‘Cryptic’ Covid variant found in NYC subway could come from rats, research suggests

The next Covid variant may come from New York’s subway rats, a new study has suggested.

Research published in Nature Communications in February claims the “cryptic lineages” in the sewage system are surprising and different from all other Covid variants – and these could potentially be transferred through the rodent population.

Scientists have regularly used samples of the city’s wastewater to get an estimation of the number of Covid cases among residents, as viral RNA can be found in faeces.

While scientists searched extensively, they haven’t yet found any rats with Covid in New York’s subways and sewers – but the combination of human waste from those with Covid, which ends up in the sewage system, and the same place being a rat’s habitat, could be the ripe conditions for a new variant to emerge in the rodents.

“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,” Marc C Johnson, co-author of the study, and a University of Missouri virologist, told Curbed.

According to Mr Johnson, rodents are not susceptible to the first strain of Covid, but could be infected by its Alpha, Beta and Gamma variants.

Study co-author and Queens College virologist John Dennehy added that rats are “probably drinking sewer water, and I heard they eat faeces, 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.”

There have been reports of hamsters transmitting Covid in Hong Kong and theories that farmers were infecting minks with coronavirus in Denmark, but whether a potential new rat variant would infect humans in New York remains to be seen.