We shouldn’t worry when a virus mutates during disease outbreaks

So says a remarkably stupid article in Nature.  Of course we should.

I have at least ten readers that can explain why.

 

 

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310 Responses to We shouldn’t worry when a virus mutates during disease outbreaks

  1. Polymath says:

    In the very long run, pathogens tend to mutate to become less virulent so their hosts are able to pass them on for longer, while pathogens that mutate in the other direction burn through the host population and are more likely to die out eventually.

    But in between, there’s that “burn through the host population” bit that you don’t want to be in the middle of, so it’s not reassuring.

    • Isolation is a revolutionary act says:

      They evolve to forego burning through us only if we kowtow in submission to their use of our bodies as replicator-vehicles and as slaves transporting them to their next victims as we betray our own kind over and over again.

    • Coagulopath says:

      And things get complicated when the disease transmits person-to-surface-to-person (or person-to-reservoir-to-person), instead of just person-to-person.

      Cholera never needed to be mild. Infected patients produce lots of waste, and someone has to clean it away.

    • Space Ghost says:

      In the very long run, pathogens tend to mutate to become less virulent so their hosts are able to pass them on for longer

      We’ve been over this. Smallpox has been around for at least 2,000 years and has a 30% fatality rate.

    • ha1597 says:

      In the very long run, pathogens tend to mutate to become less virulent

      They also tend to mutate into forms that are resistant to the drugs being used to prevent them (i.e. they, in effect, also tend to become MORE virulent in the long run).

      in the case of AIDS, doctors eventually managed to find a cocktail of orthogonal treatments that each attacked HIV in a different way, which meant that lightning would have to strike several times simultaneously in order for the virus to become resistant to all those treatments at once. But that took a long time.

  2. Frau Katze says:

    Is it not just as simple: it might mutate into something worse.

    Plus it will be harder to create a vaccine for a virus that mutates a lot. Consider the common flu. They need a new one every year.

      • Frau Katze says:

        His nickname is Dr Bad News. Yes, he correct that we need to get the percent exposed (and hopefully immune) up to 60%. That sounds worse than it might be. If all the young people get it that would be a lot.

        I hope we can get a situation where the elderly and vulnerable youths are shielded. Now that’s one thing for me or an older married couple living alone. It’s doable. And not many seniors of European descent live with their kids.

        Some cultures are different. And there are some young people with comorbids. Not sure what can be done but we need to do something fairly quickly or the whole economy will collapse.

        • gothamette says:

          As predicted, the deniers are using the infection rates as evidence that this is no worse than flu.

          It’s ridiculous because if the IFR is Bergamo level (half a percent, or NYC level – possibly 1%) then we are screwed.

          • Frau Katze says:

            The deniers can’t be reached. The success of the lockdowns is seen worldwide. So we flattened the curve and now we have to get the economy moving.

            It’s hard to prove a counter factual.

            Suppose that during WW2 by some means the Allies had been able to stop Hitler from his killing agenda. Then people would just say he never had such an agenda at all.

            • gothamette says:

              They still say it. They still deny it.

            • gcochran9 says:

              I could reach any of them.

              • saintonge235 says:

                Well yeah, but cutting their throats will get you talked about in polite society.

              • gothamette says:

                “Viruses don’t often switch species…” So far this damn virus has infected bats, humans, ferrets, an unknown possible intermediary species, felines big & small, and now minks.

                https://www.corona24.news/c/2020/04/26/covid-19-detected-at-two-mink-farms-news-item.html

                WTF?

              • John Massey says:

                And dogs.

              • gothamette says:

                I actually had an intelligent thought last night. It was so remarkable I remembered it.

                This virus seems to switch among species with rather remarkable ease.

                So…. it may well have been percolating among any number of species in Guangdong or Hubei for months. Is there a way to tell how old a virus is by analyzing its genome?

                OTOH, there would be the lab-created theory. Create an all-purpose virus that readily infects lots of species… it would be a very useful virus, no? I’m not suggesting that eevil scientists created it to kill people. Just as a research tool.

                View at Medium.com

                Finally, there is this lady, whose life has been made a misery by those wonderful guys who brought you this virus, whether natural or man-made:

                https://www.cnn.com/2020/04/27/tech/coronavirus-conspiracy-theory/index.html

              • John Massey says:

                But it infects felines more easily than canines, and sickens them more; the few dogs which are known to have been infected had only mild symptoms.

                I think the default assumption should be that it can infect all mammals, but the effects on them will range from asymptomatic to severely ill (it doesn’t seem to do macaques much good). By now it has probably passed through many millions of rats, which is not a good thought.

              • gothamette says:

                The article by Yuri Deigin, whether right or wrong, is nicely descriptive for amateurs like me.

                “The spike protein also determines which animals the virus can or cannot infect, as ACE2 receptors (or other targets for other viruses) in different species can differ in structure.”

                I wonder how many other species this thing can infect, which it hasn’t yet, because it hasn’t had the opportunity? It’s an all-purpose utility player of a virus.

              • gothamette says:

                In baseball, there is a utility player – the guy who can play a variety of fielding positions. This virus is the utility player of pathogens.

              • gothamette says:

                In short, what we don’t know about this virus far outweighs what we do know. Because it’s novel, duh.

                I guess we’ll find out what a novel virus does in the states that are lifting the lockdowns prematurely. And Sweden. The side of me that likes watching trainwrecks is morbidly fascinated with this.

  3. lg says:

    no guarantee a virus will mutate to less aggressive forms, by replication through humans it can just as easily mutate to be more infectious. plenty of historical examples.

  4. I’m guessing this is the article you’re referring to: https://www.nature.com/articles/s41564-020-0690-4.pdf?proof=true1 From mid-February, by two Yalies and an Aussie.

    Couple of points:

    For a fast-spreading pathogen like this one, you can use something like the Born-Oppenheimer approximation. The human genome won’t evolve to respond to Wuflu in the next year; the virus can evolve without dealing with backpressure.

    They point to a couple of historical examples of epidemics where known mutations that increased virulence occurred. E.g., Zika (couple of million cases, vector-transmitted) had a variant that probably increased virulence before the 2015 epidemic in the Americas. SARS1.0 (8000 cases, respiratory transmission) had some big changes early on that suggested adaptation to humans. A single mutation in Ebola (~30000 cases, fluid transmission) increases infectivity in humans. They’re trying to argue that because we’ve had multiple diseases where a key mutation preceded an epidemic that then got controlled, we can’t have a key mutation in the middle of an epidemic that makes it worse. But there’s no reason why, it’s just asserted.

    Epidemic size and shape matters. More cases, and the higher number of passages through human hosts, the more likely you are to get mutations that cause problems. Fisherian acceleration of evolution. The 8000 cases of SARS1 gave a lot fewer opportunities to evolve than the millions of cases of SARS2. The longer the chain is, the worse as well – if everyone on earth had simultaneously gotten infected with the very first strain, there would have been no adaptation to human hosts.

    As they correctly say, most viral mutations will be worthless or bad for the virus, and the mutation rate is enormous for these RNA viruses. But most isn’t all, and for a respiratory virus like this, we know that the initial virus introduction to a patient was of a successful, infectious virus, and growth inside each patient will rapidly select out any utterly broken viruses (e.g., those that can’t infect other cells). So strains with higher infectivity/transmission rates will start to dominate as they spread faster. That’s especially true in somewhere like NYC where spread is already rapid. Rapid spread is worse in itself because it means more people will end up with this before the epidemic dies out.

    As far as damage or lethality, I don’t see how it comes into this disease much. There’s a high # of pre- or a-symptomatic cases, and my reading suggests that (outside of healthcare workers in hospitals) most infections are from people who aren’t showing serious symptoms. So a mutation that, say, increases the danger of the critical phase of the virus, or pushes more people into the critical phase, isn’t going to have much impact on transmission.

    You also have the concern that you get a mutation that disrupts previous immunities. Any such mutation wouldn’t have much impact now, but during the downphase of the epidemic it would be rapidly selected for. So take NYC, where ~20-25% of the population has this. What happens if, in a couple months when they’re overshooting past herd immunity, we get a virus there that can reinfect old patients? It’ll get selected for, because it’ll have ~4x the susceptible population to work with.

    • Kyle Rowland says:

      “So a mutation that, say, increases the danger of the critical phase of the virus, or pushes more people into the critical phase, isn’t going to have much impact on transmission.”

      If the virus could costlessly make you live forever, it would. However, rapid replication using a host’s cells is inherently damaging.

      Say a mutation makes the virus render you immobile 20% faster, but increases viral shedding causing 30% more infections per unit time: favored.

      Nature has shown us a spectacular variety of successful long term strategies by pathogens. Some involve an awful lot of killing. Best to minimize how much surface area you present to this kind of process.

    • Coagulopath says:

      You also have the concern that you get a mutation that disrupts previous immunities.

      This was my thought, too. Isn’t the great hope for the Flatten the Curve crowd that eventually 40% of the population have antibodies to the disease, and traditional herd immunity math comes into play?

      And doesn’t a new strain of the virus almost set us back to square one, even if SARS-COV-3 is no more dangerous than SARS-COV-2?

      Also, why is it formatted like a scientific study (with three co-authors) when it’s basically a blog post?

      • saintonge235 says:

        #QuestionAskedAndAnswered dept.:

        “Why is it formatted like a scientific study (with three co-authors) when it’s basically a blog post?”

        Because people trying to sell you a bill of goods always try to make what they say resemble authoritative pronouncements that you can depend on.

        #SurpisedIHaveToPointThisOut

        #NextQuestionPlease

    • gcochran9 says:

      That’s the one: I screwed up the link. Fixed now.

    • gcochran9 says:

      I sure as hell hope that it doesn’t materially change the human genome in the next year.

      Their argument for why it couldn’t happen in the middle of an epidemic would work better as an argument why it’s likely.

      Then there’s the 1918 flu: the last comparable epidemic faced, and it did indeed change – for the worse – right in the middle of the epidemic.

      The authors have of course never heard of Fisherian acceleration.

      • It strikes me that the approach we seem to have settled on — get the R0 down to ~1 but not much lower — is suboptimal not just because it will drag out the epidemic and its attendant economic damage as long as possible, but because it provides optimal conditions for malignant evolution of the virus. R0 of 1 means maximum number of passages and opportunities for compounding mutations.

        • ha1597 says:

          It strikes me that the approach we seem to have settled on…is suboptimal not just because it will drag out the epidemic

          For a novel virus, dragging out the epidemic is a wise policy — at least, initially. That gives doctors time to figure out which treatments work best. The supply chains are then able to be rerouted so that no one has to scramble or get scalped in order to get masks, gloves, sanitizers, HCQ, etc. Tests can also be made available so that doctors at least know what it is they’re treating.

          All that takes time. Admittedly, flattening the curve is a costly endeavor, and at some point we reach a stage of diminishing returns. But assuming I haven’t been exposed already, I’d rather catch this thing today than two or three months ago when doctors had no clue as to what it could do or even whether someone had it, or when nurses were scrambling for masks and gloves.

          • The correct approach would have been to suppress the epidemic as strongly as possible as early as possible, and then kept it suppressed using methods that are too expensive or difficult to use on large epidemics.

            Personally, I’d rather not catch this thing at all. That was on the table back in February.

            • Dmon says:

              If the virus mutates into a more virulent form, doesn’t that essentially put us back in February with respect to the mutation? As long as we seize the opportunity to test and quarantine for the mutated virus?

              • gcochran9 says:

                Not necessarily. The more-severe version of the 1918 flu was antigenically similar to the earlier version, enough so that contracting it protected you against the later, more dangerous version.

            • saintonge235 says:

              You’re right that suppressing the epidemic would have been the correct approach, but how could that have been done?

              Answer: By saying, in early January: ‘The Chinks are hiding the truth, so we have to assume human-to-human transmission takes place, and is rapid.’

              Instead, the CDC jerked off till February 26th before bringing themselves to admit that there was evidence of human-to-human transmission in the U.S. Saying the Commies were lying as they always do would have been politically incorrect. Taking action on the basis they were lying would have been politically impossible.

              A CNN story just out says the first U.S. death was on February 6th, and that it indicates the virus was circulating in the U.S. by mid-to-late-January (January 16th to 23rd, approximately). I made Facebook posts coming to the same conclusion, based on observed rates of spread.

            • Yes, thank you. A stitch in time, …etc. Somehow this point gets lost. UK planning seems based on an open legs approach, that the virus will come and get us so there is nothing we can do about it, nothing polite, anyway.

        • gothamette says:

          That’s what Osterholm is saying.

    • gothamette says:

      You def have to watch the Osterholm interview I linked to, above.

    • saintonge235 says:

      As Kyle says, you’re wrong about lethality.

      Most viruses, afaik, work by reproducing inside the cell till it bursts. BURSTING THE CELL KILLS IT. The faster the virus reproduces, the faster it kills cells. The more cells it kills per unit time, the more likely it is to kill the host.

      If fast reproduction lowers the rate of infection in new hosts, it will be selected against. If it raises that rate, it will be selected for. And it will be more lethal.

      Read any history of lethal epidemics, and you see this. A new disease getting loose in a population quite often gets more lethal quickly.

      • saintonge235 says:

        Turns out I was wrong here about the #CCPVirus. The cell actively expels the virions via the Golgi apparatus. But that in turn let’s the virions spread through the body more quickly, and out of the body more quickly. A greater number of infected cells seems to increase the death rate for humans, and increase the spread of the disease.

        It keeps coming back to ‘the faster the virus spreads, the more likely it is to be lethal’, as far as I can tell. This certainly fits with what is observed historically.

    • gothamette says:

      Esp for AR & Greg, NY finally has some official numbers. I got this yesterday:

      https://www.governor.ny.gov/news/amid-ongoing-covid-19-pandemic-governor-cuomo-announces-results-completed-antibody-testing

      NYC is nearly 20%, in line w/previous findings. But I’d love to drill deeper into boroughs and even zip codes. It’s not possible that Manhattan has as many infected as parts of Queens and Bronx. See this:

      https://untappedcities.com/2020/04/28/interactive-map-coronavirus-cases-nyc-zip-code/

      I assume you both speak fluent Github; she links to it.

  5. Frau Katze says:

    Excerpt

    Headlines featuring ‘DNA sleuths’ searching for ‘dangerous mutations’ in the new virus inculcate an expectation that the virus will inevitably mutate to become more deadly1. News reports warning that mutating viruses may spread more rapidly evoke visions of a doomsday scenario in which public health efforts to control the epidemic are rendered futile2.
    Unlike science fiction, however, the dramatization of virus mutation is not innocuous, and we need only look to other recent outbreaks to realize the extent to which overinterpreting the impact of mutation directly affects our health and safety.

    What to make of the millions of natives of the Americas who died of smallpox? Although it does have different strains, some worse than others, smallpox just roared through the unexposed population. It didn’t kill everyone, but from the reports it killed a great many. (Other diseases were waiting in the wings for the unfortunate natives.) Smallpox didn’t mutate to help them. (a DNA virus might be slower to mutate of course.)

    The death of an estimated 90-95% of the natives (spread over the centuries) should make us wary of new viruses.

    • Coagulopath says:

      The story’s a mixture of non-sequiturs (searching for mutations is bad because it might…make the public scared?) and scientific solipsism (nobody can know what mutations will appear, so it’s pointless to even think about).

      It may have gotten published solely because it has a provocative title and references Marvel Comics and The Hot Zone in the lede. They should have sexed it up even more by talking about Trump.

  6. peter y connor says:

    The fact that Nature published such rubbish is much more concerning than its content …

  7. gabriel alberton says:

    Yes, we should very much worry. The reason is simple. If it mutates so that a more contagious strain comes up while other things are kept equal, that strain will overtake the others because it is more contagious. Duh. Less contagious strains will, of course, tend to vanish, because they are less contagious. So if the ”virus is quickly mutating” condition is true and it is widespread as it is now, it is actually likely this will happen. Not as likely as ”total entropy of the Universe will increase over time”, but likely.
    Whether the other strains will be overtaken by a more deadly strain is different. All else kept equal, there is no strong tendency for it to mutate to become more deadly. There is no tendency for it to become less deadly, either, not in the timespan that matters to us. There’s no viral popolice preventing a strain that kills 10% of young infected studs from coming up.

  8. j says:

    This new SARS-2 virus has been working its way through the human species for five-six months, passing through some 10^7 individuals. In this period it has been mutating non stop and we alreay have about 20 variants. None is fitter than the original in Wuhan wild animal market. What is the probability that it will re-invent itself to a more efficient killer till we find a vaccine? Almost none, I think. Of course I can be wrong. Most human viruses just “jumped” readymade from some other mammal. This SARS-2 is 96% the same as SARS-1 and the 4% are fragments of other existing bad virus. Was this substitution spontaneous (most improbable) or was somebody experimenting with it? We shall soon know.

  9. another fred says:

    A few years ago I realized that the primary objective of the mainstream media is to tell us to be calm and don’t panic, that we will live in the best of worlds if we just all love one another and obey the dictats that emanate from the “cathedral”.

    While being calm and not panicking is the best policy (barring a Josey Wales type fight for your life), the “cathedral” is likely to get lots of people killed.

  10. Pingback: Chicago Boyz » Blog Archive » Mutations

  11. Lowe says:

    Greg, total US deaths are ~50k right now. Infections are stable or in decline. There have been antibody tests in a few places, and a large number of people were infected already.

    Even if we don’t consider how old the median person dying is, and how padded these death numbers probably are with people suffering from heart disease, etc, it looks like this is nowhere near the disaster you feared.

    Except the 23% unemployment rate, of course. Are you going to make a post about this? Why don’t you?

    • reader506 says:

      We’re holding Rt to around 1 (maybe) with distancing and shut downs (https://rt.live). There are currently about 870k confirmed cases in the US. That’s 0.26% of the population. Even if we’re off by an order of magnitude on test coverage, we’re still a LONG way from herd immunity. “Stable infections” means the virus will continue to spread (and mutate).

      Meanwhile I’ve seen no solid evidence that IFR will be lower than 0.6%. Bergamo’s PFR was 0.57% (https://www.unz.com/isteve/new-estimate-of-population-fatality-rate-in-bergamo-province-0-57/). Of course IFR is affected by multiple variables like age of population, treatment effectiveness, and virulence of particular strain. But with 98% of the US still not infected, it’s reasonable to guess that there’s plenty of potential for vulnerable populations and virulent strains to hit them.

      Death numbers aren’t padded. Of course there’s some margin of error in classifying deaths, and idiots jump on these anecdotes as proof of over-counting (while ignoring the anecdotal evidence against it). But excess mortality rate analysis tells a very different story. Covid deaths have likely been under-counted.

      • Lowe says:

        They did a study in California and 4% were infected. They did it in New York and it was 21% in the city, although lower in the state overall. So there is evidence the infection rate is at least an order of magnitude greater than what you say.

        Regarding the death numbers being padded, this is clearly true. But say I concede they are legit, whatever. This is still not the disaster that we were warned about. If our shutdown was what made the difference, then why is Sweden not markedly worse off?

        • Frau Katze says:

          Sweden is not doing as well as Canada. Now maybe we could have lived with those numbers too, but stop saying it’s not markedly different:

          Sweden: population: 10.1 million, cases: 16.7 K, deaths: 2 K
          Canada: population: 37.7 million, cases: 43 K, deaths: 2.2 K

          I picked Canada because I live there.

        • Frau Katze says:

          The death rates based on excess deaths are not very padded. It’s down to saying, well maybe a heart attack victim didn’t go to the hospital because of Covid.

          They death rates based on excess deaths is much higher than the Covid death certificate counts in New York City and the UK. The data is in the previous post. I can get it if you want. Two separate calculations.

        • gabriel alberton says:

          ”Regarding the death numbers being padded, this is clearly true.”

          I can almost see it already: if this thing does go on to kill hundreds of thousands in the US (something that may still be prevented), there will be those claiming the deaths are fake. Deathers. Show the death certificates! Those people never existed! etc. More: they will keep saying that regardless of the number of deaths, but they will grow more vocal the more deaths there are (in the US: other countries will be completely ignored one way or the other), like the glutton who grows hungrier the more whoppers he gobbles.

          • Lowe says:

            The irony here is that you describe a hypothetical situation where people, other than you, are ignoring the evidence.

            • gcochran9 says:

              The thing is, he’s right: you’re utterly full of shit.

              • gcochran9 says:

                You can’t get a big increase in the TOTAL death rate by falsely reclassifying deaths. Can you understand that? Not that they’re doing so, by the way.

            • gothamette says:

              It’s not hypothetical in NYC. Do some simple arithmetic. IFR is nearly 1%.

            • gabriel alberton says:

              You there with the Slinky avatar: from where you got your evidence that, nationwide, US daily infections are stable or in decline? Tell me, so we can point it out to the 1point3acres people, as well as to the Johns Hopkins University people, as both counters show daily cases increasing, not decreasing, for the last several days. We could also tell the WHO people, as they show the number of daily confirmed infections in the US going from 24k to 29.1k to 30.7k in the last three days, and the CDC people, who reported an increase from 865k cases to 895k cases last I checked, consistent with the counters.

              Even if one takes the view that it’s all really noisy (it is) and the number of daily cases will soon decrease again (if only because it’s the weekend now), even a sane optimist can see the number of daily infections is holding up. Saying they are maybe really in decline, according to the data there, right now, is using your imagination, seeing what you want to see.

              https://coronavirus.1point3acres.com/en

              https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

              https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports

              If you are one of those who want to open things up, then go for it, but why say things that aren’t so in order to justify it? Oh yea open it up baby open it up

              • gcochran9 says:

                He makes stuff up because the actual facts aren’t sufficiently supportive of his case.

              • saintonge235 says:

                I visit https://www.worldometers.info/coronavirus/country/us/ daily, and look at the prior days totals of cases and deaths. Here’s the info for the last two weeks, from a spreadsheet I keep, cases first.

                Fri, 2020-April-17 709,735 37,154
                Sat, 2020-April-18 738,792 39,014
                Sun, 2020-April-19 764,636 40,575
                Mon, 2020-April-20 792,759 42,514
                Tue, 2020-April-21 818,744 45,318
                Wed, 2020-April-22 854,385 47,894
                Thu, 2020-April-23 886,274 50,234
                Fri, 2020-April-24 925,23 52,191
                Sat, 2020-April-25 960,651 54,256
                Sun, 2020-April-26 987,160 55,412
                Mon, 2020-April-27 1,010,356 56,796
                Tues, 2020-April-28 1,035,765 59,265
                Wed, 2020-April-29 1,064,194 61,655
                Thu, 2020-April-30 1,095,023 63,856

                The rate of increase is dropping, but the cases are deaths are increasing.

          • Frau Katze says:

            That’s exactly what would happen. Repeat of Holocaust deniers.

        • gothamette says:

          I don’t buy the NYC infection rate as 21% – they were checking people in the process of shopping. But let’s say that 15% are infected. That would make an IFR of nearly 1%. You check my the arithmetic. (In Bergamo it’s 6/10 of a percent.)

          When 70% of NYers are infected, won’t the number of deaths in the city alone go up to 40-60 thousand? Is that acceptable to you? It’s not to me.

          How many will die if the country achieves herd immunity at 70% infection? You do the simple arithmetic.

          Look, Lowe, and the rest of the herd immunity herd. Tell us what we do as we approach herd immunity. Give us YOUR numbers. How many will be hospitalized? How do we treat them? How much will this cost? You shriek about what it’s costing us now, but how much will it cost us to treat and hospitalize the hundreds of thousands of cases?

          But we won’t treat them. We’ll just put them in barracks to die. I think that’s what you guys really think we should do.

          • gcochran9 says:

            Total number of excess deaths in NYC is at least 17k.

            • gothamette says:

              Then the IFR is at least 1% in NYC.

              Oh, and this. The IHME has again revised its death projections upward, this time to nearly 68K. Absurdly optimistic.

              • Pincher Martin says:

                “Absurdly optimistic” is understating it.

                Have you seen the back side of the IHME projections? They have daily deaths dropping from over 1,000 deaths on May 1st to just 30 deaths on May 31st. That drop in deaths is just as dramatic as the rise in deaths from mid-March to mid-April.

                Crazily optimistic is more like it.

            • gothamette says:

              20,900, according to the NY Times interactive map today.

            • gothamette says:

              *“My quick take is that something really odd is going on with Ioannidis,” wrote Alexander Rubinsteyn, a geneticist and computational biologist at the University of North Carolina at Chapel Hill, in an email to Undark. Rubinsteyn suggested that Ioannidis may simply be “so attached to being the iconoclast that defies conventional wisdom that he’s unintentionally doing horrible science.”

              He added: “Pretty much no one with statistical acumen believes these studies.”*

              https://undark.org/2020/04/24/john-ioannidis-covid-19-death-rate-critics/

          • Rosenmops says:

            People who say “lets open everything up”….does it occur to them that many, perhaps most, people will stay home anyway? I’m sure as hell not going anywhere no matter what opens up.

            • gothamette says:

              Not gonna get your nails done?

              • Rosenmops says:

                I think I’ll give my nails a miss! But the dogs’ nails—that is another matter. I can stay out in the car at the vet, and they just take the dogs in. But I’m not sure how the hand-over goes. I hope it is not true that dogs can get it. What a horrible thought.

              • John Massey says:

                A few cases of dogs being confirmed to be infected have been noted. In the cases I have read about, the dogs were all thought to have been infected by their owners, not by other dogs or other people. In one certain case I know of in Hong Kong, a Pomeranian tested positive multiple times, and after recovery tested positive for antibodies, proving that it had been infected. But it had very mild symptoms throughout, despite being a very elderly dog (it was 17 years old). There is also no evidence that dogs (or cats) can infect humans (but that sounds familiar – there was no evidence of human to human transmission until there was, and the index patient, whoever that was, must have caught the coronavirus from some other animal, unless it was an accidental laboratory exposure).

            • Frau Katze says:

              I bet a lot of +65s stay home. Or go out a lot less. Avoid crowds.

        • saintonge235 says:

          For every three deaths the U.S. counts from coronavirus, Sweden counts approximately four. According to https://www.telegraph.co.uk/news/2020/04/03/coronavirus-swedish-experiment-could-prove-britain-wrong/, Sweden is distinguishing between deaths ‘with’ coronavirus and deaths ‘by’ coronavirus. It looks like their death rate ratio to ours would go up sharply if the death numbers were counted the same way. Can’t say for sure, though.

          But I can say for sure that Sweden’s health statistics are crappy, assuming Worldometer is reporting them correctly. The new cases and new deaths vary by a factor of four within a few days, bouncing up and down. And the recovery numbers even more artificial. Typically, there are no recoveries reported in Sweden for a five or six days in a row, then the next day over a hundred fifty. These are obviously being reported only about once a week.

          But one thing is clear: every week, the peaks get higher. See https://www.worldometers.info/coronavirus/country/sweden/.

          However Sweden counts them, the deaths per capita have been going up faster than most other countries too. A few weeks ago they were twelfth in the world in deaths per capita, now they are ten or nine.

          As for what Sweden is doing, it is along the same lines as everyone else. Gatherings of more than fifty people are banned, everyone is encouraged to distance and work from home, etc. Being rather more docile than USAmericans, little enforcement is needed. And the measures employed are getting stronger. See https://www.thelocal.se/20200310/timeline-how-the-coronavirus-has-developed-in-sweden and https://www.thelocal.se/20200425/interview-were-working-day-and-night-to-save-jobs-and-that-includes-foreign-workers-isabella-lovin-coronavirus-sweden

          One interesting statistic, though: according to https://www.hstoday.us/subject-matter-areas/counterterrorism/when-religion-and-culture-kill-covid-19-in-the-somali-diaspora-communities-in-sweden/, Sweden’s miniscule Somali community, 0.69% of the population, has 40% of the deaths. And news reports say that the Swedish government’s ‘recommendations’ on social distancing are being ignored by immigrants. So the group in Sweden that doesn’t practice social distancing is 100 times as likely to die as the general population. Gee, that is a bit suggestive, wouldn’t you think?

          So when you ask “why is Sweden not markedly worse off?”, it’s like asking why is Canada now south of Mexico. Sweden is worse off than the U.S., and getting worse off by the day.

        • saintonge235 says:

          “They did a study in California and 4% were infected.”

          They did a study, and 1.5% of the tests turned out positive. For the test used, the rate of false positives is expected to be 0%-2%. On top of that, the sample was probably biased high for suspected #CommieVirus cases from the beginning. So the paper’s results start out worthless. (https://statmodeling.stat.columbia.edu/2020/04/19/fatal-flaws-in-stanford-study-of-coronavirus-prevalence/)

          Then the authors do unexplained mathematical adjustments, and get an infection rate of 2.5%-4.2%. From this one can deduce (Let’s break out the higher math here: 100% – 4.2% = 95.8%) that at best the vast majority hasn’t been exposed yet. Somehow, this ‘proves’ that everything is all right, and no precautions should be taken.

          Man alive, the fundamental irrationality of such posts leaves me #gobsmacked every time.

  12. dearieme says:

    Well, Cochy old boy, I find myself in complete agreement with your “remarkably stupid” description.

    Could it have been written for home-schoolers of primary school children? Then why carry it in Nature? Is there an editorial insider at Nature slyly expressing his contempt for the fall of the standards of that once-great publication? You might as well rant at the decline of the Royal Society: decadence is a natural feature of the life cycle of institutions.

    On Holmesian principles I’m driven to the conclusion that it’s intended for politicians.

  13. Rob says:

    You really think you only have 10 readers who can explain why viruses mutating is bad? You don’t think much of us.

    Let’s say for a particular virus, population, and mode of transmission, there is an optimum (low) death rate from the disease.. Does the virus evolve to hit that rate and stay there? No! There isn’t ‘a’ virus. There are trillions of individual genomes all competing for you, their means of reproduction. A genome that hits on a higher virulence strategy, if that results in more rapid transmission, will be favored even though the population as a whole is harmed. Because group selection is (almost?) always swamped by individual selection.

    So why don’t colds kill you? Because your single-celled ancestors all the way to you, the pinnacle of evolution, the being all this nature red in tooth and claw crap has finally produced, have been under brutal selection to not get killed by infections. They didn’t even do such a great job. Infectious disease still kills huge numbers of people. People with genetic defects in their immune system die of “opporunistic” infections, germs everyone else’s immune system keeps in check because they were selected to survive infections. In nursing homes colds can be deadly. Viral pneumonia is caused by everyday viruses that get out of hand.

    How many genes are involved in innate and adaptive immunity? I don’t even want to guess. 30%? Even very basic housekeeping genes like the elongation factors necessary for protein synthesis are under selection to be capable of being regulated by other proteins that try to shut off protein synthesis in virally infected cells. Those proteins that try to shut them down are also under selection from infectious diseases.

    Lots of us probably carry null mutations in a few antiviral genes, but don’t suffer much from it because we’re heterozygous with a functional copy. Even when we’re homozygous for a null allele, we tend to do okay because there are so many other proteins involved in innate and adaptive immunity. But people who are null for choke point genes, genes the immune system doesn’t function without, like men with Severe Combined Immuno-Deficiency, they have to live in germ-free bubbles, because colds are deadly. But who knows, sequence the genome of everyone who dies of the flu, and there’s a good chance they have very rare alleles for some immunity genes, and very rare almost certainly means broken.

    If SARS-CoV-2 is truly asymptomatic in lots of infected people, in a way that’s good news. In another way, that is very bad news. It means there is a huge amount of headroom for genomes that cause more severe illness to increase in frequency in people, and therefore in the viral population.

    • Frau Katze says:

      What puzzles me is how children get mild to asymptomatic cases. For things like colds and norovirus, the kids get the same symptoms as the adults. I can’t seem to recall how my kids reacted to common flu. Draws a blank.

      I’m not sure about some of the now little seen infections like measles. What used to be called “childhood” diseases.

      As for Covid mutations, it’s being tracked very closely. So far no mutations that affect R0.

      If it started to hit younger people that would be a disaster.

      Elizabeth Warren’s brother died of Covid the other day, he was 85.

      • dearieme says:

        Was he a Cherokee too?

        • Jacob says:

          I hope he is respectfully interred in his people’s sacred burial grounds. Fly with the ancestors, Has-Lying-Sister.

        • Curle says:

          Mocking his sister’s fake ethnicity is the kind of hate that that causes too many Native Americans to live in fear they will fall victim to some really rude glances from probable white supremacists. That and red-lining on the Res.

      • Jacob says:

        I think the virus is selected to be asymptomatic in people who can be quarantined successfully, and symptomatic in some others (who subsequently have to go to the hospital). If it became more virulent in younger people, it might cause them to go home instead of to a hospital, thereby inducing a loss in fitness (compared to the real world, where blissfully unaware asymptomatic carriers go out into public). Ditto if it became less virulent in the old & those with metabolic/cardiovascular disease: they would no longer need to go to the hospital, but they may be sick enough to self-isolate.

        I’m also willing to put down money that the key physiological differences that enable these differential outcomes are metabolic and cardiovascular in nature.

        • reziac says:

          I’ve noted that the comorbidity/risk-factor list is exactly contiguous with serious conditions typically associated with hypothyroidism (including age-related thyroid decline, which is basically low T3 syndrome) AND that the odder symptoms are contiguous with excessive conversion of T4 to ReverseT3 — notably extreme shortness of breath prior to any pneumonia, and the unreasonable level of fatigue.

          • Jacob says:

            That’s very interesting. Let me read more about it and get back to you.

            Do you have any good reference materials for me to start with?

            • reziac says:

              Argh… I’ve read literally thousands of papers from the endocrine literature (in sheer self-defense, being one of the ~10% of thyroid patients who doesn’t fit the prescribed mold). Where to start? My brain remembers everything, but indexes nothing. sigh

              Google “300 thyroid symptoms” and you will find a non-exclusive list — it affects everything. Keep this list in mind, and note that obesity is not a cause of [insert list here]; rather, it is a co-symptom typical for hypothyroidism.

              Here’s a good jumping-off point — T3 is generally neglected (because of the wrong assumption that T4 to T3 conversion is always perfect) but is the critical factor. Anyway if you look up all the included citations, you’ll eventually reach a document with 128 PAGES of citations… read enough of ’em and a pattern will emerge, which is also suspiciously contiguous with COVID-19’s assorted symptoms and morbidities. And I’m reminded that Hashimoto’s thyroiditis can be triggered by a random unrelated infection.

              Click to access TSHWrongtree.pdf

              One of those papers somewhere down the citation chain was from a cardiac pathologist, who noted than HALF of all fatal cardiac incidents were due to low T3 syndrome. Another was from a doc in charge of autopsies at an aged-care facility (he noted that 28% had significant goiter, ie. neglected thyroid disease). There are also neurological effects (dementia, possibly MS) because of impaired cholesterol transport (may explain why a ‘respiratory’ virus is being seen in the brain and spinal cord). Just a few of many such connections… but most doctors don’t read the literature, and the few who do… often have marbles in funny colors, which does nothing for their credibility with the larger medical world.

              Blacks are more likely to be hypothyroid, with all that implies (high BP, diabetes, heart disease, dementia, and of course obesity), which probably explains their reportedly higher CV incidence/mortality (I haven’t looked up the numbers there).

              Anyway, it’s a whole bloody rabbit warren… have fun. 😀

      • Rob says:

        Is it really so unusual that an infection is milder in children and young adults. Selection is more intense on them. From memory, mumps and chickenpox are milder in children than adults. Are there any countries where colds and flu are pretty rare? If some of them immigrate here, it would be interesting to see if flu is milder in children than adults. We think of little kids as being sick all the time (snot-nosed brats), but that’s because adults are mostly immune because they had those diseases as children. Unexposed adults might fare worse. Be worth looking into. It is abou time we got some use out of immigrants.

        I seem to recall, maybe Greg mentioned it, that diseases in naive populations, like measles in the South Pacific, children had lower death rates than adults.

      • Rosenmops says:

        I recall that it was widely believed that chicken pox was less sever in children than in adults. Remember when my kids all caught chicken pox from your kids? Or was it the other way around? Barry was quite a small baby when he had it. That was almost 40 years ago.

        • Frau Katze says:

          I remember it well. I think my kids had it but the symptoms hadn’t started when I visited. All your kids caught it. I think that was it but it could have been the other way around.

          I had to take them back home on the ferry. I tried to seat us in a dark corner.

          In fact, while Athena was recovering I took her to visit Iona. Turned out that Iona had never had it, but didn’t know it. She caught it. It was somewhat worse for her but not so bad she needed any medical help. It was not a very bad sickness, except the pock marks itched. We caught it while living in Quesnel. It didn’t even keep you confined to bed.

          I think there’s a vaccine for it now.

      • saintonge235 says:

        My guess is that the symptoms are exacerbated by the immune response. Note that with the Spanish Flu, the spike in deaths among the young adults is now thought to have been caused by an over-reaction of the immune system.

        Another example is measles. Very mild in children. But doctors in the Civil War Between the States thought measles in adults was horrendous, as lethal as smallpox, or more so. (I had measles and chicken pox as a child. I recall both as so mild I basically wasn’t sick at all.)

        And polio is thought to have been a very common infection in children in medieval cities.

        So this isn’t gigantically surprising to me. Fits a pattern.

        • Frau Katze says:

          Yes, I too am old enough to have endured these childhood illnesses in the pre-vaccine days. But with Covid the children don’t seem to have any symptoms at all.

          I expect there is much to learn about this new virus,

    • gcochran9 says:

      I said ” at least ten”, and I was only considering those that post. Hard to know much about the quiet people.

    • ben tillman says:

      You need a group before you can start talking about “group selection”. A lot of “individuals” and a “group” are not the same thing.

  14. Citizen AllenM says:

    Okay, say that someone (or something like a felid) already infected in China gets the original COV-1 and they have a little bit of transcription swap-so we get something where the virus gets much more lethal while keeping the youthful asymptomatic stealth mode. That could easily up the mortality rate up to 25%- with mortality in the over 50 bunch up from this one.

    Now that would be pretty nasty, eh?
    Super COV-3 on the way!

    Where doth the flu go when summer comes?

    • Frau Katze says:

      This didn’t need to happen. It could have been contained.

      The blame lies squarely with the Communist leaders of China. They delayed, showing no respect for their own people. Then they lied, and they’re still lying.

      It should be called the Communist virus. Replay of Chernobyl. The Commies denied that too until radioactive clouds floated over Europe.

      • Rory says:

        The guilt lies squarely on our own ruling class who made a swiftly advancing global pandemic a certainty by allowing the outsourcing of production to China and the third world generally (with the side benefit of nearly destroying our middle class besides). This globalized supply chain made mass international movements of people essential.

        Also this same class are the ones who did absolutely nothing to stop the spread (all the while shouting down people who wanted to do something as racist) despite the ample warning, before it became too severe to ignore. But sure, China’s lies are the reason they didn’t do anything, not their perverse ideology and greed. That China’s lies could totally befuddle every western government for months after I was personally preparing is amazing, was it only the government they lied to, while simple citizens like myself went unmolested by chicom propaganda?

        If you’re posting here you must be at least somewhat cognizant of the way the western elite work, stop being led around by the nose by people who hate you so fucking easily. Is it China’s job to make sure our own government doesn’t screw us? If no, then it fundamentally isn’t their fault. Elites would be all too happy to shift the blame for their disinterested and evil actions to China while shipping manufacturing to India and Bangladesh instead to show “solidarity” with us peasants.

        • Frau Katze says:

          This virus would have escaped no matter how much or little was being manufactured there. China has been a source of flu viruses going back at least to the 1950s.

          • Kilo 4/11 says:

            “This virus would have escaped no matter how much or little was being manufactured there.”
            Oh hell no – we weren’t taking in 400,000 chinese a month in the ’50s, We didn’t have hundreds of thousands of Chinese student-spies here, commuting back and forth to visit their families and handlers. The chicoms WERE, on the other hand, mowing down our Marines and GIs and the Koreans we were trying to save from enslavement.

        • Kilo 4/11 says:

          /\ /\ /\ What he said! (@Rory)

          I walk the streets in Chicago where the empty lots are where factories used to be.

          In almost any street in the central part of the city there were small factories that provided the livelihood for whole neighborhoods, for generations.

          Worse than the empty lots are where the former factories have been preserved and turned into luxury loft space for the privileged of the information economy.

          Worse still is when the elites and their technocrats and management lackeys mock and taunt the remnants of our working and middle classes, for allegedly not being clever enough to see the changes coming, or for being greedy, when all they wanted was a fair share of the boom times.

          In the wake of the chicom virus, there should be harsh sanctions/tariffs placed on the China trade. But we have many collaborators among us who have escaped punishment for too long.

      • gothamette says:

        One is responsible for one’s own reactions. You can react to a provocation like an idiot, or like a responsible adult.

        New Zealand, Vietnam, Israel (Hasidim excepted), hell, even Senegal, all handled the situation intelligently.

        Look at Trump: lies, denial, evasions. It’s all bullshit. He was going for herd immunity the entire time. Look at the record.

        We should also look at Israel, because you’ve got literally 2 countries in one: a secular, rational society, surrounding a medieval fanatic one in the form of the Hasidim. And yet they ended up doing OK because the authorities welded shut their synagogues and quarantined the clusters. But can this continue? I have my doubts. We’re only at the beginning stages of this disaster.

    • saintonge235 says:

      When summer comes, the flu goes from person to person, just like in the winter. But at a rather lower rate.

      “Flu season” is a year long, in the official statistics. They just start the ‘year’ in October.

  15. dave chamberlin says:

    John Barry author of The Great Influenza https://www.amazon.com/Great-Influenza-Deadliest-Pandemic-History-ebook/dp/B000OCXFWE/ref=sr_1_1?crid=32GLGL169I79O&dchild=1&keywords=john+barry+the+great+influenza+book&qid=1587778047&sprefix=john+barry%2Caps%2C160&sr=8-1 had some really good points.
    First, as mentioned earlier by Cochran it did mutate and it kicked our collective asses after it mutated. Mutation to be more deadly can also be a mutation to spread faster or more effectively, why is that not possible? It is. That it clearly happened the last time a virus made the successful jump from another species is called proof we should fear that Covid19 can mutate to be worse. Secondly very early on in this pandemic John Barry stated if this virus spreads asymptomatically we will not be able to stop it. We now know it spreads asymptomatically a very high percentage of the time. Yea we bent the curve, but look closely at the graph over time of cases in the US, Europe, and the rest of the world. An accurate description is, with a few noted exceptions is it has plateaued, we are not beating it because our social distancing is not nearly as strict as China’s was. Strongly implying that when we back off the social distancing, which it certainly looks we are winding up to do far too early, it again starts spreading rapidly. To these authors of this article and anybody else that wants to make blanket statements about what Covid19 will or will not do in the future I say read the damn book and learn what happened last time. Thirdly and this is also clearly presented in John Barry’s book, it is not going to quit and go away. It will assault mankind for years until vaccines or effective medical therapies are mass produced which looks to be a year or so away. Add yet another ignorant optimistic assumption the list. Once we have antibodies we can never get it again. We don’t know that. It is true with some viruses and not others.

    don’t kill the messenger
    Maybe we will get some good news about how far this has spread so we can talk about herd immunity and a very low mortality rate but so far the studies didn’t think about making representative samples of the larger population so their numbers are pretty useless.

  16. gothamette says:

    Well sirs & ladies, I am not one of the 10, but I can comprehend some of the basics, here and my mind is boggling:

    https://blogs.sciencemag.org/pipeline/archives/2020/04/21/watching-for-mutations-in-the-coronavirus

    there’s a fearful amount of viral replication going on out there, and not all of it goes perfectly. A single patient may have several mutational strains going at the same time as the virus replicates, and there’s been a report of a person who turned out to be infected simultaneously by two strains with different geographic origins, which is bad luck.*

    Then comes a lot of technical stuff which is I’m sure of interest to Greg & AR and the brains here, but not to me. (Never heard of Abraham Wald.)

    Then:

    ZJU-1, whose sequence fits more with a cluster of mutations found mostly in Europe, had 19 times the viral load of ZJU-2 and ZJU-8, which are more in the Seattle/Washington state clade – these differences were already becoming apparent at 24 hours and were statistically significant (reproducibly so) at 48. And when you compare the top and bottom-performing strains, ZJU-10 had 270 times the viral load of ZJU-2 at the 24-hour mark!

    What what what what???

    Lowe – explain this!!!

    • gothamette says:

      This quote should have been italicized.

      there’s a fearful amount of viral replication going on out there, and not all of it goes perfectly. A single patient may have several mutational strains going at the same time as the virus replicates, and there’s been a report of a person who turned out to be infected simultaneously by two strains with different geographic origins, which is bad luck.

    • John Massey says:

      I already posted a link to that preprint in the last thread, and commented that it could be very important, but of course you didn’t read it, did you?

      Yes, 270x the viral load, and that is right there in the abstract of the preprint. But you didn’t read it, did you?

      • gothamette says:

        No, I didn’t. Shocking, I know, but I don’t read every word that you write, Shakespeare.

        • John Massey says:

          The preprint. The preprint. Or at least the abstract. The point of me saying it could be very important was to try to get people at least to read the bloody abstract.

          The senior author, Li Lunjuan, is a very experienced epidemiologist (although admittedly she’s a lying Commie Chink), and separately, when interviewed about that paper, she speculated that New York had got a more severe strain via Europe, while the west coast states had got a more mild strain direct from China.

          • Frau Katze says:

            The early data in B.C. showed a few cases from China but then those stopped and a whole bunch started coming from Iran. There are quite a few Iranians in Greater Vancouver but far fewer than Chinese. No idea how the virus got to Iran.

    • Couple of things to keep in mind:

      1) The cell line they’re using (Vero-E6) is monkey-derived, not human-derived. It’s obviously close enough to human for the ACE2 binding to work, but differential infectivity in human cells will be different.

      2) They found multiple nucleotide mutations (in 11 samples!) that produced the same protein mutation. T22303G (5 samples) and A22301C (1 sample) –> S247R in the spike protein. That’s very strong evidence that that particular protein mutation was under positive selection.

      3) They sequenced absurdly deep, millions of reads of coverage per locus. The genome’s only ~30K, so they managed that with a standard ~hundreds of millions of total reads per sample on a Novaseq. That let them do pseudo-phasing by comparing allele frequencies between different mutations, and look at intra-sample diversity of viral genomes. Would be nice to see real phasing, either with linked reads or pacbio or nanopore.

  17. mapman says:

    Not NatureNature Microbiology. Two very different journals. The latter is not even in the Top 5 journals in microbiology/virology. But yes, remarkably stupid. It can go either way and there is no way for us to predict the path.

  18. Frau Katze says:

    Here’s some more news, not good. It seems there are some cases of young (30’s,40’s) otherwise healthy covid-infected people having strokes, and they’re not what doctors are used to seeing.

    It doesn’t change the overall situation of serious covid complications strongly linked to increasing age. But it is disturbing.

    https://www.washingtonpost.com/health/2020/04/24/strokes-coronavirus-young-patients/

    • Frau Katze says:

      Dr Seheult explains the situation, referencing the article above.

      I can’t say I understood the whole thing but I got this much: The Covid virus, normally busy in the lungs, may get into the blood and infect the cells lining the arteries, using the ACE-2 receptor.

      It’s pretty complicated but the loss of ACE-2 receptors affects the clotting factors in the blood.

  19. uhoh says:

    Can anyone explain to me how realistically this ends (say in the US) in any way other than herd immunity? I mean, after all this effort, the number of new cases has merely stabilized. So the total number of cases is merely growing at a steady rate rather than accelerating like it used to. To make this all work instead of waiting forever in a holding pattern of economic stagnation, the number of cases needs to be dropping. R0 must be significantly less than 1, like 0.8 in Greg’s post from way back. But where we are now seems to be the limit of what the country is capable of, and all we got is R0=1. People are starting to get restless and will soon be defecting en masse, spurred on by politicians in some states. Then we’re back in firm R0>1 territory, which can only end in herd immunity.

    A few countries have been able to either nip the pandemic in the bud (Taiwan) or act decisively and nuke the curve (S Korea) or something halfway between (Australia). They might, just might, be able to take it down to near eradication. But the experience of Singapore shows that defending that is not easy. The virus doesn’t care how well you did in the past. Just as an epidemic starts with a single case, it can restart with a single case.

    At a 0.4% IFR (calculated from the random survey in Iceland) with herd immunity at about 50%, this will all work out to about 0.2% of the population dying, or 600K in the US, say plus or minus 100K. But quibbling about these numbers feels a bit academic, not really relevant to policy, when all we seem to be capable of is stretching out the curve instead of nuking it, when the only question is whether those deaths come now or a few months later.

    Or is everyone holding out for a vaccine? I don’t think we’ll last anywhere close to that long. Or do people think the we’ll be able to keep it down with testing and contact tracing. Maybe in some countries.

    • dearieme says:

      I suspect that people are just hoping that something turns up. If not a vaccine, a treatment. If not a treatment, a spontaneous petering out. If not that, maybe the death rate will fall because nearly all the most vulnerable people will have been killed already.

      • gothamette says:

        If not that, maybe the death rate will fall because nearly all the most vulnerable people will have been killed already.*

        If they think that, they are thinking wrong.

        Only the most vulnerable of the ones already infected have been killed already.

        Funny guy you are, dear one. You badgered me for an answer about funeral practices, but you didn’t pay much attention to all the care I put into explaining infection fatality rates.

        Do some thinking about that. And do grow up.

        • kpkinsunnyphiladelphai says:

          So let’s review, shall we?

          Arguably Wrong thinks the IHME model is too optimistic. In fact his view turns out to be TOO pessimistic, and gothamette, his sycophantic acolyte goes right along nonetheless..

          Greg Cochran, who argued from the very beginning that “there is no substitute for victory” now apparently seems to wonder if victory is impossible because, you know, those “stupid” contributors to Nature are putting forth argument the virus might not mutate into something more deadly.

          So, is there victory Greg? What the fuck does “victory” look like now? Don’t even bother answering, because you think anyone who has different view than you is “insane.”

          Meanwhile, the one thing that IS in insane is a certain strain of political mediocrities who are making public policy in choking the economic life out of the nation, throwing 30 million people out of work, forcing farmers to throw out eggs and milk and pigs that might lead, you know, to REAL shortages of, you know, basic stuff to EAT, because if they think they do that, they will save all the 80 year olds with COPD.

          Of course, this lockdown — presumably an effort that should lead to Cochran’s “victory — has super-duper benefits for Whitmer, Cuomo, Murphy, and Pritzker. It gives them an unending hard on — yes, for Whitmer too — since they can let their authoritarian freak flag fly, while destroying their economies for which they can blame Donald Trump because he didn’t shut down the country on February 1st.

          What if it turns out that 20% of the final death toll is from nursing homes? Take away the those aged 70+ with co-morbid conditions and nursing home patients, and what is the IFR now?

          But no, we have to close every greasy spoon and nail salon in the nation in a frenzied panic, have normal healthy people wear more or less useless masks amongst other healthy people while they are all scrambling for toilet paper, and just generally destroy our economy, rather than calmly tell old and sick people to stay inside, and have the authorities descend upon nursing homes and make sure their shit is order.

          • dave chamberlin says:

            You are not reviewing you are ranting. Arguably Wrong has a name that admits he can be wrong, if you had read what he wrote you would know he admitted to a huge potential range in outcomes. Your name is gibberish, which I find appropriate. You sound mad as hell that them thar dang fool smarty pants liberals over reacted to a flu bug and wrecked your life. I don’t know where to begin and why bother. In the words of Robert Heinlein “never try to teach a pig to sing; it wastes your time and annoys the pig.”

            • gothamette says:

              “while destroying their economies for which they can blame Donald Trump because he didn’t shut down the country on February 1st.”

              Dave:

              The reason why Mongolia shut down was because they wanted to sabotage Donald Trump’s re-election.
              The reason why New Zealand shut down was because they wanted to sabotage Donald Trump’s re-election.
              The reason why Australia shut down was because they wanted to sabotage Donald Trump’s re-election.
              The reason why Israel shut down was because they wanted to sabotage Donald Trump’s re-election.
              The reason why Spain shut down was because they wanted to sabotage Donald Trump’s re-election.
              The reason why Italy shut down was because they wanted to sabotage Donald Trump’s re-election.
              And so on.
              The key to these idiots is their gargantuan, towering narcissism, which has been projected onto Trump.
              Who is a gartantuan, towering narcissist.

          • gothamette says:

            “gothamette, his sycophantic acolyte goes right along nonetheless.”

            Nice to know that I’m so important I’d get on your nerves. I don’t kid myself. I’m one of the lesser lights here.

            Anyway….about IMHE.

            IMHE has now revised upwards. Aug 4: 67,641 deaths. To date, US has 54,941 deaths. See you on August 4th.

          • gothamette says:

            People like this guy are impossible, but for the record: we never had a real lockdown. Pizza shops in NYC are open. (Really.)

            If we had had competent leadership this thing would have been bolted shut and we could have gone on bloodied but unbowed.

            As it happened, we had the worst of both.

            But Cochran doesn’t do politics, so I’ll stop here.

          • Maciano says:

            Jesus you are an idiot

          • gothamette says:

            We’re up to 74,073 at the IMHE site.

          • gothamette says:

            “and gothamette, his sycophantic acolyte”

            And proud of it!!

    • saintonge235 says:

      If we can get really massive testing on an ongoing basis, we can identify most of those currently infectious and quarantine them.

      if we can develop treatments, we can stop it that way. Revive the horse serum industry, anyone?

      So we can maybe stop this without herd immunity. But the deaths are going to be high. So far, only two in three closed cases are closed because the infected person recovered. The other one in three is dead.

      What we know of asymptomatic cases indicates around fifteen or sixteen for every symptomatic case. That makes the indicated case fatality around 2%. Yuck.

    • dave chamberlin says:

      With this being as infectious as it is, and sneaky as it is I would say herd immunity will have to be a lot higher than 50%. The seniors will practice strict social distancing until a vaccine gets here. They are the bulk of those that you project to die and a high percentage of them won’t. So that changes the numbers around, I am pessimistic the US will do anything right but a number of other countries can keep bending the curve. They can very slowly come out of the social distancing for those under the age of 65 with a careful hand on the valve making sure that they do not repeat the disaster of Wuhan and New York City where the hospitals are flooded and people do not get even minimum care. Pervasive testing is indeed crucial for this to work.

      If the seniors can continue strict social distancing and the population eases out of social distancing in a carefully controlled manner we may be able to reach herd immunity and the mortality rate is reduced to a minimum. Because of the preliminary antibody tests showing a mortality rate of well under 1% including the seniors, maybe just maybe, we can knock that mortality rate quite a bit lower if the socially distanced seniors stay uninfected. Just trying to counterbalance my last bleak post with something constructive and positive.

    • Gkai says:

      Indeed, the death rate (and profile of people dying) is just wrong : bad enough for it to be a real issue, but not bad enough to keep modern countries shutted down for long, it’s not frightening enough to let the economy go down and risk riots.
      Not Long enough to eradicate the epidemy, not long enough to get a vaccine. Maybe long enough to improve treatment and get a lower death rate, and for sure a flatter curve so less overwhelmed hospitals…

      • Jon says:

        The NHS Pandemic Preparedness report 2016 looked in detail at the question of public compliance during lock down conditions. (Probably it’s more relevant here in England given our rowdiness and tendency to low level anti-social behaviour!)

        Although the Media has been playing it’s part until now corralling the masses I sense growing “antsy-ness” in my city and I’d say we can count on maybe another two or three weeks of hassle free compliance, especially as the weather is warming up.

        • Gkai says:

          Not only England. All European countries are relaxing their measures during the next 4 weeks. They can not continue further with the nice weather, young and middle aged citizens becoming more nervous and less frightened, and too many shops and industries depending on money injection not to go bankrupt. I do not know which is the deciding factor: population unrest or fear of unrecoverable economic crash…in both cases, goind back to more lockdowns during the summer will be difficult, hopefully transmission is much more efficient indoor that outdoor in summer, and that will be enough to keep transmission low

    • gothamette says:

      “Can anyone explain to me how realistically this ends (say in the US) in any way other than herd immunity? ”

      Everyone else is saying, “if” and “should” which doesn’t answer your question. So, to answer your question bluntly and honestly, that’s how it’s going to end. Look at Georgia. Look at the people lining up at such essential businesses as nail salons. Yes, in the middle of an epidemic, women must get their nails done!

      If we can get really massive testing on an ongoing basis, we can identify most of those currently infectious and quarantine them.

      Won’t happen.

      But starting so late and with half the country openly defiant and elected officials undermining any coordinated push in that direction, is that realistic?

      Again, I don’t talk about politics here, I come here to learn about the science, but since you asked, no, it’s not.

      Why? The buck stops somewhere. Where is that?

      • Frau Katze says:

        I was listening to an interview with Victor Davis Hansen a day or two ago. He lives on a farm in southern California. He said the recently arrived Hispanics (likely illegals) have created their own outlets for most shuttered shops. No lockdown for them. The new outlets aren’t as glitzy as the shuttered shops but they get job done. They’re in a rural area, no one had tried to shut them down.

        No idea if Covid is present. Even if it was, they wouldn’t have brought their elderly relatives with them.

        • Tl Howard says:

          Hanson lives in Central CA, the Valley.

        • gothamette says:

          Of course they have, and of course COVID will get them, and of course, it will seep into the general populace. The US is a sieve, and it is fucked.

        • gothamette says:

          @FK,

          W/r to Hanson, he’s a decent conservative but a bit thick, IMO, and his loyalty to Trump has deformed his reasoning faculties. So he’s reduced to carping – not that his carping is totally w/o merit. But it’s carping and doesn’t get to the heart of the matter, which is that in order to stomp this virus in the bud we’d all have to sacrifice liberty in the short run to save freedom in the long run.

          Unfortunately I think that libertarian-leaning democracies aren’t well-suited to crushing viral pandemics. I suspect that Trump is enacting the herd immunity strategy. He just isn’t saying so.

          All I can say is, watch out for yourselves, guys.

          • gothamette says:

            Addendum: a few posts back (which seems like an eternity) Greg was laughing at people who thought our economy was so fragile it couldn’t withstand a pause to take care of an epidemic. I laugh at those people who think our liberties are so fragile that they couldn’t stand a temporary adjustment to kill a pandemic. I expect that one of the local libertarians will quote Franklin, so I’ll do it for them:

            “Those who would give up essential Liberty, to purchase a little temporary Safety, deserve neither Liberty nor Safety.”

            Franklin was writing about a tax dispute. He lost his own son to smallpox. He was a scientist. I think he’d have been in favor of strict quarantines.

          • Frau Katze says:

            He didn’t seem to understand that these Hispanics were putting themselves (and by extension, others) at higher risk for Covid.

          • Frau Katze says:

            The libertarians are obsessed with the idea that the government must be bad. just because it’s a government. I realize it can be bad, but you have to look at each scenario separately. Ranting about the lockdown being unconstitutional seems stupid to me.

            You might have other reasons to oppose a lockdown, especially if it goes on for a long time. But being unconstitutional doesn’t sound like a good reason. You see them going crazy about contact tracing, for example.

            • Maciano says:

              Covid19 proved Libertarianism and classical liberalism to be idiotic belief systems.

              For that reason they must now prove COVID19 to be not so deadly. If that means killing their parents, grandparents and sickly cousin, so be it.

              During war, disasters and pandemics we need a government. No further word needs to be spoken about it. It’s like saying apples don’t fall down.

            • saintonge235 says:

              Lockdowns are NOT unconstitutional. Look up “police power.” It’s one of the ones specifically reserved to the states by the Tenth Amendment. And remember that Typhoid Mary died in jail, all quite legally, because the police power was used to protect the public from her. Check out the history of mandatory quarantines while you are at it.

              It astounds me how many people run around with a ‘personal’ Constitution in their head that they think is binding on the nation.

              • gothamette says:

                Where are the lockdowns? Here in NYC with the highest amount of cases we are being advised to stay home. Yet every day that it isn’t raining people are out and about. Way less than before. Masks. Enforced social distancing in essential stores. Life is not normal. But no one is being shot on sight, no one is being forced to stay home. Ask me how I know? Because I go out.

                Pizza shops are open. In NYC, that is an essential service. /sighs/ The pizza makers wear masks and gloves. I would never in a thousand years go into a NYC pizza shop now & order a slice but I offer this an example of how lax the rules in the country are. The militia LARPers are reacting to a fantasy.

                Plus a lot of people are getting a thousand a week to rid out the storm, more money than they made before. I don’t begrudge them, just saying. I hope that they save some money, but given the way Americans behave, I doubt it.

                That said, the measures have caused great economic suffering and we do need a rational exit plan. But we won’t get it.

                Modern America is the worst of libertarianism & the worst of excessive state control.

                And oh yeah, Trump is going for herd immunity, he just isn’t saying so.

              • Frau Katze says:

                Sorry if I do not know US law, I don’t live there.

      • Again, I don’t talk about politics here, I come here to learn about the science, but since you asked, no, it’s not.

        Are you being sarcastic? Literally all you do is whine about Trump and how your present unhappiness is totally his fault. Complaining is obviously not making you feel better, just go donate to senile child-sniffer Joe Biden’s campaign already. He’ll totally make all your problems go away.

        People need to get real. The hyper-connected modern world is a house of cards, massive catastrophic “tail risks” from things like pandemics (and a dozen other things) are wholly inevitable.

    • reader506 says:

      Ultimately, there are many possible ways out of the mess other than herd immunity. None are easy, but almost all of them benefit from having more time.

      We may discover more efficient means of thwarting transmission, such that we can increase (economic) activity without increasing Rt and possibly even lower it. Masks may help. Testing, tracing and isolation seem like a long shot but a lot can happen in a few months when such a large portion of our workforce is focused on solving these problems. Almost every scientist and engineer I know is working on something related to covid-19. A factory near the rust-belt town where I grew up, barely scraping by in recent years, has been working ’round the clock producing parts for medical equipment. Ramping up domestic production on effective testing is not an impossibility. A solution doesn’t have to be perfect to help.

      Even the herd immunity approach benefits from more time. Overwhelmed healthcare aside: IFR can be reduced with effective treatments, which take time to discover. A vaccine is not the only option. There are also antibody treatments, which take take time to develop and produce but not as much time as a vaccine (since you use it on sick people). Hospitals can become more efficient. We can get better at early detection of severe symptoms so people get treatment more quickly.

    • Rosenmops says:

      “People are starting to get restless and will soon be defecting en masse, spurred on by politicians in some states”

      Plenty of old, vulnerable people like me are not getting restless to rush out and be infected by a lethal virus. They can open things up all they want. I’m staying home.

  20. Peter Shaw says:

    Nature has 6 other examples of coronaviruses that have not mutated in that way. Stop being alarmist

  21. j says:

    We all have been barking at the wrong tree, trying to figure out if the mutated virus will be more virulent or weaker. As expected, the virus has been mutating like crazy and has split into twenty different corona viruses. One may be infected by variety A and celebrate that has been cured, and then get infected by variety B.

    • Gkai says:

      They are testing vaccines originally intended for mers, itself originally developed for sars version 1. If it works for sars v2, it may well work for v2a, v2b, v2c…
      doesn’t need to be 100% effective, just be effective enough (~60%) for herd immunity to kick in. Given how far gouvernements went for lockdown, forced vaccination is a given, once a vaccine is proven efficient and safe enough.
      Of course, if variant 2g is not affected at all, we will be back to square one quickly…

  22. Othmar Haele says:

    Excess death rates in European countries:
    https://www.euromomo.eu/graphs-and-maps#z-scores-by-country

    Looks like at least in parts of Europe (except UK) the first wave is over.
    There is a common perception that no one is immune to Covid 19 but there are people like Christian Drosten who think (active T Cells in people never infected by Covid 19) there is some cross immunity with other Corona Viruses. Not sure about the Nicotine making immune though.

    • j says:

      We have the official mortality numbers of Israel for the last 3 months. In the category of people over 67 there are NO EXCESS DEATHS, on the contrary, significantly LESS people died that in comparable periods in former years. The doctors say that the reasons are (1) less traffic accidents, (2) no occupational safety issues, (3) no elective surgery was performed in this period. Surgery causes complications and deaths. (4) Hospital environment is dangerous in itself. For many, home is safer.

      • gothamette says:

        Except for the Hasidic clusters Israel has done quite well.

        So has Senegal. Nine deaths to date.

        Reporting? UV rays? Youthful population? Or intelligent management?

        https://sn.usembassy.gov/covid-19-information/

        • John Massey says:

          He shouldn’t need one – you should take his word for it. I might not always agree with J’s theories about things, but he doesn’t just make shit up, just like I don’t. And what he has said is logical and what you should expect.

          During the relevant period, Hong Kong has also recorded fewer deaths, because the closure of pre-schools, schools and universities ever since January 25, universal voluntary wearing of masks in public (which began at the same time, because that was when HK got its first case), social distancing and other measures in place have dramatically cut short the influenza season, so ‘flu deaths are way down on previous years, while we have had precisely 4 deaths from Covid-19 (one of whom was a 39 year old man with chronic heart disease who died from sudden heart failure, so only 3 elderly people have died from it). I can’t help but think that having the warmest January on record also helped to snuff out the influenza (and possibly also played some role in limiting SARS2 transmissions, but there is no solid evidence for that yet – but note that India has surprisingly low Covid-19 deaths).

          If you don’t want to believe it, then don’t. I don’t give a damn. But it’s the truth. I don’t tell lies, and neither does J.

          • Frau Katze says:

            Look, it is not that I don’t believe him. But I’m puzzled by why it’s so different from Canada and the US. It is a compact small area, and so is HK, even more so. Maybe that’s the reason?

            I thought there be might an article about it. It wasn’t that I was accusing him of lying, I’m just trying to understand what’s going on.

            I am definitely not accusing anyone of lying.

            Maybe despite my attempts to stay current, I can’t keep up with it.

            • John Massey says:

              In relation to people, it’s cultural. In relation to government and health care systems, it’s organisation and preparedness. The reality in 2020 is that the UK, USA, Canada, Italy, Spain and France are basket cases; corrupt oligarchies masquerading as liberal democracies. I enjoyed the comment by one American commenter on Peter Turchin’s blog: “I can hardly wait to find out which lying corrupt senile rapist gets to drive this worthless dumpster fire of a country over the cliff in the next 4 years.”

              • Frau Katze says:

                I am not very impressed by the leaders in the UK, US, Canada, etc either.

                Unfortunately a great many people are still determined to live here.

              • John Massey says:

                No doubt the Cree and Ojibwe thought the same thing.

              • Frau Katze says:

                @John The natives were really hit hard. The ones living in tropical climates had to endure malaria and yellow fever. In Canada the worst disease was smallpox, it must have been bad. The article about viruses growing less virulent: it did not happen with smallpox. It is an example of how wrong the writers are.

              • John Massey says:

                But this is a disease that is new to all humans, so it’s a matter of whether there are genetic factors that influence the response (there are) and whether those factors vary between different populations – I have seen nothing published about that.

                The worst co-morbidity appears to be hypertension, to which African Americans are particularly prone (they seem to have particular sensitivity to sodium). Next worst appears to be obesity, as an independent risk factor, in which African Americans are also over-represented. I don’t know anything about other ethnic minorities.

              • TB says:

                This strikes me as at least a bit wrong. It’s a corona-virus, so humans do have quite a bit of experience going back thousands of years. Not a totally novel attack.

              • John Massey says:

                Which presumably explains why we did so well against the 1918/1919 Influenza. And various strains of Yersinia pestis – we have had experience of that going back thousands of years, which explains why people were so resistant to it during the 14th Century. How do you feel about eating some raw marmot liver, to prove your point?

              • TB says:

                I grant the point.

                I see it as the difference between, say, Ebola and a new flu variant or this corona.

              • gothamette says:

                @TB,

                Well, yeah. 80% of people seem to shake it off, no problem. Is it because they have a bang-up immune system that can fight off literally anything thrown at it, like a great returner in tennis? Or because their immune system remembers something from prior infections?

                I asked my PCP and he said, “We don’t know.”

              • TB says:

                No idea. It certainly presents as a typical viral respiratory disease. But there are all those other weird complications. We have endothelial cells throughout the body, so I suppose it could spread via respiratory route and pass to other areas.

            • j says:

              Sorry. My source was a radio interview on the local radio. There may be printed sources too, but it would be in Hebrew, and anyway, the doctors interviewed are well known functionaires and professors, and to me they sounded authoritative. The total corona deaths here amount to 200 in four months, which is statistically imperceptible and insignificant in a country of nine-ten million. Only in the construction industry there are – in normal times – five to ten deaths per month.

            • Frau Katze says:

              A data point about climate: Ecuador has two large cities, Quito (about 8K feet elevation) and Guayaquil at sea level. Guayaquil has a terrible problem with the virus, Quito is doing much better. I don’t know anything else about the cities, but it was mentioned by Bret Weinstein and his wife.

            • Frau Katze says:

              This article describes the dreadful conditions in Guayaquil, Ecuador (it’s 150 miles south of the equator). There is much inequality in living standards. Many well to do residents visited Spain and Italy earlier in the year and apparently brought the virus back with them.

              https://www.latimes.com/world-nation/story/2020-04-26/no-more-bodies-on-the-streets-but-coronavirus-illnesses-deaths-batter-ecuador

          • Frau Katze says:

            I’ve read a bit about India. It sounds potentially bad. But warm weather may kill it off. Even in Italy, it took off in the north.

          • gothamette says:

            “He shouldn’t need one – you should take his word for it. I might not always agree with J’s theories about things, but he doesn’t just make shit up, just like I don’t. And what he has said is logical and what you should expect.”

            “If you don’t want to believe it, then don’t. I don’t give a damn. But it’s the truth. I don’t tell lies, and neither does J.”

            Belligerent, hostile, always spoiling for a fight – and speaks for other people. Because someone asked for proof? You must suck to work with.

          • gothamette says:

            You claimed repeatedly that the first five cases of the disease had nothing to do with the wet market.

        • John Massey says:

          Admittedly, having smaller populations and land areas makes identification and contact tracing easier, but if the USA and UK has their shit together, they could have done it. They obviously didn’t have their shit together; nowhere close.

          Another comparison: South Korea and Japan. South Korea had its shit together, Japan is a basket case.

          • Frau Katze says:

            Strange about Japan. Perhaps it is down to small size. After all, it started in China, but South Korea was very efficient in getting it under control. I read they learned from SARS. But China and Canada didn’t. (SARS hit Toronto in Canada).

            • John Massey says:

              SARS hit Toronto twice, and they still didn’t learn.

            • gothamette says:

              Well, here is what I’m wondering.

              NYC seropositive is about 20% or so – but it’s not evenly distributed throughout the boros. I’ll bet that highest positives are in Bronx and Queens (where most of the deaths were). Manhattan is pretty low.

              A lot of rich Manhattanites left town to spend the quarantine in their country homes. When they come back, and as we approach herd immunity, will they get hit? A lot of them are older. And just in time for flu season.

          • saintonge235 says:

            Have to agree with Mr. Massey here.

            Ironically, Bush 43 was very impressed by THE GREAT INFLUENZA, John Barry’s book, and tried to get comprehensive preparations made. But the bureaucracy resisted him. Then Obama got elected, and continued undid most of what 43 had accomplished.

            Disaster preparation is like insurance. Right up to the day before you need it, it’s all a big waste of time, effort, and money. Then you do need it, and you wish you had three times as much.

            If we are really lucky and moderately wise, the response to the this mess will be a determination that NEXT time,we can shift into high gear very, VERY quickly. Get the CDC to forget its fantasies of being the govt. dept. that cures obesity, and stick to microbial infections. Drop the PC nonsense and face that many govt.s around the world will lie, so we need infection surveillance that does NOT depend on cooperation. Stockpile equipment, and machinery to make make equipment. Get the Dwight D. Eisenhower School for National Security and Resource Strategy involved, formerly The Industriai College of the Armed Forces. (The ICotAF was set up in the 1920s to preserve the knowledge gained the hard way in Great War about what it took to shift over from peace-time to wartime production rapidly.)

            Not that I’m holding my breath. There is something in USAmerican culture that desperately resists preparation for bad times.

            • Frau Katze says:

              None of the capitalist Western countries will learn anything. The scientists might learn something. But that’s about it.

              100 years till the next one, is what the businesses will be thinking.

              Unless somehow the ultimate source of virus is found (lab or wet markets?)

              The Chinese should shut those markets down. They’ve been a source of flu viruses for a long time.

      • gothamette says:

        Have most of the deaths been among the Hasidim?

        The largest per capita rate of disease in the US has been in Rockland county – where there is a large Hasidic cluster.

  23. TB says:

    This article is about flu, not Covid-19, but if anyone is unclear on how mutations can change infectivity etc, it’s a pretty easy read.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5600439/
    By the way, going to get tested. I work with covid positives daily, and have this dry cough I just can’t shake.

    • j says:

      My daughter had the same. The doctors gave her nothing, just stay at home 2 weeks and she was cured. She was tested negative but was told that the result is almost meaningless. Be well.

    • gothamette says:

      Keep us posted.

      • TB says:

        Got the test in the parking lot of a local high school. They swabbed deep into each nare for 30 seconds each. Very uncomfortable! Said they will call me with the results within 7 days.

        • gothamette says:

          The IMHE model still includes ventilator shortage – don’t you all think this is a bit dated?

          The virus attacks ACE2 receptors where ever it can. This results in all sorts of bad outcomes. It doesn’t cause a disease that is necessarily treated w/a ventilator.

        • TB says:

          Got the call today, and negative! Now to figure out why this endless dry cough.

          • Kilo 4/11 says:

            Ever tried Ricola? Most drug stores, yellow bag, Swiss herbal lozenges. I prefer the original formula, keep a bag all year round. Two or three in quick succession. Eases a sore throat, too.

        • gothamette says:

          What I’d like to do is get an antibody test. What does it matter if I was sick? I’m OK now. The antibody test is a simple blood test.

          I had a rotten cold from Feb. 10-Feb. 15. Probably not C19. But I’d like to know.

          Another question, perhaps idle, is whether other colds caused by corona viruses have anything in common with this. For example, half the time when I get a cold I lose my sense of smell and taste. The other half, not. Is losing sense of smell and taste a hallmark of coronaviruses?

  24. Rob says:

    I was thinking about Hanson’s variolation idea, and I thought of a problem with infecting people with very small doses of virus. I’m not sure it has a name, but it probably does. There are some viruses, like Eastern Equine Encephalitis, that have microRNA binding sites to ablate infection in professional antigen presenting cells. Because their proteins don’t get expressed in APC, the immune system has a much harder time fighting them.

    Let’s say your infected with two very similar strains of EEEV. There’s no protein differences between the guys. The only difference is that one has the three(!) microRNA binding sites, so it doesn’t replicate in APC. The other does. What happens? The strain that replicates everywhere has it’s antigens presented, so the immune system makes an adaptive response, and can better defeat both strains.

    Infect someone with a lot of virus, and they probably get both strains. They defeat both, and don’t spread the infection. Infect people with a little, and some will get only a strain that does not replicate in APC. They don’t defeat the infection, and so spread the disease. A worse disease than if they had been infected with a bunch of virions.

    I’m not saying SARS-CoV-2 has any miR sites like that, but it seems to be pretty good at evading the immune system in some people. If by dumb luck a strain arose that did have restricting miR sites like that, wouldn’t you do better to be infected with a strain that didn’t as well?

    Does that have a name, Greg?

  25. Bert says:

    The paper linked here is the first really worthwhile accomplishment that I have seen from epidemiologists.

    View at Medium.com

  26. gothamette says:

    Since Greg’s latest podcast, which I learned about elsewhere, Greg being the opposite of a self-promoter, New Zealand has announced a temporary victory. Ardern emphasized that they had to be vigilant.

  27. Citizen AllenM says:

    Looking at the current numbers, herd immunity will kick in at roughly 70%, with that taking two or three winters. In the USA, the overall death rate of infected looks to be 1%- so call it 2.1 million deaths over the next three years. The most likely scenario is we accept summer reopening, and have a fall outbreak that follows the colder weather- just like the traditional flu, and the 1918 pandemic history.

    Now, worldwide, I guess (and let us just call it a guess) that the overall death rate will be double that 1%-so 2% in the third world without drastic efficient Chinese style steps to contain the virus.
    So- India- over the next 2-3 winters will experience 35 million deaths- most of which will not be recorded from the virus.

    So, breaking the world up into efficient versus inefficient camps 1% versus 2%, plus 70% infected to reach herd immunity- 3 billion in the efficient camp- 20 million dead over the next 3 winters- 4 billion in the inefficient camp 56 million in the inefficient camp.

    Total dead at the end of the third winter- 76 million- yielding just a 1% total mortality worldwide.

    The funny part is I think these are really the lower bound of the overall deaths.

    The really interesting part is the statistical check provided by the excess death rate in Britain showing how it really is hitting the elderly and sick the hardest.

    Of course, just like the 1918 pandemic, there will be various hotspots and winners of the isolation and shutdown games.

    There, without advantageous mutation, is ultimately a speedbump for humanity.

    • dave chamberlin says:

      You are right about herd immunity kicking in at 70%, but the numbers from two sources lower the mortality rate considerably which is great news. 25% of New Yorkers that go shopping have antibodies to Covid19. https://www.youtube.com/watch?v=gx3Z1Un7M5w Forward to 4:02 of Governor Cuomo’s press conference for that source. I don’t buy that this is a representative sampling of all New Yorkers but it’s the best we can do at this point. This study combined with a Netherlands antibody study of 10,000 blood donors indicates something around a 10 maybe even 15 fold increase in people exposed to Covid19 beyond the formal number of cases listed.

      That if true completely changes the fearsome mortality rate in New York and Europe. That is great news but there is some bad news mixed in with it. It spreads easier than expected because the asymptomatic population is the overwhelming majority of cases. Whatever the percentage of New Yorkers exposed to Covid19, it’s astonishing how far and how fast it spread.

      I predict we will reach herd immunity far faster than you are predicting in the United States. It spreads really quickly when people ease off social distancing and that will start May1st for the rational people and when the Covididiots get a whiff of this lower mortality rate that will put wind in their sails and hopes in their tiny heads. The same flawed study I linked to above also found a 2 to 3% infection rate in upper New York which is probably far more indicative of the rest of the country. We are just at the beginning of this pandemic.

      The mortality rate I calculate is much lower than yours is both for the world and the United States even if we reach herd immunity at 70% before a vaccine comes to the rescue. Seniors like myself have to continue strict social distancing while scientists direct the greater population to carefully ease out of the lockdown. As you mention some places will succeed, some will fail. The numbers also indicate that the third world with their vastly larger proportion of young skinny people won’t be hit nearly as hard.

      • gcochran9 says:

        There are 20k excess deaths in NYC. With 24% infected, the NYC IFR, from the current numbers, is about 1%.

        • Citizen AllenM says:

          I was using the English Doc’s weekly excess mortality for the estimates- and since absolute excess mortality is a pretty good proxy, I feel I am in the ballpark.

          The large scale will be hidden from all but the demographers of the third world.

        • dave chamberlin says:

          70% of 1% of 330,000,000 million is 2.3 million dead in just the United States. But I will tell you what. Me and and old fart buddies ain’t gonna join the count. Nope. We don’t need your restaurants, shopping malls, movie theaters, shopping sprees or social butterfly lifestyle. We like living and we like it just fine. So cross us off your list and kindly subtract us from your death toll.

        • gothamette says:

          I’d love to see the borough breakdown of the 24%. That’s an overall. Isn’t it reasonable to assume that there are higher percentages in Bronx and Queens (heavily hit) and lower percentage in the heavily populated island of Manhattan? Lots of prosperous white people. Many have decamped to 2nd homes in the country. Lots staying home, sheltering in place, ordering out. So lower infection rate, while Bx and Queens achieve herd immunity.

          When they come back, just in time for flu season, and virus is still circulating — BOOM.

          Sound reasonable?

  28. Philip Neal says:

    Off topic, except that there is only one topic at present.

    Neil Ferguson of Imperial College, London has today (28 April 2020) released the <href=”https://github.com/mrc-ide/covid-sim”>C++ code of the model which informs British government policy, (c) Neil Ferguson 2004-13. Has anybody been looking at it?

    I used to document C/C++ APIs for a living and so, though I make no pretence of being mathematically minded, I took a first look. The procedural code seems to be at lines 2199 to 3068 of the file covid-sim-master\CovidSim.cpp – the rest is data, either sample or hypothesis. A morning and an afternoon are not enough to make sense of something like this, but the motivation and data structures are clearly motivated and comprehensible.

    What interests me is this. Observational data is organised by counties of the UK, by states of the USA, and similarly for other countries. Cities, large or small, do not seem to come into it. Data structures below this level go down to the level of places, cells and microcells (9 to a cell) and people live in cells, but these are all model, not empirical observation, and – by the same token – population, not sample.

    People don’t move. Instead the simulation employs spatial mixing probability distributions (spatial kernels) that control the probability that people in cell X will infect people in cell Y located in another spatial region.

    “People do not move” – that is to say, the hypothetical individuals assumed by the model – do not move from place to place. At first glance, the model does not allow for crucial events such as a church group visiting Wuhan and returning to Seoul. Events (infectons) are seemingly supposed to be a function of places with a population in the millions with an assumed constant rate of flow of people between them.

    Is Neil Ferguson right?

  29. John Massey says:

    No doubt the Cree and Ojibwe thought the same thing.

  30. dearieme says:

    This morning’s Times reports on a report.

    ‘Researchers gathered data from almost 17,000 patients admitted to 166 NHS hospitals between February 6 and April 18.

    By that time 49 per cent had been discharged alive, 33 per cent had died and 17 per cent continued to receive care. The study is continuing and the scientists behind it said they had found Covid to be a complex disease quite unlike other respiratory viruses. The details of how it kills people were still unclear, they said.

    “It’s a common misconception, even today, that Covid is just a bad dose of the flu,” Calum Semple, a professor in outbreak medicine at the University of Liverpool who is leading the study, said. “I’m going to choose my words very carefully here: Covid is a very serious disease. … The study followed patients for 14 days. Some of those receiving care were expected to die, bringing the case fatality up from the 33 per cent reported in a paper released yesterday to somewhere between 35 and 40 per cent, Professor Semple said. …

    “Despite the best supportive care that we can provide, the crude case fatality rate for people who are admitted to hospital – that is, the proportion of people ill enough to need hospital treatment who then die – … is similar to that for people admitted to hospital with ebola.”

    The median age of the patients included in the study was 72 and for those who died it was 80. The median duration of symptoms before admission was four days. The median duration of a hospital stay was seven days.

    The most common underlying health conditions were chronic cardiac disease (seen in 29 per cent of patients), uncomplicated diabetes (19 per cent), non-asthmatic chronic pulmonary disease (19 per cent) and asthma (14 per cent). However, almost half of the patients had no reported underlying illness. …

    60 per cent of patients were male. “Those who have poor outcomes are more often elderly, male and obese,” the report says.’

    • gothamette says:

      ” The study is continuing and the scientists behind it said they had found Covid to be a complex disease quite unlike other respiratory viruses. The details of how it kills people were still unclear, they said.”

      The doctor at Medcram thinks that C19 is a disease of endothelial cell disruption, resulting in organ failure, not a respiratory disease, as it had at first seemed. He has an entire series about this.

      Thank you Dave Chamberlin. That series is a gold mine.

      • Frau Katze says:

        That linkage to strokes was surprising. It indicates that Covid it definitely not a “bad flu”.

        I’m hoping that only a minority will be affected by blood clotting problems.

        NYT has yet another article thing morning on how excess deaths point to the Covid death rate being worse than imagined.

        But the libertarians will ignore it. I do concede that the lockdown must be lifted or the whole economy will collapse, even if it causes a few more deaths. I just wish the libertarians would stop trying to deny that.

        • gothamette says:

          We are lifting the lockdowns in most states. I don’t know what they are bitching about. And we’ll see how that goes.

  31. Frau Katze says:

    Two California doctors. This video was banned from Youtube. Unfortunately, they just give a lot of numbers, no charts or graphs. They also don’t seem to use per capita but keep saying, extrapolate to the total number at various locations.

    Per capita is how two different areas should be compared. Extrapolating emphasizes how few people are affected. I’m not denying that. They compare Sweden and Norway.

    But what would the picture look without the lockdown?

    https://banned.video/watch?id=5ea4994ea881fd00808e95ad

    • Jon says:

      It’s on Youtube

      • Frau Katze says:

        They must have changed their mind. I don’t know.

        • gothamette says:

          I’m not wasting 53 minutes of my life on this. At 17:53 he’s actually claiming that flu is more lethal than Covid, citing stats from the CDC which they have stated are deaths arising from flu, not deaths caused directly by flu. And then they’ll turn around and say that we shouldn’t do the same with C19. In fact if we did, deaths would be way more than the official count.

          He claims that our response to C19 has caused suffering that will last a lifetime. I agree with him. It was abominably handled. He should take that up with the management.

          • Frau Katze says:

            I didn’t watch more than about 10 minutes or so. Reading out a whole bunch of numbers is a poor way to present them. A graph or chart is what’s required. Maybe that wasn’t available. I quit after several minutes of numbers.

  32. dave chamberlin says:

    N.E.W.S.
    it is an abbreviation. North East West and South. It’s supposed to be an abbreviation for all the important information gathered from all directions.

    Those were simpler times when people believed in high notions for mankind. Yep. We are going to give you the truth from all directions. Here it is….

    Now the N.E.W.S, better stands for Nonsense Everybody Wants Sickness because there is no intention by new sources to tell the truth and conversely the public doesn’t give a rat’s ass about the complex truth, they just want confirmed what they already believe.

    Meanwhile….back at the ranch…. the truth is kinds wondering what happened to it’s once actual status.

    I’m wondering too

    • TB says:

      Well, the news from my small town west of Chicago is that we are nearing our covid capacity in our ICU, to the point that patients who were in ICU are being sent out to the cardiac unit for monitoring, and we are almost out of negative pressure rooms. Last night I took care of 2 covid-positive patients.

      I am learning to notice trends. Both these patients respiration rates were faster at the end of my shift than the beginning. Both had gradually declining blood oxygen saturations. Just like my patient from the day prior, who we transferred to ICU early in my shift. All three patients had been symptomatic for over a week before coming in, so the expectation was that they should be recovering, but in fact they were going down. None of these people are elderly, the oldest 60s and the youngest 30s. Lots of covid positives in their 30s. Lots with none or few pre-exisiting conditions.

      It’s a brutal disease, like the worst flu you ever had, but it just doesn’t seem to stop. A flu is a few days of fever and muscle aches. Covid is a week or weeks of struggling to breath, with fever, diarrhea, nausea, so weak that a burly muscular guy who works outdoors for a living can’t walk to the bathroom, can barely sit up.

      • dave chamberlin says:

        It’s important you get the message out TB, and thank you.

      • gothamette says:

        @TB,

        The young pulmonologist who runs MedCram on Youtube has done a bang-up series about Covid. (Thank you Dave Chamberlin.)

        He thinks that Covid is essentially a disruption of the endothelial cells, resulting in organ failure, and not really a respiratory disease. But of course if you have time check out his series. He’s up to 65 but you don’t have to watch them all. The last 10 are enough to get his drift.

        https://www.youtube.com/channel/UCG-iSMVtWbbwDDXgXXypARQ

  33. tc says:

    What do you make of the claim that the numbers for flu deaths are just statistical estimates and not “true” counts, and in fact the CDC has been overselling flu deaths for decades, in order to scare people into getting their shots?

    https://blogs.scientificamerican.com/observations/comparing-covid-19-deaths-to-flu-deaths-is-like-comparing-apples-to-oranges/

    “In the last six flu seasons, the CDC’s reported number of actual confirmed flu deaths—that is, counting flu deaths the way we are currently counting deaths from the coronavirus—has ranged from 3,448 to 15,620, which far lower than the numbers commonly repeated by public officials and even public health experts…

    The CDC should immediately change how it reports flu deaths. While in the past it was justifiable to err on the side of substantially overestimating flu deaths, in order to encourage vaccination and good hygiene, at this point the CDC’s reporting about flu deaths is dangerously misleading the public and even public officials about the comparison between these two viruses.”

    • TB says:

      Doesn’t bother me, normally. This year with the covid complication it is a difficulty, since we can’t be sure which is which without the test. I know we are doing a lot more respiratory panels (very expensive) on the suspected covid patients, to rule out other common ills. Now that covid-specific tests are common and easy and fast (one day for us) we may start doing fewer panels. By next year we will have covid-19 added to the respiratory panel and it’ll be easy again (but expensive).

    • gcochran9 says:

      The CDC estimates are reasonable: lots of bad things become considerably more likely to happen if you have influenza. Like heart attacks: https://www.statnews.com/2018/01/24/flu-diagnosis-heart-attack/.

      The big mistake people are making is comparing the overall impact of a bad flu season ( like the Hong Kong flu OF 1968) – one in which ~50-70% eventually caught it – with a more virulent epidemic ( higher IFR & higher R0)) that is just beginning ( < 5% of the US infected so far by coronavirus. ) something like comparing the casualties of the first three months of WWI with the casualties of all of WWI.

      Well, they’re making other mistakes too, but then they want to.

  34. Frau Katze says:

    I read today that people who were infected with SARS 1 (outbreak was in 2003) are apparently immune to Covid-19.

    There was another group who had not had SARS 1 but were immune anyway. One guess was a coronavirus that occurs in some animals such as dogs. The virus doesn’t cause noticeable symptoms in humans.

    They ruled the common cold. Even if you had all 99 variations. It’s not similar enough to SARS 2.

    Still, the finding of any infection that can cause immunity (for at least 17 years) is good news for the vaccine makers.

    • John Massey says:

      Anecdote, sample of one: my old schoolmate and his wife went on a cruise from Australia to South America in March this year. Everything turned pear shaped, they were not able to disembark anywhere, my old mate got infected, as did a group of their friends and some other people on board, and they were confined to their cabins, so he was locked in with his wife. Long story short, they only just made it back to Australia, quarantined and he tested positive, but had only mild illness for 2 weeks before recovering completely.

      But here’s the thing – his wife tested negative multiple times and never did catch it, even though they were sharing a cabin together, eating together, etc. Seems like she has natural immunity. She used to be a nurse, so who knows what she was exposed to during her working life.

  35. John Massey says:

    Another anecdote: I have a friend living in Seattle, with his wife and daughter. His wife was infected and was bed ridden at home for 5 weeks before she finally recovered, but seems to have no bad after effects. I don’t know if she had access to oxygen during those 5 weeks, but if she was bed ridden she must have been fairly sick.

    But here’s the thing again – he and his daughter never got sick, despite sharing the house with his wife, taking her meals, etc. So maybe they both had asymptomatic infection, or maybe they just didn’t catch it.

    Given that in other circumstances it is crazy infectious, these cases seem strange. There is really a lot that people don’t understand about this disease yet.

    • John Massey says:

      Forgot to mention – they had a very old dog, which always slept in my friend’s work room next to his desk, so he was in close contact with the dog for a lot of the time over a long period. Material? Who knows?

      • Frau Katze says:

        In reading anecdotes about Covid I’m struck by how unpredictable it is. Unlike influenza, it varies dramatically even amongst people without comorbidities.

        Even amongst those who survive, some can’t seem shake it off, but remain feeling wiped out for weeks.

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