Researchers Find Coronavirus Mutations in NYC Sewage, Pointing To Possible Rat, Dog Infections

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A group of researchers charged by New York City with scouring human sewage for signs of the coronavirus — and its many mutating variants — made a startling discovery in April.

After months of testing and re-testing, they found four combinations of COVID mutations that, when compared to a global database of more than 2.5 million sequenced variants, had not been seen before. The four variants are at least somewhat antibody-resistant, which could reduce the effectiveness of vaccines, the researchers found.

The team of virologists and microbiologists from CUNY’s Queens and Queensborough colleges, the New School and the University of Missouri have been studying sewage from the city’s 14 wastewater treatment plants since June 2020, collecting samples in plastic bottles once a week and analyzing them to see concentrations of the virus. Since January, the researchers have gone a step further, analyzing the sewage for different COVID-19 variants.

The data is preliminary and has not been peer-reviewed or published in a scientific journal. Some outside experts say it’s far too early to raise alarms. But there’s one troubling possibility about where the new sewer mutations are coming from, according to a preprint study published by the researchers on Thursday.

As with other animals, COVID-19 could be infecting dogs and rats, leading to new mutations and an outbreak in New York City’s sewers. While animal-to-human transmission of the virus is exceedingly rare, it has been seen in the U.S. in minks.

‘Do It Ourselves’

Despite the potential implications, the researchers say the presentation last month of their findings to city officials earned a muted response.

They were told they could investigate further, but the city’s Department of Environmental Protection initially offered no additional funding or support for their efforts.

“The city officials basically told us if we wanted to do any kind of surveillance of the rats we would have to do it ourselves,” Dr. Marc Johnson, a virologist at the University of Missouri, wrote in a June 9 email obtained through an open-records request by the Documenting COVID-19 project. “They had zero willingness to help explore this potential public health risk.”

In a statement, city Department of Health and Mental Hygiene officials said they had reviewed the team’s findings, which they called “preliminary,” and were working to determine the origin of the mutations.

The city noted that there have been no confirmed infections of rats. They pointed to a study in Antwerp, Belgium, last winter that found no rats were infected with the virus, though that study left open the possibility that mutations could leave rodents susceptible to the virus.

“There are various possible explanations for the mutations identified and we will discuss theories with scientific and government partners,” wrote Patrick Gallahue, a Department of Health spokesperson. “One thing we do know from clinical testing and surveillance is that COVID-19 is circulating in NYC and the best way for New Yorkers to protect themselves and others is to get vaccinated.”

When contacted by the Documenting COVID-19 project and THE CITY about their study, the researchers said they are barred from speaking publicly.

But the preliminary wastewater findings, coupled with the initial reluctance by city agencies to investigate reflects New York’s scaling back of resources aimed at combating the virus, at a time when evolving variants and case rates in the city and across the country are climbing, experts say.

“There’s so much we don’t know about this virus,” said Dr.Kartik Chandran, a professor of environmental engineering at Columbia University, who has done similar wastewater work in Bergen County, N.J., Provincetown, Mass., and in correctional facilities in the southern U.S. “And we need to be asking these questions and looking for answers.”

Wastewater Collected

Since last year, New York City has been testing sewage for signs of COVID-19. At the Newtown Creek plant in Greenpoint, Brooklyn — the largest facility by volume in the city, handling the waste of millions of New Yorkers — workers descend four stories to a concrete basin that opens to a river of raw sewage.

They then fill two 500-milliliter bottles with wastewater, which they analyze at the DEP’s on-site laboratory.

Starting in January, the team of city virologists and microbiologists began using a novel way to analyze the samples for the presence of COVID variants — including the new Delta variant, which was first found in India, and has quickly become the dominant strain in the U.S. — by isolating and sequencing RNA from the virus.

The researchers began testing the city’s wastewater as a complementary approach to studying the virus’ mutations instead of strictly relying on clinical samples. Most lab samples come from seriously ill patients, not those who are asymptomatic or mildly ill recovering at home.

All viruses mutate and some mutations are more problematic for human health than others.

By sequencing the COVID RNA and focusing on the spike protein mutation, researchers can identify new vaccine-evading variants early and serve as a warning system for outbreaks, weeks before positive-test and hospitalization rates rise. In the process, they also found four new COVID “lineages,” or variants, of coronaviruses in the city’s sewer system, on spike protein mutations Q493K, Q498Y, H519N and T572N.

‘Necessitate Further Study’

Their work is funded through a more than $300,000 contract with the city. The Missouri Department of Health and Senior Services with the University of Missouri is assisting in analyzing the data, through a $2 million National Institutes of Health grant.

The team began testing rat feces for the coronavirus to see whether that was the source of the new spike protein mutations — but nothing matched their initial finding.

They then surveyed the sewage, using a process called “deep sequencing,” for animal DNA. They found evidence of various mammals, such as cows, pigs, and sheep, which likely came from human food consumption, along with evidence of dogs, cats and rats.

But most of the mutations were found over three different wastewater plants spanning months. That meant the “animal reservoir” would have to be living in or near the sewershed; largely constrained to their geographic location; in big enough numbers to sustain an epidemic for six months.

The most likely culprits: rats and dogs.

“These novel lineages could be relevant to public health and necessitate further study,” the researchers wrote in the study.

As for the mutations themselves, their origin remains an open question.

The researchers hypothesize that since not all COVID-19 cases were diagnosed and not all positive samples were sequenced, the “cryptic lineages” could come from “asymptomatic, vaccinated, immunosuppressed, pediatric, or chronically infected patients who are not being sampled in clinical settings.”

COVID-19 could also linger in different areas of the body, such as the gut, long after it’s been cleared in other areas, like the respiratory tract — potentially explaining the presence in wastewater.

An ‘Unbiased Look’ at Spread

New York City is not the only city using this method to test for coronavirus on a wide scale as a way to predict community outbreaks. Similar work is being done across the country in cities in Missouri, Massachusetts, California and Nevada, where wastewater helps predict spikes in cases in Las Vegas.

“For the most part, In Vegas, it aligns pretty well so when we start to see the cases, the concentrations in the wastewater are also increasing,” Daniel Gerrity, principal research microbiologist for the Southern Nevada Water Authority, said in an interview. “In general, wastewater provides an unbiased look at what’s happening because it doesn’t require people to go get tested.”

The CDC is expanding its local wastewater testing, with $33 million spread across dozens of public health labs.

A Massachusetts company, Biobot Analytics, is working on a federal grant to collect samples from 320 treatment plants across the U.S. In Missouri, the state health department sends weekly reports from Johnson’s research to its local health counterparts, and that data has largely tracked the spread of the Delta variant across the state.

In New York, wastewater testing is not only conducted on a citywide scale, but also with smaller samples, including at Columbia University residence halls. The university began ramping up testing in September 2020, with the help of a $2.5 million grant from the National Institutes of Health, to detect traces of the genetic material from the coronavirus in dorms. That data is then cross-referenced with student positivity rates.

The university is currently testing six dorms and will begin examining wastewater in all 16 residence halls once students return in the fall.

“The surveillance can be really important to give us a signal because we are not doing regular testing of the vaccinated,” said Dr. Waafa El-Sadr, an epidemiology professor at Columbia University who is spearheading the school’s response to the virus. “But if we get a spike in the wastewater then our intent is, we immediately must test all the residents in that facility.”

‘Get the Vaccine’

In Bergen County, which is larger than five states and the District of Columbia, Chandran and his team from Columbia found signs of a looming “third wave” in mid-October. Those signals from the New Jersey county hardest hit during the pandemic were eventually seen in soaring testing and hospitalization numbers by Thanksgiving.

Another recent uptick in COVID-19 sewage signals — usually a two-to-three week leading indicator of cases — has been seen in a handful of urban and suburban communities in southern Bergen County, resulting in coordinated vaccination drives and messaging to local leaders, according to officials.

“It allows us to put our plans into place and mobilize our mobile units, begin outreach for testing and vaccination in the heart of these communities and explain to people that the science and data is supporting what we’re telling you: Get the vaccine,” said Bergen County Executive Jim Tedesco in an interview. “Fortunately, we don’t have a rat problem like New York does and, as a predictor of information, this is somewhat vital in putting our response plan together.”

Bergen County is seeking to continue its wastewater program, which collects samples six days a week from its Little Ferry treatment plant and employs AECOM, an infrastructure consulting firm, to analyze the data.

So far, the program has cost $370,000 in federal CARES Act funds along with an additional National Science Foundation grant. Bergen County officials and researchers now meet once a week to discuss the latest findings.

In New York City, researchers are hoping wastewater will similarly provide answers to how to deal with future outbreaks and target resources to the most vulnerable populations.

Signs of More Rats

If the new spike protein mutations the researchers discovered points to an outbreak of coronavirus among city rats, they would not be the first animal to contract the virus.

There have been reports of dogs, cats and even a New York City tiger catching the virus, according to the CDC.

A study published Wednesday by the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service found that white-tailed deer populations in New York, Michigan, Illinois and Pennsylvania had coronavirus antibodies, meaning they had previously contracted the virus, although they did not show signs of an active infection.

In November, Denmark culled 17 million minks after the virus jumped from a human handler to the minks, then back to humans. In Michigan, a taxidermist became infected with coronavirus and, after his test results were sent to a lab, it was determined that there was a mutation in his sample that came from an infected mink.

Rats, notable disease carriers, have long been a scourge on the city and, as with human New Yorkers, the coronavirus has had an outsized impact on them. There were increased reports of aggressive behavior among the rodents during early months of the pandemic due to a shortage of garbage to eat — so much so that the CDC issued a warning about their behavior in March 2020.

The lack of food also led to a drop in the rat population as many either starved or turned on each other. Bobby Corrigan, an urban rodentologist dubbed the city’s “rat czar,” estimated that millions of rats died in New York throughout the pandemic.

However, since then, the rat population has surged past its pre-pandemic levels in some rodent hotspots because of the increased food and space available, according to Corrigan.

“There’s certain blocks within certain boroughs in New York City where it’s the perfect storm for rats,” Corrigan said. “In those areas, I suspect they are actually back now in greater numbers than before the pandemic.”

In New York City, 311 complaints about rats dropped during the peak of the pandemic, only to skyrocket as the city reopened. According to Corrigan, the increase in calls could either be due to the increased rat population or because the rodents migrated from commercial areas, where restaurants used to leave their food, to areas with more housing as people shuttered themselves in their homes.

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