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How scientists traced a mysterious covid case back to six
toilets
This article first appeared in The Checkup, MIT
Technology Review’s weekly biotech newsletter. To receive it in your
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This week I have a mystery for you. It’s the story of how a
team of researchers traced a covid variant in Wisconsin from a wastewater plant
to six toilets at a single company. But it’s also a story about privacy
concerns that arise when you use sewers to track rare viruses back to their
source.
That virus likely came from a single employee who happened
to be shedding an enormous quantity of a very weird variant. The researchers
would desperately like to find that person. But what if that person
doesn’t want to be found?
A few years ago, Marc Johnson, a virologist at the
University of Missouri, became obsessed with weird covid variants he was seeing
in wastewater samples. The ones that caught his eye were odd in a couple of
different ways: they didn’t match any of the common variants, and they didn’t
circulate. They would pop up in a single location, persist for some length of
time, and then often disappear—a blip. Johnson found his first blip in
Missouri. “It drove me nuts,” he says. “I was like, ‘What the hell was
going on here?’”
Then he teamed up with colleagues in New York, and they
found a few more.
Hoping to pin down even more lineages, Johnson put a call
out on Twitter (now X) for wastewater. In January 2022, he got another hit in a
wastewater sample shipped from a Wisconsin treatment plant. He and David
O’Connor, a virologist at the University of Wisconsin, started working with
state health officials to track the signal—from the treatment plant to a
pumping station and then to the outskirts of the city, “one manhole at a time,”
Johnson says. “Every time there was a branch in the road, we would check which
branch [the signal] was coming from.”
They chased some questionable leads. The researchers were
suspicious the virus might be coming from an animal. At one point O’Connor took
people from his lab to a dog park to ask dog owners for poop samples. “There
were so many red herrings,” Johnson says.
Finally, after sampling about 50 manholes, the researchers
found the manhole, the last one on the branch that had the
variant. They got lucky. “The only source was this company,” Johnson
says. Their
results came out in March in Lancet Microbe.
Wastewater surveillance might seem like a relatively new
phenomenon, born of the pandemic, but it goes back decades. A team of
Canadian researchers outlines several historical examples in
this story. In one example,
a public health official traced a 1946 typhoid outbreak to the wife of a man
who sold ice cream at the beach. Even then, the researcher expressed some
hesitation. The study didn’t name the wife or the town, and he cautioned that
infections probably shouldn’t be traced back to an individual “except in the
presence of an outbreak.”
In a similar study
published in 1959, scientists traced another typhoid epidemic to one woman,
who was then banned from food service and eventually talked into having her
gallbladder removed to eliminate the infection. Such publicity can have a
“devastating effect on the carrier,” they remarked in their write-up of the
case. “From being a quiet and respected citizen, she becomes a social pariah.”
When Johnson and O’Connor traced the virus to that last
manhole, things got sticky. Until that point, the researchers had suspected
these cryptic lineages were coming from animals. Johnson had even developed a
theory involving organic fertilizer from a source further upstream. Now they
were down to a single building housing a company with about 30 employees. They
didn’t want to stigmatize anyone or invade their privacy. But someone at the
company was shedding an awful lot of virus. “Is it ethical to not tell them at
that point?” Johnson wondered.
O’Connor and Johnson had been working with state health
officials from the very beginning. They decided the best path forward would be
to approach 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 there’s a dangerous new variant lurking in our community,” Ryan
Westergaard, the state epidemiologist for communicable diseases at the
Wisconsin Department of Health Services, told Nature. But they also
wanted to try to help the person who was infected.
The company agreed to testing, and 19 of its 30 employees
turned up for nasal swabs. They were all negative.
That may mean one of the people who didn’t test was carrying
the infection. Or could it mean that the massive covid infection in the gut
didn’t show up on a nasal swab? “This is where I would use the shrug emoji if
we were doing this over email,” O’Connor says.
At the time, the researchers had the ability to test stool
samples for the virus, but they didn’t have approval. Now they do, and they’re
hoping stool will lead them to an individual 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
lineages, the more I am convinced that they are replicating in the GI tract,”
Johnson says. “It wouldn’t surprise me at all if that’s the only place they
were replicating.”
But how far should they go to find these people? That’s
still an open question. O’Connor can imagine a dizzying array of
problems that might arise if they did identify an individual shedding one of
these rare variants. The most plausible hypothesis is that the lineages arise
in individuals who have immune disorders that make it difficult for them to
eliminate the infection. That raises a whole host of other thorny questions:
what if that person had a compromised immune system due to HIV in addition to
the strange covid variant? What if that person didn’t know they were HIV positive,
or didn’t want to divulge their HIV status? What if the researchers told them
about the infection, but the person couldn’t access treatment? “If you imagine
what the worst-case scenarios are, they’re pretty bad,” O’Connor says.
On the other hand, O’Connor says, they think there are a lot
of these people around the country and the world. “Isn't there also an
ethical obligation to try to learn what we can so that we can try to help
people who are harboring these viruses?” he asks.
By:- STEPHANIE ARNETT/MITTR | ENVATO
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