How researchers traced a mysterious Covid case to six toilets
It sounds like the question in an exciting puzzle: How was a US research team able to trace a Covid variant from a wastewater treatment plant in the state of Wisconsin to six toilets in a single company? But there are also privacy concerns that arise when you use the sewer system to trace rare viruses back to their source.
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The virus likely came from a single employee who happened to shed an enormous amount of a very strange variant. The researchers would like to find this person. But what if that person doesn’t want to be found?
A few years ago, University of Missouri virologist Marc Johnson became obsessed with the strange Covid variants he found in wastewater samples. They were strange in several ways: they did not correspond to any of the usual variants and they did not circulate. They appeared in only one place, appeared there for a certain period of time and then often disappeared again. The outlier first appeared at Missouri State. “It drove me crazy,” Johnson says. “I asked myself, ‘What the hell is going on here?'” With the help of colleagues in New York, he pointed out a few more.
From the sewage treatment plant to the outskirts of the city
Hoping to uncover more lineages, Johnson posted a call for wastewater samples on Twitter (now X). In January 2022, he received another hit in a wastewater sample that came from a wastewater treatment plant in Wisconsin. Together with David O’Connor, another virologist at the University of Wisconsin, he began working with state health officials to track the signal: from the wastewater treatment plant to a pumping station and then to the outskirts of the city, “one manhole at a time ” says Johnson. “Every time there was a junction in the road, we checked which junction [das Signal] came.”
They followed some questionable leads. The researchers suspected that the virus could have come from an animal. O’Connor once took people from his lab to a dog park to ask dog owners for fecal samples. “There were so many distractions,” Johnson says.
After taking samples from about 50 storm drains, the researchers finally found the last drain hole in the pipe section that had the variant. You were lucky. “The only source was this one company,” Johnson says. The researchers recently published their results in the journal Lancet Microbe.
Wastewater monitoring appears to be a relatively new phenomenon brought about by the pandemic, but it has been around for decades. A Canadian research team has described several historical examples. In one case in 1946, a public health official traced an outbreak of typhus to the wife of a man selling ice cream on the beach. Even then, the researcher expressed some concerns. The study didn’t name the woman or the city, and he warned that infections probably shouldn’t be traced back to one person “unless it’s an outbreak.”
In a similar study published in 1959, scientists traced another typhus epidemic to a woman who was subsequently banned from the restaurant industry and eventually persuaded to have her gallbladder removed to eliminate the infection. Such publicity can have a “devastating effect on the wearer,” the scientists said in their report on the case. “From a quiet and respected citizen, she becomes a social pariah.”
Don’t stigmatize anyone
Things got correspondingly dicey when Johnson and O’Connor traced the virus back to that last shaft. Until this point, researchers had suspected that these mysterious virus strains came from animals. Johnson had even developed a theory involving organic fertilizer from a source further upriver. Now they were limited to a single building that housed a company with about 30 employees. They didn’t want to stigmatize anyone or invade anyone’s privacy. But someone in the company had shed a whole lot of virus. “Is it ethical not to tell them at this point?” Johnson wondered.
O’Connor and Johnson had worked with state health officials from the start. They decided it would be best to contact the company, explain the situation and ask if they could offer voluntary testing. The decision wasn’t easy. “We didn’t want to cause panic and say that there is a dangerous new variant lurking in our community,” Ryan Westergaard, a communicable disease epidemiologist with the Wisconsin Department of Health Services, told Nature. But they also wanted to try to help the infected person.
The company agreed to a test, and 19 of the 30 employees had a nasal swab. They were all negative. This could mean that one of the people who did not get tested had the infection. Or could it mean that the massive Covid infection in the gut didn’t show up on a nasal swab? “At this point, if we were doing this via email, I would use the shrug emoji,” O’Connor says.
50 cryptic Covid variants in wastewater
At that time, researchers had the opportunity to test stool samples for the virus, but they did not have permission. Now they have one, and they’re hoping the chair will lead them to a person infected with one of these strange viruses who can help answer some of their questions. Johnson has identified about 50 of these cryptic Covid variants in wastewater. “The more I study these strains, the more convinced I am that they multiply in the gastrointestinal tract,” says Johnson. “It wouldn’t surprise me at all if that was the only place they reproduce.”
But how far should they go to find these people? This is still an open question. O’Connor can imagine a dizzying array of problems that could arise if they identified an individual who sheds one of these rare variants. The most plausible hypothesis is that the lines appear in people whose immune systems are impaired, making it difficult for them to clear the infection. This raises a whole host of other thorny questions: What if, in addition to the strange Covid variant, this person also had a weakened immune system due to HIV? What if that person didn’t know they were HIV positive or didn’t want to reveal their HIV status? What if researchers educated them about the infection, but the person didn’t have access to treatment? “If you imagine the worst-case scenarios, they’re pretty bad,” says O’Connor.
On the other hand, O’Connor said, it is believed that there are many of these people in the United States and around the world. “Isn’t it also an ethical obligation to try to find out as much as we can so that we can help the people who harbor these viruses?”
(jl)
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