“To have something in a sewershed that you’re detecting, you need a fair bit of it around,” said Dr. Adam Lauring, a virologist at the University of Michigan, who was not involved in the research.

Dr. Johnson, the Missouri virologist, agrees. He favors the hypothesis that the sequences are coming from animals, perhaps a few specific populations with limited territories. In May and June of 2021, when the number of human Covid-19 cases in the city was low, the mysterious lineages made up a greater proportion of the viral RNA in wastewater, suggesting that they may have come from a nonhuman source.

The researchers initially considered a diverse array of potential hosts, from squirrels to skunks. “This is a very promiscuous virus,” Dr. Johnson said. “It can infect all kinds of species.”

To narrow down the possibilities, they went back to the wastewater, assuming that any animal that was shedding virus might be leaving its own genetic material behind, too.

Although a vast majority of the genetic material in the water came from humans, small amounts of RNA from dogs, cats and rats were also present, the scientists found.

Dr. Johnson has been considering rats, which roam the city by the millions. In his lab, he created pseudoviruses — harmless, nonreplicating viruses — with the same mutations present in the cryptic sequences. The pseudoviruses were able to infect both mouse and rat cells, he found. The original version of the virus does not appear able to infect rodents, although some other variants, like Beta, can.

“So in and of itself, that isn’t huge data, but it is at least consistent with the idea that it’s coming from rodents,” Dr. Johnson said.