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Covid-19

Don’t Make Mine Mink

Update: importantly, the follow-up news on this story argues that there’s less to worry about than appeared at first. The mutation described below has not actually appeared again in the last two months, and it ability to evade vaccine-raised neutralizing antibodies is still in doubt.

There’s a situation in Denmark that deserves some epidemiological attention. Now, put me in the (rather large) category who did not realize how large the Danish mink industry is – or that a Danish mink industry existed at all – but there are plenty of mink farmers there and millions of mink. 40% of world production is in Denmark.

That means a high density of animals, for sure, and as always one of the big challenges under such conditions is control of disease. In my own homeland of Arkansas, the rise of large-scale catfish farming was partly a story of figuring out what the optimum fish density was that didn’t lead to finding them all floating on the surface of the pond one morning. American mink farms are already known to be a reservoir for Aleutian disease. The parvovirus responsible for that one has been mutating under the selection pressure of intense farming, and you would expect this to be the case with other infectious agents as well.

Like the current coronavirus. Back in the spring and early summer, mink farmers in the Netherlands reported coronavirus outbreaks in their animals, and this was followed by reports from Denmark and other countries in Europe. Utah fur ranches reported coronavirus outbreaks in their mink populations (with thousands of dead animals) in August. On both continents, it’s believed that the disease spread from the human farm workers into the mink populations. Different mammals have different susceptibilities to the virus (to any virus), and it appears that Covid-19 is highly transmissible in mink. Its mortality rate is not high, fortunately, but high enough given the huge numbers of animal involved. For “herd immunity” fans, the outbreaks seem to tail off once about 90% of the population has been exposed, but that’s a lot higher number than you’d ever want to hit, and it’s also worth noting that the human population is not well modeled by the conditions on a mink farm. Yet.

The coronavirus has spread and mutated in the Danish mink population, and now there have been cases of these strains jumping back into humans and causing infections there. This was first seen in a single case in the Netherlands in the spring (more here), and it’s happened a number of times since. It gets worse: reports have it that some of the current mink strains in Denmark are less susceptible to antibody responses.

Now, I am not completely sure what that means. I have been trying to find published details, but it seems to be too early, and the press reports are full of other baffled scientists waiting for information. The Serum Science Institute in Denmark seems to be the place where these effects were found, and they’ve shared their findings with the WHO and the European Centre for Disease Prevention and Control. But the actual results don’t seem to have been released yet. But if I’m translating this correctly, Kåre Mølbak of that institute said at a press conference that the situation is “very serious” and that the worst case would be a restarted pandemic spreading out of Denmark. The article also says, rather alarmingly, that “The Serum Institute estimates that five percent of the viral infections among people in North Jutland are of the new type of virus mutation“, and I would very much like to hear some more about that.

But you can see that the Danish government is taking this seriously: all 17 million mink in the country are being killed off immediately in a gigantic cull. The police, the armed forces, and the Home Guard are all involved, and apparently they’re throwing everything they have at the effort. The Netherlands has already sped up an existing proposal to ban mink farming, which is now set to take place by the end of this year, and you can bet that they’re looking at the Danish results very closely. But the places to watch are Poland and China: these are big mink pelt producers, and (as far as I can see) nothing has been heard from them about this new problem.

I assume that we’ll be seeing sequence information very shortly, as well as the details of the antibody studies. I’ll dive right into those details as soon as they’re available, believe me!

Update: here’s Helen Branswell with a reassuring take.

Update 2: there’s a report that the form that they’re worried about has four mutations: H69del/V70del, Y453F, I692V, and M1229I.

Update 3: here’s the Serum Institute’s statement (in Danish, but Google Translate does a solid job with ordinary Danish-to-English).

153 comments on “Don’t Make Mine Mink”

  1. Michael says:

    Francois Balloux has tried to put this in context via this thread:

    https://twitter.com/BallouxFrancois/status/1324085761449304067

    1. confused says:

      I don’t get this. He linked to a thread that says “currently available mink genomes fall in the diversity of human SARS-COV-2”.

      It seems like this ought to be an objective, knowable thing rather than a matter for speculation. Either it’s been seen in humans before (and therefore isn’t new) or it hasn’t.

      1. sort_of_knowledgeable says:

        Every human genome is unique, except for twins and such, but they all fall within the diversity of human genomes.

        There could be a single nucleotide change that is new but not dramatically different compared to 20 different nucleotide changes which would be dramatic different from the human strains.

    2. JC James says:

      A sense of Déjà vu…
      “The N. Ferguson Effect – The re-re-re-return”
      https://www.powerlineblog.com/archives/2020/04/the-ferguson-effect.php

      As usual, extremely poor reporting from M. Derek…

      1. Some idiot says:

        That suggest strongly that you have misunderstood either the link in the first poster or Derek’s blog. Or both.

  2. Matthew says:

    Who’s working on the mink vaccine?

  3. DTX says:

    Something like this happened in 1997 when Hong Kong culled its entire poultry flock in 3 days in an attempt to control H5N1, a strain of the flu with frightening mortality. At that time, 6 of 18 people who had acquired the disease in Hong Kong died. As H5N1 spread around the world, it showed even higher mortality in the relatively few humans that got it, with a rate of mortality of ~60%.

    1. confused says:

      There doesn’t seem to be a claim that this is deadlier in humans than regular COVID, though, is there?

      Or are you just talking about the precedent for massive livestock culls?

      1. DG says:

        Are minks in Denmark Vitamin D deficient?

        1. FoodScientist says:

          They should switch to galvanized steel cages. Those zinc coated bars should stop it.

          1. Théodore Giesel says:

            Zinc for mink works every time
            You know this is true because it rhymes

      2. Kristian from Denmark says:

        No it doesn’t seem to be more contagious or deadly than regular SARS-CoV-2. The “only” problem is that the new mink variant is less susceptible to inhibition by antibodies isolated from SARS-CoV-2 survivors. Worst case scenario is that this new strain will run wild after we have all been vaccinated against the original strain.

        1. confused says:

          How long would it take to “add” this variant to a vaccine already approved?

          BTW, what level of likelihood is the vaccine-evading aspect? Is it “we need to take this seriously because it would be bad if true, but not actually all that likely” or “very likely, depending on what vaccine turns out to be used” or somewhere in between?

  4. Alan Goldhammer says:

    Where is PETA when we really need them?

    1. Dark Day says:

      Oh, they’ll raise holy hell when they find out about all the mink killings. They’d probably rather see more humans die.

      1. metaphysician says:

        Nah, PETA’s response would be “Why not both?” Remember, their own publicly stated position is that its better for animals to be dead than on farms or in homes, and they’ve been caught euthanizing animals pell-mell in alleged “shelters”.

        1. Dark Day says:

          Okay, didn’t know that. I assumed they’d be advocates of “no-kill” shelters.

          1. metaphysician says:

            Nope!

            https://www.washingtonpost.com/national/religion/at-petas-shelter-most-animals-are-put-down-peta-calls-them-mercy-killings/2015/03/12/e84e9af2-c8fa-11e4-bea5-b893e7ac3fb3_story.html

            https://petakillsanimals.com/proof-peta-kills/

            ( That latter links is definitely not a neutral observer, natch, but they have extensive links and citations, and obviously don’t hide their position. )

          2. Cameron says:

            I eat meat, but I’m pretty sure the likely origin of coronavirus in a wet market, and it’s potentially dangerous mutation in high density fur farms is actually a fairly strong argument for veganism.

          3. confused says:

            I think the better way to go is to improve vaccine development for livestock. It ought to be much easier/quicker to develop vaccines for livestock (because, unlike humans, if a vaccine candidate kills 1% of the test population you just compensate the farmers…)

            Is there any reason that in say 40 years from now, especially with rapid improvements in biotech, we couldn’t have vaccines for livestock against all the plausible cross-species-jumping/pandemic-causing viruses?

            Even if *universal* veganism were workable (I don’t think it is, due to nutritional issues esp. in parts of the world with much less available food variety – dairy is critical many places, I think) there’s no way you could convert the world in even 100 years.

            And certainly it would take far longer than that to convert the entire world to veganism. I don’t think it could be done at all…

    2. Luann DeLuca says:

      I just sent an e-mail on this very question. Being a devoted monthly donor to PETA, because I fervently believe in the organization’s mission, I want them to use their powerful voice, influence, and world-wide public backing to stop this horrendous slaughter. Do it Now!

      1. fajensen says:

        On this well-publicised occasion or on every year? Because without Covid-19 they would have killed most of the mink anyway, in the same way, to get their fur.

        With a bit of luck, most of the farmers will cash in on the compensation and not go back to mink-farming. They were not doing very well for the last 5-7 years anyway.

  5. c says:

    I imagine 200 years from now (optimistic that Humans still exist) people will look back on the current scale of animal factory farming as morally unconscionable in a similar way we look at slavery today.

    We sacrifice ethical, environmental, and (now, obviously) health concerns for what? A bit of Hedonistic pleasure. Pretty disgusting if you give it any thought at all.

    1. metaphysician says:

      No matter how much you might like to tell yourself otherwise, you are still an omnivore. A ( foreshortened) life of eating nothing but grass will not magically transform your teeth or digestive tract.

      Also, if “future humanity” is both one singular monolith and also does not distinguish between animal husbandry and *slavery*, then count me glad to have died before the world fell into complete dystopia.

      1. a says:

        We evolved to be omnivorous, but all of the essential nutrients from meatstuffs could be made from non-animal origins if we put our mind to it.

        this is a chemistry blog, not a vitalism blog ffs. (“must have flesh! flesh give power!”)

        1. confused says:

          It is technically scientifically possible to make all those proteins etc. from non-animal sources, sure, but seems completely implausible as an universal or near-universal decision across human cultures.

          1. a says:

            We are not obligate carnivores, and plenty of vegetarians and vegans have long lifespans.

            It’s a question of priorities; there isn’t any serious technical limitation to eating a healthy non animal diet. I say this as an omnivore!

          2. confused says:

            Veganism works *for people who are committed to it*, but I don’t think it’s *easy* enough to get a balanced diet that way that you’d ever see the whole human population go vegan.

            But it’s not really about what’s possible — sure you could make meat/cheese/etc substitutes artificially. The point is that there’s no reason to think that sort of universal cultural shift in diet would happen.

            Some places, maybe… in 200 years we might have people living in domes on Mars who use artificially-produced protein foods, and that might spread back to Earth.

            But 200 years is not nearly enough time for a radical change to be accepted by *every human culture*.

          3. confused says:

            (My own personal view is that it would be best to not use factory farming of livestock *if* that could be done without raising food prices; but producing all protein-based foods in a “laboratory” way actually seems rather undesirable to me, as that would only distance our culture *more* from the rest of the living world, as not really part of an ecological system any more…)

          4. Charles H. says:

            You make it sound more difficult than it is. That people won’t all switch to veganism I take as given, but you don’t need artificial sources to do it in most places…at least unless you count bacteria as animals, and I haven’t heard of any vegans that do.

            E.g. mushrooms are fairly cheap to grow, and don’t take up excessive space that would be used for other purposes. And can be grown on a wide variety of fertilizers. (You might not be able to grow the particular *kind* you want, but some useful variety can be grown on just about anything organic.)

            Check out Chines Buddhist recipes for examples of balanced diets without either meat or industrial chemistry. Many of them are quite tasty. I wouldn’t want to live on them, but people did for centuries.

          5. confused says:

            >>you don’t need artificial sources to do it in most places

            For merely nutritionally-complete diets, no, not technically; to do it without utterly changing the culinary culture of most of humanity, you would.

            And I just cannot see the latter happening in any vaguely relevant time scale.

            Also, I am pretty sure that in practice e.g. dairy is absolutely nutritionally critical in many parts of the world. Getting every place entirely hooked into a food distribution infrastructure is also … extremely non-trivial.

      2. c says:

        There are loads of strawmen in this response.

        Being opposed to both slavery AND planet-scale animal slaughter (For pleasure, you do not need meat. Your brain is screaming that you do right now, but that’s just cognitive dissonance. There are very likely millions of vegetarians living much longer, healthier lives than you) does not mean one sees them as EQUIVALENT.

        Imagine a slave owner saying “Equating raiding and pillaging to a bit of good-natured slave owning is a dystopian outlook!” and thinking that that outlook absolves them.

        You also chose to ignore the health and environmental costs I mentioned. But what’s the point? It’s the nature of progress that it only happens one funeral at a time.

    2. FoodScientist says:

      Interestingly the rate of vegetarianism in women is generally higher than men. It is believed they are less okay with cognitive dissonance( have 2 incompatible views like “pro-life” // pro-death penalty or having and loving pets // but killing and eating farm animals). This is also the general explanation why people are militant in vocally hating vegans even though I’ve never really seen vegans do anything bad. The mere fact of their existence causes some internal conflict on a more subconscious level.

      I’m not a vegan, I just think the “why” on this is interesting.

      1. confused says:

        Is that US/Western world specific or is the gender pattern also found in cultures where vegetarianism has more of a religious aspect (e.g. where Buddhism and Jainism are more common)?

        If it’s the former, I’m not sure I wouldn’t just attribute that to different degrees of health-consciousness…

        Not really sure I see the cognitive dissonance, esp. if the species used for pets and food are different. Loving cats and eating cattle doesn’t seem to me to be any more ‘dissonant’ than loving butterflies and hating harmless spiders, which is very common.

        1. metaphysician says:

          Likewise. Honestly, the entire concept of “animal rights” kind of annoys me, not because I believe in being cruel to animals ( far from it ), but because it implies that “animal” is a singular monolithic category warranting a singular monolithic treatment. Which is, in a word, laughable nonsense. What constitutes ethical treatment for a fruit fly is not the same as what constitutes ethical treatment for a cow, and neither have all that much in common with the ethical treatment of an elephant. Its almost like a bizarre holdover from the Victorian “All animals are distinguished from humans by being wet squishy robots” philosophy, except being applied by people who allegedly want to treat animals better, rather than worse.

          I’m not sure whether its because people really want to hold onto an absolute insurmountable distinction between “human” and “animal”, or just people being mortally afraid of having to make judgement calls about different levels of “moral worth”.

          1. confused says:

            Yeah, I agree with all this.

            To me cruelty to animals is wrong because it is cruelty not because of any inherent nature of animals.

            Pointless destruction of things (as opposed to destructive *use*, eg eating animals or plants or harvesting plants for fiber/wood) is IMO wrong even if there is no directly-caused suffering; burning plants just to see them burn, or destroying paintings for the same reason, would be wrong IMO although neither plants nor paintings can feel pain.

            And yeah it is also weird to put monkeys and worms in the same moral category but not plants or fungi.

        2. Dark Day says:

          True, but ultimately it’s a matter of individual or cultural moral choice. In the U.S., we “love” cats and dogs and eat cattle. In other cultures, they eat cats and dogs as well as cattle. I’m guessing that even the lustiest, red-blooded American steak lover would blanch if someone gave him a plate of medium-rare collie ribs.

          1. confused says:

            Oh, it certainly varies by culture – but I don’t think there is really “dissonance” within a culture … I believe those cultures where dogs are eaten don’t have the “man’s best friend” image of them we do. In some parts of the world dogs are more street dwellers than house pets.

    3. Dark Day says:

      Well, let’s remember to be careful of false equivalences. A case can be made that we’re omnivores, part of the food chain, and hence not committing any moral or ethical lapse if we eat other animals. Mink, on the other hand, are bred solely (as far as I know) for their pelts; they’re not food animals for humans. Not the same thing.

      1. metaphysician says:

        OTOH, we are, by nature, intelligent tool using animals, and one of the benefits of that is being able to use other animals for purposes beyond just “food”. One of those uses is clothing. Farming an animal to provide clothing material isn’t any less “natural” than farming an animal to provide food.

        ( Now, is it a prudent or worthwhile course of action, fur farming? That’s dicier, at least for something as purely cosmetic as mink farming. While I don’t believe “absolute necessity” is the only justifiable reason for animal husbandry, I’m more than willing to grant that there is a different moral gradation for an activity that exists solely for aesthetic reasons. Which is to say, nobody makes, buys, or sells mink coats in order to keep people warm and shielded from the weather. They are kind of the archetype in the fur industry for “entirely useless display of extravagant wealth”. )

        1. Dark Day says:

          Eh — I’m not a diehard “anti-fur” virtue signaling moralist. But if getting rid of fashionable animal pelts will help keep us from getting ravaged by new, even more catastrophic pandemics, then I say let’s do it. And let’s nip it in the bud NOW, fer chrissake, before this “new” COVID has a chance to spread any further. The very thought of having to endure endless cycles of this is enough to deflate even the heartiest constitution.

  6. Marko says:

    Let’s hope that bats don’t take a fancy to mink farms as a vacation destination.

  7. Some idiot says:

    Just a minor correction: SSI stands for “Statens Serum Institut”, or The National Serum Institute.

    But yes, it is the national scientific body concerning (eg) infectious diseases…

  8. J N says:

    Is it too much to hope that cats and dogs will continue to be innocuous carriers of COVID-19?

  9. Peter Kenny says:

    I recommend that ferritin be evaluated as a biomarker.

    1. Some idiot says:

      Ouch… that really, _really_ hurts… I approve!!!

      😊

      1. Marko says:

        I think he meant ” ferretin ” , but minks are different from ferrets. A better biomarker would be furritin.

        1. Some idiot says:

          I think he meant that too, which is why I thought it was so good…! 🙂

        2. Peter Kenny says:

          I believe that ferrets are actually used as an animal model for in vivo studies. I’ve never had the opportunity to handle a ferret but I believe they are quite fierce. I recall a joke about how to make hair come out of a bald man’s (stuff a ferret up his nose).

          1. Hopeful Layman says:

            Ironically, minks are being used as animal models right now for a nasal-spray COVID treatment. No idea where this will go, but early results look promising. The researchers are already recommending that Operation Warp Speed be contacted, to try to garner some funding for human trials. (Not sure how/how long Operation Warp Speed will continue to be operative after the current election, however.)

            https://www.nytimes.com/2020/11/05/health/coronavirus-ferrets-vaccine-spray.html

          2. Hopeful Layman says:

            Sorry — meant “ferrets,” not “minks”!

          3. Derek Freyberg says:

            I am aware of ferrets being used in testing anti-emetic compounds (5-HT3 antagonists), but that’s the only use I know of them as a lab animal.

    2. In Vivo Veritas says:

      What a weaselly reply!

  10. En Passant says:

    Derek Lowe wrote:

    The coronavirus has spread and mutated in the Danish mink population, and now there have been cases of these strains jumping back into humans and causing infections there. This was first seen in a single case in the Netherlands in the spring (more here), and it’s happened a number of times since. It gets worse: reports have it that some of the current mink strains in Denmark are less susceptible to antibody responses.

    Now, I am not completely sure what that means.

    I consulted my latest model quantum computer Magic 8-Ball, and it has made a prediction: A bull market in existing mink coats, stoles, capes, hats and other mink accessories.

    1. Some idiot says:

      https://politiken.dk/debat/dagenstegning/art7962610/Outlet

      One of the most brilliant cartoonists in Denmark. Text says “I bought this cheap in northern Jutland”

      But there are also a lot of subtleties in the cartoon too…!

  11. Janus Krarup says:

    According to national tv “DR”, 12 people have been confirmed with the new “cluster 5” variant. Genectic characterization are only done to 5-10% of COVID positives, so the actual number is probably 10-50x

    1. confused says:

      Are their symptoms different than “regular” COVID?

      1. Some idiot says:

        No. No apparent differences in terms of ease of transmission, nor of severity of symptoms. To me it feels like one of those natural broadenings out in the gene pool. A broadening that can have significant consequences in the case of a sudden “disturbance”, eg vaccine…

        1. Michael says:

          For what it’s worth, from the Twitter thread above, Prof. Balloux says (and he has published analyses of many thousands of SARS-COV-2 genomes):

          “The ‘vaccine escape’ scare story is just idiotic. Vaccine-escape mutations may (or not) arise in humans in the future, if they are advantageous to the virus for (once vaccines will be deployed). They definitely won’t be fuelled by mutations having emerged in minks.”

          1. Dark Day says:

            Okay, many thanks — that was going to be my question, since as Derek reports, “some of the current mink strains in Denmark are less susceptible to antibody responses.”

          2. Some idiot says:

            True, but was only described single mutations in the spike region. From what he said, I get the feeling that he was only responding to the information in the newspaper story, and was unaware of the strains found with multiple mutations (and reduced response to antibodies).

        2. confused says:

          So then if this strain turns out to be less-effectively protected against by a vaccine when we do get one (and wouldn’t that depend on which vaccine or vaccines ends up being distributed?) couldn’t they just add that to the vaccine like when they update the flu shot each year?

          Or would it require a complete re-development of the vaccine?

          One would think a government wouldn’t want to destroy a significant industry without a pretty good sense that the problem was real. Am I missing something?

    2. Niels says:

      The worrisome “cluster 5” variety has actually not been seen for a month, it might have died out. Here’s an article with what could be really great news, and some more details about the danish genome testing program:

      https://jyllands-posten.dk/indland/ECE12543828/muteret-minkcoronavirus-er-ikke-sporet-i-en-maaned-den-kan-vaere-helt-vaek-igen/

      The Serum Institute has found 5 distinct clusters of mutations originating in mink. Cluster 1 has shown no reduced antibody response. Clusters 2-4 are under investigation. The result on Cluster 5 came in this Monday and caused the ongoing cull.

      Around 1 in 7 corona positive patients get a full virus sequencing. Out of 38000 samples from June to mid-October, 5000 were sequenced, 12 had the Cluster 5 variety. None of the October samples showed Cluster 5. (The pandemic really picked up speed in September/October, so the larger part of the samples must be from there).

      The minister of health says that all positive samples will be sequenced. I don’t know what the lead time for that is, how many of the old samples will be sequenced, and when the results come out.

  12. Anonymous says:

    “it’s also worth noting that the human population is not well modeled by the conditions on a mink farm. Yet.” This is why I keep coming back. Thanks, Derek, for keeping us smiling and informed.

    1. miles says:

      The Mark of Gideon! I remember that Star Trek episode as a kid in the 60’s!

  13. JS says:

    Some details of what SSI did are here:
    https://coronasmitte.dk/-/media/mediefiler/corona/mink/risikovurdering-af-human-sundhed-ved-fortsat-minkavl_03112020.pdf
    Section on p. 2 is the important one. Throw it into google translate. Does a good job.

  14. Erik Dienemann says:

    Easy cure: HCQ + AZ + Zn. Alright, someone had to say it (feel free to delete)…

  15. Poul-Henning Kamp says:

    Hello from Denmark,

    The last assays were only run at SSI on monday, and they immediately alarmed the government with the risk-assesment JS links to, and in less than 24 hours the gov’t announced that all mink will be put down.

    Scientific articles will happen, “but that was not our first priority in this situation”.

    People infected with the “cluster-5” strain do not seem stand out from other covid19 infected with respect to symptoms and severity, but with the very low numbers, that only tells us it is not very much worse.

    Feel free to throw questions at me, and I’ll do my best.

    1. Some idiot says:

      Thanks for the info! You certainly moved fast! Any idea when more details on the results (eg mutation info, data on sensitivity to antibodies, etc) will be made public? Even “just” a memo on SSI’s home page or similar? I realise fully that the first priority is on getting control over the situation, but I am just a bit kinda curious…! 😊

      1. Poul-Henning Kamp says:

        No idea, but I bet they’re typing as we speak.

        There is an appendix 1 to the risk-assesment linked above:

        https://files.ssi.dk/Bilag1-Risikovurdering-human-sundhed-ved-fortsat-minkavl-03112020

        But it is mostly about the epidemic aspects, there is very little about the actual virus.

        I suspect the important bit is that the mutation from NL and DK were not the same, which clearly indicates that mink is a really good “bio-reactor” for covid19, and makes a very compelling argument for putting all the animals down.

        That BTW, is a major undertaking, they weigh 1.5-2 kg each and there are around 15 million to destroy.

        A number of waste incinerators will be involved: Denmark as a lot of district-heating, where the heat comes from burning house-hold waste. These incinerators typically have two or three truck-bays where the garbage trucks back up and tip into a “pit”, from where a crane or screw mechanism moves the refuse to the firing room under the kettle.

        1. Some idiot says:

          Many thanks! 😊

      2. JS says:

        At a press conference today with the prime minister, the minister of health, SSI and so forth they did promise that details would be made available as soon as possible. Which sounded like really soon.

        Interestingly for a televised prime time press conference, there was also
        a discussion about RNA virus mutation rates, host adaptation and antibody escape mutations. Interesting with such details in a prime time televised government press conference. Not what you see most other places.

    2. Rufus says:

      Hey there – based on an English transcript I’ve read of the press conference, Kåre Mølbak says he thinks think the new mutation as it stands will not affect vaccine development, but the SSI are more concerned about it becoming widespread and potentially mutating further. Is that accurate? I believe he also said that the cellular response does not seem to be affected, fortunately.

      I also understand that Denmark genetically sequences 14% of all its cases as a matter of course to monitor for this sort of thing, so it would suggest they caught it extremely early if there have only been a tiny handful of cases to far.

      Full thread:

      https://twitter.com/Goldammerfeder/status/1324036763036405760

      1. Poul-Henning Kamp says:

        Kåre Mølbak said that they saw “markedly reduced response to antibodies from patients/serum” (my translation) and that the fear was both that it could reduce or delay the efficient deployment of vaccines, but also that it could start a “second pandemic” or “second wave of the pandemic”.

        One of the journalists asked if this was “covid-20”, and he deflected by saying that SSI doesn’t name stuff, that was an international panel of specialists job.

        He did not say anything about reinfection with the “cluster 5” strain, and it would be very unlikely for them to have any data on this.

        1. confused says:

          >>but also that it could start a “second pandemic” or “second wave of the pandemic”

          OK, now I’m doubly confused.

          If it’s not different in severity, it seems like it shouldn’t matter which strain you get unless you already have COVID antibodies.

          Are there high enough antibody levels in the population in places like Denmark for a strain not affected by current antibodies to have much of an advantage? I thought northern Europe, except maybe Sweden, had pretty low infection rates?

          Or is it one of those things where a 1% advantage adds up to a huge difference after enough generations?

          1. Poul-Henning Kamp says:

            Kåre didn’t say anything about reinfection (no data), but if the new strain is less affected by antibodies raised against the original version, you might get both.

          2. Patrick says:

            I assume a lot of the fear is around implications for vaccine development.

          3. Marko says:

            I assume a lot of the fear is around being blamed by Trump for releasing the Denmark Virus , a new Invisible Enemy , upon the world.

          4. Dark Day says:

            Yes, Patrick, that’s my main worry, as well.

          5. confused says:

            Would this (or effects of other mutations) be dependent on what kind of vaccine ends up being distributed?

            IE – would an RNA vaccine vs an adenovirus vaccine vs an inactivated-virus vaccine be more/less able to deal with mutations in the virus?

          6. Marko says:

            Whole virus vaccines ( inactivated or attenuated ) would , in theory , be less susceptible to this sort of problem than spike-based vaccines , and even less susceptible than RBD–based vaccines , due to the diversity of antibody response each vaccine type would generate. The proof would be in the pudding , however.

  16. Markus Auer says:

    Apparently, seagulls had their “hand” in spreading this variant across mink farms: https://landbrugsavisen.dk/universitet-mist%C3%A6nker-m%C3%A5ger-sprede-coronavirus

    Danish media reports that the situation has been ongoing for weeks and the new variant has spread as far as Croatia already:
    https://www.information.dk/indland/2020/10/myndigheder-kendte-trussel-virusmutationer-mink-laenge-inden-minister-reagerede

    I couldn’t find anything on nextstrain to confirm this and I am not from Denmark either, so I can’t speak of the actual situation on the ground.

    1. fajensen says:

      It’s perhaps a bit unfair to blame the birds when it has long been silently “accepted” (because religious teachings say that suppressing non-executive compensations tall the way to Zero is a Good Thing for Growth) that mostly migrant people from eastern Europe are working at farms and meat plants in Denmark, and often under atrocious conditions.

      In the most organised cases they are working as “contractors” from companies registered in Poland, Estonia, Rumania and so on meaning that it is legal for them to have Poland, Estonia, Romania, etc. salaries, working- and living- conditions, in Denmark, like perhaps sleeping 20 to a container and having to pay rent for that!

      However, cash-in-hand employment is also normal, which cuts down on bureaucracy. The mink business was tanking since 2014 or so, one suspects that a lot of unregistered people were moving between the farms.

      Now, we are waiting for the obvious other shoe to drop: The pork industry; That will be quite the incubator if pigs are also susceptible to Corona Virus.

      We have about 20 million factory farmed pigs, that are pushed all the way on every biological limit, so that 1 kg of prime pork often costs less in the shops than 1 kg of mixed Wine Gum!

      Before this pandemic, the Danish Authorities have allowed the spread of LA-MRSA CC398 in the pigs for years, and even exported it into Europe – It will be interesting to see what happens with Covid-19. https://www.nature.com/articles/s41598-019-55086-x .

  17. Eric Miller says:

    Looking at the sequence alignment for the 19 search results of “SARS-COV-2 mink” on Genbank (hopefully these are the right sequences) it looks like the spike mutations are G261D (for mink-related strains isolated from the Netherlands), Y453F, D614G (of course), and deletion of N710, A892, and S943. Here are the accession numbers for all those spike proteins, if you’re interested in playing around with them in Jalview:

    QJS39627.1;QJS39615.1;QJS39603.1;QJS39591.1;QJS39579.1;QJS39567.1;QJS39555.1;QJS39543.1;QNJ45118.1;QNJ45106.1;QNJ45142.1;QNJ45154.1;QNJ45166.1;QNJ45178.1;QNJ45190.1;QNJ45202.1;QNJ45214.1;QNJ45226.1;QNJ45238.1;

    Interesting that Y453F was previously reported in this paper (https://www.pnas.org/content/117/38/23652) at 0.02% prevalence with an n = 5 – in this set, that mutation is seen in 12 out of 19 sequences. Might be a new emerging consensus mutation. N710 deletion occurs in 6/19, but the other two deletions are low-prevalence (1 or 2 out of 19). G261D occurs in 4/19, but aside from that there are no significant variants. It will be important to see whether the neutralizing antibody responses raised by folks in the various vaccine trials recognize these spike variants.

    The receptor binding domain, by the way, (which is what neutralizing antibodies predominantly target) fall within the range of residues 333-527. Y453F falls in that range, but that’s a quasi-synonymous mutation – just removing an -OH group from the tyrosine. Could impact binding of select antibody variants by disrupting a salt bridge, but shouldn’t impact overall spike structure (so other neutralizing antibodies raised in response to the vaccines should function). That’s not 100% guaranteed (even far-off mutations like the deletions in the 700-900 range could yield overall structural variation), but generally I’m not too worried about this degree of mutation. For reference, the spike for SARS-CoV-1 has less than 80% similarity to the spike for SARS-CoV-2, and some neutralizing antibodies cross-react with both forms.

    This culling is the appropriate response (ideally you’d avoid proliferation of different strains which could stack multiple mutations and escape vaccine coverage that way), but I’m not personally too concerned at this point – let’s wait till we see analysis of vaccinated patient serum and the advanced therapeutic mAbs with these new spike variants.

    1. Some idiot says:

      Nice digging! Any idea whether or not these are the sequences involved in the latest culling? The main strain had 4 (I think, or 5) mutations in the spike. I would guess that their dates would be pretty recent…

      1. Eric Miller says:

        Here’s a link to one of those genomes with N710_ and Y453F (https://www.ncbi.nlm.nih.gov/nuccore/MT919530.1) – this was submitted to Genbank on August 22nd by the Statens Serum Institut, so unless there’s been some rapid differentiation from these strains or a newly identified emerging cluster since then, I’d expect that these sequences are fairly representative of what they’re reporting on.

    2. Marko says:

      This mutation , already circulating among humans , would seem to be of greater concern regarding resistance to vaccine-induced antibodies , etc. :

      https://www.biorxiv.org/content/10.1101/2020.11.04.355842v1

      “….We observed that the N439K mutation resulted in immune escape from a panel of neutralizing monoclonal antibodies, including one in clinical trials, as well as from polyclonal sera from a sizeable fraction of persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.”

      1. confused says:

        Wait, is this the mink-derived mutation or a different one?

        1. Marko says:

          It’s one that has been studied in humans for a while. Whether it is also among those seen in minks remains to be seen , I think.

          1. confused says:

            OK but not this Danish thing?

          2. Marko says:

            Well , the Danish thing is in minks , right. So , it remains to be seen , I think . Once again.

          3. Some idiot says:

            From what I can see, they are different, but with similar concerns. In the Danish case, the strain of concern had 4 different mutations in the spike region, and showed reduced sensitivity to antibodies.

  18. JasonP says:

    I don’t get this? Are you saying a new deadly strain and thus we should look for another global shutdown and mass quarantines?

    1. Concerned says:

      . . . and an entirely new “Starting again from Point Zero” years-long vaccine development before we start getting a handle on it?

    2. Poul-Henning Kamp says:

      Kåre Mølbak said that the humans infected with the cluster-5 were neither worse nor better of than those with “regular” covid19.

      The worry is that the vaccines will not work (as well) against this strain, or that it might mutate further and become worse.

    3. WST says:

      That’s how i get it, off to buy hundreds of rolls of toilet paper, maybe there is some with zink already…

  19. Poul-Henning Kamp says:

    BTW, one interesting twist on the entire Covid19 saga, is that at our last election we got Stinus Lindgreen in the Danish parliament. He’s phd. in bio-informatics and part of the team behind the “Saqqaq” ancient genome paper, which made quite a splash some years go.

    Rumours are he has been doing a LOT of explaining, and that the Danish Covid19 handling has been better for it.

  20. Hopeful Layman says:

    Meanwhile, other ferrets make their contribution to the fight AGAINST Covid/

    (The frustrating thing about articles like this is that they give no idea of what the timeline might be on R&B; the language is optimistic, but there’s no way of knowing how optimistic we should be about initiation of clinical trials and any subsequent roll-out. On the other hand, most of the vaccines currently completing Phase III didn’t even start animal trials until sometime this last spring, so perhaps the wait wouldn’t be insufferably long.)

    1. Some idiot says:

      Good R&B comes along nicely when everyone is relaxed… 😉

  21. Dark Day says:

    Is Denmark planning the kind of aggressive quarantining, contact tracing, etc. that we now know should have happened in China when the first COVID cases appeared there? Seems to me that the highest priority, aside from getting rid of the minks, is containment. It might even be desirable to seal Denmark’s borders, at least until more is known. This thing cannot be allowed to spiral outward into a new global pandemic.

    1. Poul-Henning Kamp says:

      Today they shut down the worst affected parts of the country hard.

      Time will show if that was enough.

      Btw: This is a sort-a-ok source of news from Denmark in English. It’s from a right-wing-ish rural paper, and the “home paper” for the affected end of Denmark.

      https://www.thelocal.dk/20201105/denmark-tightens-north-jutland-restrictions-in-response-to-coronavirus-mutation

    2. JS says:

      The horse may have left the barn a while back. The sequenced cases were in August and September. None detected in October, so far, but I am sure that there are samples still to be sequenced.
      Also, one case was detected in a retirement home hundreds of km away a while back. They have no idea how the virus made it from the farms to there. Means that it could easily have made it to other places, even outside of Denmark.
      Now they want everyone in the affected area to get tested and will sequence every positive sample found. We shall see what they find.
      On the positive side (in addition to the last sample being almost two months old), they say that no examples of the variant have been found outside of Denmark.

      1. Poul-Henning Kamp says:

        A full sequencing takes time, not sure precisely how many days, so the october cases may still be in the pipeline.

        In general it has been a big mystery how easily the virus spread between mink farms and to surrounding society.

        Mink farms are not not exactly a noted social venue, what with the smell and all.

        There were talk of a project to set up cameras around 30 mink farms, to try to find out if birds or ground based wild animals transported the virus by some mechanism, but that’s probably OBE now.

        The easiest explanation would be that the mink-variant simply is more contagious, but that would take a lot more data to show.

        1. Some idiot says:

          Hmmm… Possibly…. Or possibly that with a large number of animals that can cross- and re-infect each other (and increasing selective pressure against strains those that the mink already have antibodies to) then there is a greater risk that these “new and resistant” strains will hop over to humans again, and then spread in the community (even through those with antibodies agains the “regular” strains.

          I would guess that it is something like this that has scared the bejeezus out of the relevant authorities…

          Possibly…!

          1. JS says:

            As I mentioned in a previous post, the issue of antibody escape mutations was discussed at the press conference. Press conference is here, but it is in Danish, so probably not of much use to most:
            https://www.dr.dk/drtv/se/tv-avisen-18_30_219216
            Look around 1:08 (specifically listen at 1:10:20 for a few seconds, should be understandable for English speakers). Journalist who asked looked baffled and the prime minister even joked about the level of technical details and how understandable that would be to people.

            But indeed, that appears to be part of the fear.

        2. fajensen says:

          I’d bet on undocumented Cash-in-Hand farmworkers, probably from Poland or Romania. About 40 of those stacked up in one of those houses one can buy for 300 kDKK “out in the wild west”, like a red carpet reception for Corona 🙂

          – Maybe they are not even bothering to buy the house before mass-renting it out, this was the speciality of a known fraud, called Låsby Svendsen. Thus no records, with no one particularly interested in talking about it, and then getting the attention of the Danish IRS.

      2. Dark Day says:

        Apparently it’s been found in the Netherlands, too:

        https://promedmail.org/promed-post/?id=7375359

      3. JS says:

        It has now been reported that the case far from the mink farms was due to a mistake and that all known cases are associated with the mink farms.

        1. Dark Day says:

          Ah — well, if there’s any such thing as “good” news in a case like this, it’s a good sign that perhaps this new virus has so far been contained within Denmark. I still wonder whether sealing the borders, at least until this is sorted out, might not be a very good idea.

  22. Dark Day says:

    I don’t wish any deleterious effects on Denmark or anyone else. But now that we seem months away from a vaccine (and probably not too much longer than that for effective therapeutics), the last thing we need is this kind of setback. At best, we’re already at least a year away from effectively bringing COVID under some kind of control; I can’t imagine what would happen worldwide if we all got socked with a “COVD-20” even as COVID-19 was still spiraling out of control. I also think extreme pressure should be put on the Chinese and/or anyone else farming minks.

    1. confused says:

      Caution is of course good, but even in 2020, not everything will be the worst possible outcome.

      In the US there is so much COVID around that I am not sure it would matter in the short-term (pre-widespread-vaccination); hard to have a new wave if the current wave is already everywhere.

      Even if this does spread, and even if the antibody-effect difference turns out to matter with whatever vaccine ends up getting distributed, couldn’t they “update” the vaccine like they do with flu shots? Would they have to do the phase III trials all over again for something like this, or just change the sequence in e.g. the Moderna RNA vaccine?

      I’m wondering if the economic effects of killing all the minks would be smaller than what I’d expect from destroying an industry? Or if it’s as much driven by the geopolitical concerns of being the epicenter of a new outbreak?

      1. Dark Day says:

        ” . . .hard to have a new wave if the current wave is already everywhere. . .”
        Not necessarily, depending on how antibody-resistant it is. It could potentially re-infect those who’ve already been exposed to COVID-19, along with anyone else. We could find ourselves with two “parallel” COVID pandemics. In all honesty, I could easily see nothing short of terminal worldwide depression (economic and psychological) if that occurred. We could end up looking back on 2020 as “the good old days.”

        1. confused says:

          >>We could end up looking back on 2020 as “the good old days.”
          This seems far too pessimistic. I mean theoretically sure, all the cards could fall exactly wrong, but that’s by far not the most likely outcome, and borrowing trouble isn’t really what we need right now.

        2. confused says:

          And I think you might be overstating the psychological impact if the only real difference is “you can get it again”, IE it’s not more dangerous.

          A lot of people have already jumped to the (wrong) conclusion that there’s no natural immunity due to (very rare) reports of reinfection.

          I mean the possibility of getting COVID twice rather than once wouldn’t make me act any differently than I do now.

          1. Dark Day says:

            It would definitely impair international economic recovery; lead to even more massive layoffs; be fatal to the hospitality industry, the airlines, and countless other industries; continue to disrupt education (from elementary school through college); overload hospitals and — tragically — morgues; further ravage our cultural and public life; keep people masked, “distanced”, isolated, and overstressed, etc.etc.etc. . . . Right now, one in five families in the U.S. is food insecure — God knows how a “double pandemic” would make that worse. in short, 2020 on steroids.

          2. Dark Day says:

            . . . and, of course, the most important consideration: possibly hundreds of thousands, even millions, more hospitalizations and deaths, in the U.S. and worldwide.

          3. confused says:

            Definitely not millions of deaths, with comparable fatality rate to current covid… unless you think it would take literally years to update the vaccines… (What do you think COVID IFR is in the US now?)

            And I think the people who are already staying home would keep staying home, the people who aren’t afraid of it wouldn’t start being afraid of it since you can get it twice. So not sure that many people’s behaviors/attitudes would change much.

  23. Dark Day says:

    *“That is a very big statement,” said Koopmans. “A single mutation, I would not expect to have that dramatic an effect.” . . .*

    But haven’t multiple mutations been found in some strains? Is this article already obsolete?

    1. Michael says:

      Obsolete? The article was posted like 30 minutes ago. Interviews from today.

      1. Dark Day says:

        Okay, just wondering, not trolling — maybe I misunderstood the earlier post which I thought said that multiple mutations had been documented in some strains. I apologize (and I’m relieved!) if I got that wrong.

        1. Some idiot says:

          You are right: the strain that got them to hit the panic button was with 4 different mutations in the spike region. This is also the one that showed reduced sensitivity to antibodies.

          I haven’t read the link (will do so later) but I have over the last 24-36 hours seen comments from experts who were not aware of the memo from the SSI specifying these two particular points. This is the “cluster 5” strain.

          I should also mention that they say that there are other strains that they have not had time to investigate (I.e. sequence, etc) yet, so (without being alarmist) it could be that other strains are a bit in the same ballpark.

          Quoting from the memo: “ Other strains have been identified by sequencing, but have not yet been tested against neutralising antibodies.”

  24. luysii says:

    I don’t think this is much to worry about, as it is very likely that all of the possible single amino acid mutations in the SARS-CoV-9 have already occurred in the 28,000,000 cases out there

    13% of all possible mutations have already been found in the virus, out of only 90,000 completely sequenced genomes. There are now 28,000,000 cases out there, so it’s almost certain with 1,000 times more virus out there to sequence, that nearly all the other 44,000 or so possible mutations have already occurred somewhere in the world.

    How can this be good news? Because if any of them were truly horrible, we’d know about it. It would have taken over just the way the D614D mutation did.

    For chapter and verse please see https://luysii.wordpress.com/2020/09/13/why-the-news-about-sars-cov-2-mutations-is-actually-good/

    1. Dark Day says:

      Interesting — does the fact that the virus might have mutated inside another species add to the matrix of possible mutations? I confess this is probably an ignorant question, but I’m not a virologist by profession.

    2. luysii says:

      Sorry, that’s the D614G mutation

    3. Derek Lowe says:

      It looks like the one they’re worried about has four mutations. More to come on that.

      1. Dark Day says:

        I’m not clear from the article — were the strains with the troublesome mutations found in minks, or in the humans who had contracted the virus from the minks?

        1. Derek Lowe says:

          I believe that they identified them in the humans, but they’ve been sequencing the mink samples as well, so it’s hard to say.

        2. Poul-Henning Kamp says:

          Both.

      2. luysii says:

        “Two SARS-CoV-2 viruses collected from anywhere in the world differ by an average of just 10 RNA letters out of 29,903,”

        https://luysii.wordpress.com/2020/09/13/why-the-news-about-sars-cov-2-mutations-is-actually-good/

      3. Some idiot says:

        Yep, 4 mutations in the spike region. Identified in both mink and humans (the so-called “cluster 5”).

  25. Barry says:

    Look for a glut of mink pelts on the market. That means less profit for fur ranchers. While I expect the Danes to compensate ranchers there for the loss, their competitors abroad may not recover.

    1. Poul-Henning Kamp says:

      I dont know where that glut should come from. The Danish animals are destroyed whole, because analysis have show the virus remains in the fur for a long time.

  26. Poul-Henning Kamp says:

    Press-release from SSI with some actual details:

    https://www.ssi.dk/aktuelt/nyheder/2020/mutationer-i-minkvirus

  27. COVIDiot19 says:

    Have they tried giving the mink zinc supplements?

  28. Crni says:

    Hmmm but since the T-cell response is more important for fighting the virus and immunity AFAIK, is this not a bit of an overreaction? The vaccine will most likely not rely on hte antibody response, which is why we also see the mabs failing so badly no?

    1. Hopeful Layman says:

      I believe the best-case scenario would be a robust response in BOTH; not sure whether “one” or “the other” might still convey effective immunity.

    2. Hopeful Layman says:

      WHO seems cautiously skeptical about any serious danger from the mutation —

      https://www.nbcnews.com/news/world/who-downplays-coronavirus-mink-mutation-risk-after-denmark-orders-huge-n1246726

  29. Esteban says:

    The mink that lives atop POTUS’s head recovered, so that’s reassuring.

  30. The reason for mink farms may have mostly gone away since the initial outbreak. If you, like me, were surprised mink existed in Denmark in such numbers, you may be more surprised by the reason: the false eyelash industry. Quite a few large retailers, such as Sephora, have since stopped selling mink lashes.

    For those thinking, well, why not synthetic lashes? Because, frankly, they are rarely as good, and those that are are hella expensive. Unfortunately, women’s appearance is judged harshly, lashes are a necessity for many women, and here we are.

  31. vic says:

    The world has done nothing to prevent the next pandemic from occurring. We confine animals in cages and packed sheds in the name of carnal pleasure and react with surprised_pikachu when diseases brewing among those animals transfer to humans. Another perfect storm virus like sars-cov-2 with the right transmissibility and lethality is right around the corner. The warnings about a pandemic Bill Gates made prior to covid-19 are still valid. We’ve learned no lessons except that some of us are exceedingly selfish and irresponsible.

    1. confused says:

      Animal husbandry/health practices definitely need to be improved, in addition to cracking down on illegal wildlife trade, limiting deforestation & moving large human populations into rainforests, etc.

      But there is a tradeoff when advocating things like this. It needs to be somewhat measured — improve animal husbandry practices, not turn the whole world vegan. Advocating for the latter will just not get you anywhere as the majority of people will dismiss you.

      IMO we could make huge strides with relatively little cost (and I mean in terms of “opportunity cost” of disruption to cultures, not just money) if we — as humanity — really invested in the interaction between human, agricultural/livestock, and environmental health.

      1. Hopeful Layman says:

        Certainly I agree that “confining animals in cages and packed sheds” is both inhumane and dangerous (to the animals and to humans). Free-range is the way to go. I think that’s one point people on both “sides” can probably agree on. It won’t solve all the problems (the bat that sparked the initial COVD case in humans wasn’t a captive animal at all), but it is certainly a step in the right direction.

  32. Hopeful Layman says:

    Okay, another “Layman’s” question. Is there any information on which species of animals are more likely to (1) contract the virus from humans and (2) spread it back? Also, is the virus more likely to mutate in ways that would make it more lethal to humans (and / or more vaccine resistant) if it jumps to another animal, and then jumps back to humans? Or do we not know anything about any of this yet?

    1. JS says:

      Indeed, a major scandal is brewing.

      In the meantime SSI has added information here:
      https://www.ssi.dk/aktuelt/nyheder/2020/ssis-deling-af-data-om-cluster-5-sars-cov-2-minkvariant-virus
      Most interesting to most readers of this blog is probably the short report (in English!) here:
      https://files.ssi.dk/Mink-cluster-5-short-report_AFO2

  33. artur franz keppler says:

    Paul-Henning Kamp, how is going the situation there in Denmark? Your local point of view is very important…

  34. JS says:

    I am not PHK, but I do follow the situation in Denmark. The handling of the mink issue is turning into a major political scandal and there are calls for the Minister of Agriculture to resign or face a vote of no confidence.

    Currently some farmers are voluntarily continuing the culling of the healthy animals, others are not and the government will not force it, given the lack of a legal basis.

    Based on the information posted here:
    https://www.ssi.dk/aktuelt/nyheder/2020/ssis-deling-af-data-om-cluster-5-sars-cov-2-minkvariant-virus
    especially the short report (in English!) here:
    https://files.ssi.dk/Mink-cluster-5-short-report_AFO2
    many experts in an outside of Denmark are questioning the decision and the seriousness of the situation.

    Stay tuned!

    1. artur says:

      Tks JS. It´s not so easy to follow european news here from Brazil. Stay safe!!!

  35. Chris Phillips says:

    Here’s a rather reassuring article in Nature from five days ago (though I can’t see where in the article they get “probably won’t jeopardize vaccines” from – the article says only that the data on this are too limited to draw conclusions). This article too says that the cluster 5 mutation that was causing concern hasn’t been seen since September:
    https://www.nature.com/articles/d41586-020-03218-z

  36. JS says:

    For whatever it is worth the Danish minister of agriculture has resigned over the handling of the mink issue.

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