There’s something mysterious in New York City’s wastewater, and some think the city’s rats are to blame.

Since the early days of the pandemic, scientists have used samples of New York City’s wastewater to track the rise and fall of COVID-19 cases in the population. People shed viral RNA in their poop, and it all ends up at the city’s sewage treatment plants, making it relatively easy to track more significant infection trends and monitor the emergence of new variants.

But in a new academic paper published in Nature Communicationsxc2xa0this week, a group of researchers reported finding mysterious viral RNA fragments with mutations that don’t belong to any case of COVID ever sequenced in a person. They refer to these mutations as “cryptic lineages” and reported finding them consistently in several, but not all, of the wastewater treatment locations they sampled.

While the paper offers a few possible human explanations, it also proposes an unusual hypothesis: the city’s rat population may have developed its own unique strain of COVID.

Marc Johnson, a virologist at the University of Missouri and one of the paper’s authors, told Thrillist that his first instinct after discovering some of these unusual mutations was to Google it.

“What came up immediately was that this is a mutation they had made in the virus when they made a rodent-adapted SARS-CoV-2,” he said. “When you mutate this position, it gains the ability to infect rodent cells. And a light went off, like, ‘Oh, maybe these aren’t coming from people.'” He successfully infected rodent cells with a harmless version of the mutated virus in his lab, showing that the explanation was at least plausible.

The rates of these viral mutations in the wastewater were not connected to the ebbs and flows of the virus in the human population, another sign pointing to a possible animal reservoir. In fact, the mutations made up a larger share of sequencing when cases in New York City were low.xc2xa0

After considering many of the animals that call NYC home, the team narrowed it down by analyzing animal DNA found in the wastewater samples. “The ones we really thought about were rats and dogs, predominantly,” said Davida Smyth, a microbiologist at Texas A&M University and another paper author. “We see this consistently over time, and we’re not seeing it with people. The most likely thing, we’re thinking, is rats because of the density.”

Thus far, the rat theory is missing one key ingredient. The team hasn’t been able to identify the virus in rats. “We’ve looked like crazy to try and find it in rats, and we have not succeeded,” Johnson said.

The paper also proposes several other explanations, such as inadequate test sequencing, long-term immunocompromised patients, or even a virus that’s not being caught by testing because it develops in the gut rather than the nose.

“The fact that the mutations aren’t spreading throughout the city, the fact that they’re geographically constrained to a specific regions of the city, limits which of those hypotheses are the most likely,” Smyth said, noting that their investigation is constrained by the financial realities of New York academia. “With limited resources, money, and manpower, you can only do so much. Without funding we can’t go crazy, and that limits us considerably.”

Although there haven’t been any documented cases of rats transmitting COVID to people, incidents with hamsters in Hong Kong and minks in Denmark show that there are risks that need to be monitored. “It is something we should keep our eye on just like we do for influenza… in wild birds,” Johnson cautioned. “I think the same would be appropriate for this virus.”

While the mystery hidden in NYC’s poop has yet to be solved, New Yorkers’ feelings about the rodent citizens they share a home with are no secret. The city saw a record number of rat complaints last year.

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