The International Olympic Committee said Sunday it will order testing for disease-causing viruses in the sewage-polluted waters where athletes will compete in next year’s Rio de Janeiro Games.

Before, the IOC and local Olympic organisers in Rio said they would only test for bacteria in the water, as Brazil and virtually all nations only mandate such testing to determine the safety of recreational waters.

But after an Associated Press investigation published last week revealed high counts of viruses directly linked to human sewage in the Olympic waters, the IOC reversed course after being advised by the World Health Organisation (WHO) that it should expand its testing.

“The WHO is saying they are recommending viral testing,” IOC medical director Dr Richard Budgett said. “We’ve always said we will follow the expert advice, so we will now be asking the appropriate authorities in Rio to follow the expert advice which is for viral testing. We have to follow the best expert advice.”

On Saturday, the International Sailing Federation (ISAF) became the first to break with the IOC’s insistence on bacteria-only testing, saying it would do its own independent tests for viruses.

“We’re going to find someone who can do the testing for us that can safely cover what we need to know from a virus perspective as well as the bacteria perspective,” said Peter Sowrey, chief executive of the ISAF. “That’s my plan.”

That came after the WHO said on Saturday that it had advised the IOC to test for viruses.

A five-month Associated Press analysis of water at each of the venues where about 1,400 Olympic athletes will have contact with water showed dangerously high levels of viruses from sewage.

The Associated Press commissioned four rounds of testing in each of those three Olympic water venues, and also in the surf off Ipanema beach, which is popular with tourists but where no events will be held. Thirty-seven samples were checked for three types of human adenovirus, as well as rotavirus, enterovirus and faecal coliforms.

The Associated Press viral testing, which will continue in the coming year, found not one water venue safe for swimming or boating, according to global water experts who analysed the data. A risk assessment done based on the Associated Press’s study found that athletes who ingest just three teaspoons of water have a 99% chance of being infected by a virus – though that does not automatically mean they would fall ill. That depends upon a person’s immune system and a number of other factors.

The concentrations of the viruses in all samples were roughly equivalent to that seen in raw sewage – even at one of the least-polluted areas tested, Copacabana beach, where marathon and triathlon swimming will take place and where many of the expected 350,000 foreign tourists may take a dip.

In Rio, much of sewage goes untreated and runs down hillside ditches and streams into Olympic water venues that are littered with floating rubbish, household waste and even dead animals.

A doll’s head floats in the polluted waters of a canal at the Mare slum in Rio de Janeiro, Brazil. Photograph: Leo Correa/AP

The pollution problem has been around for decades, and has sparked what top medical experts in Rio call an endemic public health crisis because of the dirty water in the otherwise stunning city circled by Atlantic rainforest and golden sand beaches.

On Sunday, athletes competed under a blazing Rio sun in an Olympic test event in the triathlon.

“It’s been an interesting learning experience over the last few days. I think some athletes went back to biology 101 to learn the difference between bacteria and viruses,” said American triathlete Sarah True, who has qualified for next year’s Olympics. “It’s kind of eye-opening for me that people didn’t differentiate the two.”

She said that for the athletes, “obviously it’s a concern – it’s a risk” but that “ultimately the Olympic dream is so strong that sometimes we put the pursuit of excellence above our health”.

True said she didn’t think the Olympic venue could be moved from Copacabana even if the IOC’s tests also find high viral counts.

“We can’t move,” she said. “Ultimately too much money has been invested.”

So far, neither the IOC nor the sailing federation has said who would do their testing. Virology experts in Brazil say there are only three or four labs with the molecular biology equipment and trained scientists who can carry out the testing for viruses in water.

The Associated Press’s tests are being conducted by Fernando Spilki, a respected virologist who is a board member of the Brazilian Society for Virology and editor of its scientific journal. He is not being paid by the Associated Press to conduct the testing, though the Associated Press is purchasing the lab materials required to carry out the research.

When Rio was awarded the games in 2009, it promised cleaning its waters would be an Olympic legacy. But Rio Mayor Eduardo Paes has repeatedly acknowledged this will not be done, calling it a “lost opportunity”.