In New York’s sewage, a mysterious coronavirus signal

“To have something in a sewer that you detect, you need a good chunk of it,” said University of Michigan virologist Dr. Adam Lauring, who was not involved in the research.

Dr. Johnson, the Missouri virologist, agrees. He favors the hypothesis that the sequences come from animals, perhaps a few specific populations with limited territories. In May and June 2021, when the number of human cases of Covid-19 in the city was low, mystery lineages made up a greater proportion of the viral RNA in the sewage, suggesting they may have come from a source not human.

The researchers first considered a wide range 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 the possibilities, they went back to the sewage, assuming that any animal that shed a virus might also leave behind its own genetic material.

Although a large 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 envisioned the rats, which roam the city in their millions. In his lab, he created pseudoviruses – harmless, non-replicating viruses – with the same mutations present in cryptic sequences. The pseudoviruses were able to infect mouse and rat cells, he found. The original version of the virus does not appear capable of infecting rodents, although some other variants, such as Beta, can.

“So by itself it’s not huge data, but it’s at least consistent with the idea that it came from rodents,” Dr Johnson said.

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