In New York City Sewage, a Mysterious Coronavirus Signal

In the city’s wastewater, these mysterious sequences, or cryptic lineages, have continued to appear.

Humans are not at risk from these lineages, which have circulated for at least a year without overtaking Delta or Omicron. On Thursday, the researchers published their findings in Nature Communications, but they still don’t know where they came from.

“We have not found the cryptic lineages in human databases, and we have looked everywhere,” said Monica Trujillo, a microbiologist at Queensborough Community College.

The origins of the lineages are a source of controversy among researchers. According to some, the virus comes from people whose infections aren’t being captured by sequencing. Nevertheless, others suspect the lineages may have come from virus-infected animals, possibly rats in the city. It is still possible for the favored theory to change from day to day or hour to hour.

There are still no answers.

“Finding the source is really important, but we haven’t been able to do so,” said John Dennehy, a virologist at Queens College.

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Strange sequences

Since June 2020, the researchers – including Marc Johnson, a virologist at the University of Missouri, Davida Smyth, a microbiologist at Texas A&M University, and others – have been sampling wastewater from 14 treatment plants in New York City. Targeted sequencing of the virus’s spike protein gene began in January 2021, focusing on part of the gene.

While this method provides a limited view of the viral genome, it allows researchers to extract a great deal of information from wastewater, which contains fragmented viruses.

Researchers found that viral fragments with novel mutation patterns appeared repeatedly at a handful of treatment plants. According to them, they were unable to disclose the specific plants or areas of the city.

“We have not seen these variants among clinical patients in New York City,” said Michael Lanza, spokesman for the city’s Department of Health and Mental Hygiene.

Rose Kantor, a microbiologist at the University of California at Berkeley, found similar sequences in one California sewershed.

The researchers’ continuing quest to figure out where the sequences come from highlights both the potential of wastewater surveillance, which can help scientists keep tabs on how the virus is evolving, and the challenge of making sense of any anomalies pulled out of the murk.

“Trying to figure out what we had was really difficult,” Doctorsaid.

There is a possibility that the lineages came from people whose infections have escaped detection or whose viruses have not been sequenced.

According to the researchers, the fact that they kept showing up at the same few wastewater plants makes this theory less plausible, since New Yorkers and any variants they may be carrying move freely throughout the city.

Nonetheless, Doctor speculated that the sequences could be coming from people who are confined to long-term health care facilities in just a few areas of the city. However, he has not been able to prove it.

Doctor said the problem was confined to a very small area of the sewershed. In those areas, I emailed doctors and hospitals and never received a response.”

People with compromised immune systems may have difficulty fighting off the virus, which allows it to mutate more easily. According to many scientists, Omicron originated from an immune-compromised individual.

Some of the cryptic lineages have the same mutations as Omicron, or mutations at the same locations. These lineages may also be able to evade some antibodies, according to laboratory experiments.

Some of the body’s immune defenses might have been evaded by the New York City lineages, the researchers theorize.

An animal origin?

In contrast, according to some scientists, the lineages have been circulating for long enough to have appeared in at least one sample sequenced from an infected person.

“In order to detect something in a sewershed, you need a fair amount of it around,” said Doctor  Lauring, a virologist at the University of Michigan.

Doctor, a Missouri virologist, agrees. A few specific populations with limited territories could be the source of the sequences, according to him. When the number of human Covid-19 cases in the city was low in May and June of 2021, the mysterious lineages made up a greater proportion of the viral RNA in wastewater, suggesting that they might not have been human.

In the beginning, researchers considered a variety of potential hosts, including squirrels and skunks. According to Doctor, this virus is very promiscuous. “It can infect all kinds of animals.”

As a result, they went back to the wastewater, assuming that any animal shedding virus might have also left behind its genetic material.

Researchers found that RNA from dogs, cats, and rats was also present in the water, despite the vast majority of genetic material originating from humans.

Doctor has considered rats, which roam the city in millions. Using the same mutations found in the cryptic sequences, he created harmless, nonreplicating pseudoviruses in his lab. Neither mouse nor rat cells were resistant to infection by the pseudoviruses, he revealed. Rodents can’t be infected by the original virus, but some variants, such as Beta, can.

“In and of itself, that isn’t a huge amount of data, but it supports the idea that it comes from rodents,” Doctor said.

The scientists have been working with Animal and Plant Health Inspection Service at the U.S. Department of Agriculture to test blood and fecal samples from rats in the area for signs of the virus. As of now, they haven’t found anything.

“We might not be hitting the right animals,” Doctor said.

Maybe rats aren’t the source of the mystery lineages. Scientists have repeatedly discovered that humans can transmit the virus to animals, especially pets, zoo animals, farmed mink, and others with whom they are in frequent contact. It has raised concerns that the virus may establish itself in an animal reservoir, where it might mutate and spread.

Rats, however, have not typically been of concern, and there has been no evidence that the virus is circulating in wild rats. Rats were also not infected by humans through unknown pathways.

According to Doctor, nothing makes perfect sense.

Scientists said animal origins remain a possibility.

Doctor believes it is equally plausible, if not more so, than a human origin.

As a result, the search continues. Johnson has developed a new technique that amplifies only non-Omicron sequences, making it easier to detect lineages. Also, he has begun searching for similar lineages in sewage samples from other states, which may provide further clues.

Doctor said, “We’ll find out eventually.”.

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