Passages

Viruses don’t often switch species: there are many barriers.  In order to succeed, viruses must interact correctly with hundreds of proteins – ones they make use of, and immunity proteins that might destroy them.  Not easy, and so less than one in a thousand bird and mammal viruses seem capable in infecting humans.  This can’t be a product of gradual evolution: the viruses has to be capable of infecting human cells from day 1. Virologists often attempt to grow important human pathogens in laboratory animals, and usually it doesn’t work. Second, the virus, even at at the very beginning, has to have an R0 > 1, else it will quickly burn out. So, even at the beginning, it has to be able to infect humans and be transmitted at least moderately efficiently to other humans.

That doesn’t mean that there isn’t room for improvement. Once our new virus starts spreading, mutations that further its spread will be favored by natural selection. That selection is extremely rapid.  Virologists make practical use of that rapid selection. For example, they wanted a mouse model of SARS.  They did manage to get SARS to infect mice, but it didn’t cause as serious a disease as in humans.  They passaged the virus 25 times: infected a mouse, injected a sample from that infected mouse into another mouse, and so on,  resulting in a strain that was highly lethal to mice. Natural selection in the course of the infection of a single mouse led to a better-adapted strain of coronavirus:  repeated 25 times, it transformed the virus from not too serious to highly lethal.

In an analogous experiment, researchers took a subtype of an avian influenza virus (one not known to infect humans)  and passaged it in ferrets.  Originally, it could infect ferrets but was not transmitted noticeably to other ferrets: but after 10 passages. it could – without losing virulence.

“At this point, the virus population will experience selection for variants with increased capacity to spread through the human population.”

Covid-19 has been not in humans very long and is probably changing fairly rapidly.

 

 

This entry was posted in Uncategorized. Bookmark the permalink.

408 Responses to Passages

  1. NonLinear says:

    Well, you can take a look here:
    https://nextstrain.org/ncov/
    Most leaves have only a handful of nucleotide substitutions and 1-4 AA substitutions. There is also a 300 bp deletion that showed up in Singapore. Granted it’s only 3400 sequences out of the sextillions of genomes out there, but seems reasonably well-sampled, roughly proportional to testing activity in the affected countries. By uncalibrated eyeball test the S protein seems to be under more purifying selection, which would be consistent with reports from the structural folks that S is already pretty well optimized for human ACE2, but it’s not a strong signal.
    GISAID.org also does predicted structures for S – ACE2 binding on any AA subs in the binding pocket, but I think one needs to register to get at that.

    • P says:

      Don’t let the facts get in the way of a good story…

      • gcochran9 says:

        Ten passages routinely results in significant evolutionary change. Interesting if running through a few million people produces none.

        • Gkai says:

          This would mean the virus entered human population well before first sequencing and was already at optimum, no?

        • gothamette says:

          “Covid-19 has been not in humans very long and is probably changing fairly rapidly.”

          To become less lethal?

          • gcochran9 says:

            To be transmitted more efficiently, but that might mean more or less lethality. If a change hiked virus count, increased transmission 20% while increasing lethality 5%, that would be favored.

            • j says:

              Improved and more effective transmission certainly will be favored, but why increased lethality would benefit the virus? For start, countermeasures (such as social separation and hygiene as well as development of vaccines) would become more frenetic.

              • reiner Tor says:

                The virus is not thinking forward. The countermeasures would hit the more and less lethal strains equally, so for a selfish virus particle to maximize its own replication it could still go for higher lethality, even if it results in more countermeasures.

              • j says:

                Reiner, virus are chemical machines, they certainly do not plan ahead or care. My question is: say you have two similar virus competing for humans (their “food”). one that kills its “food” and the other that harms them only a little. The harmless survives while the other disappears, no?

              • reiner Tor says:

                It depends on a lot of parameters. For the virus, it doesn’t matter if, after, say, three weeks of illness, you get cured or you die. Either way, it just has to stop replicating in your body. Why would the first scenario (getting cured after three weeks of illness) help its spread relative to the second scenario (dying after three weeks of illness)?

                By being more virulent, the virus would be replicating at a faster rate inside the body, which could mean that relatively speaking a higher portion of virus particles within the body would be from the more virulent strains (so, selection within the body would favor the more virulent versions, though within one body the differences would be small), but this would also mean a higher number of virus particles in your saliva, which in turn would increase the probability of you infecting others.

                So there’s certainly a chance of the more virulent strain being better at infecting others. As already mentioned, the virus wouldn’t care for lockdowns, because lockdowns would hurt less lethal strains either, they are hurting even the flu. So there’s no benefit for less lethal strains relative to more lethal ones. Now, of course, there are other scenarios, so it’s possible that for some reason a less lethal strain would be better at transmitting itself. The flu, for example, is normally way less lethal than SARS-CoV-2. So it’s possible that selection will favor less lethal strains, but nowhere near a certainty.

              • gothamette says:

                “It depends on a lot of parameters. For the virus, it doesn’t matter if, after, say, three weeks of illness, you get cured or you die. Either way, it just has to stop replicating in your body. Why would the first scenario (getting cured after three weeks of illness) help its spread relative to the second scenario (dying after three weeks of illness)?”

                I believe you are overthinking this. There have been charts published online about the time periods (there is probably a technical term for it, but I don’t know it) one is maximally infectious.

                A lot of this depends on showing symptoms, and dammit, symptoms are notoriously subjective.

              • j says:

                Reiner: According to new data (species inquirenda, those “cured” and released from the hospital continue shedding virus and are infective.

              • gothamette says:

                Interesting article about transmission. No, really, y’all read it:
                https://quillette.com/2020/04/23/covid-19-superspreader-events-in-28-countries-critical-patterns-and-lessons/

                Selective quote to piss some people off: “But China’s policy of selective disclosure and, in some cases, outright dishonesty, has made me skeptical of many reported details.”

          • kpkinsunnyphiladelphia says:

            Greg’s post is a classic case of expressing evolutionary hubris, even anthrpomorphizing the little bugger.

            If you believe in evolution — and yes, it is a belief system when it comes to speciation, as opposed to intra-species variations — then you also really have to believe that Nature doesn’t give a shit about whether biological adjustments are good, bad, or meaningless.

            They just are.

            Besides, it appears that the virus does quite nicely in horse shoe bats — so I’m sure the little buggers are thinking — “If this human host thing doesn’t work out in the long run, we still have our bats!”

            Interestingly enough, the horseshoe bats are more common in Yunnan province, not in Hubei province. Though the horseshoe may be quite native to the Wuhan labs.

            Oh, and guess what? Covid 19 is threatening bats!! But not in the way you might think: Even Science is in thrall to political correctness. Ah, yes, this virus might kill people, but it won’t kill environmentalism.

            https://science.sciencemag.org/content/367/6485/1436.1

            • Frau Katze says:

              I see! Chinese people are growing suspicious of bats. I can’t blame them. Until recently, I didn’t think much about bats. I’ve even seen one. Do they prefer warm climates?

            • Frau Katze says:

              I meant, I have never seen a bat.

              • Gkai says:

                Not sure how far north they go, but here (Belgium) you can see plenty of them. A warm night with lots of insects or and you should see some.
                Apparently they can be found north of Sweden, so as long as there are flying insects chances are they are around. I like bats, but would not try to eat them 😉

              • Frau Katze says:

                @Gkai I avoid warm evenings outside because of mosquitoes, whose bites I react badly too. Likely that’s why I haven’t seen them.

            • gcochran9 says:

              “it is a belief system when it comes to speciation, as opposed to intra-species variations” how silly.

              • kpkinsunnyphiladelphia says:

                Silly?

                Prove it.

                Show me the fossil evidence. You know, the stuff that happened before the Burgess Shale.

                When you find, it, claim your Nobel Prize.

        • NonLinear says:

          One study did 4 passages through HEK293 (I think) and found none. Unfortunately the link to their data is down.

          This study that found some intra-host variation: https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa203/5780800

          but that those variants weren’t being transmitted.

        • gothamette says:

          Ioannidis is up to his tricks again.

          https://analytica.com/adjusting-the-santa-clara-county-antibody-prevalence-results-for-self-selection-bias/

          Would appreciate Mr. Cochran’s analysis of the latest data dump.

  2. david says:

    I guess that’s why they say some less infectious diseases have higher mortality rates, like ebola, HIV,etc. So after a few rounds of animals “sharing needles,” did some researcher eventually catch this from simple handling of an animal test subject? Or were there possibly a few rounds of human test subjects receiving it intravenously? Ill pour out a shot of hand sanitizer for the first researcher to share needles with a mouse in the name of science.

  3. JayMan says:

    As soon as you mentioned this on Twitter, I though that one selective pressure we’re putting the virus under with our social distancing measures is to be more effectively transmitted in the presymptomatic stage.

    • I’d guess the evolutionary pressure driven by social distancing is the opposite. Even in normal life a symptomatic person bunkers down. Whereas an asymptomatic person meets huge numbers of people every day. Now the symptomatic people still meet many folks in hospitals and the asymptomatic people only meet their family.

    • saintonge235 says:

      You seem to ass/u/me that only the symptomatic engage in “social distancing.” This is the opposite of the truth.

  4. jbbigf says:

    Any idea of the nature of the modifications? Do we see whole-protein inactivations, single amino acid alterations, duplications ….? It seems to me that part of the reason we see rapid adaptation is that there are huge numbers of copies, so lots of opportunities for mutation. But which opportunities are actually exploited?

  5. swampr says:

    A putative, undisclosed chain-of-ferrets gain of function experiment, similar to the infamous bird flu experiment, seems to be at the heart of the escape from the lab speculation. The idea is it would look like selection rather than bioengineering because it would be selection.

    Ferrets have been shown to be highly susceptible to Covid-19 and have airborne transmission. A computational analysis of 47 species found that ferrets and tree shrews obtained the top two binding free energies for ACE2 receptors, much more than pangolins or primates. The authors conclude these animals are likely candidates to be the intermediate host. Of course, the reason ferrets are used in experiments in the first place is because they have similar receptors to us, so the theory has a somewhat circular logic.

    https://www.biorxiv.org/content/10.1101/2020.04.04.025080v1

    • gothamette says:

      “I’ve been in a market in Bangkok which was almost a mile by a mile inside – you can find almost any animal imaginable. I have a picture where there are cages full of ferrets and on top of them are chickens. From an influenza standpoint, birds and animals together are not good,” he said.

      He’s referring to a wet market in Bangkok but let’s examine the one(s) in Wuhan. Of course, they are probably cleaned up now, or they’d just lie. So far everyone’s been looking for bats in that market and they ain’t there. Or so they say.

      https://www.telegraph.co.uk/global-health/science-and-disease/coronavirus-outbreakchinese-live-animal-markets-recipe-disaster/

      • Frau Katze says:

        The bats wouldn’t need to be at market. The bats could pass on the virus to another animal that ended up at the market. The Chinese themselves were theorizing a certain bat, horseshoe bat (I think that’s name) was the source.

        You’d think they could be persuaded to come up with some alternative. All these flus and SARS (but not MERS) seem to come from there.

      • Garvan says:

        @gothamette:
        There is no market in Bangkok this size. The biggest, Chatochak market, is 110,000 m2, so who ever you are quoting has a tendency to exaggerate. There are pet shops selling all kinds of birds and puppies, pet fish – every kind of pet you might want. They probably have chickens, but I did not see any the last time I was there. And I will bet there are no ferrets. Ask him to show you the photographs.

        • gothamette says:

          @Garvan,

          I’m not quoting anyone, just providing a quote from a link – click on the link. But you’re right – we have to be very leery of fake news.

          @Frau,

          I know about the horseshoe bats. I was suggesting that ferrets may be the intermediary species, and may have been sold at the notorious Huanan wet market in Wuhan. Pangolins and civet cats have apparently been excluded. But we’ll never know.

          BTW, the NY Times has a PDF of bombshell emails being traded in the US government. Highlights here:

          The one from Dr. Eva Kee validates my belief that the Diamond Princess was a model of transmission that warranted close scrutiny, regardless of it’s supposedly “unnatural” environment.

          • gothamette says:

            @Garvan,

            I wish I cd’ve edited my response – meant to say I didn’t stand by the sentence I quoted.

          • Frau Katze says:

            Thanks for the link. It seems that the federal government, including the CDC, should have acted faster. I only read the few they quoted.

            I’m trying to recall a previous case when the federal govt made an enormous fuss and the whole thing fizzled out. It was back in the 1900s. Might been under President Ford. I can’t remember the details.

            Others have pointed out that if strict measures were put in place right away and we were spared, there’d be a huge backlash over the restrictions. “You made us do all that and nothing has happened.” People would not believe that the strict measures were what stopped it. They’d say it was wild overreaction.

            Likely it would fall strictly in partisan camps. I’m going to try to dig up that early case. I still have lockdown-brain fog.

      • swampr says:

        I doubt there were any horseshoe bats in that market. They are tiny, insectivorous “microbats”. Most bat consumption is of large fruit eating “megabats” that live in warm climates like southern China (and not the Wuhan region). This extensive review found that insectivorous bat eating is limited to Africa and less commonly SE Asia. There’s an obscure reference to villagers in one place in N. Italy eating horseshoe bats in the 19th Century, but that’s clearly not the area it started in.

        https://link.springer.com/chapter/10.1007/978-3-319-25220-9_12

        Perhaps the Chinese will find a wild intermediate host as was done with SARS. Nothing so far.

        • reziac says:

          Saw video from a wet market, with several vendors selling bats. The bats were about the size of a pet type rat, and solid black. No idea what species but all shown by the camera were the same.

          As to SARS for mice… would someone please come infect my barn??

          • Frau Katze says:

            It’s roast bat for dinner! Yum!

            Bats exist in most places. I’ve never of any other group eating them. People with European backgrounds tend to fear them as they may be rabid.

            Maybe I’m wrong. Maybe they taste great. Although immigrants typically bring diet habits with them and open restaurants, causing mass immigrant supporters to be impressed with this “diversity”, I have not of restaurants serving bats. Maybe I don’t get out enough.

          • swampr says:

            Looking at youtube wet market videos I only see fruit eating bats. They have a sort of canine appearance. Insectivorous bats are tiny. They have weird, ugly faces and huge ears. There is a famous video of a Chinese woman eating fruit bat. She is a food show host on a visit to the Pacific island of Palau, where bat eating is customary.

            • John Massey says:

              There is a video floating around of an infamous market in Sumatra that sells all kinds of weird stuff, including bats. But those are fruit bats – the corpses are black because they kill them by putting a blow torch to them.

  6. jbbigf says:

    Thinking about this a little further, it seems like the optimal strategy, for a virus, would be to become essentially asymptomatic.Most of the damage we receive from infection is due to our own immune response. So, the virus that practices restraint — let’s say, the “enlightened” virus — would mange to hijack the mechanisms of a small set of cells without seriously harming the host. After which, it would be in a position to become a symbiote.

    • gcochran9 says:

      Think further yet.

      • jbbigf says:

        I’m afraid I am reasoning by analogy, and the analogy doesn’t go any further.

        The logic of the situation says that reproducing is the goal, not controlling reproductive resources. The fact that the virus “wastes” a huge reproductive resource in the course of reproducing is irrelevant, if it reproduces successfully. But we also know that when organisms compete for a limited resource, the more efficient organism wins. I suppose that as long as the resource is not exhausted, it is not necessary to compete. After it kills us all, the virus will die itself. But that is irrelevant until it kills us all.

    • Frau Katze says:

      A virus is pretty intrusive. It hijacks your cells to make copies of itself. I’m not convinced that there can be asymptomatic attacks for such an intrusion. Of course I’m very far from being an expert.. But just saying.

    • Frau Katze says:

      It’s just a series of chemical reactions. How could it be limited to only a few cells?

      • jbbigf says:

        Oh, that’s easy. It needs a receptor to enter the cell. Different cells have different receptors.

        • gothamette says:

          “Different cells have different receptors”

          Women and children last in this case, apparently.

          • Frau Katze says:

            I think that in the case of women, their immune systems seem to to fight off many infections better, for some reason or other. Maybe because each woman is a potential mother, whereas with men, you don’t need as many of them to create the next generation. An individual man isn’t valued as much (from an evolutionary perspective).

            It makes women much more likely to get autoimmune diseases (but many of these come on after childbearing age and most aren’t fatal).

            The ability of children to survive so well is a mystery to me. They readily catch other infections. But in some cases, catching the same disease in adulthood gives more severe symptoms. Covid-19 is already famous for this.

            • gothamette says:

              I’ve heard the “why” many times and it seems reasonable to me. What I want to know is the “how.” (about women’s superior immune system)

              About children? Perhaps the innate immune system gets old and tired, like everything else.

            • Smithie says:

              With women, it might be about having XX. That is to say, two copies of genes for the X, as opposed to one for males with their XY. That’s thought to be why women live longer than men.

              It’s a testable premise since sex-determination works the opposite way in some animals, and the evidence from comparing them seems to support the theory. The sex with the double chromosomes seems to almost always live longer on average, whether male or female.

              Maybe, it helps with purifying selection, if males with bad genes on the X die off. Also, might hurt, with autoimmune diseases, to have two copies.

              • gothamette says:

                “With women, it might be about having XX. That is to say, two copies of genes for the X, as opposed to one for males with their XY. That’s thought to be why women live longer than men.”

                Can’t buy that. Look up X inactivation.

              • gothamette says:

                “XX”

                Women don’t get two doses of X chromosome genes because of X inactivation, so I can’t buy that.

              • Frau Katze says:

                @gothamette Take an example of a woman carrying one copy of a gene on the X chromosome that causes hemophilia. Half her sons will be hemophiliacs (on average).

                Presumably half her cells have the bad gene, due to inactivation. But such women do not get hemophilia. The other half of her cells will not have bad gene. Apparently that’s enough to stop hemophilia.

                Perhaps the genes that affect lifespan are like this. I’m just suggesting it.

              • gothamette says:

                @FK,

                Right. My problem is with the wording of this: “With women, it might be about having XX. That is to say, two copies of genes for the X, as opposed to one for males with their XY. That’s thought to be why women live longer than men.”

                People who don’t know about X inactivation erroneously think, “Women get a double dose of the good stuff,” which is completely inaccurate.

                X inactivation is quite astonishing – why are Turner’s syndrome women disabled, but normal women not? Presumably Turner’s syndrome women get the same dose of X chromosome gene product. But they do not.

              • Frau Katze says:

                @Gothamette Yes, I don’t know much about it.

              • gothamette says:

                @FK,

                I don’t think anyone does. It’s a very complex process. Although obviously some know more than we do.

              • Smithie says:

                @gothamette Actually, I’m familiar with X inactivation. I’m mainly talking about different cells expressing different copies of genes. There are definite benefits to that, and perhaps drawbacks as well. That’s possibly more unique antigen on the surface of cells, for the immune system to get excited about.

                But it should be said that X inactivation is a complicated process, not well understood. It’s probably not like a coin flip. A small percentage of genes might possibly have both copies active. It is also possible that bad Xs are more likely to be inactivated.

                Presumably, if you were trying to mess around with DNA to make men live longer, one way to do it might be to fix bad mutations on the X.

            • gkai says:

              IMHO it does not work like this, “An individual man isn’t valued as much” is group, or worse, species selection thinking. Selection works at the individual (or even better: at gene level, so you get kin selection as a bonus). So from man genome point of view of course anything that makes transmission of this genome more likely is favored. Including resistance to pathogens.
              A man/woman difference would imply there is a tradeoff which is different for man and woman, like increased immune response making you physically weaker, or any other effect most damaging to male-male competition.

              • Frau Katze says:

                Yes I know group evolution is a no-no. How did it arise? Just by chance?

              • gkai says:

                Not by chance: A different tradeoff for immune response in men/women is to be expected by default. This happen for a lot of other biological functions, because of different lifestyles, pregnancy adaptation, and different reproductive strategy (more variation in number of descendents for men).
                So while it do not make sense for men immune system to be globally less efficient, it may make sense to be more variable in efficiency for specific pathogens. Maybe the optimum is frequency-dependent and you have a polymorphism equilibrium with multiple variants for men, but not for women…

              • gothamette says:

                This is a virus that attacks the respiratory system. Everywhere the virus kills 2X as many men as women.

                That is all I know.

                That, plus Africa seems to have escaped so far relatively unscathed. Now, since African-Americans are getting slammed, it ain’t ethnic. So what is it?

                I’d say youth, UV rays, time and maybe lack of testing (although Senegal has done brilliantly, with two deaths).

              • gkai says:

                Not only Africa. South-east asia is also relatively unaffected.
                Thailand for example had a first wave from Chinese tourists…that died quickly.
                Then currently is facing a second wave from Western tourists. But again, it seems to die quickly.
                This time they implemented lockdown measures and were more serious about tracking too….but not before a lot of people fled to countryside (lost their income in tourist areas and they knew th lockdown was imminent), so I do not think the lockdown alone was enough.
                All the region (Laos, Myanmar, Thailand, Cambodia, Vietnam) seems mostly OK like Africa, so indeed it’s like there are places where the virus do not spread. UV, Warm and local genetics may be it. Or protective effect from other tropical pathogens? Who knows, but it’s now too long imho for it to be a timing issue, so I am not longer expecting those countries to be hit soon.

              • Frau Katze says:

                But an improved immune system for women would increase a given woman’s chances. Couldn’t it select just that way?

                Male children don’t get the advantage but they do no worse. Neutral.

              • Gkai says:

                Of course, but this would as true for men so this would explain the difference: both sexes would get the best possible immune system, as long as it does not decrease fitness by negatively impacting other biological systems. That’s the trade-off i was speaking about, and to get an évolutive explanation you should show how the trade-off is different for men and women. It could even be indirect, like other biological systems are different enough between men and women (because under differential selective pressure) that they constrain differently how good immune system can be. But in the end it’s again differential trade-off…

              • gothamette says:

                Vietnam instituted a total quarantine. No foreigners allowed in after March 31.

        • Frau Katze says:

          True. I’m not thinking straight these days. HIV famously attacks only certain cells.

    • nllssn says:

      Except for the symptoms that promote the transmission. Sneezing and coughing cause virus containing water droplets to be projected from the host to a significant distance, promoting the spread. A totally asymptomatic carrier wouldn’t be nearly as efficient at transmission.

      • gothamette says:

        That’s half a good point. But asymptomatic people sneeze and cough esp when there is an airborne irritant. They talk to others. It’s amazing how much schmutz comes out of your mouth when you speak. Not you personally. I would say “one” but that’s Brit-speak.

  7. dave chamberlin says:

    I am sure a lot of us keep checking the statistics on Coronavirus statistics on a day to day basis. What jumps off the page, besides the United States leading the world in screwing this up, is the large variation is death rate to confirmed cases. https://www.worldometers.info/coronavirus/

    Now I know that there are a lot of variables but even taking them into account I keep thinking Spain, France, United Kingdom, and Italy with an over 10% death rate and Germany and South Korea with a 2% death rate is a huge spread and they should have closed by now with all the testing and the virus spreading through more age groups. The gap has closed some but there is still 5 times the death rate in some modern nations than others. Question. What’s going on? Yea, i know it ravaged the old folks in Italy and over in South Korea they tested way more early on, and the wave of death follows three to four weeks after infection so the nations with more recently infected people have much lower death rates but these differences are not what one would expect in variation, it’s 500 percent, and there has been a lot of testing in all of these nations now.

    • mapman says:

      Probably early hospitalizations (both Germany and Korea have tons of beds and are not afraid of filling them). It’s a double-edged sword but with competent nursing it’s a net life-saver.

    • Frau Katze says:

      It hit Italy hard. I suspect there were some incorrect diagnoses. See my comment further down about Covid deniers. They are feeding off these inconsistencies.

      I think it’s important to figure this out. 10% sounds far too high. It can’t be right.

      Mark you, some early US cases came from a care home in Seattle, Washington.

      I’d think the death would be higher than 10% in a care home. In B.C. (where I live) we have had fairly low numbers. But at least one care home was involved.

    • Gkai says:

      The death rate, if we speak about dead linked to covid 19/ detected covid 19 cases, does not mean much. The numerator vary (attribution to covid 19 can vary from findings the virus to died from respiratory problems, and deaths outside the hospital are not necessarily counted.
      but this is nothing compared to denominator problem : tests are done very differently depending on countries, Germany does a lot of testing compared to most other European countries. In many other countries only people having symptoms are tested, sometimes only when they are hospitalized…
      Even the 2% is probably too large, in a very recent study germany sampled 1000 random people in a town with a lot (for germany) of cases: 2% with the active virus, 14% with antibodies. So much more than the detected cases catched the virus and either didn’t got sick enough to seek medical help, or did not even feel sick.
      covid-19 is getting close to it’s peak in Europe, hence the slow down of hospital admissions. How much this peak was lowered by lockdowns is difficult to say, we will see once antibodies tests are done large scale accross Europe. Gut feeling (from wuhan number after 1st set of measures, posted here in some previous thread) is that it was reduced from 3 to 1.5. Instead of 60%, we got 30%. We will relax lockdown soon (in practice, people relax it already.), and go back to R0 around 2. A small rebound, or more likely a longer peak, can be expected, but 50% antibodies is likely. Curve was flattened, not squashed.

      • Maciano says:

        The virus is nowhere near its peak in Europe, so we’re not flattening peaks. We’re at 1-5% at most. Some areas a little more than others, that’s it.

        We‘ve put much of Western Europe under lockdowns, so we’ve temporarily stalled fast contagion (at extreme costs).

        • Gkai says:

          I believe it’s at least 10% in europe, most countries more around 20% and a few at saturation under lock down. It’s number out of thin air like yours, except that:
          https://spectator.us/covid-antibody-test-german-town-shows-15-percent-infection-rate/
          If it was 1-5% it would mean the current lockdown, with people buying their groceries, exchanging kids in shared custody, walking around and even working for quite a few, decresed R0 from 3.5 to below 1. You believe that? I don’t even speak about those who do not follow the lockdown instructions, they are a quite a few but even without taking that into account R0 below one is not believable.

          • Gkai says:

            Oh and for what it’s worth, 1% do not fit my personal experience: i know to many cases personally for that. Given that my social circle is more toward the small side, and from people not esprcially at risk (not usually going to large gatherings like churches or music festivals), even 5% do not feel right.

            • gothamette says:

              I don’t really care about any of this.

              What I want to know is: what is the overall number of deaths in Lombardy/NYC/Hamburg/Fill-in-the-Blank compared to overall number of deaths last year, during the pandemic months.

              It’s real simple. Compare number of deaths in any area you choose from Feb-May 2019 and compare it to Feb-May 2020. (Or beyond May, just giving that as an example.)

              What do we find?

              • Gkai says:

                I try to find this for Belgium, but 2020 data is not easy to find. Probably not available.
                i expect excess death will be very visible for April and may, maybe visible but barely for March. It was about 9000 deaths per month last year. I expect about 5000 deaths for april. Let say 4000 for may (long peak/rebound) and 1000 (overestimating) for March. 8000 total excess death in 2020 (some death removed less than a year of life) , which is 8%. Clearly visible, but imho, now largely unchangeable by any lockdown measures or treatments…

              • gothamette says:

                I tried to find it for New York City, but I can’t. The New York City Department of Health releases a lot of data, most of it very difficult to understand.

              • Frau Katze says:

                I’d like to see those numbers too. The person who called me a panic-monger on Youtube claimed he had see the numbers and there was no difference. I should have asked for a source but the Youtube commenting is not very good. Not designed for discussions.

                I just ignored him and unfollowed that channel.

              • gothamette says:

                It’s very hard to get one’s hands on something so basic. There’s a NYC website that’s as easy to read as the Rosetta Stone.

              • gothamette says:

                OK, there’s this:

            • Frau Katze says:

              @gothamette I only just noticed this now. I must have passed it earlier when I was in the Covid fog. I was waiting for excess death data.

              The winter spikes are what? Elderly and people with co-morbids dying of regular flu?

              I’ve got a comment further down about the same stats for the UK. The article finds a large number of excess deaths but most are over 75.

              Thing is, if a young person died there would have to be some cause.

              But with 75+ you think, well their time had come. (That happened with my mother who died at 78 for no particular reason that we knew. We would have had to pay a lot for an autopsy we were told. This was many years ago.)

              • John Massey says:

                Winter spikes are mostly elderly/people with comorbidities and infants dying from seasonal influenza or complications from seasonal influenza like pneumonia and bronchitis (which is a killer in countries like the UK, whereas it’s little more than an irritation in Australia). Things is, with social distancing, hand washing, mask wearing, cessation of a lot of normal activities, etc. the winter influenza season this year has been mild and finished early in many places, so reduced deaths from that, but also people with other life threatening conditions are not seeking medical attention when they should because they are avoiding going to hospitals and clinics, and many hospitals and clinics are clogged with Covid-19 patients, so have no spare capacity to treat those other folks, so increased deaths from other causes.

                So, unfortunately, it is not as simple as attributing all excess deaths to Covid-19 – need to factor in those other things, which can only be roughly approximated (which I suppose is a polite way of saying guessed).

              • Rosenmops says:

                She was 79. There was something wrong with her lungs. She was coughing up blood. (never smoked) But she wouldn’t go to the doctor. She was always very suspicious of doctors. She died suddenly, at home, as you know. We should have had an autopsy, Too late now.

              • Frau Katze says:

                But it’s a start. I bet the majority are Covid. That huge spike for NYC can’t be due to just heart attack victims not going to the hospital.

                But I admit part of the spike must be other causes. Perhaps a combination of excess death data plus examining death certificates for a cause would help.

                What do they put on the death certificate of, say, an 80 year old person who dies in their sleep? (as apparently happened to my mother, she had one of those buzzer things to summon help but it was not used.)

              • John Massey says:

                Fair comment. In fact, because of reduction in deaths due to influenza, the true number of fatalities due to Covid-19 could be higher than indicated by the excess deaths above the seasonal norm. But I guess as a first approximation, it will do, especially if it is a big spike relative to the norm.

              • Frau Katze says:

                @Rosenmops So what was on the death certificate?

          • Maciano says:

            You mention 1 town that was specifically hard hit and therefore tested. Why wld that be representative for all of Europe?

            I wish it was true, we cld put this nightmare behind us, but it isn’t.

            • Gkai says:

              Hit hard for Germany. Gangelt is in NRW, which indeed is lander with most cases. But compared to other countries, it’s nothing special. Certainly not Italy or Spain level.
              Btw, while not living in Germany, my home is 90 km from Gangelt. The region is a densely populated area, people routinely cross the Netherland /german /belgian border there. So yes, i am quite confident my country is above 15%, especially as the study is probably a snapshot of the situation one or 2 weeks ago…1-5%, on the other hand, do not make sense.

              • Maciano says:

                Gangelt is interesting because it’s hard-hit and can show us a bit of the future. But not much more than that. The attack rate isn’t nowhere near its potential. Right now, we stalled the full attack, but it will come back as soon as we release the distancing rules.

                Btw, the high amount of Belgian deaths is similar in the Netherlands. You count the nursing home deaths, while we (the Dutch) don’t. This week GPs have agreed to add the excess mortality to the Dutch RIVM (Dutch CDC) data. (We rly are brothers.) The similarity between Belgian Limburg, Dutch Limburg & Dutch Brabant is striking — and horrible to watch.

                I’m not surprised that Western NR Westphalen (like Gangelt) is also one of the worst hit German areas. It’s all so close to each other.

              • gothamette says:

                @Maciano – Ed Conway of Sky News has charts showing that Belgium per capita is the worst hit European country. Scroll down:

                http://www.edmundconway.com/2020/04/covid-19-data-qa/

              • gkai says:

                Clearly we do not agree about the probable contamination rate in Europe, or even in Benelux. This is interesting in itself, but even more interesting is the reason why we disagree: there is still no antibodies test. That those tests are too few to do systematic testing I can understand, the demand is high and supply chain wrecked. But there is no need to do systematic testing of all to get an idea about contamination rate, a representative sampling would be enough.
                So why European governments can not get hold of a few thousands sero tests and do a representative sampling of their population? Those tests were available 2 weeks ago (at least that’s what was said then, and the Gangelt study would not have been possible without those tests so they should exists).

                Contamination rate is a fundamental data to plan for lockdown measures and give a timing for relaxing those measures. Basically without that it’s extremely difficult to even interpret the other numbers given they are all suffering from large uncertainties and bias.
                So why do we only have a small study in Germany(Gangelt)? Is it sheer incompetence, or should I put my conspiracy hat?

              • Gkai says:

                Just got the news i was waiting for : a belgian firm is ramping up quick antibody test (answer in 15 minutes), and will market it end of April. Production will be 1 million tests per month. Belgian government ordered some… but did not want to say how much or how they will use it… WTF?
                So yes, i will put my conspiracy hat and believe they already know how many belgians are covid-seropositive… And do not tell, for unknown reasons. Guess it’s the same for most western countries.

              • Gkai says:

                Correction : they say they will tell how those tests will be used in a few days. Ok, let’s wait for this announcement 😉

    • nllssn says:

      I saw a youtube video where the guy was pretty confident that the reason why the death rate in Germany is so low is that the average age of the infected is much lower. The largest influx of infections to Germany was from young people returning from ski vacations. So the original popuation of the infected was skewed much younger.

    • gothamette says:

      Dave –

      Read carefully. This is prob the closest we can come right now to a random sample. The numbers floored me. Nearly 14% of asymptomatic women who were admitted to a NYC hospital to give birth were positive:

      https://www.nejm.org/doi/full/10.1056/NEJMc2009316

      • Frau Katze says:

        14% positive with 215 women. That’s really high. Decent sized sample too.

        • gothamette says:

          Drives down the CFR. Some are saying that pregnant women have a higher %age because they go to the doctor a lot.
          Maybe.

          • John Massey says:

            Suggestion from the local CCP spy here: pregnant women have suppressed immune systems.

            Another CCP spy suggestion: In the USA at the end of winter, averaged over the whole population, 42% have Vitamin D deficiency. But among African Americans it is 82%, and Hispanics it’s 70%. (You can do your own research to get these data, as an exercise.) What does Vitamin D deficiency do to the immune system? Yes, I get that there are socio-economic-employment factors as well to explain why minorities are over represented in deaths, but you can add Vitamin D deficiency to that, and it is something that is very easy to fix.

            Roger Seheult covered this. A meta-study found that a small daily Vit D supplement optimised immune response but, counterintuitively, considering dose-response, a large daily supplement does nothing. What is needed is a long term regular Vit D supplement.

            I have read that some foods in the USA (bread, milk, whatever) have Vit D supplementation, but that is clearly not working if 42% of the whole population is deficient (and I assume a pretty high % of Af-Ams and some lesser % of Hispanics are lactose intolerant).

            So the best thing you can do for your black and Hispanic friends (of whom I have absolutely no doubt you have lots) is to suggest they pop a small Vitamin D pill every day.

            Now I’ll get back to studying Xi Jinping Thought and classifying American women and my personal stalker Pincher Martin into various categories of mental illness.

            • gothamette says:

              ” The generalization of pregnancy as a condition of immune suppression or increased risk is misleading and prevents the determination of adequate guidelines for treating pregnant women during pandemics”

              https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025805/

              It’s complicated.

              Vitamin D? Maybe a factor, but I’d think that the stress of having to commute to a shitty job in a crowded subway while your society is falling apart would have more to do with it than that.

              Still, I have indeed recommended to my black and (one Texpat Latino) friends that they take Vitamin D.

            • gothamette says:

              This twitter thread mentions ‘weaker’ immune systems of preg women, then qualifies:

            • dave chamberlin says:

              You’ve got that little red book in your back pocket dontcha. This is winding up a lot of us too tight, me included. My home town Chicago just lost a home town hero John Prine to Covid19 who wrote some of the best songs ever written. Our answer to Mark Twain. https://www.youtube.com/watch?v=7zGQJhZGFTY Put this on the background when you read, that man is a treasure. Make yourself a Handsome Johnny, a diet ginger ale and vodka, and listen/watch to this. https://www.youtube.com/watch?v=l0EiV423j0M.

              • John Massey says:

                Hi Dave. Yep, I never leave home without the little red book. Oh no, that’s my wallet. Being a bit of a country music fan, I knew about John Prine from way back, and was downhearted to read he hadn’t made it.

              • John Massey says:

                Oh, that version of Magnolia Wind was with Emmylou Harris – I’ve been an ardent fan of her singing ever since Gram Parsons’ album Grievous Angel. I bought my daughter every album she ever released, plus the Trio albums with Dolly Parton and Linda Ronstadt, and lately she has been buying tracks ripped from first pressings because they sound so totally different, like hearing them for the first time. My daughter has outstripped me now, researching little known American country singers who deserved more recognition than they got.

              • David I Chamberlin says:

                Oddly John Prine’s last album is his best selling. It blew me away. The Tree of Forgiveness. listen to it.

            • gothamette says:

              Here is more about how wonderfully open the Chinese have been.

              • gothamette says:

                I linked to a letter. Arguably Wrong (go to his blog to see our exchange there) read the pre-print studies linked to in the letter, which gave indications of the demographics.

                They weren’t exactly the same populations, but the pre-print article gave an indication: Upper Manhattan and Bronx. So probably heavily black and Hispanic. (Also obese. That has nothing to do w/infection, but is another indication that the women were almost completely Af-Am and Hispanic.)

                I believe that both populations are way more infected than whites and Asians, who together are 40% of NYC.

          • Frau Katze says:

            I thought of that too. Just going to the doctor’s office is high risk now.

      • Frau Katze says:

        The other thing: none of those women were over 60!

      • dave chamberlin says:

        Interesting link and good news, oddly enough. We are hoping that this nasty virus had a much much lower mortality rate because there was a huge hidden population of people that were infected but showed no symptoms. Young pregnant women apparently shrug Covid19 off a very high percentage of the time. Great. Who knows when large scale antibody testing will be available but it is coming.

      • gothamette says:

        This study has blown up Twitter and thrown some people into a tizzy.

        Do some arithmetic. If 14% of NYC’s population is infected, and deaths are now above 10K (google it), the CFR is

        0.83%.

        Not the flu.

        • gcochran9 says:

          14% is probably a little high: I think that hospital caters to Hasids, where it started early and who may not have fully followed guidelines.

          • gothamette says:

            Also a lot of blacks & Hispanics.

            “follow guidelines” – I’ll say. Most of the non-compliance stories I heard were of Hasids were of men, who refused to stop gathering in the 10-man quorum. (Women have no such religious obligations.)

            But of course men brought home the virus, and as China showed, the virus got passed around in family clusters.

          • An interested reader says:

            I think that hospital caters to Hasids <<

            Not so much – catchment area for those two hospitals (Allen, Irving) is Upper Manhattan and Harlem, not Brooklyn.

            • gcochran9 says:

              Then I heard wrong. Happens.

            • gothamette says:

              Also Bronx. Arguably Wrong actually read the notes and found earlier pre-print studies which described the population as obese, and hailing from Upper Manhattan & Bronx.

            • gothamette says:

              Did you hear about this?

              • R49 says:

                Hello,

                yes of course. It was all over the news.

                The one afterthought I had was (conspiracy theory alert): Did the Chinese authorities suppress the early warnings like from Dr. Wenliang because the virus accidentally broke free from Mrs. Shi Zhengli’s lab, the Wuhan Institute of Virology? I know the accusation really isn’t proven at all, however, it would just make a better justification for authorities to suppress the news about the new virus discovery and its spread.

                Any thoughts?

            • sthomson1971 says:

              There are a lot of Orthodox Jews up here in the heights (24,000 seven years ago according to the Times) disproportionately young and fertile.

              • An interested reader says:

                Modern orthodox != Hasidic. In particular, their behavioral patterns with respect to a challenge like this are quite different.

          • dearieme says:

            “who may not have fully followed guidelines.” Probably followed different guidelines. Carved in stone.

          • gothamette says:

            Black and Hispanic; see my comment about Arguably Wrong & pre-print article

  8. mapman says:

    Yup. And the longer we let this thing run, the more replication cycles it goes through, the higher is the probability of selecting a virus that infects us better. Its sheer mutation rate is on the same order as that of the other RNA viruses such as flu (but no reassortment which is the biggest problem with flu), so yeah, it’s just a matter of time before it becomes more infective and starts selecting humans (could be long time though). For that matter, a really deadly new flu is also just a matter of time.

    • Rob says:

      Ackshually, coronaviruses have an exoN gene that codes for a proofreading exoribonuclease. They have a mutation rate much lower than other RNA viruses. Hoping they don’t mutate to spread better is putting a lot of faith in one protein, I admit.

  9. Frau Katze says:

    This is also this circulating: Covid deniers. I’ve only just encountered them so it’s unclear whether or not they believe that Covid doesn’t exist, or they accept that it exists but insist that the number of reported cases is wildly inflated. More likely the latter.

    Since deaths often occur with some some other illness, they think the other illness caused the death.

    Motive: hospitals allegedly get extra funding for Covid cases.

    The chaotic situation in northern Italy is the jumping off point. The deniers allege (no doubt correctly in some cases) that the Italians took to calling all sorts of things Covid.

    But assume there were such mistakes. On the same day I saw the first denier video, I also later saw a news story that some Italian towns reported no Covid at all, because they couldn’t test for it.

    One of them who called me a “panic-monger” also insisted there no excess deaths in the Italian case. I find that hard to believe.

    Another variant: saying it’s pneumonia. But pneumonia seems to a set of symptoms, not a particular disease.

    • gothamette says:

      @FK: the COVID deniers have been around from the start, some here, many on Twitter, and they shift with each new development.

      • Frau Katze says:

        The first denier video I saw did not seem at first to be outrageous ranting. I was quite willing to believe the Italian numbers were inaccurate.

        It was seeing a Wall Street Journal report on the same day noting that some Italian towns reported no C19 at all because they couldn’t test that I realized he was only considering one side, the over-reporting side. I trust the WSJ report.

        He’s only getting worse with time and I stop following the channel. There’s no point getting entangled with such people.

        • saintonge235 says:

          In addition to the lack of tests, there were a bunch of towns in Italy that reported much higher than normal death rates. No tests were conducted, but it’s hard to believe multiple towns had sudden increases in natural deaths do to multiple unrelated diseases. It’s also hard to believe that there was one disease that wasn’t the Commie Virus killing them, but no one noticed it.

          But people are basically emotional reactors, not thinkers. Many of them don’t like the lockdown, so they insist the problem must be too small to warrant the measures taken./

          It’s impossible to have an intelligent discussion with such unless you can get them to agree what counts as data on both sides of the question, and how to evaluate the data, before attempting to talk about these matters.

          • Frau Katze says:

            I accept that the Italian data is inaccurate. The situation there sounds as if it was very confused and chaotic

            I think the data is more accurate in other European countries. And more accurate still in South Korea.

            But this man has gone off on the wrong tangent.

            • John Massey says:

              Frau Katze: This very well illustrates ‘the problem’, but it takes a bit of getting through:
              https://fivethirtyeight.com/features/a-comic-strip-tour-of-the-wild-world-of-pandemic-modeling/

              • dave chamberlin says:

                Too bad that comic strip isn’t read and understood by more people. Lots of insight into the difficulties of pandemic modeling. It should be mandatory reading for every crackpot out there who thinks his or her simple answers to complex questions on Covid19 are the truth. Render onto Caesar the things that are Caesar’s, Render onto scientists the things that are science.

            • gothamette says:

              @FK,

              Right now, I’m treating everything as provisional, except dead bodies.

              There’s a Sky News reporter named Ed Conway who is doing very good graphs on deaths. Head on over there and look at his stuff. In short, more people are dying than normally. Lots more.

              • Frau Katze says:

                I’m going to check him out.

              • dave chamberlin says:

                I was looking for graphs over time comparing different countries and Ed Conway did exactly that. Thanks and I will continue to follow him. It scares me how the four countries England, France, Italy, and Spain are clumped together in these graphs and it scares me that they all have insanely high mortality rates. I have no idea about what it means but it is concerning.

    • reziac says:

      My personal faves are those who claim that while there may be a disease involved, it’s really not so bad (not as bad as flu!), and the whole shutdown response is a leftist plot to gain control. Granted there are enough little tin gods misinterpreting various stay-home orders to fuel that notion, but I look at all the regulations going out the window and wonder how they plan to accomplish it.

      And none of ’em can answer: Cui bono?

      • Frau Katze says:

        One of the deniers told me that the hospitals benefit because the hospitals get extra funding for C19 cases.

        Trying to gauge the validity of that statement is not simple. There must be different policies in different areas. Trying to figure it out for Italy is beyond me. One would need to be fluent in Italian.

  10. j says:

    Is that the original virus that hit Wuhan around December 2019 had a low Ro but its evolved descendants in New York are much more virulent? Or evolution is pushing this virus, like others in the past, into some kind of silent flu?

    • Анисимов Дмитрий says:

      No, apparently most New York vulnerable demographics (“minorities”) has just more hand-to-hand contacts that population in Wuhan.

      • j says:

        Why should New York well-fed well-cared minorities be more vulnerable to the virus?

        • gothamette says:

          The hardest-hit populations in NYC are the usual (old, or with comorbities) and those with jobs that forced them to take subways and deal with people even after the city was supposedly locked down. It was a very soft lock-down. Non-essential people were “asked” to say home. Minorities are heavily repped in the “essential services” sectors.

          Just for now, keep the nasty cracks to yourself.

          • j says:

            I was innocently wondering if, being the average age of the victims about eighty or so, why is the NYT attributing “racial discrimination” to the virus. Two months ago I guessed that Europeans would be passed over since they have less receptors than Wuhan residents, but I am refuted by the massacre in Lombardy.

            • j says:

              Well, I read in the WSJ that in Chicago the Blacks are 70% of the corona-dead. It is hard to speculate on the why.

              • saintonge235 says:

                Good article on why in THE SPECTATOR. https://spectator.us/coronavirus-racist-african-americans/

                TL,DR: Blacks and Hispanics have higher rates of co-morbidities (25-66% greater), and that make them especially vulnerable; they are more urban in most of the U.S., and urbanites are more likely to catch infectious diseases; minorities are poorer, and poor people get sick more often; minorities are less likely to have jobs where they can work from home; and finally:

                “African Americans’ response to recent public health dictates has been less punctilious than in the population at large. There was ‘natural pushback’ against shelter-in-place orders, as ProPublica put it discreetly. There was the widely-circulated theory that melanin protects blacks from the disease. Non-compliance has been so pervasive that Dr Anthony Fauci, in the White House’s April 8 press briefing, said that he pleaded ‘particularly with our brothers and sisters in the black community’ to protect the elderly from infection by observing social distancing.”

        • Curle says:

          Look up the YouTube video for police in LA breaking up an ‘block party’ just days ago.

  11. zeev says:

    info question. Do the cov-2 need enter the cell’s nucleus to accomplish replication?

    • John Massey says:

      Yes, the coronavirus RNA needs to enter the cell nucleus in order to replicate. So a lot of effort is going into finding things that will prevent the coronavirus cell ‘spikes’ from binding to the ACE2 receptors to prevent this from happening.

      Greg, what do you make of this?
      https://www.scmp.com/news/china/science/article/3079491/deadly-coronavirus-comes-three-variants-researchers-find

      Feel free to ignore if you don’t want to spend the time. I fully appreciate you can’t be expected to read and comment on everything.

      • gothamette says:

        That SCMP article is small potatoes, and old ones. This is not new. I asked you about the two, or three, strains and you dismissed its importance – and now suddenly they are important?

        *Sidney Bell, a computational biologist working with the Nextstrain team, cautions people not to read too much into these new mutations themselves. “Just because something is different doesn’t mean it matters,” Dr. Bell said.

        Mutations do not automatically turn viruses into new, fearsome strains. They often don’t bring about any change at all. “To me, mutations are inevitable and kind of boring,” Dr. Bell said. “But in the movies, you get the X-Men.”*

        • John Massey says:

          Not the same. And I didn’t say it is important, I asked Greg what he made of it.

          Don’t put words in my mouth, and don’t twist my words.

          • gothamette says:

            The NY Times article is way better.

            “Don’t put words in my mouth, and don’t twist my words.”

            I’ll say whatever I want.

    • nllssn says:

      No, I don’t think so. It just has to enter the cell. Not the nucleus. Here’s a youtube video that explains it pretty clearly and why zinc ionophores like hydrochloroquine (and green tea extract) have antiviral activy (spoiler, pushing zinc ions into the cell interferes with viral replication) :

    • gothamette says:

      Watch Medcram on Youtube.

  12. Robert McLindsay says:

    How likely is it that covid-19 came from a Chinese lab?

    • swampr says:

      Pro lab theory:
      -Wuhan labs seem to have been at the center of Chinese bat CoV research
      -One of the Wuhan labs, the older and less secure of the two, is a few hundred yards from the market.
      -It’s unlikely that horseshoe bats were kept in the market
      -A chain-of-ferrets gain of function experiment could account for a virus appearing to have resulted from natural selection, as this one does
      -The virus is well adapted to respiratory ferret transmission
      -Plenty of scientists are on record saying the moratorium on gain-of-function research should not have been lifted

      Against lab theory:
      -Ferrets are used in experiments because the receptors in their lung tissue is a good model for humans anyways
      -Wuhan is an NYC scale megacity. There are only so many of those and many of them have virology labs. Perhaps more than have massive bush meat markets
      -Some villagers in the area of the cave where the closest wild relative of Covid-19 was found have antibodies for CoV viruses. They don’t hunt or eat bats
      -They took 500 samples from the market and say that 30 out of 32 positive samples were from the wildlife area

      • Janet says:

        Some more comments in favor of the lab theory:

        — The only places within 900 km of the city where horseshoe bats were found… were two virology labs in the heart of the city, both of which were doing research specifically on coronavirus transmission to humans and gain-a-function, and one of which was only BSL-2 (i.e. the same level as a normal hospital laboratory).
        — In other Chinese labs, staff have been convicted of selling lab animals to wet markets for food, in lieu of euthanizing them. This could have been the ferrets, as well as the bats.
        — Note that it appears that large amounts of virus is shed in feces, and all reports indicate that the wet market in question routinely had fecal and blood slurries on the floor, tables, and butchering tools. The market was also literally downstream from the two labs in question, and may well have used raw river water for washing and watering the animals.
        — Staff from those labs “disappeared” very early in the timeline of the outbreak and have not been seen in public since that time. Some of these same staff were part of a documentary in 2017 that showed them collecting bats in extremely unhygienic conditions (e.g. being exposed directly to bat blood, urine and feces, and not wearing any PPE while collecting in caves); this was presented as an example of their dedication to duty and courage in the face of danger.

        Against the “against” points:

        — The market was hurriedly “decontaminated” with bleach in early January, by exactly the same authorities who have been caught out spreading false information (e.g. saying no evidence of human-to-human spread, well after they imposed severe anti-contagion measures on their populace). I would put very little faith in the “results” these authorities are publishing, particularly when they make sure that nobody outside of their control can double-check the facts.
        — At this point, villagers who show positive for COVID may well have gotten it from another human, e.g. one who returned from Wuhan for lunar new year, rather than from bats.

        • John Massey says:

          All ‘he said-she said’ stuff. Of course they would close and disinfect the market – they thought that was where it came from. It takes a certain talent to paint that as something sinister. You are just repeating a load of horse manure.

          • saintonge235 says:

            That the Wuhan authorities disinfected the market is not suspicious. That the Wuhan authorities lied tremendously makes whatever they say now suspicious, especially if it point the finger of blame away from them.

        • gothamette says:

          That they disinfected the market isn’t particularly noteworthy. What else did they remove? Ferrets? Civet cats? Pangolins?

          I don’t think the Chinese are lying about the numbers. They may well be lying by omission and suppressing things. In fact, I’d bet on it.

        • gothamette says:

          ” Of course they would close and disinfect the market – they thought that was where it came from.”

          They wiped down the crime scene.

          ” It takes a certain talent to paint that as something sinister. You are just repeating a load of horse manure.”

          Just half a brain cell and a healthy dose of skepticism towards a regime that runs these:

          https://en.wikipedia.org/wiki/Xinjiang_re-education_camps

          And which refused to shut down these dirty markets.

          Everything this guy says is a lie, including the words “and” and “the.”

          50 points if you can tell me who said that first.

      • saintonge235 says:

        I can’t help but notice that only one of the “Against lab theory” reasons are actually reasons to doubt the lab theory.

        —Why ferrets are used in labs says nothing about where the disease came from.
        —Many big cities have virology labs says nothing about where the disease came from.
        —The antibodies of villagers not in Wuhan says nothing about how the disease was introduced to Wuhan.
        —The antibody tests do provide some support for the idea the virus took hold there first.

    • John Massey says:

      That has been thoroughly debunked by some non-Chinese scientists. I would give you the link, but I can’t be fucked.

      • gothamette says:

        But you can be fucked to keep coming around here and taunting people. I asked several times for a link to your claim that the “first five cases” had no link to the Huanan wet market but you didn’t answer. I found a NEJM cite that directly refuted your claim. I won’t link to it again because I can’t be fucked.

        There is a NY Times article with damning emails that I also can’t be fucked to link to because I already have. In it, Dr. Eva K. Lee who works with the CDC, explains how relevant the Diamond Princess is to the spread of SARS2. Which I thought all along, and which you dismissed.

        • John Massey says:

          Eva K. Lee didn’t explain at all how the Diamond Princess was relevant, because it wasn’t like she said it was – it was far more confused and complicated than that, and had more elements to it, and they were all bottled up in close quarters for weeks – not analogous to the situations she cites at all. None of what happened on the DP has been properly documented, just a lot of random passengers’ recollections. I recall that I based my guess at maximum % infected on rate of infection on the DP, and you challenged me on it by saying it was time limited, so could have been higher if not for that. My memory is better than yours.

          The earliest case of someone infected with Covid-19 that Chinese scientists have found was a guy elsewhere in Hubei Province (i.e. not in Wuhan) who had it in November, and he had no link to the Huanan market. But they said he was not ‘patient zero’, and that person is important to find, to try to get clues to the origin. And in your classic style you cite that as MY CLAIM, when it was not my claim at all – I was citing some Chinese scientists. You have a major problem with objectivity. I see this as a scientific puzzle to be solved. You seem to think it’s a propaganda war, and that I’m on one side of it. I am not.

          • gothamette says:

            It was an email, not a peer-reviewed paper, in which she explained quite well how the DP was relevant to free living conditions.

            “The earliest case of someone infected with Covid-19 that Chinese scientists have found was a guy elsewhere in Hubei Province (i.e. not in Wuhan) who had it in November, and he had no link to the Huanan market.”

            Link, please.

            “You have a major problem with objectivity.”

            Ditto.

            ” I see this as a scientific puzzle to be solved. ”

            So do I.

            “You seem to think it’s a propaganda war, and that I’m on one side of it.”

            The one thing you said that is accurate.

            Glad to see I struck a nerve.

          • gothamette says:

            Yes, John, I think you are totally compromised by your loyalty to China and Chinese culture.

            I come here to learn things, not to get into arguments with people, especially hostile jerks who don’t answer questions directly.

            What can you tell us about this pandemic that we don’t already know? I want to hear it. I’m not.

            You keep insinuating that the disease doesn’t come from the wet market, and I keep asking where you get that from, and you won’t say. You make ridiculous criticisms (Eva K. Lee’s email was incomplete, well, duh), you say that the virus has been circulating for 30-40 years without citation, and you accuse ME of not being objective, and of denying facts?

            You really are in a parallel universe.

            So, tell us something useful. Give us the citations for your claims. Not SCMP. Peer-reviewed articles.

            • Pincher Martin says:

              Yes, John, I think you are totally compromised by your loyalty to China and Chinese culture.

              Bingo. But don’t forget his loyalty to the CCP.

              • gothamette says:

                All I want to know is where he gets his facts from. That’s all. And he accuses me of being a crazy lady?

                /scratches head/

              • gothamette says:

                Moving on, FYI, about 600 sailors on the USS Teddy Roosevelt (out of approx 5,000?) have tested poz. Let’s keep an eye on that number.

          • gothamette says:

            This is the last thing I’m gonna say to you.

            Cochran doesn’t do partisan politics, so I haven’t said anything about it. But for the record: the response of the political authorities in the US, from right to left, has been abysmal. The one thing you said that was right was the crack about the baseball bat. Even that wouldn’t have worked.

            What passes for the left in this country wouldn’t have allowed quarantine, because that would have been “racist.” Racist to shut off all flights from China. Racist to quarantine NYC in February.

            But the buck stops in the Oval Office. One sentence from the dunce in the White House would have depoliticized the matter, and turned it from a partisan issue into a public health issue. Trump did the opposite. In a sane society, we’d have removed him from office a month ago.

            This pandemic has revealed the strengths & weaknesses of both the US and China. China’s weakness was in creating the virus. It’s strength was in stamping it out as far as humanly possible.

            The US has been revealed as a fatally flawed society.

            That’s it, Massey. I’m done with you.

          • gothamette says:

            “Hubei Province (i.e. not in Wuhan) who had it in November, and he had no link to the Huanan market. But they said he was not ‘patient zero’, and that person is important to find, to try to get clues to the origin. And in your classic style you cite that as MY CLAIM, when it was not my claim at all – I was citing some Chinese scientists.”

            It is YOUR claim. You continually claim that it is so, without citing the source.

            This is a freaking website, not a peer-reviewed article. If I say, in idiomatic English, that “you claimed” something, I don’t mean that you, yourself, wrote the peer-reviewed article, but that you base YOUR claim on something reputable and reliable.

            So give us the source, and I’ll read it, and decide whether it’s reliable.

            Stop taking things so personally.

          • gothamette says:

            “The earliest case of someone infected with Covid-19 that Chinese scientists have found was a guy elsewhere in Hubei Province (i.e. not in Wuhan) who had it in November, and he had no link to the Huanan market. But they said he was not ‘patient zero’, and that person is important to find, to try to get clues to the origin. And in your classic style you cite that as MY CLAIM, when it was not my claim at all – I was citing some Chinese scientists. “

            It is YOUR CLAIM until you supply a reliable link. Then it will become a cited claim.

      • swampr says:

        They are only certain that it was not directly engineered, not that it didn’t come from a lab.

        “bat coronaviruses have been studied at such labs in and around Wuhan, China, where the new coronavirus first emerged. ‘As a result,’ Ebright says, ‘bat coronaviruses at Wuhan [Center for Disease Control] and Wuhan Institute of Virology routinely were collected and studied at BSL-2, which provides only minimal protections against infection of lab workers.'”

        https://thebulletin.org/2020/03/experts-know-the-new-coronavirus-is-not-a-bioweapon-they-disagree-on-whether-it-could-have-leaked-from-a-research-lab/#

      • John Massey says:

        No, not accidental release either. One paper (not Chinese authored) says it has been circulating for 40 to 70 years, and they don’t mean circulating in bats.

        Taunting? Hardly.

        gothamette, you have a talent for misquoting people, twisting their words, shifting goal posts and a host of other little tricks. Precision of language is important. If you are going to quote me, you better quote me precisely.

        • gothamette says:

          “No, not accidental release either. One paper (not Chinese authored) says it has been circulating for 40 to 70 years, and they don’t mean circulating in bats.”

          Link, please.

  13. dearieme says:

    I see that Boris Johnson has been released from hospital. Which makes me wonder: do they ensure that a patient is non-infectious before they release him? If so, how do they check?

    • Janet says:

      They don’t check that patients are non-infectious when they leave the hospital. They are discharged when they no longer need intensive nursing care and immediate access to emergency treatment. Presumably, most of the people who leave the hospital are still symptomatic, thus assumed to be infectious, but are instructed to self-quarantine at home. I don’t know if, in the UK, that instruction has the force of law behind it or not.

      • dearieme says:

        Here’s the man himself, wielding his rhetorical trowel.

      • Safe Assumption...? says:

        Jan, “Showing symptoms = infectious” may not be a safe thing to equate. In fact it probably isn’t. E.g.

        https://www.cambridgeindependent.co.uk/news/cambridge-virologist-explains-what-we-know-and-dont-know-about-covid-19-9104220/

        “Q: Can you relapse after recovering from the virus? A: That doesn’t happen with these respiratory viruses. The symptoms that drag on are your body’s response to the virus, but the virus is gone after a few days. I take great umbrage at the lengths of time you are meant to be infectious for because it is just not true. Nine days is nonsense. You don’t excrete a live virus that long. Those studies are not checking for live virus, they are checking for genome. They do something called a PCR test (polymerase chain reaction), which is the test we are using to diagnose patients. It doesn’t tell you that you have live virus in your nose, it tells you have had it. For about 72 hours of a viral infection you have a live virus. In children it can last for longer – four or five days have been observed in flu

        Symptoms may often (and probably are in most of the duration they are actually observed) simply a the legacy left by the virus; the virus produces them in you in order to increase its reproductive potential, but that doesn’t mean the symptom only last as long as you are infectious and have a live virus in you. It doesn’t have an fitness interest in whether the symptom takes ages to heal from after it has used it to spread, only that you have it for enough time as it needs.

        In the case of BoJo, who has had it for a long time, it seems not so likely that he is still infectious. But of course, this virus may have a longer infectious horizon than influenzas.

        • Frau Katze says:

          What do you make of this? I’m hoping it’s caused by inaccuracies in the tests.

          https://globalnews.ca/news/6805414/coronavirus-south-korea-reinfection-canada/

          • Safe Assumption (replying) says:

            Don’t know what to make of it.

            Other than that it would be bizarre in the extreme that this is being picked up in South Korea and Japan where you have supposedly very low community prevalence of infection, and not in Western Europe where the general trend seems to be to think that it’s at least in the 3-5% by now, and much higher in regional concentration.

            You’d think that for true symptomatic reinfection, it would be obvious in places where the infected are statistically likely to come back into contact with contagious people (though lockdown makes that hard to estimate), not like SK where that supposedly is highly improbable to happen.

            I’d guess there’s also the issue that PCR doesn’t tell you much about live virus vs dead virus. If the virus gets back into your cavities and then gets killed by your immune response, maybe it’d still show up.

        • gothamette says:

          “For about 72 hours of a viral infection you have a live virus”

          I’ve read descriptions of doctors who intubate patients and they say that the virus is shedding liberally from the patient’s nose and mouth.

  14. Smithie says:

    Some ferrets are quite aggressive and will sink their needle-like teeth into you, if you don’t show them attention. They also stink to high heaven. I am not a fan.

    Though weasels are certainly interesting creatures to see in the wild, if you don’t have chickens. Some of them have winter coats which match the snow.

  15. John Massey says:

    A bit of light relief:

    • Frau Katze says:

      I remember that one!

    • John Massey says:

      He was married to one of the McGarrigle sisters (Kate) for a while. Think I don’t know Canadians? A lot of them were shipped in at the request of Winston Churchill and died trying to defend HK against the Japanese. It was an appalling disgrace – Churchill knew that HK was indefensible and had no intention of wasting British troops trying, so just used Canadians as cannon fodder. Also you rarely hear Canadian troops mentioned when people talk about the D Day Normandy landings, but they took one of the beaches.

  16. Rob says:

    Cochran, I am sure you know that passaging was used to attenuate a large chunk of the diseases used in standard vaccines, from tuberculosis to measles to polio. By and large, modern biotechnology has not been applied to attenuate pathogens, because live attenuated vaccines have fallen in popularity.

    There’s a technique in bacteria called PACE, Phage Assisted Continuous Evolution. As i recall, they have a chemostat full of E. coli with some plasmids and a phage. A gene they want to evolve in the phage genome, an accessory plasmid with a necessary phage protein, a mutagenic plasmid to increase variety of the to-evolve protein, and some way of coupling the accessory plasmid expression to the evolved. In cells where the evolved protein works, the accessory plasmid’s protein that the phage needs to make infectious particles is expressed, and the evolving gene on the phage genome is packaged and can go on to infect other cells fed into the chemostat. Versions of the evolved gene that don’t work aren’t packaged into infectious phages.

    The original experiment evolved T7 RNA polymerase to recognize a different promoter. A later experiment evolved a split RNA polymerase where the two pieces could be attached to different proteins, and if the proteins interact, a gene is transcribed and translated.

    I saw a recent experiment where a coronavirus with a defective version of exoN, the 3’ to 5’ exprobonuclease that proofreads during genome replication and keeps the mutation rate down, was passages in cell culture to see if it regained fitness and lowered its mutation rate. They stopped passaging when a new version of the spike protein increased fitness, and stopped forming syncitia. The virus did regain some fitness, but the disabling mutations in exoN were not reversed.

    It seems to me that PACE could inspire a method of passaging to attenuate a virus for vaccines. Put all the genes you don’t want to change, like the spike protein, because you want that to be immunogenic for the wild type virus, integrated into the cells’ genome so they don’t evolve, and have a low fidelity genome replication.

    The advantage is twofold, first, the high mutation rate means the virus will adapt to the cell culture, and likely lose fitness in human hosts, and the high mutation rate means lower-fitness variants will fix in the population due to Muller’s ratchet. Keeping some genes from evolving means chosen paths to revert to higher virulence are closed off.

    The big problem with SARS vaccines was not that inactivated virus or purified protein vaccines weren’t immunogenic. The problem was that when vaccinated animals were challenged with wt virus, they developed lung damage due to Th2 hypersensitivity. An attenuated virus vaccine would probably not cause hypersensitivity, because live viruses tend to produce Th1 responses.

    Finding the epitomes that cause the Th2 reaction is probably the most pressing need for making a vaccine to SARS-CoV-2.

  17. James Thompson says:

    Excess deaths in Europe can be seen here:
    https://www.euromomo.eu/index.html

    With 2015 as a baseline, excess deaths are now higher than seasonal flu in Italy, Belgium, France, Netherlands, Spain, and UK.
    I think this is a real effect, particularly when Covid-19 is relatively restricted in focal outbreaks, rather than widely spread as in the case of Influenza A and B.

    • dearieme says:

      How do you correct for (i) reduced rates of accidental deaths in, for instance, car crashes, (ii) increased rates of death from untreated illnesses, (iii) reduction of non-Wuhan iatrogenic deaths in hospitals, (iv) and so on and so on.

      Have we any reason to be confident that such effects are small enough to ignore?

      • gothamette says:

        You don’t.

      • Frau Katze says:

        I think these other sources, while they definitely exist, are quite a bit smaller than C19 (at least in any place that has had a high spike.). They go both ways too.

        If we had the same data for South Korea (that was and is testing a lot) the “other factor count” might emerge, by comparing the excess death count with count from the tests.

  18. Maciano says:

    It really is SARS2. Less lethal, but more contagious.

    Did it evolve in bats or did it get evolved by Chinese virologists? Hard to say.

  19. gothamette says:

    New Zealand “nuked the curve.” “In western countries it was also becoming apparent that the mitigation strategy of “flattening the curve” was failing”

    https://www.theguardian.com/world/2020/apr/10/elimination-what-new-zealands-coronavirus-response-can-teach-the-world#

    • Frau Katze says:

      Quite apart from government policies (and I’m not criticizing them) there’s the island effect.

      I live on a large island (Vancouver Island) that can only be reached by ferry. The capital of BC is on the on Island. Normally there are ferries at frequent intervals (the crossing takes about 1 ½ hours. They’ve been cut back to discourage typical tourist crossings.

      The rates are very low here. It’s because we’re on an island. New Zealand is larger but in a very remote place. Rates are even relatively low in Australia too.

      • gothamette says:

        New Zealand’s low rates are due entirely to government policy. Mongolia and Vietnam have also done a great job. And so has Senegal. Yes – Senegal. They can turn around tests in 4 hours. Look it up.

        The US response has been an epic fail.

        • Frau Katze says:

          While admiring the New Zealanders, I still hold that being on an isolated pair of islands can’t hurt. Plus how do you account for the low rate on Vancouver Island, where we have the same (increasingly awful) medical system all through the province? Nor has our government been particularly proactive.

          • gothamette says:

            Definitely being an island helped, no doubt about that. But it also could have hurt. Import a few cases, let it rip, and Bob’s your dead uncle.

            Vancouver Island. Luck?

            • Frau Katze says:

              Whatever the reason, we have been lucky in one way. Victoria has the mildest climate in Canada. It attracts retired people. You can identify with those escaping the prairie winters, that can hit -40° (this number is the same for Fahrenheit and Celsius). I’ve encountered it. It’s incredibly cold.)

              There are a lot of care homes. And elderly people in general. We’re like dry tinder for a fire. The easing of the lockdown will initially be easy for us. But we’re almost all vulnerable.

        • Frau Katze says:

          Re, Senegal. I know very little of this country, but I noticed this, about the Middle East.

  20. Tim Burr says:

    Been hiding in my underground virus proof bunker for 3 weeks … what’s the USA death toll? 5 million? 6 million?
    Mexico must be worse – no real lock down. 10 million? Oh, my poor Chihuahuans! Maybe a chance to pick up a Baja casa on the cheap.

  21. j says:

    Bad News, Friends. There is no “Herd Immunity” of COVID-19. Korea found that those “cured” are not immune and can be re-infected.

    • NonLinear says:

      In a scenario where the assays used to declare individuals COVID-19 negative had a low false negative rate that might be a reasonable conclusion. However, the false negative rate for the PCR tests (https://www.medrxiv.org/content/10.1101/2020.04.07.20051474v1.full.pdf), squared (you need 2 negative tests to be declared “cured”), multiplied by thousands of tests, would also account for dozens to hundreds of cases exhibiting this course of events (declared negative, later testing positive). Given that this null scenario is more consistent with our priors on immunity, I’m sticking with it until more compelling evidence for re-infection shows up.

  22. gothamette says:

    This is what I’m talking about. He’s got a lot of good graphs illustrating excess deaths:

  23. John Massey says:

    On the subject of whether islands are refuges or prisons/captive populations, this from the BBC:

    “A European island off the coast of Estonia has been labelled by locals as ‘corona island’ after becoming the hotspot for the virus and being placed into strict quarantine. The first Covid-19 cases on the island of Saaremaa emerged a month ago after a sports event was held there with a team from Italy. Now health officials estimate that half of the island’s population have contracted the virus.”

    First time I have seen a reference to a rate of infection of a population anywhere near as high as ‘half’, so I just updated my priors.

    • Frau Katze says:

      A small island doesn’t sound good.

      Vancouver Island is a big island. But it will get in due time (we do have some cases already). The number of care homes is also a problem.

      New Zealand sounds more promising. Get it down to zero and quarantine anyone coming in.

      • Rosenmops says:

        I’ve noticed comments on the Global News site about Vancouver Island. Some Islanders want a lot more restrictions on who is allowed on the ferries. Some say only essential workers and residents. Some extra people crossed over on the Easter Weekend, and there was much wailing and gnashing of teeth about it. But with the reduction in sailings, and the capacity of each boat being reduced by 50% to maintain social distancing, there was only a small fraction of the usual Easter weekend crowds. Thank goodness the pandemic didn’t happen later in the year when cruise ships dock in Victoria. There won’t be any cruise ships this year. It will be hard on small businesses.

        Small private boats also take people to the Island, and planes. But still the numbers in the Vancouver Island Health District are low.

        Population of Vancouver Island (where Frau lives) is about 870,000, and there are 97 cases, 3 deaths.

        Population of the Interior Health Region (where I live) is 750,000. and there are 150 cases and 1 death.

        Overall BC has had 1,647 cases and 81 deaths, mostly in the Vancouver area.

        • Frau Katze says:

          But we can’t stop people from coming. I suppose reduction in ferries would keep tourists down. It sounds like a bad time time to travel just for a vacation.

          I’d have thought tourism was not going to be a thing this year.

          There’s really not that many in BC overall. But enough to encounter one of them working in a drug store near your place.

          • Rosenmops says:

            Yup. It is like a bowl of candies that all look and taste identical, but some small percent are deadly poison. You have to avoid all of the candies.

            • Frau Katze says:

              We have a lot of care homes here. It’s a popular place for retirees due to the mild climate.

              I finally started reading the book about the 1918 pandemic again. It was bad, very bad. It killed young adults (cytokine storms?). It started as a fairly mild flu but somewhere it mutated (I suppose) into something much worse.

              Also, in 1918 news travelled much slower. Few had an overall picture of the geographic spread.

              People of that time were quite accustomed to serious infectious diseases. So while it was bad, it didn’t have shock factor associated with Covid. We are spoiled. Some of us had measles and mumps as children but that a long time ago and only dimly recalled. Vaccines were available by the time my children were born.

              Infectious diseases seemed on the way out. Then there was HIV. But it did not spread by aerosol. Still… new diseases could appear, seemingly out of nowhere.

              And now one has done just that.

    • John Massey says:

      Something curious that you can see in a lot of the epidemic records, and South Korea is a good case of this – there is a long string of isolated cases with no evident increase (which tempts you to think not very infectious, or maybe no human to human transmission, or maybe infection is a function of viral shedding/load, or maybe it was just flying under the radar all along, maybe just passed off as cases of old people dying of pneumonia, which happens, or maybe lots of things), and then suddenly you get an explosion. In their case it was attributed to a super-spreader at a large religious gathering who is alleged to have infected ~ 1,000 people. So, I have a lot of half-formed thoughts about that.

      So, as much as I wish for you that it doesn’t happen, it seems possible that you might suddenly see a big outbreak on Vancouver I. and it is as well to be prepared for that.

      Because we have relatively few cases in HK and good contact tracing, we have seen some weird things happen, e.g. a singer with a band was infected (not known from where, possibly in the Philippines, because a lot of live bands in HK are Filipinos (much more musical than Cantonese)), and that band performed at two particular ‘night spots’ (bars with live music), and so far that has resulted in a string of more than 100 cases, all traceable back to that one person. Another one was a particular Buddhist temple where a whole lot of people who visited the temple got infected, and then infected their family members. It turned out the temple had been visited by two Buddhist monks from the Mainland last November, and they were subsequently traced and confirmed in the Mainland to have been infected. So were they already infected in November when they came to HK?

      The more I see these long chains of infections stretching a long way back, the more half-formed thoughts I get about when and where the virus might have first become a lot more contagious in humans. But further open discussion and thinking aloud about that is now impossible, unfortunately.

      • Frau Katze says:

        Yes, it will get here.

        I haven’t been out for 3 weeks. I shop for groceries online and they’re delivered. I leave the non perishables for a few days. Delivery men generally now leave stuff at the door to reduce contact.

        I’m worried about my daughter, a surgeon in Edmonton, Alberta, who recently did emergency surgery on a patient who then tested positive. But I can’t do anything so I just try not to think about it.

        My sister and I are prepared for a long period at home. We’re both high risk on account of age (and she has rheumatoid arthritis). She says she won’t go put even when restrictions are relaxed (as they must be, and pretty soon).

        We’re both retired (as is her husband, who also had Type 2 diabetes), so we don’t have to go out.

        I have heard that South Korea and China (and HK I assume) track people by their phones, which greatly aids in contact tracing.

        I doubt any Western country could take that route. I don’t entirely understand it but many people become almost hysterical at the thought of their movements being tracked. It doesn’t sound that bad to me. I have nothing to hide.

        • John Massey says:

          No, no tracking of people by their phones in HK. People here would go apeshit about something like that. Tyranny! Oppression! Well, those things come in many guises and from many quarters.

          • John Massey says:

            Well, I should qualify that – precision of language is so important, although some people clearly don’t seem to have any problem with playing fast and loose with misquoting others, misattributing statements to them, putting words in their mouths, etc., at which point you realise that it is all about propaganda and sheer vindictiveness, not truth seeking.

            Contact tracing in HK is done by the Police, to relieve health care workers of the burden of trying to do it and because they are good at it, and because HK has a pretty high ratio of Police to population. And when they are seeking to establish someone’s contacts they will respectfully ask the person if they can look at their phone, to get a list of their contacts. If the person says no, that’s invasion of privacy, then it’s no and the cops won’t push it. Most people, when asked politely, don’t seem to mind, so long as they know what it is the cops are looking for and why, and what at.

            • gothamette says:

              “Well, I should qualify that – precision of language is so important, although some people clearly don’t seem to have any problem with playing fast and loose with misquoting others, misattributing statements to them, putting words in their mouths, etc., at which point you realise that it is all about propaganda and sheer vindictiveness, not truth seeking.”

              True that. The person who said this is a lying SoS: ““The earliest case of someone infected with Covid-19 that Chinese scientists have found was a guy elsewhere in Hubei Province (i.e. not in Wuhan) who had it in November, and he had no link to the Huanan market. But they said he was not ‘patient zero’, and that person is important to find, to try to get clues to the origin. And in your classic style you cite that as MY CLAIM, when it was not my claim at all – I was citing some Chinese scientists. “

              Until we learn who the referenced Chinese scientists are, this is worth as much as soiled PPE.

        • John Massey says:

          Frau Katze: This is a good read about people who are immunocompromised for various reasons, including due to medications for e.g. rheumatoid arthritis (and also due to pregnancy), but it does kind of leave one thinking, well, what the hell do they know or understand about this thing?

          https://theconversation.com/what-does-it-mean-to-be-immunocompromised-and-why-does-this-increase-your-risk-of-coronavirus-135200

          • Frau Katze says:

            She said she was tapering off the med that decrease immune system functions.

          • Frau Katze says:

            Excerpt:
            ——-
            Meanwhile, a 47-year-old woman from Wuhan who was taking steroids to suppress her autoimmune disease lupus, contracted the coronavirus and didn’t fall ill. But her compromised immune system couldn’t efficiently clear the virus and she spread it to her father and sister before testing positive.
            ——-
            Didn’t fall ill but passed it on! What if the index case didn’t fall ill?

        • reiner Tor says:

          I have nothing to hide.

          At least as long as it’s not a crime to comment on a racist site like this one. It could perhaps be used to destroy a few careers. And perhaps some people have something to hide, perhaps only shameful but not illegal things, which could then be used to blackmail them.

          But yeah, against this virus, using cell information for contact tracing is probably inevitable.

          • John Massey says:

            Hell, I’m hoping it will get me in the good books of the CCP so much that they start paying me to be an agent provocateur, and I can start doing this stuff professionally.

          • gothamette says:

            At least as long as it’s not a crime to comment on a racist site like this one.

            True. I tell friends that I was first alerted to the virus on this site by having them open a vein and swear that they will never ever tell the truth about me. Well, not quite but close. Even in the middle of a pandemic you have to be careful, because this will end.

            A lot of the shit I read on Twitter & the NY Times is people profiteering from now and positioning themselves for advantage and profit after.

            I could name names, but I won’t.

          • Frau Katze says:

            I’m retired. But my pseudonym dates back a while. I’m not entering racist comments by any standard. Well. by most standards.

            • reiner Tor says:

              You can manage to do that either by avoiding certain topics, or by being dishonest about them. Okay, a couple more options are never having thought long and hard about those topics, or being a total moron. But I’d eliminate those options here, because obviously you are not a moron, and because you are at the Cochran blog.

              So let me ask you, do you believe that a substantial portion of the measured IQ difference between whites and blacks is due to genetic differences, or not? Do you believe that for genetic reasons, all else being equal, blacks will be more impulsive and more aggressive than whites, and thus more likely to commit violent crimes? Just asking for a friend.

              • Frau Katze says:

                My beliefs are standard for this blog. You know what that means.

                It’s currently irrelevant anyway. I’m over 65 and worried the Covid virus. Many here on the blog provide interesting comments plus interesting links.

                I’m also sheltering in place and am alone. Of course, I cannot visit friends or family. I miss this and this blog lets me at least communicate with other people.

            • reiner Tor says:

              By the way, even if you are retired, you might understand that most people are not. You wrote above that you didn’t understand why people were “almost hysterical” about the government further increasing its surveillance over ordinary citizens.

              I agree it’s probably inevitable (or a horrible price is to be paid) temporarily, but I think it’s perfectly understandable why people get “almost hysterical” about it.

              I wish you and your family the best of health and avoiding Covid-19 as well as other serious illnesses.

              • Frau Katze says:

                The whole thing has an unreal quality, like I’m in a bad dream. I simply said the South Korean approach seemed to work. Still, how long can they keep that up? The threat is still there. I doubt it would even work in Canada, the country is too big.

                OTOH, I’m quite concerned about our current economic situation. It cannot continue like this. I spend as much time reading about economic news as about the virus. I restarted my subscription to the Financial Times. My son and his wife are out of work because of the lockdown. My daughter is working at high-risk job. Her young son is worried about her.

                I’m now more sympathetic to the natives of Mexico confronting smallpox (far worse than C19) brought by the Spanish.

        • gothamette says:

          Allegedly the Mossad was tracking people by phone. I read that in Haaretz, not some alt right website.

          They haven’t done brilliantly. I haven’t kept up on the stats but last I checked they had 11K cases and the usual 1% death rate.

          Senegal, OTOH, has done quite well. Maybe they aren’t reporting. I don’t know. But so far out of a pop’n of nearly 16M, they have…. two deaths.

          Two. Count ’em. Two.

          • j says:

            It is public knowledge here in Israel that the Mossad has been authorized to assist the police in this nasty epidemic. Netaniyahu said so on TV. Normal people know that the Mossad is working for their safety and it is OK.

            • gothamette says:

              I didn’t mean to imply it was wrong. I just think it may not have been as good as old-fashioned methods after all.

              Take a look at Senegal’s numbers. Better than Israel’s. (Yes that may be a matter of reporting.)

              • j says:

                Yes, the epidemic is hitting us hard. I can point at two difficulties specific to this country: (1) A tradition of rescuing our people at any price, like sending planes to New Zealand, Ecuador, New York, etc. to bring in those stuck there. Many of the Newyorkers are infected. (2) The existence of disaffected communities that resist government orders, like the Haredim and some Arab villages.

        • random observer says:

          Well, necessity is its own law, always, and public health sometimes is like national security. I figure if I would accept it in a state of war or rebellion, then I’ll likely accept it in a state of plague.

          Even so, wildly troubled by the idea that we might have to transition to the kind of society where our locations can be known and our movements tracked at any time, especially as a norm, not just an emergency. Technology has already taken us near to that point, it just hasn’t driven every country to do it. I’m only 49, but may be the last generation to automatically assume I am not being and cannot be tracked in everyday life. Perhaps already wrongly, but it was long true enough. I didn’t have cellphones until the age of 40 and still remember that they can track me. If public telephones still existed, I’d not carry my private one and my work one not all the time.

          That’s a profound end to a particular state of being as a human, since in general no premodern society could do that above the village level [which admittedly covered most people’s lives but was usually informal] and in particular in English-speaking cultures, which long made a political and moral fetish of it. I inherited that fetish for good or ill. I take the view that I am free to walk about my own country without being asked who I am or what I am doing, or to produce papers, or to be tracked. At least under normal conditions, none of these are the business of the authorities or anyone else. Whether or not I have anything to hide, which is irrelevant.

          I can see its end, and why, and perhaps the necessity of it in a crisis, but I’ll miss it.

          FTR, I’m in Ottawa. Work 3 afternoons/week at work in a critical function, so still out at times. Have a couple of moderate comorbidities, but at least social distancing is proving easy here. 2 metres easy to do except the very intermittent passage on the street of less. Not sure how I’d react if I heard a cough from such a person while passing them. Part of me would be annoyed at the statistical chance. Trying to bear in mind that allergies, colds, and sniffles from sleepless nights [like my own natural symptoms] probably still more common. Nevertheless, checking temperature often. Grocery stores are limiting numbers, insisting wait lines keep social distance, quizzing us about symptoms, travel etc. A lot of it’s theatre, sure, but it is keeping numbers and distance controlled pretty well.

          I hope the island continues to do well- take care.

          • Frau Katze says:

            It’s odd how people react differently. I would think any phone tracking would be temporary. I doubt it work very in Canada anyway. It’s too big.

            I’m worrying my daughter on the front lines but for some strange reason I’m not worrying about myself, aged 68. That’s likely because I have so little contact with anyone. I’m getting groceries by ordering online and having them delivered.

            I might be more concerned if I lived in New York. Or maybe if it hits Vancouver Island hard.

            • gothamette says:

              “I might be more concerned if I lived in New York.”

              I go on and off. Rationally, I say to myself that I am unlikely to get the virus unless I am sneezed on or coughed on by an infected person. Viral load, etc.

              I wear a mask and gloves (although I’ve read that the latter may not be all that effective…) and I avoid close contact w/strangers. Wash hands, etc. Carry around a spritz bottle of alcohol, which I use obsessively.

              Then sometimes I say to myself, “this is the day you get it. I just hope that I inherited my mother’s iron constitution.” She was one of 7 sibs – 5 lived past 90, the oldest to 104 1/2.

          • gothamette says:

            Guess what? A few months ago, I was shocked to receive from Google a log of my movements around the tri-state area.

            This was before SARS2.

      • gothamette says:

        “open discussion”

        The fact is that even in NYC the SARS2 attack has been very uneven. Being totally honest, where I live it hasn’t been terrible. I don’t know one person on my block who’s gotten it, and I would have learned.

        (OTOH, the brother of one of my neighbors lives in Paris and he has lost three co-workers to SARS2. Middle-aged professional men who work in some globalized office. So, in NYC I have zero acquaintances who have been infected, but three French 2nd degree acquaintances.)

        Click to access covid-19-data-map-04032020-1.pdf

        Things are not that bad where I live. Perhaps I’m kidding myself but I think if I’m smart, avoid crowds, getting sneezed or coughed on, wash my hands a lot, wear gloves & a mask, and carry a spray bottle of alcohol w/me and use it every five minutes, I can avoid this thing.

        If I had lived in zip code 10452 and took the #2 subway every day, that would have been a different thing entirely. I think viral load is crucial. I heard a nurse saying she was being sent into germ warfare every day. So is taking the subway, working in a people-oriented business and then going home to others who have been exposed. There’s only so much your immune system can take.

        I also don’t understand why obesity and high blood pressure would be such a risk factor for what is (ostensibly) a respiratory disease.

        Then there’s this: all the people who get it, get a little sick, and shake it off. I hear it’s 80/20 – but are those statistics really accurate?

        So many questions.

        • gothamette says:

          A couple more things.

          NYC has a lot of strengths – a truly excellent and extensive public and private hospital system. Lots of hospital beds. World class medical schools (the residents and interns have contributed heroically), many many great doctors, a responsive emergency medical system, to make up for our stupid, abysmal mayor.

          The system hasn’t cracked. It’s been very stressed but it hasn’t cracked. Bill Maher just released a very funny video, for which of course he was slammed, for criticizing pandemic porn. (He was right.) One of the stats he mentioned was that NYC’s system didn’t come close to being overwhelmed.

          But we saw pictures and videos of hospitals overwhelmed…. yet all were in Queens. I have a sneaking suspicion that Mount Sinai at 105th/5th never came close to being full – but I don’t know. I’d love to know.

          You can’t mention this without being accused of being part of the “it’s just flu bro” crowd,” which I definitely am not.

          I just heard, right now, on the news “the New York epicenter” – when you drill down you see it just isn’t so.

          We need to drill down into the grainy details and analyze. This will help save lives. But if it doesn’t fit a narrative, we’ll have a hard time finding out.

          • Rosenmops says:

            Maybe a lot of people in Queens aren’t practicing social distancing. Is it a different demographic from where you are?

            In Canada Quebec. especially Montreal, seems to be the epicenter. Many more cases and deaths in Quebec than Ontario, though Ontario has a larger population. Maybe people in Montreal don’t like being told what to do.

            • Frau Katze says:

              Didn’t they have several care home cases in Quebec? Of course they are in many places. I wonder what fraction of care homes have had Covid infestations?

              There are a lot of care homes in Victoria.

            • gothamette says:

              It’s a hugely different demographics. I predicted and I was right, that the biggest single plurality in NYC would be Hispanic. They don’t practice social distancing because they can’t. They travel on subways to service jobs that are “essential.”

              The next biggest demographic in NYC is blacks, because of some of the above but mostly I think comorbids.

              NYC stats are more racially equal than other US towns.

              Asians are the least likely to die in proportion to their population.

              • Rosenmops says:

                The usual suspects are losing their minds about the disproportionate number of blacks dying, saying it is because of racism. The cormorbids could be genetic.

              • gothamette says:

                I doubt that the obesity and diabetes rates among Af-Ams are solely genetic – although genes are always implicated. Sub-Saharan Africans are pretty thin, until they get a hold of KFC. (Yes, there’s a NY Times article about that – look it up.)

                Also Indians & Pakistanis are very prone to developing diabetes in the West. Genes or environment?

  24. Frau Katze says:

    I’ve just found that Sweden has a taken a very relaxed approach to the pandemic and has 10% death rate. (Approx 12K cases and 1.2K deaths according to the Hopkins chart). See also:

    https://www.thelocal.se/20200414/swedens-coronavirus-strategy-sparks-fierce-debate-as-deaths-pass-1000

    There’s is a video by an unhappy Sweden. There are a lot of elderly, that contributes to a higher rate. The article says immigrants have been hit hard (I don’t know why). Well, there’s lots elderly in Canada and the USA too. Canada had 28.2K cases, 1.4K deaths. The US, 636K cases, 27.8K deaths

    • gothamette says:

      I have a nasty theory that the Swedes thought it would clear out the immigrants, and that old folks were collateral damage, and the rest of the herd would survive.

      • Frau Katze says:

        So why do Swedes keep electing the same old leftist, pro-mass immigration politicians.

        There’s an active opposition but the state, the elite, big business, universities (the usual) fight against them tooth and nail. Antifa started in Europe and they’re given free reign to attack the this opposition.

        Maybe I’ve answered my own question. But this ruling class wouldn’t of hurting their precious immigrants. I can well believe the elderly could safely dispensed with though.

        • gothamette says:

          “So why do Swedes keep electing the same old leftist, pro-mass immigration politicians.”

          I can’t answer that. I have known a few Swedes and maybe they are self-selected but they were always hyper-professional and rather conservative. Perhaps they are just voting for the status quo. The devil you know.

    • gothamette says:

      “The article says immigrants have been hit hard (I don’t know why).”
      I cynically suspect that the authorities knew that and thought it was a feature, not a bug.

    • gothamette says:

      That was a very funny video. The guy is basically saying that Swedes do not like to be individualistic, but they as a group consider their society to be exceptional. They take joy and pride in bucking the worldwide consensus – but only as a collective. They like to be exceptional – but only as a herd.

      It’s an interesting paradox.

      We’ll see if it works.

    • gothamette says:

      That Swede has a dry sense of humor.

  25. swampr says:

    Iceland just published valuable data.

    They tested a random sample of 2000 people and their outbreak appears to be tailing off. 0.6% were positive. With a population of 364,000 and 8 deaths that means 2,200 infections and a 0.4% death rate. Another critically 8 are critically ill so that will likely rise a few tenths. These are such small numbers you can’t extrapolate too much from the death rate. Had it gotten into a nursing home and killed a dozen people it would have more than doubled. More interesting is that they halted the epidemic at such a low level without the more economically crushing measures.

    https://www.nejm.org/doi/full/10.1056/NEJMoa2006100

    • reiner Tor says:

      I think Scandinavians practice pretty extreme social distancing even without a pandemic. Like queuing up for a bus they keep 2 meters distance from each other, I’ve seen some pictures. Old people usually live alone. They are highly developed, and probably the elderly are often competent at using the internet, ordering groceries online. So socially isolating the elderly is something which might be difficult to replicate elsewhere. Icelandic population (like that in the USA) is relatively young for a first world country, which reduces mortality rates further. I’d expect their mortality rate to eventually reach 1%, though happily it looks like two people in critical condition have just recovered (a couple days ago they still had 10 people in critical condition), which increases the chances of me being proven wrong.

      By the way, Icelanders tested fewer cases relative to those tested positive than South Koreans, according to the worldometer statistics, almost 5% of those tested were positive in Iceland, whereas less than 2% of them in South Korea.

      https://www.worldometers.info/coronavirus/

      • swampr says:

        I find Iceland interesting because it’s a random sample, not the overall testing which is incomplete like anywhere else. They tested a couple thousand people, selected at random regardless of symptoms. No other case of that except for the Diamond Princess, which was not random (skewed older). It’s still not perfect because some who tested negative had probably already recovered or became infected later on. A random sample antibody test will be more accurate, but hasn’t been done other than for small towns so far.

    • Frau Katze says:

      If a small island with a few hundred thousand residents can’t eliminate it, I don’t know who can.

  26. Frau Katze says:

    With respect to the lab vs market question.

    Maybe the Chinese don’t know either. Suppose it infected a lab worker, but he didn’t know.

    After work he heads to the market on his way home, as is his habit. Say he does that for several days and gets mild case that he assumes is just a routine ailment. Suppose several market people catch it from him?

    How could the Chinese figure it out if the worker didn’t know he was infected? If he didn’t know how could anyone know?

    • reiner Tor says:

      Yes, that’s what I was thinking, too.

      • j says:

        At this point, the lab vs market debate is irrelevant. Those labs are a danger to humanity. To each one of us.

        • John Massey says:

          And so are the markets, even those that sell only live domesticated things like chickens and guinea fowl, and they should be illegal everywhere. Not seafood, that’s not a problem.

        • reiner Tor says:

          It was reported that they increased their safety levels since the epidemic. I don’t think they are now any worse than similar labs elsewhere. I also don’t know if such a lab would or could produce any net benefit to humanity. Is it a good idea to have labs studying dangerous viruses? I’d think it is, with appropriate safety, but maybe not.

          Can anyone with some knowledge of the issue weigh in?

          • German_reader says:

            “I also don’t know if such a lab would or could produce any net benefit to humanity.”

            If I understand correctly, they were studying those coronaviruses as preparation for a Sars-like pandemic which was seen as inevitable sooner or later, given the prevalance of potentially dangerous viruses in bats and the close proximity of bats to human settlements (e.g. they found antibodies for certain viruses in villagers which seems to indicate zoonoses from bats are a not uncommon occurrence):
            https://www.scientificamerican.com/article/how-chinas-bat-woman-hunted-down-viruses-from-sars-to-the-new-coronavirus1/
            It would be of course highly ironic if that research had brought about just the pandemic scenario which it was meant to mitigate.

          • swampr says:

            It’s worth doing. A virus that spreads like the flu with a death rate like SARS, as bird flu might would be, is so dangerous a threat we need to do this kind of work to understand how to fight it. But not at minimal level 2 security (per Richared Ebright) in the middle of a dense Asian megacity. Maybe at an isolated location with a two week quarantine for anyone leaving. Perhaps much of physical work could be done by a few techs while the scientific work was handled remotely.

            • gothamette says:

              I really don’t get the benefit. Please explain it because there’s a huge gap in my brain between understanding how this thing works in reality and why they were actually handling infected bats in a lab. Were they working on serums? Vaccines?

        • Maciano says:

          Amen, J.

          These markets are cruel to animals and dangerous to humans, lab origin of SARS2 or not

    • swampr says:

      The closest official sample from a wild bat that they have is only a 96% match. That’s apparently different enough that there would have to be either another undisclosed bat sample that’s closer or an intermediate step. The contention is that intermediate step could have been ferrets or tree shrews that it was passaged through. If either were the case it’s very easy to imagine them hiding it.

  27. dearieme says:

    Lab safety: years ago I heard two young research fellows at Cambridge indulging in competitive boasting about how they avoided paying heed to their chemistry lab safety regulations. Their particular acts of reckless bravado involved radioactive material. I dare say they, and their colleagues, and the people who dealt with the lab waste, survived thanks to the regulations being (probably) absurdly conservative, by virtue of the linear no-threshold model of the dangers.

    Similar antics in a bio lab would scare me stiff. And it’s not just bravado, there is also incompetence to allow for, and corruption. Even just moments of inattention or stupidity when one is feeling tired, or below par – from a virus infection, say. Asking for a zero defects safety policy is simply not realistic.

    In my experience there is a particular problem with bio, namely that people with a background in, say, chemistry, physics, or engineering will often reckon themselves woefully underinfomed about biology and therefore ill placed to serve on safety committees covering bio labs. Certainly when I was on a safety committee that covered a Level 3 bio lab I felt that the burden of my ignorance was pretty uncomfortable.

    But to leave that duty to biologists is rather like having poachers police the poachers – too much danger of trading favours with each other, complacency, group think, and putting the interests of the researchers ahead of the interests of the rest of us. I’ve never felt any reason to believe that there are fewer fools or scoundrels among biologists than there are among physical scientists.

    Maybe I’m unduly influenced by the fact that I’ve never known a university science lab that took safety as seriously as it was taken at a commercial firm I once worked for. Or maybe I am “duly” influenced by that.

    • Frau Katze says:

      Didn’t someone at one of those labs contract smallpox?

      • dearieme says:

        Birmingham.

        I assume that such leaks are usually covered up in Russia, China, and the USA. Or am I being too hard on the USA?

        • gothamette says:

          As usual, yes, you are being too hard on the US. But what else can one expect from a man who jeered at my sadness for Italians who died without a proper Catholic funeral? Not once, but twice? (“Oh do grow up.”)

          I’ve already told you about the outrageous case in the NIH. I supplied a link. You appear to have forgotten. You can look it up yourself, lazybones.

          • dearieme says:

            I asked an entirely serious question: what happens if the corpses are still shedding virus? Your answer was to emote emptily. So, yes, do grow up.

            • gothamette says:

              I wasn’t emoting at all. I simply pointed out that it was sad Catholics couldn’t have a proper religious burial. Your response was to jeer. So do fuck off.

              • dearieme says:

                But what if the corpses are still shedding virus? Do you plan to avoid this elementary question to the end of time?

              • gothamette says:

                Enough of this. I didn’t answer your question because it was stupid, but I will answer it now, in italics and allcaps.

                OF COURSE NOT.

                Never once did I suggest that grieving family members contravene medical procedures.

                Not once.

                I merely expressed sympathy that people could not bury their relatives in accordance with natal religious funerary procedures.

                I do admit that I expressed sympathy for this primitive feeling of love and devotion. It never occurred to me that anyone would question that, much less mock and jeer at it. I was so astonished at that, I reacted with outrage. Learn a new thing everyday. People are crazier than I can possibly imagine. For that, I do not apologize.

      • gothamette says:

        Live smallpox in vials was discovered in a closet at one of the NIH labs. No infections. But very embarrassing. Hope someone lost his job over it.

        • Frau Katze says:

          The fatality occurred in the UK:
          ——
          The 1978 smallpox outbreak in the United Kingdom resulted in the death of Janet Parker, a British medical photographer, who became the last recorded person to die from smallpox. Her illness and death, which was connected to the deaths of two other people, led to the Shooter Inquiry, an official investigation by government-appointed experts triggering radical changes in how dangerous pathogens were studied in the UK.

          The Shooter Inquiry found that Parker was accidentally exposed to a strain of smallpox virus that had been grown in a research laboratory on the floor below her workplace at the University of Birmingham Medical School. Shooter concluded that the mode of transmission was most likely airborne through a poorly maintained service duct between the two floors. However, this assertion has been subsequently challenged, including when the University of Birmingham was acquitted following a prosecution for breach of Health and Safety legislation connected with Parker’s death. Several internationally recognised experts produced evidence during the prosecution to show that it was unlikely that Parker was infected by airborne transmission in this way. Although there is general agreement that the source of Parker’s infection was the smallpox virus grown at the Medical School laboratory, how Parker contracted the disease remains unknown.
          ——-
          https://en.wikipedia.org/wiki/1978_smallpox_outbreak_in_the_United_Kingdom

          • gothamette says:

            Wow. We’re talking past one another – I was referring to this. I didnt’ know about the British case.

            https://www.cnn.com/2014/07/11/health/smallpox-found-nih-alive/index.html

            • Frau Katze says:

              I know. But my original statement was asking about the case that resulted in someone dying of smallpox. I was lazy, I should have looked it up then and there.

              I don’t recall the NIH case but it sounds alarming.

              I can’t imagine working in a place where there might be loose smallpox lying around.

              • gothamette says:

                No problem.

                It is alarming that in two labs, one in US, one in UK, live smallpox was dealt with so carelessly.

                Makes it more plausible that this SARS2 virus was inadvertently released from that lab…

                I’m suspicious of it because it sounds a little too convenient. Trump and his press flacks (and yes I am aware that the story was first floated in the anti-Trump WaPo, but governments and journalists play a complicated game) want to deflect from his miserable performance.

                OTOH, it could be true.

            • Frau Katze says:

              “ It is alarming that in two labs, one in US, one in UK, live smallpox was dealt with so carelessly. Makes it more plausible that this SARS2 virus was inadvertently released from that lab…”

              Good point. And SARS2 is way less dangerous than smallpox. Conditions wouldn’t have to be so tight.

              Part of the problem of SARS2 is that it’s so new.

              But I’ve never paid much attention to regular flu, and that is apparently different every year too. I’m sure I got the 2009 version but I didn’t think of it as serious, although it took 3 weeks to get back to work.

              The 2009 version didn’t cause the same furor, Was the just because most people got flu shots?

  28. Rob says:

    Cochran, I was thinking about passaging to create live attenuated vaccines, and I found a paper that modeled virus interactions with the innate and adaptive immune systems in the context of attenuation for vaccines. They modeled several interaction terms to try to find ways that a virus could interact with innate and adaptive immunity to find the sweet spots of reducing pathogenicity while leaving the end magnitude of the adaptive immune response increased or unchanged. They found “unintuitive” relationships that could be rationally altered in attenuation to make safer, more effective vaccines. I’ll leave a link, because I can’t make a meaningful summary without just quoting big chunks, because they’re parameters to differential equations.

    “Using directed attenuation to enhance vaccine immunity” Antia, Ahmed, and Bull. 2020.
    https://www.biorxiv.org/content/10.1101/2020.03.22.002188v1

    While the paper was about live attenuated vaccines, it struck me that it could apply to why some diseases appear to get milder. Beyond the ‘well, people used to get German measles and smallpox, and now we just get colds and flus, so obviously infections are getting milder.’ But ‘cowpox’ (prolly horsepox) was passages hundreds or thousands of times, sometimes from one person’s arm to the next person’s arm after causing a sore without significantly(?) increasing in virulence or reducing immunity to smallpox. Sure, pox viruses have dsDNA genomes and relatively low mutation rates, but a huge chunk of the genome is dedicated to manipulating host immunity. Maybe the eons of passaging in horses left all those immunity-influencing genes adapted to manipulating a different host. Maybe that’s why so many live attenuated vaccines cause decent immunity. Possibly passaging viruses in other hosts or cultures causes adaptation to their slightly different interferons, toll-like receptors, adaptor proteins, etc, not just genome replication.

    It seems that genomic manipulation could help us attenuate by passaging in genetically modified hosts. Knocking enough mouse genes out and human genes in order to grow p falciparum in mice is probably too tall an order for the foreseable future (maybe), but knocking out all the toll-like receptors, myd88, and trif, along with other PAMP sensors (in separate experiments run in parallel) in human cell culture would be a good start for attenuating viruses when we don’t know what all the polypeptides do. Like if, say, nsp10 of SARS-CoV-2 accumulates lots of errors in an interferon knockout line, but not in a TLR9 knockout line, then maybe that protein is involved in regulating the interferon response. Maybe knock all those receptors out of a mouse (assuming it’s viable) and knocking in human furin and cox2 proteins, and the virus will grow in mice. Then we wouldn’t have to use a mouse coronavirus as a model with iffy transferability to covid19. We could use SARS2 and be well on the way to an attenuated vaccine.

    Oh yeah. Saponin adjuvant is used in some veterinary vaccines and causes Th1 and CTL responses to subunit antigens or killed pathogens, so we could maybe even do a non live-attenuated coronavirus vaccine without inducing Th2 hypersensitivity. The adjuvant would have to be approved for people, though.

    • R49 says:

      Can’t you be a bit more polite to our host, instead of just “Cochran,”? There is “Hello Greg”, or “Dear Mr. Cochran”, and so on.

      • dearieme says:

        Please note that if Rob is a ninety-five year old who has served as an army officer then “Cochran” is polite. Or polite enough. At least he didn’t spell it “Cochrane”.

      • Rob says:

        Well, I believe ‘Dr. Cochran’ would be the more polite form. But I can try that, or ‘my nigga’, or ‘hey boo’. Whichever you think is best.

  29. tc says:

    Michael Mina, Harvard epidemiologist and someone who has been involved in the testing effort since the beginning, seems to be edging towards the “more widespread than thought” position.

    • tc says:

      Serological study of Santa Clara county by Stanford guys, including Ioannidis, is out. Estimates a lot more cases than were detected by PCR.

      https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1

      “Under the three scenarios for test performance characteristics, the population prevalence of COVID-19 in Santa Clara ranged from 2.49% (95CI 1.80-3.17%) to 4.16% (2.58-5.70%). These prevalence estimates represent a range between 48,000 and 81,000 people infected in Santa Clara County by early April, 50-85-fold more than the number of confirmed cases. Conclusions The population prevalence of SARS-CoV-2 antibodies in Santa Clara County implies that the infection is much more widespread than indicated by the number of confirmed cases.”

      • Craken says:

        I very much doubt the reliability of the Santa Clara study.
        The participants are probably not a representative sample. The authors solicited volunteers via Facebook. How many of their volunteers were seeking a quick test because they suspected prior infection? It wouldn’t take many with that motivation to badly skew the results.
        Another problem is that the test’s specificity range is 98.3-99.9% according to the study authors. But the positive rate on the Santa Clara test group was only 1.5%–lower than the maximum rate of false positives.
        This fellow goes into far more detail on these points and others:
        View at Medium.com

        • An interested reader says:

          The criticisms re sampling and test calibration are well taken.

          People are finally getting their hands on serological tests – and all they can figure out to do is run these uninterpretable convenience samples.

          SCAN (Seattle/King County) has the same problem, their “working to mirror the area’s population as closely as possible” language notwithstanding.

          My kingdom for a decent-sized, randomized population survey…

        • Frau Katze says:

          Self selected groups are generally verboten for statistical accuracy.

          • gothamette says:

            I’ve read that they got a lot of ppl who wanted to be tested because they had symptoms, and a lot of Asian Silicon Valley folks recruited friends via social media. Not a random sample.

    • gothamette says:

      He’s not taking into account the demographics limitations of the NEJM pregnant women study.

      We still don’t know how many are infected.

      But why can’t Arguably Wrong do another simulation, based on 100 infected in NYC area around Feb 1? (That’s the number I recall from somewhere – don’t ask me to cite a link because I won’t be able to.)

  30. John Massey says:

    https://www.pnas.org/content/early/2020/04/07/2004999117

    For those who have trouble with reading comprehension, this is not the theory put forward earlier by Chinese scientists of two strains, which they labeled S and L.

    Watch for the next paper from Forster et al., which will suggest that the origin could have been in southern China as early as September 2019. By origin they mean when it mutated into a form that could be harmful to humans, so I guess they mean the location and timing of the index patient. It could have been circulating in humans or some other animal for a long time before that. By southern China, they do not mean Wuhan, which is in central China (for those whose world geography might not be their strongest subject).

    The Cambridge (UK) group are not lightweights, so I venture to suggest that people can probably quit fixating on a lab release in Wuhan – but only if they want to, obviously.

    • gothamette says:

      Not my usual reading, but I did note this:

      “There are two subclusters of A which are distinguished by the synonymous mutation T29095C. In the T-allele subcluster, four Chinese individuals (from the southern coastal Chinese province of Guangdong) carry the ancestral genome, while three Japanese and two American patients differ from it by a number of mutations. These American patients are reported to have had a history of residence in the presumed source of the outbreak in Wuhan.”

    • John Massey says:

      “If I am pressed for an answer, I would say the original spread started more likely in southern China than in Wuhan,” said Cambridge geneticist Peter Forster, adding that concrete proof “can only come from analyzing more bats.”

      • gothamette says:

        I downloaded the paper – I’ll give a link later.

        Unsurprising confession: it’s beyond my pay grade. Forster said somewhere that the virus originated no earlier than 13 September and no later than 7 December.

        He’s a geneticist who came up with a model, and as we know, “all are wrong, some are useful.” I learned that here.

        But to me this is something like smoking. There’s never an end to what we can learn about how smoking damages your body, down to the very genetic structure. But even before we knew about genes, cigs were called “coffin pegs.”

        It would be rather strange for a virus to circulate for months in Europe, in the US, Australia, and somehow explode like a bomb in Wuhan w/o something weird going on in Wuhan. Did the virus hate Wuhan?

    • Frau Katze says:

      These the people who used a self selected sample. Right there, with me knowing little about biology but something about statistics, I’m ready to write them off.

      Random sample must be the start of any argument based on statistics.

  31. Anonymous says:

    Podcast update soon?

  32. gothamette says:

    How do people get infected?

    “When an infected person expels virus-laden droplets and someone else inhales them, the novel coronavirus, called SARS-CoV-2, enters the nose and throat”

    This may be the best way to get infected, but it’s not the only way that at least 123K people (those are confirmed cases in NYC, I realize it’s more) got infected in 3 months.

    https://www.sciencemag.org/news/2020/04/how-does-coronavirus-kill-clinicians-trace-ferocious-rampage-through-body-brain-toes#

  33. kpkinsunnyphiladelphia says:

    Hey, Greg, the “insane” John P. Ionnadis has co-authored a medRxiv prepint on a Wuhan statistical study done of seroprevalence in the population of Santa Clara County.

    https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1

    “If our estimates of 48,000-81,000 infections represent the cumulative total on April 1, and we project deaths to April 22 (a 3 week lag from time of infection to death), we estimate about 100 deaths in the county. A hundred deaths out of 48,000-81,000 infections corresponds to an infection fatality rate of 0.12-0.2%.”

    Enjoy!!

    • gothamette says:

      I’ve asked Greg to analyze it, and put a link to a criticism on Arguably Wrong’s blog. Even I can see the problems.

      • An interested reader says:

        At this point it’s not worth Greg’s time. It’s been demolished quite thoroughly by others. Latest to weigh in is Andrew Gelman:

        https://statmodeling.stat.columbia.edu/2020/04/19/fatal-flaws-in-stanford-study-of-coronavirus-prevalence/

        • gothamette says:

          Thanks – Gelman murdered it.

          So why does Ioannidis have such a reputation?

          • John Massey says:

            Going purely from memory, and stating it as simply as I can, he showed that the findings of 70% of medical association studies subsequently turn out to be false, and why.

            This turned him into a kind of public hero, because suddenly people could understand why they keep seeing conflicting headlines about what is claimed to be good or bad for health. “Coffee is bad for you.” “No, coffee is good for you.” “Well, only if you drink 3 cups/day or less.” “No, it’s OK to drink as much coffee as you like.” That sort of thing, endlessly back and forth.

            Unfortunately, he has now evidently reached his level of incompetence, as demonstrated by numerous people who have now discredited the Santa Clara preprint. That is putting it as charitably as I can, and preferring not to impute some unethical motive.

          • An interested reader says:

            Because he’s written some usefully thought-provoking stuff in the past, calling attention to systematic, deep-rooted defects in how biomedical science has been done. That sensitivity to methodologic flaws has made the current episode all the stranger for those of us who have followed his work.

    • I was working on a post, and decided it wasn’t worth my time. It’s nuts; he’s making simple statistical errors.

      • An interested reader says:

        Still more:

        • Yup. You can see some quick pass Bayesian sensitivity/selectivity estimates from their training data here: https://twitter.com/arguablywrong/status/1251365286885781504

          That paper was so bad that either:
          1) The primary authors are morons. Surprising, but dementia is a thing.
          2) The primary authors are highly motivated to get a low infection fatality rate. Why? Well, lucre or wishful thinking would be my bet.

          • An interested reader says:

            Gelman dug into the authorship:

            “The first author of the paper is a professor of medicine—I think that means he’s a doctor, not an epidemiologist. His graduate degrees are an MD and a masters in health services. The second author is a medical student with a masters in economics and a masters in public health. The third author has a PhD in policy analysis. The fourth author is a medical student with a masters in health policy. The fifth author is a medical student with a masters in epidemiology. The sixth author is a medical student. The seventh author is a medical student. The eighth author is a medical student. The ninth author . . . I don’t see his training on the web. He works for a nonprofit called Health Education is Power, Inc. I doubt he’s an epidemiologist but I can’t be sure. The tenth author runs a company that does lab tests. The eleventh author is a psychiatrist. The twelfth author is a biologist. The thirteenth author has a PhD in pharmaceutical sciences. The fourteenth author has a PhD in medical science and is an expert on blood doping. The fifteenth author is a masters student in epidemiology and clinical research. The sixteenth author has an MD but he’s been a professor of epidemiology. The seventeenth author has an MD and a PhD in economics.”

            https://statmodeling.stat.columbia.edu/2020/04/19/fatal-flaws-in-stanford-study-of-coronavirus-prevalence/#comment-1307481

            I hasten to add that author credentials are neither necessary nor sufficient for validity – either the work was done competently or it wasn’t. But this looks awfully like negligent supervision of a large group of trainees and amateurs (relative to this kind of analysis).

            • An interested reader says:

              OK, I’d missed this angle – read on for a JetBlue (!) connection:

              https://www.dailywire.com/news/neeleman-stanford-professors-coronavirus-study-could-be-game-changer

              • gothamette says:

                Thanks for that link. Dated April 7.

                Why is this so important for all of us searching for a ray of hope amid the dire predictions? As of today, the US is approaching 400,000 confirmed cases of the COVID-19 virus and, tragically, more than 10,000 deaths.

                April 22, 2020:

                Coronavirus Cases:
                819,321
                Deaths:
                45,356

                https://www.worldometers.info/coronavirus/country/us/

                Yeah. Some people have a lot of economic incentive to put lipstick on this wild hog.

            • gothamette says:

              Here’s a statistic I just came across.

              On March 20, the death toll in the United States was 225. By April 20, the coronavirus had killed more than 42,000 Americans.

              • Tim Burr says:

                Only 5 million short of the hysterical predictions. LOL
                But it has definitely killed almost as many as a regular flu season. Mind, you, nowhere near as many as a bad flu season.

                Of course, the typical victim – an obese 70 year old guy who spent time in bathhouses and is recovering from chemotherapy – might have died WITH the virus, not so much because of it.

              • gcochran9 says:

                I can’t think of any reason to put up with this guy. Does anyone speak for him?

              • gothamette says:

                I’d be interested if Arguably Wrong would do a model of how many would have died if we hadn’t adopted the mitigation practices that idiots like Tim Burr mocked and jeered.

                Burr is what my dad used to call “a real bum.”

              • Frau Katze says:

                @gcochran9 He illustrates the dilemma of taking a certain action to forestall a bad outcome. If it works, you can never prove your actions made the difference. A certain subset of the population will always believe your actions made no difference and it would have turned out just fine without them.

                Sarcastic comments free of charge.

                Furthermore: find a flu season that killed substantial numbers of residents of any care home it found. Or when was the UK PM or other prominent politician put into intensive care at age 55 by the flu? Prince Charles managed to survive at home.

              • gothamette says:

                Or, do nurses & doctors have to get dressed for germ warfare when they treat flu patients?

              • Tim Burr says:

                Frau Katze, more than half the planet didn’t take any serious precautions, we have comparisons all over the place. Pointing to single incidences here and there don’t prove anything.

                You people have engaged in childish name calling from the start when someone tried to sober you up. You have all succumbed to some bizarre neurotic groupthink. There’s no sign of self-reflection by any of you over how wrong you were from the start or the damage you’ve done to other people’s lives.

              • gothamette says:

                @FK:

                Don’t feed the troll.

                They never answer with any specificity (“we have comparisons all over the place”) and they always say: You did it first!

                The world has moved on, and so should we. All this little worm has is an unmoderated blog to spout off on.

                49,963 deaths so far in the US. And it isn’t even flu season!

                Which brings up another question. If the virus is still lurking around by next October, what will happen? Coinfections? Flu PLUS COVID19?

              • Frau Katze says:

                @Tim So what exactly your theory? That this just another flu, maybe bit worse than average? How do you account for the excess deaths (on this page, you can find excess deaths for New York City and the UK. The numbers are large. If it’s so benign, why is it killing so many people?

                Your nasty comment “Of course, the typical victim – an obese 70 year old guy who spent time in bathhouses and is recovering from chemotherapy – might have died WITH the virus, not so much because of it.” sounds like you’re quite happy to see anyone over a certain age culled.

  34. Frau Katze says:

    You don’t need to watch the whole vid. It’s an interview with ER doctor from “Reason”, a channel that usually attracts somewhat intelligent viewers.

    The comments are full of angry and dismissive people. There’s real hostility there. Calling it a “scamdemic” is one example. I have never seen any of their vids attract this reaction.

  35. dave chamberlin says:

    Good news. My earlier concern about a very high mortality rate in the heart of Europe appears to be wrong. Watch the first 5 minutes of the following John Campbell Youtube video to see why. https://www.youtube.com/watch?v=2w7F_hzqIhM . We are all interested in the actual number of people have been exposed to Covid19, have showed little to no symptoms and now have built up antibodies. We can’t trust the data yet for statistical accuracy, we need a large sample size of random people who did not self select because they were suspicious that they had Covid19. The Netherlands tested 10,000 people that donated blood for Covid19 antibodies. 3% of that group have antibodies, which translates to a half million people if blood doners are representative of the nation. So instead of a fearsome 11.2% mortality rate it drops 15 fold to .066% mortality rate.

    Well alright. People keep squawking we need more testing before we can ease off the social distancing and they absolutely should keep insisting on it. This shows why. Put a flashlight on more of these pervasive studies and we will finally know the infection rate of the general population. Then and only then can knowledgable decisions be made.

    • dave chamberlin says:

      I will throw my two cents into the modeling projections that uses the assumption of a .066 % mortality rate. Which is good news however here comes the bad news. Covid19 is a combination of highly infectious and very sneaky, the vast majority being asymptomatic combined with a widely distributed vaccine being appoximately a year away a 70% infection rate for our 330 million United States is what I would guess at this time. What did that influential IMHE https://covid19.healthdata.org/united-states-of-america study project? 60,000 with a range of 38,000 to 140,000. I am predicting just a smidge higher, 1.5 million and I might add this IMHE projection that everyone else takes seriously is pure horseshit. I mean come May 1st we shall be flying by the 50,000 dead number so the bottom end of the range is already stupidly ignorant.

      Now IF we behave like the Chinese citizens did yes we can do what they did and reduce the mortality rate to near zero. Are we? Nope, ain’t happening. We will go back to work and the old farts will keep dropping until a large enough percentage of the population is infected that the virus stops spreading. But as our fearless orange leader has said maybe one day just like magic this virus will disappear. Could happen but then again a ten mile across rock could blast us into extinction too. Who knows, I don’t, my guess could change next week and it probably will with new information.

    • swampr says:

      Interesting. You mean .66%, not .066% right? The only way to square the results of some of these antibody tests with the death totals in NYC or Bergamo Province is to assume most people there have been infected. I’m aware of the tests of birthing women (15% positive) in NYC, but that was women who had ongoing infections. Many would have cleared already it or got infected later in the study period.

      • dave chamberlin says:

        Yes, two thirds of one percent is what I meant to say.

      • dave chamberlin says:

        Random antibody testing is rolling out in Germany and New York this week. This is what we need to determine the denominator in the mortality percentage. I do not not know what percentage of the population will be infected but I am guessing 70%, it could be far lower.

        • dave chamberlin says:

          That is not clear at all. What I meant to say is I am guessing 70% of the population will be infected before a vaccine is made available. Right now a very small percentage of the population has been exposed, much higher in New York City than anywhere else in the country.

          • gothamette says:

            I would love to be tested except…. I understand they have to stick that nasal swab WAY back, and that not doing so is resulting in some false negatives.

    • John Massey says:

      Read above. You are a little late to the party.

    • gothamette says:

      Have to admit, he’s making a lot of sense here.

      • gothamette says:

        On 2nd thought, he’s making some obvious points about getting infected in hospital, which is clearly a factor, but the rest of what he says is either obvious or not relevant.

        And his Santa Clara county study was crap. Read Andrew Gelman.

    • gothamette says:

      Ioannidis says something that sounds right but probably isn’t. People are exhibiting what the docs call “care-seeking behavior” and they go to the hospital – and get sick there. Maybe some of that happened early on, I don’t know. But I do know that we in NYC were strictly advised NOT to go to the hospital unless we were symptomatic.

      Now an article comes out in the NY Times which says that this accounts for why so many come to the hospital already half dead with pneumonia. Because they aren’t going to the hospital early enough. So I don’t buy his reasoning.

      • Frau Katze says:

        Quote:
        “ Even patients without respiratory complaints had Covid pneumonia. The patient stabbed in the shoulder, whom we X-rayed because we worried he had a collapsed lung, actually had Covid pneumonia. In patients on whom we did CT scans because they were injured in falls, we coincidentally found Covid pneumonia. Elderly patients who had passed out for unknown reasons and a number of diabetic patients were found to have it.”

  36. Frau Katze says:

    Possibly of relevance: NYT has written a huge attack on “far right” Youtube channels.

    They’ve seized on the rather eccentric Stefan Molyneux. But the reasoning! It’s is partly because he is a believer in “race realism.”

    Mind you, in the previous attack, the reporters never got around to print blogs. Even a site as odd at the Unz Review was ignored. Too much stuff to read.

  37. John Massey says:

    Patient-derived mutations impact pathogenicity of SARS-CoV-2.
    https://www.medrxiv.org/content/10.1101/2020.04.14.20060160v1

    They only sampled 11 patients, but this could turn out to be very important.

    Incidentally, Li Lanjuan was the first scientist who suggested that Wuhan should be completely locked down, with no one in or out.

  38. Eponymous says:

    Greg: Will you have another podcast soon?

  39. Frau Katze says:

    At the Financial Times, they’ve got an estimate of Covid deaths based on excess deaths. Official figure is 17,337 Covid deaths for the UK. Their estimate is about 41,000.

    There were 18,516 deaths registered for week ending April 10 (England and Wales). Previous 5 year average was 10,520. Similiar pattern in Scotland and Northern Ireland.

    https://www.ft.com/content/67e6a4ee-3d05-43bc-ba03-e239799fa6ab

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s