olympic Committee (IOC), the Tokyo metropolitan government and the Olympic Organising Committee to bring in the ban.

"It is extremely regrettable that the games will be staged in a very limited manner in the face of the spread of novel coronavirus infections," president of the organising committee Seiko Hashimoto said.

"I am very sorry for ticket holders and local residents who were looking forward to the games."

At the same time, athletes from around the world are beginning to arrive in Japan en masse to finalise their Olympic preparations.

One-by-one, team-by-team, they're making their way to the Olympic village, which has long been seen as a potential Covid-19 seeding site for a super-spreader games.

The head of the Biosecurity Program at the Kirby Institute, Professor Raina MacIntyre, calls the village a "petri dish of variants".

"I think it's a very, very risky situation and I would expect to see some of these variants that have been geographically confined spreading more following this event," she said.

So what danger is there of Covid-19 spreading in the village, and what potential is there for it to break out into the Tokyo population?

First, the good news:

"The village itself is really controlled quite closely, so teams are kept in bubbles and kept apart from each other and people," Deakin University epidemiology chair professor Catherine Bennett said.

The IOC says that about 84 percent of Olympic delegations will be vaccinated - that includes the 11,000-odd athletes who will make their way through the village over the course of the Games, and perhaps an equal number of support staff.

And they won't all be there at the same time. Athletes are only allowed to arrive five days before they compete and must leave no later than two days after they finish.

The Australians will be leaving one day after their last event.

The Covid-19 protocols are strict. Anyone going to the Games has to have two negative Covid-19 tests in the four days before they fly to Tokyo, and another on arrival at the airport.

Athletes will be then tested daily.

Those tests have already caught out a Ugandan athlete and coach, and a Serbian athlete.

We don't know who isn't vaccinated

What isn't known is just which athletes make up the remaining 16 percent who have refused to get vaccinated.

The United States, for instance, will have the largest team at the Olympics, and while all athletes have the option of vaccination, not everyone has taken it up.

It is the same with the Australian team of 484 athletes.

The Australian Olympic Committee says about 98 percent of athletes will be fully vaccinated, which equates to 10 deciding not to get a jab.

At the village, athletes are discouraged from congregating in places like the food hall. Instead they'll be encouraged to pick up the food and eat outside, or in their rooms.

The Australians will not be using the village gym, they will build their own and make sure everyone who uses it will be wearing masks.

The bad news is that despite all the checks in place, the virus can and potentially will spread in the village, which was designed before Covid-19.

MacIntyre is concerned about the potential for airborne spread of the virus in the village despite the precautions in place.

"We've seen lots of breaches in hotel quarantine in Australia, [and] the same issues are there," she said.

"There's infection being brought in by athletes, and it will still get in even with the protocols, because you can get several false-negative tests before finally testing positive, and you can be asymptomatic.

"So you're then getting a petri dish of variants potentially in Japan from the athletes and ancillary people coming in from all over the world, and these can spread."

But Bennett said she thought the checks in place would control Covid-19 if it did come into the village.

"I think it'll be controlled if there is an issue, I think it'll be contained very quickly and I don't think it will impact lots of people in terms of infection," she said.

But there is a caveat.

"I think the risk is probably amongst teams," she said.

"If you do have someone who either contracts the virus while in Tokyo or did unknowingly bring the virus to the village before they're discovered to be positive, there is a risk that there'll be disruption.

"Other people will then be forced to isolate or may not be able to be involved in events, even if they're not positive."

And that's the worse-case scenario for Olympic organisers and athletes. A positive test means that not only will that athlete be out of the Games, but their close contacts will also have to stop competing.

That could potentially shut down an entire sport - particularly high-contact sports or ones that are held indoors.

Which is what happened to some tennis players who couldn't train at this year's Australian Open.

"If they were on a plane with someone who was positive, even if no one else on that plane contracted the virus, it was a disruption to their preparation, so I think that's the reality of trying to run these events in Covid-19 time," she said.

Crowd ban to protect the wider population

Bennett thinks the decision to ban spectators has minimised the risk to the broader Japanese population, although she said the ban was always about stopping transmission within large crowds, given the relatively high level of virus circulating in the community.

But she said it could still leak out of the village through volunteers or workers at the village.

This week two staff tested positive and later admitted they'd been eating in a group with two other village workers, which was a breach of the organising committee's rules.

"And of course, that works both ways, like our hotel quarantine workers - the issue of taking the virus out of the village," Bennett said.

As we've all found out over the past 18 months - and Sydney residents are learning yet again - the best laid plans can fall apart if people don't comply with the rules.

The basics of wearing masks and keeping socially distanced as well as the high vaccination rate will all help, but there's one thing that some athletes might find hard to comply with.

"You've got a bunch of young people going and they all want to have a good time," MacIntyre said.

"The other thing that's never accounted for, but contact tracers know all about, is sexual contact, right?"

The eyes of the world will be watching over the two weeks of the games, and organisers will be desperate to suppress and isolate any positive cases.

If the Olympic village is indeed a petri dish as Professor MacIntyre suspects, it will be one watched closely by the world's epidemiologists, because no experiment like it has ever been carried out.

- ABC