Just days before the start of the Olympic Games the waterways of Rio de Janeiro are as filthy as ever, contaminated with raw human sewage teeming with dangerous viruses and bacteria, according to a 16-month-long study commissioned by The Associated Press.

Not only are some 1,400 athletes at risk of getting violently ill in disciplines such as sailing and open water swimming, but the AP’s tests indicate that tourists also face potentially serious health risks on the beaches of Ipanema and Copacabana.

The AP’s survey of the aquatic Olympic and Paralympic venues has revealed consistent and dangerously high levels of viruses from the pollution, a major black eye on Rio’s Olympic project that has set off alarm bells among sailors, rowers and open-water swimmers.

The first results of the study published over a year ago showed viral levels at up to 1.7m times what would be considered problematic in the United States or Europe. At those concentrations, swimmers and athletes who ingest just three teaspoons of water are almost certain to be infected with viruses that can cause stomach and respiratory illnesses and more rarely heart and brain inflammation — although whether they actually fall ill depends on a series of factors including the strength of the individual’s immune system.

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Since the AP released the initial results last July, athletes have been taking elaborate precautions to prevent illnesses that could potentially knock them out of the competition, including preventatively taking antibiotics, bleaching oars and donning plastic suits and gloves in a bid to limit contact with the water.

But antibiotics combat bacterial infections, not viruses. And the AP investigation found that infectious adenovirus readings — tested with cell cultures and verified with molecular biology protocols — turned up at nearly 90% of the test sites over 16 months of testing.

“That’s a very, very, very high percentage,” said Dr Valerie Harwood, chair of the department of integrative biology at the University of South Florida. “Seeing that level of human pathogenic virus is pretty much unheard of in surface waters in the US. You would never, ever see these levels because we treat our waste water. You just would not see this.”

While athletes take precautions, there is also concern for the 300,000-500,000 foreigners expected to descend on Rio for the Olympics. Testing at several of the city’s world-famous beaches has shown that in addition to persistently high viral loads, the beaches often have levels of bacterial markers for sewage pollution that would be cause for concern abroad — and sometimes even exceed Rio state’s lax water safety standards.

In light of the AP’s findings, Harwood had one piece of advice for travelers to Rio: “Don’t put your head underwater.” Swimmers who cannot heed that advice stand to ingest water through their mouths and noses and therefore risk “getting violently ill,” she said.

Danger is lurking even in the sand. Samples from the beaches at Copacabana and Ipanema revealed high levels of viruses, which recent studies have suggested can pose a health risk — particularly to babies and small children.

“Both of them have pretty high levels of infectious adenovirus,” said Harwood, adding that the virus could be particularly hazardous to babies and toddlers who play in the sand. “You know how quickly an infant can get dehydrated and have to go to the hospital,” she added. “That’s the scariest point to me.”

Dr Fernando Spilki, the virologist and coordinator of the molecular microbiology laboratory at Feevale University in southern Brazil whom AP commissioned to conduct the water tests, says the survey revealed no appreciable improvement in Rio’s blighted waters — despite clean-up promises stretching back decades.

“Unfortunately, what we’ve seen throughout all this time is that there is a variation in the levels of contamination, but it fluctuates much more as a result of climactic conditions than due to any measures that may have been taken to try to remove this contamination,” said Spilki, one of Brazil’s most respected virologists.

The most contaminated points are the Rodrigo de Freitas Lagoon, where Olympic rowing will take place, and the Gloria Marina, the starting point for the sailing races. In March, 2015, sampling at the Lagoon revealed a figure of 1.73bn adenoviruses per liter; this June, adenovirus readings were lower but still worrying at 248m adenoviruses per liter. By comparison, in California, viral readings in the thousands per liter are enough to set off alarm bells.

Facebook Twitter Pinterest Water and sand samples are collected from Copacabana Beach. A study has revealed and dangerously high levels of illness-causing viruses. Photograph: Silvia Izquierdo/AP

Despite a project aimed at preventing raw sewage from flowing directly into the Gloria Marina through storm drains, the waters remain just as contaminated. The first sampling there, in March, 2015, showed over 26m adenoviruses per liter; this June, over 37m adenoviruses per liter were detected.

While local authorities including the Rio mayor, Eduardo Paes, have acknowledged the failure of the city’s water clean-up efforts, calling it a “lost chance” and a “shame,” Olympic officials continue to insist Rio’s waterways will be safe for athletes and visitors. The local organizing committee did not respond to multiple requests for comment, though it has previously said bacterial testing conducted by Rio state authorities has shown the aquatic venues to be within state guidelines.

The crux of the issue lies in the different types of testing used to determine the health and safety of recreationalwaters.

Bacterial tests measure levels of coliforms — different types of bacteria that tend not to cause illnesses themselves but are indicators of the presence of other, potentially harmful sewage-borne pathogens such as other bacteria, viruses and protozoa that can cause cholera, dysentery, hepatitis A and typhoid, among other diseases. Bacterial tests are the worldwide standard because they’re cheap and easy.

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But there’s a growing consensus that they’re not ideal for all climates, as bacteria break down quickly in tropical weather and salty marine waters. In contrast, viruses have been shown to survive for weeks, months or even years — meaning that in tropical Rio low bacterial markers can be completely out of step with high virus levels.

That disparity was borne out in the AP’s testing. For instance, in June, 2016, the levels of fecal coliforms in watersamples from Copacabana and Ipanema Beaches were extremely low, with just 31 and 85 fecal coliforms per 100ml, respectively. But still, both had alarming readings for rotavirus, the main cause of gastroenteritis globally, with 7.22m rotaviruses per liter detected in the waters of Copacabana, while 32.7m rotaviruses per liter were found in the waters of Ipanema Beach.

The testing also revealed alarming spikes in fecal coliform levels — the very measure the state government uses to determine the safety of Rio’s recreational waters.

“If these were the reported values in the United States, let’s say in California, there is definitely an indication of a problem,” said Dr Kristina Mena, a waterborne virus expert at the University of Texas Health Science Center.

According to California’s bacterial tests standards, 400 fecal coliforms per 100ml is the upper limit for a beach to be considered safe for swimming. AP’s tests revealed that Copacabana Beach, where the marathon and triathlon swimming are to be held and thousands of tourists are likely to take a dip, exceeded California’s limit five times over 13 months of testing.

Nearby Ipanema Beach, which is not playing host to any Olympic sports but is among the city’s most popular tourist spots, exceeded California standards five times over 12 months, once spiking to nearly 50 times what would be permitted in California. One of two testing spots along the beach in the Olympic hub neighborhood of Barra da Tijuca once hit more than 60 times that limit over the five months testing was conducted there.

“If we had exceedances that consistently were in the thousands like I’m seeing here, there would be a high likelihood that that beach would be put on our list of impaired water bodies,” said Rik Rasmussen, manager of surface water quality standards at California’s State Water Board. That would lead to water quality warnings posted on the beach, possible beach closure, and the development of a program to root out the source of the contamination, he said.

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The beaches even violate Rio state’s own standards, which are much less stringent than those in California, many other US states and countries such as Australia and New Zealand. In Rio, beaches are considered unfit if bacterial tests turn up more than 2,500 fecal coliforms per 100ml — more than six times higher than the upper limit in California. But Copacabana and Ipanema even violated those much higher limits on three separate occasions. The state environmental agency, INEA, did not respond to repeated requests for comment.

Rasmussen acknowledged that the higher thresholds might make sense in Rio, where sewage pollution has been a perennial problem, meaning that locals are regularly exposed to the pathogens lurking in raw waste from an early age and therefore build up immunities. But visitors are unlikely to have such immunities, putting them at risk for illnesses.

After the AP’s initial report on the findings of the study in July of last year, the Olympics’ adviser on health matters, the World Health Organization, said it would carry out its own viral testing in Rio’s Olympic waterways. The agency later flip-flopped, finally concluding that bacterial tests alone would suffice.

Athletes who have trained years for a chance at Olympic glory have resigned themselves to competing in the filth.

“There’s been a lot of talk about how dirty the water is and all the viruses,” said Finnish team sailor Noora Ruskola. “I’m mentally prepared for this. Some days the water is totally OK, and some days there are bad days.”