Did the rodents population explosion in all big cities worldwide last several years play some causal role in the Covid Pandemic 2019 - 2022?
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Does Rodents' abnormally aggressive behavior suggest that they are infected with some variants of Sars-Cov-2 or other Coronaviruses that can be transmitted to humans? - Google Search https://
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The Ratpocalypse is Here - Why Rat Populations Are Booming During The COVID-19 Pandemic
May 19, 2020 7 min read
The recent COVID-19 pandemic has emptied city streets all over the world. Packed urban-centers jammed with cars and foot traffic are now empty, quiet, and devoid of humans. One population this is impacting is the urban rat. While food sources from scraps and trash deposits continue to deplete, rats have turned desperate and emboldened as the odds of survival stack up against them. Hungry, cannibalistic, and panicked, rats continue to search for their next meal. While the apocalypse may not be right around the corner, according to many experts, a Ratpocalypse could be!
It's the perfect storm for the year of the rat. The temporary closure/scaleback of countless restaurants and businesses have depleted rat food sources. Many rodents rely on scraps, trash and leftovers in urban areas as a means of survival.
According to experts, there is now a significantly larger prevalence of rodents in major U.S. cities than there was at the beginning of the novel Coronavirus pandemic. This has been reflected in numerous outlets and cities reporting a spike in rat activity.
Ratpocalypse Reports Increasing From Major Publications Around The World
Publications across the globe, have continued to report on the increase in rat activity:
12/3/21:‘You Dirty Rat’: Experts Posit That Omicron Hatched in Rodents - Infection Control
11/18/21:The next coronavirus could come from RATS: Rodents may be asymptomatic carriers of SARS-like viruses, study warns - Daily Mail
06/18/20: Rats at food markets and restaurants found to carry several strains of coronavirus - Independent
06/5/20: 5 reasons you might be seeing more wildlife during the COVID-19 pandemic - ScienceNews
05/28/20: Rodent sightings increase in residential areas during the pandemic - ABC News
05/26/20: Centers for Disease Control and Prevention says people may see an increase in "aggressive" rodent behavior since lockdowns - CBS
05/25/20: Rats growing more aggressive, even eating each other during pandemic - KTVU News
05/25/20: CDC warns of hungry rats roving empty streets, advising home and business owners to cover trash bins - The National Post
05/23/20: With restaurants closed, rat sightings are increasing across the United States - CNN
05/23/20: Rats are getting aggressive hunting for food amid restaurant closures, CDC warns - The Washington Post
05/19/20: Rats resorting to cannibalism, searching homes for food amid drop in restaurant diners - 22News/WWLP
05/18/20: Rats Adapt To A World In Pandemic Mode - WBUR
05/12/20: Hungry City Rats Are Looking for a New Lunch Spot Near You - Wired
05/07/20: Rats turning on each other, resorting to cannibalism in Pittsburgh during COVID-19 outbreak - WPXI News
05/04/20:New Yorkers now have to deal with cannibalistic rats during COVID-19 pandemic - Ladders
05/04/20:One More Thing to Think About during COVID-19: Rats in Your Engine Compartment - Car & Driver
04/30/20: ‘They’re climbing’: Exterminators say calls for rats in Baltimore homes have doubled during coronavirus pandemic - The Baltimore Sun
04/30/20: NYC to Step Up Rat Fight as Rodents Take Advantage of Social Distancing - NBC New York
04/28/20: Seeing more rats in Toronto during the pandemic? Pest control experts explain why - CBC
04/24/20: The rats are coming. Here’s how we can keep them away. - The Washington Post
04/21/20: As Chicagoans eat at home because of COVID-19, rats used to dining out on restaurant scraps follow the food supply - The Chicago Tribune
04/13/20: Starving, angry and cannibalistic: America's rats are getting desperate amid coronavirus pandemic - NBC
04/13/20: Rats! COVID-19 is bringing another problem to Canadian streets - CTV
04/13/20: Hungry rats may turn to cannibalism during the coronavirus outbreak, and it could lead to a breed of aggressive, resilient rats in the future - Insider
04/07/20: Coronavirus: Why more rats are being spotted during quarantine. - BBC
04/03/20:Rats come out of hiding as lockdowns eliminate urban trash - National Geographic
Hungry Rats Search For Food
One example of a growing Ratpocalypse comes from mid/late March 2020, from the famed New Orleans' French Quarter. The district boasted huge new swarms of rodent visitors who were perusing its historic streets. The YouTube videos and news reports quickly went viral.
Shortly after the COVID-19 pandemic forced restaurants and bars to close down in the historic center of Louisiana, the rats came out to play. Rats were spotted in packs like gangs, per some rodentologists.
For commensal rodents like the rat who depend on human litter and trash (whether it is in New York, Washington D.C., or Seattle), it was time to come up with another plan to feed themselves.
Because the pandemic induced a dearth in trash, rats are now even willing to risk coming out by day to find viable food sources.
Some are turning increasingly to residential areas to feed on household trash, which is more plentiful than ever with most cooking at home. The combination of food scarcity and desperation has caused some to speculate on a rat population boom or at least a visibility boom. In short, the Ratpocalypse could be coming to your doorstep in search of a food source.
The British-based National Pest Technicians Association warned earlier in April that closing down pubs, hotels, restaurants, schools, tourist hangouts, and similar public places in order to maintain social distancing rules will have unintended consequences for rat populations. Larger populations could quickly spring up in now-empty buildings and grow bolder because there are no people around (granted they find a viable food source).
Across major cities of the United States, there has been an increase in sightings of rodents in the last month. Seattle, Chicago, New York, and New Orleans have especially seen rising complaints regarding rat populations while under lockdown. The Baltimore Sun has reported some Baltimore exterminators have seen calls regarding rat infestations double.
Canada has also seen its share of increased rat activity. The CBC reports some exterminators in Toronto have seen a 20% increase in rat infestations. An article from CTV says increased calls are also coming in from Halifax, Winnipeg, Montreal, Regina, and Vancouver. The trend is disturbingly similar in other parts of the world too.
Rat Wars On City Streets; Cannibalism Among Rodents Becomes More Common
Another by-product of food scarcity has cause stressed rat colonies to increasingly turn to cannibalism to feed themselves. Rodents will first kill one of their own. Next, they then clean the meat off of the unfortunate victims down to the bone in no time. This grisly behavior in New York is becoming all too common. Some experts warn this continued cannibalism could lead to a breed of more agressive, smarter rats.
Expert rodentologist Bobby Corrigan shared the graphic image below in a Tweet on 4/16/20:
Rats Are Grand Masters of Adaptation
Rats are formidable animals that have become greatly successful by locating reliable sources of food using their sensitive noses. The COVID-19 pandemic has proved no different, they are easily able to reduce such barriers as plastics, doors, and fabrics in minutes. The pests are everywhere in the world because they are so adept at adapting to different conditions and circumstances.
The lockdown presents the perfect opportunity for rats to claim back city streets as municipalities struggle to engage with pest control professionals or develop control rodent control plans to deal with the boom of unwanted infestations. New Orleans has been doing precisely that while the French Quarter is closed down. They hope to control the city's thriving and growing rat population this way.
Rats Are Most Unwelcome House Guests
Hungry, angry, wandering rats can threaten the well-being of homes and their human and pet occupants. Besides potentially causing considerable damage as they enter and move about a house, they are also quite capable of spreading dangerous diseases to the home occupants. Unchecked, the rodents could end up in a child's bedroom or living in a nursing home or even a hospital ward. The bad news is that rats are historically connected with around 55 individual pathogens. Fortunately, so far no vermin have been positively linked as direct carriers of the coronavirus, although research still continues.
A specific danger in a home or business is that these rodents are able to easily gnaw through electrical wiring and wood, which can lead to house fires. Besides these more unlikely but still possible dangers, you do not want to let the rodents become overly familiar with your kitchens or to share your dinner meals with them now that times are hard for the pests. Car & Driver also warns of costly damage rats can do to your car by chewing engine wires.
Keeping Rodents Out of Your House During the Coronavirus Pandemic and Lockdown
An effective means of keeping the rodents from your own house is to deliberately seal up all areas that allow for the pesky creatures to enter the structure. This includes holes and cracks that exist near the pipes, utilities, or even foundation. From the inside of your home, you should eliminate all hiding places for them that you possibly can. Also, make an effort to clean up and eliminate any food source that rats could return to such as trash, pet food, unpackaged food.
We also recommend the use of effective and automatic traps that can allow you constant control without having to reset them daily. Our brand new Home Trapping Kit is the perfect addition to any home or business looking to protect against an ensuing invasion. The kit comes with a portable trap stand to move your A24 automatic trap around easily and our Quick Start Guide walks you through set up and the best places to set up your trap.
Weathering The Ratpocalypse
Traditionally, rat problems are human problems. Wherever we go, this opportunistic pest follows. That's because of the abundance of food that all species of rats have come to depend on from us. With the food scarcity reaching new levels across the globe for all types of rats, expect to hear and see more from these adaptable creatures.
Photo: Gary Hershorn/Getty Images
Over the past year, scientists keep seeing a COVID-19 oddity showing up in New York City’s sewer system: bits and pieces of virus in the wastewater that suggest there’s a mysterious new variant in the city. Thankfully, there’s no evidence that it’s particularly infectious or deadly. But scientists aren’t sure where the “cryptic lineages,” as researchers call the fragments, are coming from. One theory is that the virus is coming from people whose strains have yet to be sequenced. But another is totally and utterly alarming: that this variant could be courtesy of the city’s rats.
A new paper about the mystery was published in Nature Communications last week. Curbed spoke with four of the co-authors — John Dennehy, a virologist at Queens College; Monica Trujillo, a microbiologist at Queensborough Community College; Marc Johnson, a virologist at the University of Missouri; and Davida Smyth, a microbiologist at Texas A&M University — about whether or not New Yorkers should be bracing themselves for a rat-COVID wave.
What’s the argument that this variant is coming from rats?
Marc Johnson: 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. In immunocompromised patients, you see a lot of similar mutations, but this one particular mutation right at the receptor binding site has just not been found. If these lineages are coming from an immunocompromised patient, it is probably that, a single patient, and it’s really hard to believe that this much signal could come from one person.
How could rats even catch COVID?
Johnson: Alpha, Beta, and Gamma have gained the ability to infect rodents, but the original strain of COVID could not.
John Dennehy: They’re probably drinking sewer water, and I heard they eat feces, 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.
What points toward rats over other animals?
Johnson: There was a figure in the paper where we actually show that these lineages have all gained the ability to utilize the rat receptor. It was this suspicion that led us to do the experiment that confirmed this: I was like, “Well, probably not rats, but if it is rats, then it should have gained the ability to infect rat cells,” and sure enough, the virus did.
Based on that hunch, you tested for signs of the virus in city rats. What does that entail?
Johnson: So John would go wandering around dark alleys at night and collect rat feces for me and he’d put them in Ziploc bags, label them, and send them to me. My brave undergraduates would plug their noses and extract the RNA from them the same we do with wastewater, and screened them for SARS-CoV-2 RNA. None of those came back positive. In the case of APHIS [the Animal and Plant Health Inspection Service in the U.S. Department of Agriculture, which was a research partner], they would collect blood from rats and send them to us and we would check to see if they had antibodies against SARS-CoV-2, which would tell us if they’ve been previously infected, and none had clear antibodies.
Dennehy: It’s estimated that there are at least a couple million rats. We only tested, what, almost 100? It’s quite possible we didn’t collect the right animals.
Is there any evidence that COVID-19 is widely circulating in rats?
Johnson: Not that we know of. It’s kind of haunting, but it’s coming from somewhere.
Monica Trujillo: I think the important thing to keep in mind here is that every time the virus replicates, it has a possibility to mutate. So if there is a population where you are not aware where the virus is replicating, that is worrisome. That is why it’s important to know where these cryptic sequences are coming from.
But have new variants developed in animal hosts? Has that been documented?
Dennehy: Not that we know of. Omicron is possibly hypothesized to come from animals in Africa, but that’s not proven. There are some instances where other animals have gotten infected and then spread it back to humans. I think mink is an example.
Johnson: The one that jumped into mink mutated a little bit, but nothing like what we’re seeing.
What does that say to you? Could rats, if infected, possibly reinfect humans with a new strain?
Johnson: We don’t know where Omicron came from. So we don’t know where Pi [an as yet nonexistent variant] is going to come from — but these animals sure look like likely candidates.
So … could rats potentially spread the virus in the city?
Dennehy: Yes and no. I think rodents tend to inhabit the same spaces as we do. I think probably there are often more interactions with humans and rats than we realize, not necessarily physical contact, but touching the same surfaces, that sort of stuff. Perhaps rats could exhale the virus into the air in certain areas — the subways.
Johnson: It doesn’t mean it’s an immediate, imminent threat. It’s worth paying attention to, but it’s not worth panicking over. It’s theoretically possible, but we’ve been following these lineages for over a year now and we haven’t seen it happen yet.
Davida Smyth: Rats are known to be vectors. They do transmit things, but it’s very rare. So one of the major things we see, for example, is leptospirosis. That’s something that does pop up from time to time. It’s associated with the urine of a rat, but it’s very, very rare. So in order for you to be infected by a rat, you’d have to be living in very close quarters with the rats.
What’s the worst-case scenario here? The best-case one?
Johnson: If it is in rats, it could be that it can only infect rats and loses the ability to infect humans altogether. That’s fully possible. Worse-case scenario is it spills back into humans and it’s Pi. Best-case scenario is it takes care of your rat problem. Problem solved.
This interview has been edited and condensed for clarity.
Washington, Feb. 04, 2022 (GLOBE NEWSWIRE) -- Today, in voting to approve the America COMPETES Act, the U.S. House of Representatives included a provision to ban mink farming throughout the United States, signaling disapproval of an industry that harms and kills animals for their pelts, exports them to China for a sliver of elite consumers, and presents a threat of SARS-CoV-2 spillover to people in the homeland.
The amendment was led by U.S. Representatives Rosa DeLauro, D-Conn., Nancy Mace, R-S.C., and Peter DeFazio, D-Ore., and cosponsored by Reps. Jim Cooper, D-Tenn., Andy Levin, D-Mich., and Joe Neguse, D-Colo. It is a follow up to H.R. 4310, introduced by these same lawmakers and two dozen others from both parties, including Reps. Mike McCaul, R-Texas, Jan Schakowsky, D-Ill., Lance Gooden, R-Texas, and Vern Buchanan, R-Fla.
“There’s nothing good about keeping aggressive and solitary wild mink in cages on factory farms, killing them for a product nobody needs, and then shipping their exteriors to luxury consumers in China,” said Wayne Pacelle, president of Animal Wellness Action and the Center for a Humane Economy. “The case against mink farming is clinched when one understands a new variant from one or more of these factory farms may disrupt our economy and put millions of Americans at risk.”
The amendment was approved as part of a larger bloc of amendments, including a separate measure to crack down globally on live wildlife markets because of infectious diseases risks they also pose.
“The factory farming of mink threatens public health, especially as we continue fighting against the COVID-19 pandemic,” said Representative DeLauro. “The evidence is clear: mink operations can incubate and spread new COVID-19 variants and pose a unique threat of extending the pandemic. At the same time, with virtually no domestic market, the U.S. mink industry has been in steady decline for years. Now is the time for this legislation to become law, and I am urging all of my colleagues to continue supporting this bipartisan effort.”
“One of the many lessons we learned at the beginning of the COVID-19 pandemic is the real danger of animal-to-human transmission of disease. In fact, If COVID-19 could design its perfect habitat for mutation and transmission, it would closely resemble a mink farm, where thousands of mink are kept in small, often unsanitary, overcrowded cages, for days on end,” said Representative Mace. “Today, through working together on both sides of the aisle, we have the chance to end the abusive and inhumane mink farming practice that puts Americans’ health at risk.”
There have been approximately 6.1 million mink infected with SARS-CoV-2, with approximately 675,000 mink dying from the virus. This contrasts with perhaps just a few hundred COVID-19 infections among all other captive non-human animals, including big cats, domesticated dogs and cats, gorillas, and ferrets.
“This cage-confinement environment, where mink are crowded together by the thousands, maximizes chances for intraspecific aggression, viral infections, and mutations,” observed Jim Keen, D.V.M., Ph.D., director of veterinary sciences for the Center for a Humane Economy and a former infectious disease specialist at the U.S. Department of Agriculture. “No amount of good animal husbandry can prevent this kind of aggression and the onset of disease among these captive, immune-compromised wild animals.”
Mink farms have already spawned three variants – in Denmark, France, and the United States. As such, they are a proven source of multiple novel virus variants that may compromise human vaccine effectiveness or increase human virus virulence or transmissibility. Mink are a top candidate as the “missing link” between bats which most scientists believe to be the original source of COVID, and people according to the World Health Organization.
USDA reported 2.7 million pelts sold in 2019, and 1.4 million mink pelts sold in 2020. According to a review by Animal Wellness Action, there are just 60 farms operating in the U.S. There is no domestic market for mink, and it is an export-market commodity only, with 80 percent of pelts sold to China.
“As one who grew up on and around mink farms, I can attest to the extreme aggression these creatures exhibit in their frustration with the miserable conditions on barren factory farm conditions,” said Scott Beckstead, director of campaigns for the Center for a Humane Economy.
The amendment was supported by Animal Wellness Action, the Animal Wellness Foundation, Center for a Humane Economy, the Michelson Center for Public Policy, SPCA International and dozens of other organizations, from the Idaho Humane Society to the Iowa Federation of Humane Societies to the Oregon League of Conservation Voters.
Animal Wellness Action (AWA) is a Washington, D.C.-based 501(c)(4) organization with a mission of helping animals by promoting legal standards forbidding cruelty. We champion causes that alleviate the suffering of companion animals, farm animals, and wildlife. We advocate for policies to stop dogfighting and cockfighting and other forms of malicious cruelty and to confront factory farming and other systemic forms of animal exploitation. To prevent cruelty, we promote enacting good public policies, and we work to enforce those policies. To enact good laws, we must elect good lawmakers, and that’s why we remind voters which candidates care about our issues and which ones don’t. We believe helping animals helps us all.
The Animal Wellness Foundation (AWF) is a Los Angeles-based private charitable organization with a mission of helping animals by making veterinary care available to everyone with a pet, regardless of economic ability. We organize rescue efforts and medical services for dogs and cats in need and help homeless pets find a loving caregiver. We are advocates for getting veterinarians to the front lines of the animal welfare movement; promoting responsible pet ownership; and vaccinating animals against infectious diseases such as distemper. We also support policies that prevent animal cruelty and that alleviate suffering. We believe helping animals helps us all.
The Center for a Humane Economy (CHE) is a non-profit organization that focuses on influencing the conduct of corporations to forge a humane economic order. The first organization of its kind in the animal protection movement, the Center encourages businesses to honor their social responsibilities in a culture where consumers, investors, and other key stakeholders abhor cruelty and the degradation of the environment and embrace innovation as a means of eliminating both.
Since the onset of the coronavirus pandemic, researchers have looked at sewage and wastewater for clues related to how the Covid-19 virus behaves and how it may mutate, in order to understand it better.
A group of researchers in New York who were running tests in the city’s wastewater found that there may have been chances of a new variant of Covid-19 going unreported, according to a report by New York Times. The report highlighted that the researchers found a series of never seen before mutations which were also not reported or detected in human beings.
The researchers have no idea where these undetected variants came from or whether they possess the ability to take over the dominant strains of Covid-19. Scientists are divided as to where these mutations are coming from. The report, originally published in the Nature Communications, highlights that a section feels that the virus is coming from people whose infections were not captured by sequencing while another section believes the lineages may be coming from virus-infected animals, with New York City’s rats being the main suspect.
The researchers call these lineages cryptic lineages.
The researchers of the New York study - Monica Trujillo, a microbiologist at Queensborough Community College, John Dennehy, a virologist at Queens College, Marc Johnson, a virologist at the University of Missouri; Davida Smyth, a microbiologist at Texas A&M University and others - have said that they have not fully understood what was it that they have sequenced.
Omicron In Canadian Wastewater Before Initial Detection
Researchers in Canada said that they found the Omicron variant in Nova Scotia province’s wastewater even before the strain was reported from South Africa, according to a report by Canadian news agency National Post. Graham Gagnon, professor, and director of the Centre for Water Resource Studies told the news agency that his team of researchers detected Omicron , retrospectively, in Nova Scotia wastewater in mid-November.
Like the researchers in New York, Gagnon’s team had been investigating wastewater from Nova Scotia’s four main treatment plants since December 2020. Researchers who probe Covid presence in wastewater highlight that wastewater often provides important clue related to how the virus is evolving, especially when testing systems face duress due to high number of cases.
Read all the Latest News, Breaking News and Coronavirus News here.
New York City's Rats Could Have Their Own Strain of COVID-19
Two experts weigh in on mysterious viral RNA found in the city's wastewater.
Published on 2/4/2022 at 5:44 PM
There's something mysterious in New York City's wastewater, and some think the city's rats are to blame.
Since the early days of the pandemic, scientists have used samples of New York City's wastewater to track the rise and fall of COVID-19 cases in the population. People shed viral RNA in their poop, and it all ends up at the city's sewage treatment plants, making it relatively easy to track more significant infection trends and monitor the emergence of new variants.
But in a new academic paper published in Nature Communications this week, a group of researchers reported finding mysterious viral RNA fragments with mutations that don't belong to any case of COVID ever sequenced in a person. They refer to these mutations as "cryptic lineages" and reported finding them consistently in several, but not all, of the wastewater treatment locations they sampled.
While the paper offers a few possible human explanations, it also proposes an unusual hypothesis: the city's rat population may have developed its own unique strain of COVID.
Marc Johnson, a virologist at the University of Missouri and one of the paper's authors, told Thrillist that his first instinct after discovering some of these unusual mutations was to Google it.
"What came up immediately was that this is a mutation they had made in the virus when they made a rodent-adapted SARS-CoV-2," he said. "When you mutate this position, it gains the ability to infect rodent cells. And a light went off, like, 'Oh, maybe these aren't coming from people.'" He successfully infected rodent cells with a harmless version of the mutated virus in his lab, showing that the explanation was at least plausible.
The rates of these viral mutations in the wastewater were not connected to the ebbs and flows of the virus in the human population, another sign pointing to a possible animal reservoir. In fact, the mutations made up a larger share of sequencing when cases in New York City were low.
After considering many of the animals that call NYC home, the team narrowed it down by analyzing animal DNA found in the wastewater samples. "The ones we really thought about were rats and dogs, predominantly," said Davida Smyth, a microbiologist at Texas A&M University and another paper author. "We see this consistently over time, and we're not seeing it with people. The most likely thing, we're thinking, is rats because of the density."
Thus far, the rat theory is missing one key ingredient. The team hasn't been able to identify the virus in rats. "We've looked like crazy to try and find it in rats, and we have not succeeded," Johnson said.
The paper also proposes several other explanations, such as inadequate test sequencing, long-term immunocompromised patients, or even a virus that's not being caught by testing because it develops in the gut rather than the nose.
"The fact that the mutations aren't spreading throughout the city, the fact that they're geographically constrained to a specific regions of the city, limits which of those hypotheses are the most likely," Smyth said, noting that their investigation is constrained by the financial realities of New York academia. "With limited resources, money, and manpower, you can only do so much. Without funding we can't go crazy, and that limits us considerably."
Although there haven't been any documented cases of rats transmitting COVID to people, incidents with hamsters in Hong Kong and minks in Denmark show that there are risks that need to be monitored. "It is something we should keep our eye on just like we do for influenza... in wild birds," Johnson cautioned. "I think the same would be appropriate for this virus."
While the mystery hidden in NYC's poop has yet to be solved, New Yorkers' feelings about the rodent citizens they share a home with are no secret. The city saw a record number of rat complaints last year.
Unknown lineages of the virus that causes COVID-19 have been found in New York City's sewage, raising new concerns that the novel coronavirus is finding ways to escape immunity.
The lineages don't seem poised to break out and cause a new surge at this point. Their proportion has risen and fallen along with New York's case rates, and there's no sign that these versions of the virus are becoming more common over time. But the mutations seen in the mystery lineages are similar to those that allow the omicron variant to partially escape immunity from vaccination and previous infection, said John Dennehy, a virologist at The Graduate Center at City University New York, who co-led the research.
"The fact that the omicron variant came from somewhere unknown and that it shares quite a few of its mutations with the unknown variant we see in New York City, that does pose a pretty serious concern that whatever we're seeing could find the right combination of mutations that would make it highly transmissible," Dennehy told Live Science.
Related: Coronavirus variants: Here's how the SARS-CoV-2 mutants stack up
Also troubling: The researchers don't know where the new viral lineages come from. The lineages are found only in limited areas of the city, and they don't seem to be spreading from neighborhood to neighborhood. They might arise from chronically infected humans or perhaps from an animal reservoir — but what animal? So far, there's no firm evidence for any option.
"Nothing makes perfect sense," said Marc Johnson, a virologist at the University of Missouri School of Medicine.
Unknown unknowns
Many cities monitor wastewater to try to track the amount of SARS-CoV-2 circulating in the community. Because people begin shedding virus in fecal material before they feel sick or get tested, wastewater levels of the virus precede rises in cases that show up from testing by about three weeks, Johnson said.
But relatively few places do genetic sequencing of the virus material found in wastewater. Dennehy started working on genetic sequencing in New York after the alpha variant made clear that coronavirus mutations were going to be a force to be reckoned with. After Dennehy and his colleagues Monica Trujillo, also at CUNY, and Davida Smyth, now at Texas A&M San Antonio, appeared on an episode of the popular podcast This Week in Virology in April 2021, Johnson got in touch. He'd been doing similar sequencing in Missouri and was losing sleep at night over viral RNA sequences that didn't match anything in global databases of coronavirus variants.
"I was going crazy," Johnson told Live Science.
The Missouri variants disappeared in late April 2021, never to be seen again. But the researchers began to collaborate on more thorough sequencing of viral RNA found in New York City, wondering if they'd find the same sequences they'd seen in Missouri. They didn't. But they did find a cluster of completely new unknown sequences.
The researchers expanded their efforts, testing wastewater from all of the city's 14 wastewater treatment plants two times a month, ultimately building a record spanning from January 2021 to the present.
Immune evasion
The researchers use a technique that doesn't allow them to sequence an entire viral genome, but which focuses on about half of the spike protein that the virus uses to get into cells.This region contains a key area called the receptor-binding domain (RBD). Many of the mutations that allow omicron to evade antibodies from vaccines or non-omicron infections sit on the RBD. So, too, do the mutations seen in the lineages found in the New York City wastewater. (The researchers use the word "lineages" to avoid confusion with the term "variants of concern" as used by the World Health Organization. But, Dennehy said, genetically speaking, they're the same concept: Sequences representing unique replicating populations of virus that are genetically related to one another.)
Related: 11 surprising facts about the immune system
The researchers studied four of these mystery lineages, dubbed WNY1, WNY2, WNY3 and WNY4. They found that all had abilities to partially or completely evade antibodies that easily snag the original SAR-CoV-2 virus. While blood plasma from vaccinated people or people with previous infections could partially neutralize all four lineages, this neutralization was reduced compared with the original virus.
"They were mutations exactly where you'd expect to find mutations if the virus were trying to evade an immune response," Johnson said.
Mystery origin
So where are these mystery linages coming from? The researchers checked 5,000 other wastewater samples from around the globe and found the lineages only in seven samples, all from New York State. Whatever they are, they're homegrown.
There are a few hypotheses, none of them entirely satisfactory. The first is that they're coming from unsampled human infections. Only between 2.6% and 12.9% of New York City cases are sequenced at any given time, so it's entirely possible that rare variants of the virus could sneak under the radar. Perhaps the lineages are versions of the virus that infect the gut and aren't often found in the nose or throat, where PCR swabs go.
But there are problems with these possibilities. A few studies have compared virus from the gut with virus from the nose and throat, and so far, no one's seen a difference between the two, CUNY's Trujillo told Live Science. Also, the geographical range of the viral lineages is limited — they're found in the catchment areas of only three of the 14 wastewater treatment plants in the city. If the source of the virus is humans, they're humans who don't move around much.
"We were thinking about humans that might be bedridden," Smyth told Live Science. "So long-term facility patients that are perhaps not mobile."
But that would be strange too. "It would be weird that it would spread within a local population and not go anywhere else," Johnson said.
Another possibility is that the carrier of these cryptic lineages isn't human. The mutations seen in the clusters are seen in a region of the genome associated with the virus becoming more adept at infecting rodents (which aren't easily infected by the original coronavirus). New York City's rats would be an appealing target for blame. There are a lot of them, they live in the sewers, and they don't travel far.
But the researchers could find no smoking gun linking rats to the variant. The team sequenced the wastewater for animal genes, essentially looking to find out who poops in the sewers besides people. Other than genes from the animals people eat for food (cows, pigs, chickens), the researchers found evidence of cat, dog and rat genetic material in the sewers. But none were highly prevalent. And the wastewater treatment plant with the highest proportion of mystery coronavirus had the lowest proportion of rat genes — some weeks, rat genes weren't even detectable.
Meanwhile, the stray cat population probably isn't big enough to sustain the amount of transmission the researchers inferred from the wastewater, and pet cats don't interact often with other pet cats either, Johnson said. Dogs are known to get COVID-19, but these mutations haven't been seen in dog virus cases before. And it would be very strange if a version of COVID-19 were circulating in dogs but not humans, Smyth said, given how close New Yorkers are to their pups.
Preparing for the next variant
The answer to the mystery may lie in sequencing more viral genomes from more animals on a regular basis. Smyth, in Texas, is working to get access to petting zoos to see if she can find new viral variants in different species. Testing the sewage upstream from the wastewater treatment plant in order to narrow down the source to a smaller area would also be helpful, Dennehy said, but much of that work is now moving into the purview of the Centers for Disease Control and Prevention (CDC), so Dennehy and his team will no longer have much access to upstream wastewater sources.
The omicron variant seemed to appear out of nowhere: It evolved from an earlier lineage than the delta variant that was, at the time, dominant. Its origin is a mystery. To Dennehy, Johnson and their colleagues, the origin of the next variant will remain a mystery, too, unless a more robust effort is put into place to understand where variants come from. Scientists already take regular samples of influenza from bird populations and raise the red flag when new strains that could potentially jump to people start circulating. Something similar may be possible with wastewater and regular animal sampling for SARS-CoV-2 — if research agencies prioritize funding that kind of science.
"What we are looking at here is the mechanism or potential mechanism through which different variants arise," Trujillo said. "This is where we should be doing the research."
The findings appeared Feb. 3 in the journal Nature Communications.
Originally published on Live Science.
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