“Potentially Very Bad”: Lots of New Covid Variants in New York City Rats

Our reader GM is not happy that the possible very big downside of a recent Covid discovery is not being taken seriously. Lots of nasty new variants of Covid have been found in New York City wastewater. They appear to come from rats.

Now so far, there is no evidence that one of these rat Covid variants has jumped species to humans. But as we’ll explain, were that to happen, it could be Seriously Bad. Many of these variants are novel and have the potential to escape current vaccines.

But the reaction to the wastewater study has been underwhelming. And the US already does one of the worst jobs of any advanced economy in terms of sequencing Covid cases to determine the prevalence and spread of variants. So if a ratty Covid were to infect humans, the US would be late to work that out.

From a preprint in MedRxIV, Tracking Cryptic SARS-CoV-2 Lineages Detected in NYC Wastewater:

To monitor New York City (NYC) for the presence of novel variants, we amplified regions of the SARS-CoV-2 Spike protein gene from RNA acquired from all 14 NYC wastewater treatment plants (WWTPs) and ascertained the diversity of lineages from these samples using high throughput sequencing. Here we report the detection and increasing frequencies of novel SARS-CoV-2 lineages not recognized in GISAIDs EpiCoV database. These lineages contain mutations rarely observed in clinical samples, including Q493K, Q498Y, H519N and T572N. Many of these mutations were found to expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. In addition, pseudoviruses containing the Spike amino acid sequence of these lineages were found to be resistant to many different classes of receptor binding domain (RBD) binding neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these mutations, including the possibility of a non-human animal reservoir.

GM explains:

I was never worried about minks as a reservoir, those are mostly solitary and likely can’t sustain a transmission chain.

But rats in the sewer is a completely different situation.

And it’s not just that there is an external reservoir, as the paper notes, you select for somewhat different mutations in rodents. That can still infect humans, only now the major neutralizing epitopes are taken out.

Also, this will screw up the few remaining ZeroCOVID countries too unless they start maniacally screening all cargo shipments. The Chinese might try, but they also have a gigantic land border and that effort is doomed in the long run…

Now on the one hand, New York City is estimated to have only about 2 million rats, compared (pre Covid) about 10 million humans. In London, the population jumped about 25% during 2020, so it’s reasonable to assume if anything their numbers are higher now.

If you have spent any time in New York City, you are sure to have seen them. Rat sighting is a form of spectator sport:

On the other hand, if you look at the CDC website, the very first rodent disease listed as directly transmitted to humans, Hantavirus Pulmonary Syndrome, has a primary transmission mechanism that doesn’t even require you to have been within eyeshot of a rat: “Breathing in dust that is contaminated with rodent urine or droppings.”

Most Western countries have not taken fecal aerosol transmission seriously (although some readers have pointed out the risk of airport toilets, which can’t be covered while flushing). From a post this March by William A. Haseltine, former Harvard Medical School professor, in Forbes:

Last year, I conducted an interview with a friend who traveled to Shanghai and was forced to quarantine in a hotel for 11 days under the supervision of local health authorities..

One detail, however, struck me as rather curious, if not startling. When my friend checked in, a woman handed them a blue bucket and a little bottle of disinfectant tablets. “For toilet,” she told him, then laughed when she saw the look of shock and horror on his face. “No, no, no, no. Not for that. Dissolve the tablets in water in the bucket, then dump the mixture into the toilet before you flush.” It didn’t matter whether it was number one or number two, my friend told me. He had to treat his waste as if it was potentially infectious and carrying the virus that causes Covid-19, SARS-CoV-2—using half a bucket of water and six tablets for urine, or a whole bucket and twelve tablets for feces….

In theory, the virus can travel from one person’s waste to another’s lungs through one of two routes. The first is fecal-oral route, which involves either direct ingestion of contaminated water through the mouth or indirect exposure through the eyes or nose. The second is what I call the fecal-aerosol route, whereby the virus enters the body via sewer gas or even smaller, yet still virus-laden particles known as aerosols. The ability of the virus to successfully traverse either depends on whether it can remain infectious and replicate at sufficient concentrations as it slogs through the digestive juices of the human gut.

Not to ruin your breakfasts, if you are reading this post over a morning repast, but a friend points out that rats (like other mammals) like to hang out near basement heaters and steam pipes in the winter. That means they pee and poop on them. And hot air rises….

Recall that on 1/3, if not more, of the Covid cases include digestive symptoms; some Covid cases present with those first and are initially mistaken as an intestinal bug. But because other aspects of the disease appear to be more dangerous, what Covid does in and to the gut hasn’t gotten much attention.

Mind you, even if fecal transmission is now uncommon, the rat variants are sufficiently different, um, “cryptic” that if they do start infecting humans, their behavior could also be different. GM is alarmed:

In this paper, WNY4 takes all out 3 classes of monoclonals. And WNY4 has an absolutely brutal combination of mutations:

K417T N439K K444N Y449R L452R N460K S477N Δ484 F486V S494T G496V Q498Y N501T G504D 505H H519Q

And that’s in the RBD alone.

That’s basically all the immune escape mutations from all human variants plus some more.

And it still binds the human receptor, though with a decreased affinity, but it will be infectious.

Quite possible current vaccines will not work at all against this.

Some of those mutations, like Q498 and Q493 might actually be adaptations to rodent ACE2. They just happen to be immune escape ones too.

It’s been a mystery why we don’t see them taking over in humans because in certain combinations with other mutations, they have been predicted to dramatically increase receptor affinity eve for hACE2.

P.S. WNY4 isn’t really even a “variant”, that’s a new strain by all reasonable definitions.

Rats with Covid are an obvious possible danger, given that they already transmit 26 diseases to humans, according to the CDC. But these rat infections also illustrate the way that Covid is becoming endemic in animals. The broad infections across species is reminiscent of rabies (fortunately without its level of mortality). For instance, deer, which most suburbanites regard as rats with hooves, are also showing alarming levels of Covid. A wild deer survey in Michigan found that more than half have Covid antibodies.

Rather than organizing an effort to monitor this hazard and game out responses, the CDC is instead busy defending itself on its flip-flop of asking the vaccinated to mask up. Since the National Nurses Union and the California Nurses Union were both very critical of the CDC’s “Mission Accomplished” in May, why not let them handle the PR push? Most Americans would put a lot more faith in nurses than any public health official right now.

GM points out the US isn’t deploying its genetic sequencing capabilities to get a better handle on this risk:

The one somewhat positive thing is that we still do not see these spilling back over into humans.

But on the other hand, it is not like there is much sequencing going on, even though supposedly a very large sum of federal money was dedicated to sequencing a few months ago (after which the number of sequenced samples promptly went down).

Also, for something like WNY4 that has so many mutations, it is quite possible that the current PCR primers don’t work at all, so whoever contracts that will not test positive to begin with, thus it will never get sequenced…

Speaking the Black Death though, one has to wonder what these adaptive changes meant in terms of virulence and virulence to which species.

Every time these viruses have been passaged in rodents, they go from mostly harmless to lethal.

So is the rodent population going down in NYC? Nobody is looking I guess.

How much has it spread among the rats? That’s actually kind of trivial to check — just collect a bunch of rats, there are plenty of them, test the blood for antibodies.

Is anyone going to test these viruses in the lab on mice and rats to see how they compare to the Wuhan one? That might happen.

Are they going to also be more lethal to humans? Hopefully we never find out…

Also, there is one very unfortunate aspect of the paper — they only sequenced RBDs, not whole viruses, not even whole spikes. What other mutations happened elsewhere is anyone’s guess.

Nassim Nicholas Taleb, in January 2020, warned of the risk of Covid as a pandemic in January 2020:

The general (non-naive) precautionary principle [3] delineates conditions where actions must be taken to reduce risk of ruin, and traditional cost-benefit analyses must not be used. These are ruin problems where, over time, exposure to tail events leads to a certain eventual extinction. While there is a very high probability for humanity surviving a single such event, over time, there is eventually zero probability of surviving repeated exposures to such events. While repeated risks can be taken by individuals with a limited life expectancy, ruin exposures must never be taken at the systemic and collective level. In technical terms, the precautionary principle applies when traditional statistical averages are invalid because risks are not ergodic.
Naive Empiricism

Next we address the problem of naive empiricism in discussions related to this problem.

Spreading rate: Historically based estimates of spreading rates for pandemics in general, and for the current one in particular, underestimate the rate of spread because of the rapid increases in transportation connectivity over recent years. This means that expectations of the extent of harm are underestimates both because events are inherently fat tailed, and because the tail is becoming fatter as connectivity increases.

Global connectivity is at an all-time high, with China one of the most globally connected societies. Fundamentally, viral contagion events depend on the interaction of agents in physical space, and with the forward-looking uncertainty that novel outbreaks necessarily carry, reducing connectivity temporarily to slow flows of potentially contagious individuals is the only approach that is robust against misestimations in the properties of a virus or other pathogen.

Not only are rats incubating new Covid variants (and mutations!) that could jump to humans, but the reason for additional alarm is that if that happens, the rats become a new connectivity vector for the disease, increasing the propagation modes beyond human to human. And there is no way we can rid ourselves of rats….

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  1. allan

    “the risk of airport toilets, which can’t be covered while flushing”

    Also the case for many (most?) toilets in institutional settings and public buildings in the U.S.
    Schools and universities have taken this into account in their reopening plans, amirite?

    1. amfortas the hippie

      i literally hate knowing all about aerosolised fecal matter from flush toilets
      if there were one thing i could unlearn….
      our composting toilet(diy) doesnt have that problem
      nor does it overflow or explode
      or use any water

  2. Cocomaan

    Recommended viewing is Morgan Spurlocks documentary “Rats”.

    A lot of the movie is about the titanic human efforts to kill urban rats. It’s really unbelievable to watch.

      1. cocomaan

        When I sat on an animal research ethics board, the veterinarian told great stories. She once said that students would become attached to the research animals and often would adopt them. The vet agreed with you, they made nice pets. (obviously this was for behavioral research pets, not biomedical)

        Once or twice they had to deny the adoption to the student, because the species were exotic/invasive and on escaping could have caused serious problems. I seem to remember it was some kind of quail.

        I also knew a guy who had a pet skunk. Smelly was removed, obviously. Now that thing was cute, he used to feed it raspberries.

      2. Tom Stone

        They do make nice pets, mine was named “Blackie”, he liked to crawl up my legs and perch on my shoulder.
        Burt and Diane came to our house in Piedmont to celebrate my dad’s survival on the Anniversary of his third experimental brain surgery, performed by Levin and Feinstein.
        He was the only one of the 13 subjects to live that long…you had to have 6 months or less to live to be accepted.
        I was ten and brought Blackie out to meet our guests and he climbed up Diane’s leg to say hello…

      3. Betty

        In the late 1960s, many friends did experimental psych doctoral research with mice or rats, would become attached, and upon finishing their work, ‘free’ them in Riverside Park. I’m sure this is an ongoing tradition.

  3. chris

    What’s the link for the paper on WNY4? It looks like it was intended to be included but didn’t make it in the published article. Thanks as always!

      1. ChiGal in Carolina

        So there has actually been no sequencing done on rats and this is entirely hypothetical if for the reasons you enumerate plausible.

          1. ChiGal in Carolina

            Exactly so. And neither the preprint nor what GM writes justifies this commentary from Yves stating as if fact what is merely speculative: “Not only are rats incubating new Covid variants (and mutation!)…”

            I do understand about the precautionary principle but there is so much sloppy science around it seems important to choose our words carefully.

            1. Yves Smith Post author

              I don’t take well to false assertions regarding the post, particularly you accusing me of misrepresenting GM. He reviewed it in advance and was fine with it.

              There are variants AND A MUTATION in the wastewater that do not come from humans because if they were from/in humans, the consequences would be Gawd awful. Rodents are the only plausible alternative source in these volumes and varieties.

              And as chris indicated, the sequences WERE identified, otherwise GM would not have been able to list them and discuss their significance.

              GM added:

              The issue in this case is that they did test binding to hACE2. It is reduced for WNY4, but the affinity is still higher than it was for SARS-1, and that can also be compensated in terms of infectiousness even further with mutations like P681R (a very unfortunate aspect of the paper is that they only sequenced the RBD, not the rest of the virus, which is near certain to have all sorts of very interesting features).

              1. ChiGal in Carolina

                Yes, the sequences were identified in waste water, but no sequencing was done in rats. So it is plausible but still just a hypothesis that rats are incubating new variants.

                No offense intended but when I share these posts with my ex who is a neuroscientist and works with gene expression in mice he goes ballistic. He is so frustrated by the current state of the science press because when he goes back to check the original research it doesn’t support the claims.

                For example recently it was reported that the vaccinated were carrying high titers without getting sick. He says one problem with epidemiologists is they are not strong on biology: it is nonsense that there would be high titers without symptoms because the only way the virus can reproduce is if it gets inside the cells and that is what produces the symptoms.

                After looking at the research he found that actually the titers were low in the vaccinated and the ones who got sick did so because they had underlying conditions.

                But meanwhile the idea was out there that the vaccinated were harboring high levels of virus.

                This kind of misinformation is very problematic I think you would agree. Again, Yves, this is your house and believe me no offense was intended. Just trying to figure it out like everybody else.

                1. Yves Smith Post author

                  Please see GM’s reply below. Your neuroscientist boyfriend lacked the biomedical chops to appreciate the importance of the particular mutations that GM listed. Perhaps he should stay in his lane?

                  Put it another way: if he didn’t like the hypothesis, the onus was on him to offer one with at least as much explanatory power, and not just whinge. It was obvious even to me that saying they were from humans was vastly less plausible and far more alarming if true.

            2. GM

              The evolution of the virus has been studied in rodents in laboratory conditions, and the mutational signature of these variants matches what is seen in those experiments.

              Mutations in Q498, Q493 and others reliably arise in rodents.

              On the other hand, they don’t arise in mink, other mutations happen there.

              Thus the inference that these variants most likely evolved in rats, and less likely in cats/dogs.

              The alternative is that they evolved in some humans in NYC and nobody has picked them up in actual patients.

              But then this would be:

              First, even worse news as it means they were in the human population already

              Second, somewhat unlikely because it does not seem like they have spread widely in humans, and then it would be hard to pick them up in the wastewater if just a few people have been shedding them.

          2. chris

            I found this article too. It seems as if there has been a decision to not support this research. But they have mentioned specific identification of variance in the sequences so it does seem as if the people at CUNY have done the sequencing.

  4. PlutoniumKun

    I’ve been wondering the implications of Covid becoming endemic to animals might be. Its hard to see anything good coming from this.

    A few weeks ago I was out hiking a well known route with two friends and we met another friend of mine with her (very adorable) dog coming the other way. We stopped for a chat and the dog was a hit with my other friends. Two days later the dog owner called me to say she thought she had covid. She had all the classic symptoms, although later tested negative (although its probably imo that this was a false negative). But curiously, the week after one of the people I was walking with came down with Covid too, despite her being very careful. The thought crossed my mind that the dog could have been the vector, given that he got a good hug from everyone. I’ve no proof or evidence for this of course, its just something that crossed my mind at the time, it was probably a coincidence. At least not many people give rats a hug.

    1. Anon

      Since dogs can be vectors using them to smell everyone in attempts to have the dogs sniff out Covid in airports sounds especially stupid…

    2. c_heale

      The implications are that the virus will mutate in animals into variants that human immune systems can’t defend against, and the virus cannot be eradicated. Smallpox was eradicated because it’s only host was humans. Flu can’t be because it has human and bird hosts.

  5. Big River Bandido

    Eww. Twenty five years living in NYC and I never saw a rat climbing inside one of the trains. On the platforms, all the time. Once or twice inside a car. But never like that.

    Wonder if they got hungry, desperate, and thus more brazen during the lockdowns.

    1. AnonymousAnonymous

      They have definitely gotten more brazen; they had to when all the restaurants closed and their constant access to food waned as places shut their doors, and food waste was in shorter supply.

      Having outdoors tables hasn’t helped, and what’s alarming is the rats (who usually shy away from humans) are going right up to the tables:

      “Giacomo Romano, who owns Ciccio, an Italian restaurant in Manhattan’s Soho, said rats from a nearby park have been harassing diners since the outdoor meals were permitted. “Last night, a customer had a baby rat running on his shoe, and I let you just imagine his reaction,” Romano told NBC.”


      Also makes you wonder what getting COVID does to the rats’ psyche. It’s driven humans crazy, why not them?

  6. Tom

    A similar story could be written about bats.
    However the bats keep themselves and don’t spread viruses. People have lived in cities with rats for thousands of years. The idea that we’re now going to be vaccinating people against rats is going a bit far.

    1. Yves Smith Post author

      This is either a reading comprehension fail or deliberate straw manning. A bad look and violations of our site Policies. You are accumulating troll points.

  7. Lee

    “And there is no way we can rid ourselves of rats….” But it appears that rats may be finding a way to rid themselves of us. Perhaps they have secretly learned to cultivate grain and make pizza, so that they no longer have use for us.

    1. GF

      I read Coyote America: A Natural and Supernatural History by Dan Flores a couple of years ago and he had a chapter on urban coyotes and included Manhattan. He said there are an estimated 5,000 coyotes living there and that they are voracious rat eaters and eat several a day. Rats generally are not a favorite catch for cats as they can fight back. Not a problem for the coyote. So if you see coyotes in NYC, let them do their jobs. Without them the city would be overrun with rats.

      1. Robert Gray

        > Dan Flores … estimated 5,000 coyotes living [in Manhattan]

        Erm … that’s, on average, over 200 per sq. mi. Sounds fanciful.

        > So if you see coyotes in NYC …

        With numbers like that, there must be daily, hourly, sightings somewhere on the island; that’s why the Post is full of such stories. Oh, wait.

        1. Cynical Engineer

          You’re assuming that people can tell the difference between “coyote” and “dog” on a brief sighting. Keep in mind that Eastern coyotes have crossbred to a significant extent with domestic canines and are much more “dog-like” than the Western coyote.

          Having lived in coyote country out West, I can assure you that they are very, very good at remaining unseen.

  8. Raymond Sim

    This is how big-time zoonotic spillover actually happens. See ‘The Great Epizootic of 1872’ for instance. For more fun look into the possible contribution that event made to the Great Influenza.

    Plausible worst-case scenarios resulting from our feckless response to this crisis are so terrible that feckless minds can’t even conceive of them as real.

    I nearly died in 2015, twice. Both times the pain was so terrible that I would have welcomed death, except that I wanted to see my grandchildren grow up. Now. I feel it might have been a mercy never to have seen this much of their future.

    1. Acacia

      I like the choice of a rather grizzly tale — Willard-esque, even — as a way to teach some basics of literary narration and a bit of vocabulary too. :D

  9. Ergo Sum

    NYC has combined sewer a storm drain system. Meaning that in heavy rain, storm, etc., the treatment plants are bypassed. In which case, everything goes strait out to the rivers, sea and the ocean. What is the possible impact to sea life?

  10. campbeln

    Variants of Concern versus Trial & Vaccine dates:

    Chart with these dates overlaid on Genomic Epidemiology of Novel Coronavirus – Global Sampling (Variants of Concern)


    Mar 16 to Nov 19 2020

    Samples of the COVID-19 inactivated vaccine at Sinovac Biotech Ltd, March 16, 2020. [Photo/Xinhua]
    China has 5 vaccines for COVID-19 currently undergoing phase 3 clinical trials in some foreign countries, a Foreign Ministry spokespsn said Wed

    July 27, 2020

    The Phase 3 clinical trial was designed to determine if the Pfizer-BioNTech COVID-19 vaccine is safe and effective in preventing COVID-19 disease. This trial began July 27, 2020, and completed enrollment of 46,331 participants in January 2021

    Aug 5, 2020

    Phase 3 clinical trials for the much-anticipated Oxford COVID-19 vaccine are set to begin in the United States Wednesday (Aug 5, 2020), with participants in Madison, Wisconsin rolling up their sleeves for the injection.

    Nov 16, 2020

    The phase 3 trials were a multi-centre affair with 24,419 participants aged 18 to 98 years. Bharat Biotech and the Indian Council of Medical Research recruited them between November 16, 2020, and January 7, 2021. (The Drug Controller General granted ’emergency use’ approval for Covaxin on January 3, 2021.)

    Dec 8, 2020
    Covid-19 vaccine: First person receives Pfizer jab in UK

  11. Dikaios Logos

    Within the last 2 weeks I’ve seen 2 dead rats in the open on the edge of my property (an I-95 city , not NYC). I assumed they found my traps and died of the poison therein, BUT those traps had been out for a while and i just suddenly saw these two. And in previous episodes when rats seem to have eaten the poison, there was never visible evidence of dead rats. Perhaps I’m seeing something new going through their borrows?

  12. Scott1

    I had worried about air that carried the Covid up from those grates the homeless might nap over hoping not to freeze to death. Eventually I worried about Chinese overfishing or Chinese causing famines, again, somehow I hadn’t worried about.
    I had been saying that in the US the CDC needed to be part of the DOD since Defense and Education is what governments must do at their minimum. Probably it is unattractive to politicians that fear “Big Government”. Defense from Germs and Viruses is a job for the UN, in the minds of those very interested in decreasing the power of the UN, is a guess.

  13. Skunk

    One of the worst outbreaks of the original SARS virus occurred in Hong Kong in an apartment building in a stack of bathrooms. It appears that fecal aerosols passed through defective floor traps, so that the user of one bathroom infected residents in the stack on other floors. This was very well-known at the beginning of the COVID-19 pandemic. I suspect that some of the cruise ship outbreaks may even have been connected to the way the toilets are connected, although this is just speculation.

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