New York City Might Have Rat COVID, But It’s Probably Fine

Photo: Gary Hershorn/Getty Images

Over the past year, scientists keep seeing a COVID-19 oddity showing up in New York City’s sewer system: bits and pieces of virus in the wastewater that suggest there’s a mysterious new variant in the city. Thankfully, there’s no evidence that it’s particularly infectious or deadly. But scientists aren’t sure where the “cryptic lineages,” as researchers call the fragments, are coming from. One theory is that the virus is coming from people whose strains have yet to be sequenced. But another is totally and utterly alarming: that this variant could be courtesy of the city’s rats.

A new paper about the mystery was published in Nature Communications last week. Curbed spoke with four of the co-authors — John Dennehy, a virologist at Queens College; Monica Trujillo, a microbiologist at Queensborough Community College; Marc Johnson, a virologist at the University of Missouri; and Davida Smyth, a microbiologist at Texas A&M University — about whether or not New Yorkers should be bracing themselves for a rat-COVID wave.

What’s the argument that this variant is coming from rats?

Marc Johnson: One of the amino-acid changes that we’re seeing in the virus has not been seen in patients. Ever. But this amino-acid change has been seen in rodent-adapted virus, which really says something to me. In immunocompromised patients, you see a lot of similar mutations, but this one particular mutation right at the receptor binding site has just not been found. If these lineages are coming from an immunocompromised patient, it is probably that, a single patient, and it’s really hard to believe that this much signal could come from one person.

How could rats even catch COVID? 

Johnson: Alpha, Beta, and Gamma have gained the ability to infect rodents, but the original strain of COVID could not.

John Dennehy: They’re probably drinking sewer water, and I heard they eat feces, so if there’s any clumps of material in the wastewater, I’m sure they might try to consume it. We’ve never detected live virus in the wastewater. But given the volume of wastewater and the number of rats, it’s certainly possible that they’ve gotten infected that way.

What points toward rats over other animals?

Johnson: There was a figure in the paper where we actually show that these lineages have all gained the ability to utilize the rat receptor. It was this suspicion that led us to do the experiment that confirmed this: I was like, “Well, probably not rats, but if it is rats, then it should have gained the ability to infect rat cells,” and sure enough, the virus did.

Based on that hunch, you tested for signs of the virus in city rats. What does that entail? 

Johnson: So John would go wandering around dark alleys at night and collect rat feces for me and he’d put them in Ziploc bags, label them, and send them to me. My brave undergraduates would plug their noses and extract the RNA from them the same we do with wastewater, and screened them for SARS-CoV-2 RNA. None of those came back positive. In the case of APHIS [the Animal and Plant Health Inspection Service in the U.S. Department of Agriculture, which was a research partner], they would collect blood from rats and send them to us and we would check to see if they had antibodies against SARS-CoV-2, which would tell us if they’ve been previously infected, and none had clear antibodies.

Dennehy: It’s estimated that there are at least a couple million rats. We only tested, what, almost 100? It’s quite possible we didn’t collect the right animals.

Is there any evidence that COVID-19 is widely circulating in rats?

Johnson: Not that we know of. It’s kind of haunting, but it’s coming from somewhere.

Monica Trujillo: I think the important thing to keep in mind here is that every time the virus replicates, it has a possibility to mutate. So if there is a population where you are not aware where the virus is replicating, that is worrisome. That is why it’s important to know where these cryptic sequences are coming from.

But have new variants developed in animal hosts? Has that been documented?

Dennehy: Not that we know of. Omicron is possibly hypothesized to come from animals in Africa, but that’s not proven. There are some instances where other animals have gotten infected and then spread it back to humans. I think mink is an example.

Johnson: The one that jumped into mink mutated a little bit, but nothing like what we’re seeing.

What does that say to you? Could rats, if infected, possibly reinfect humans with a new strain?

Johnson: We don’t know where Omicron came from. So we don’t know where Pi [an as yet nonexistent variant] is going to come from — but these animals sure look like likely candidates.

So … could rats potentially spread the virus in the city?

Dennehy: Yes and no. I think rodents tend to inhabit the same spaces as we do. I think probably there are often more interactions with humans and rats than we realize, not necessarily physical contact, but touching the same surfaces, that sort of stuff. Perhaps rats could exhale the virus into the air in certain areas — the subways.

Johnson: It doesn’t mean it’s an immediate, imminent threat. It’s worth paying attention to, but it’s not worth panicking over. It’s theoretically possible, but we’ve been following these lineages for over a year now and we haven’t seen it happen yet.

Davida Smyth: Rats are known to be vectors. They do transmit things, but it’s very rare. So one of the major things we see, for example, is leptospirosis. That’s something that does pop up from time to time. It’s associated with the urine of a rat, but it’s very, very rare. So in order for you to be infected by a rat, you’d have to be living in very close quarters with the rats.

What’s the worst-case scenario here? The best-case one?

Johnson: If it is in rats, it could be that it can only infect rats and loses the ability to infect humans altogether. That’s fully possible. Worse-case scenario is it spills back into humans and it’s Pi. Best-case scenario is it takes care of your rat problem. Problem solved.

This interview has been edited and condensed for clarity.

New York City Might Have Rat COVID, But It’s Probably Fine