Let me count the ways

As many virologists have stated, their expectation was that the evolution of noticeably higher-transmission variants of Cov-19 was quite unlikely.

There is solid evidence that this has now happened at least three times (D614G, A222V, and B.1.1.7)  with at least two others likely ( in South Africa and Brazil).

They failed in an important aspect of their job.

 

 

 

 

 

 

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68 Responses to Let me count the ways

  1. NobodyExpectsThe... says:

    Any chance of a new podcast episode, about the new strains and the present situation?

  2. Davidski says:

    More bad news just in. Apparently, the UK variant isn’t just more transmissible, it’s also 30-40% more deadly.

    And early indications are that the new South African and South American variants reduce the efficacy of at least one of the vaccines by 50%.

  3. P says:

    Which virologists were they? People have been talking about the possibility that it would mutate to favor higher transmissibility since the beginning, and that it was likely that vaccines would need to be updated to match changing strains. I remember them saying they thought it would be slower to mutate than influenza, but not that it wouldn’t happen.

    • gcochran9 says:

      Almost all of them.

      • Here we have Trevor Bedford, Carl Bergstrom, and Bill Hanage explaining how unprepared they were for something like this: https://twitter.com/trvrb/status/1346282228477698051

        Bergstrom was so confident that this wouldn’t happen, he’s still doubting that the UK strain is more transmissible, because he knows that more transmissible variants just shouldn’t occur. From his Wikipedia page: “Carl Theodore Bergstrom is a theoretical and evolutionary biologist and a professor at the University of Washington in Seattle, Washington. Bergstrom is an outspoken critic of low-quality or misleading scientific research.” Christ above, have mercy on us.

        Or you have Francois Balloux, the fucking director of the genetics institute at university college london, who is incapable of doing basic algebra.

        • gcochran9 says:

          Vincent Racaniello

        • Bert says:

          Apparent ignorance of Paul Ewald’s “Transmission Rate Hypothesis for the Evolution of Virulence” is scientific malpractice when it occurs in a supposedly professional person, like Bergstrom, who gives advice on public policy in the pandemic. The co-author of “Calling Bulllshit: The Art of Skepticism in a Data-Driven World” should be hearing calls of “Bullshit” directed at him right now.

          Common sense reasoning would expect a virus that is easily transmitted to be selected for greater contagiousness and virulence under the ecological conditions prevailiing:
          1) more than half-way below herd immunity, 2) a spike-protein density that was relatively low initially but could be assumed capable of being higher, 3) infection of some individuals whose immune system does not clear the virus such that there are weeks of selection in those individuals for viral modifications that evade immune response measures, and 4) greater ability to infect being based on a better cell entry mechanism, why would greater infectivity not lead to higher viral loads within the average person, and thus greater rates of morbidity and mortality.

          • Now, to be fair, I don’t know anyone who saw that third one (selection inside immunocompromised individuals) coming. I certainly didn’t. There were some early case studies that I missed though, the earliest published back in July. That should have raised some serious eyebrows and modified treatment protocols. I didn’t see it until I started digging after the UK strain emergence.

            • Sorry, misremembered: it wasn’t published in July, the patient died in July. Published in November, too late to do much about the UK strain by then. I think we need faster publication.

            • Yudi says:

              Good old Greg saw #3 coming. He told a story on one of his interviews about a cat virus that has low virulence when it first enters the cat, but gets worse and eventually kills the cat.

            • Rob says:

              Live vaccine strains reverting to virulence in immunocompromised recipients is at least a hypothetical concern in vaccinology. I do not know if it has actually been known to happen. So an already virulent disease evolving greater virulence in the immunocompromised should have been predicted.

              I blame education’s focus on diversity and hoop-jumping over intelligence and creativity. Perhaps COVID will cause a Great Relearning. As it stands, selecting for intelligence is racist against blacks and Hispanics. Selecting for creativity is racist against Asians. Group think and conformity are predictable hazards of current selection procedures.

        • dearieme says:

          “Bergstrom is an outspoken critic of low-quality or misleading scientific research.”

          How brave. That’ll show those ruffianly scientists who speak up for low-quality or misleading scientific research!

          “Or you have Francois Balloux … who is incapable of doing basic algebra.” Nominative determinism.

  4. James Thompson says:

    Could you name and rank them by Brier scores? Each variant which is more transmissible counts as one point, each variant more lethal another point. So, roughly speaking, each of the virologists in your list would be at minus 6 at the moment. (No need to square anything at this juncture).

  5. Poolnet says:

    The British government has kind of walked back that 30-40% more deadly number for the U.K. Variant. Some scientists have intimated that the studies need more scrutiny. At any rate, the Fauci of the U.K. Covid response said that if 10 >60 patients out of 1000 died of the original virus, 13 or 14 might die of the new U.K strain. Either way it’s a dangerous disease for a minority of cases.

    Also, re the South African variant, there’s a large J&J vaccine study being conducted in the US and SA concurrently that may shed some light on the efficacy of vaccines for the new strain. Answers may come very soon.

  6. Rob says:

    Perhaps a future use of virscan would be to find some of the neutralizing antibodies from patients that bind linear epitopes of the virus and see if, say, vaccinees produce 3 different neutralizing antibodies, are they all to the same epitope in all vaccinees? If they are, then that points to a vaccine that might be easily counteracted by mutation. If I remember the virscan paper correctly, most people who had antibodies to a linear epitope from a particular virus had antibodies that bound within the same 10 residue section.

    Could maybe do an assay that consisted finding the epitope(s) bound, saturation mutagenesis on those chunks of the virus, infecting a cell culture with the mutants, and seeing if the offspring visions that were successful in culture were still bound by the antibodies. If yes, fantastic. If no, then that points to a vaccine that is fairly easily escaped. While not perfect, such an assay would be another datapoint for deciding between vaccines whose producers all claim 90% effectiveness.

    • Rob says:

      It occurs to me that in silico approaches might be avoided in some places. Finding the epitopes of interest requires virscan and computer analysis, but after saturation mutagenesis and cell culture infection, patient antibodies can be added to see if the mutated viruses are still inhibited by patient antibodies at concentrations that inhibit wild type virus.

  7. Anon says:

    Been reading posts/comments here: apparently we’re expecting mutations to increase virulence/lethality because this is a new virus, and there’s a lot of evolutionary low-hanging fruit for it to pick; compare to an older virus like measles, which is largely fit for its purpose, and unlikely to make deadly new mutations. (Have I got that right?)

    Does anybody feel like explaining to me why this is a new virus whose mutations we should fear, but, say, this year’s flu strain is an old one that won’t mutate horribly? I thought coronaviruses had been around forever: is there a non-technical reason why this one should be considered new, other than “It’s sufficiently different from the last one”?

    Cheers

    • Bert says:

      The research report linked below suggests that the D614G variant has a higher density of S-protein, which presumably means more spikes. If the native host of SARS-Cov-2 was cave-roosting bats (almost certainly true), then in that environment transmission was easy, so the optimal allocation of viral resources (set by natural selection) was to have the number of S-protein spikes be relatively few. For the last year the virus has been transmitting in what may be a more challenging environment, in which any modifications (more spikes for example) that arise by mutation and that improve infectivity would increase in frequency in the virus population.
      https://www.nature.com/articles/s41467-020-19808-4

      The other aspect is evolution of virulence. See my above comment about Ewald’s hypothesis on that matter.

      As for why seasonal influenza virus mutations have not led to higher infectivity recently, I would suppose a virus with an R not much above 1 has “tried” most of the possible mutations and none so far were advantageous, meaning that influenza evolution is now less likely than a virus in the middle of jumping to a new host.

    • Esso says:

      New in this context means that the virus first started circulating in humans 1-2 years ago. Before that only some other mammals and maybe some tissue culture in a US military lab?

      There are many different coronaviruses, but they don’t exchange notes. If some have adapted to humans, that does mean that this new virus would benefit at all.

      Other human coronaviruses are older but not ancient. The concentration of pre-historic hunter-gatherers was far too lean for most modern respiratory viruses to start a burn. The more people, the more chances for viruses to make their entry into humans and better the chance to stay there. That suggests that most viruses are rather new, not “around since forever”.

    • Coagulopath says:

      I thought coronaviruses had been around forever

      Yes, but only in animal reservoirs. The nearest relative we’ve seen to COVID19 is a virus called RaTG13, which is 96% similar but only affects horseshoe bats. The virus is as old as the hills…until now, it just never crossed over to us.

      Consider the phrase “the new kid on the block”. It’s true from the block’s perspective. From the kid’s perspective, it’s the block that’s new.

      • I forgot which fake e-mail address I used on the last comment says:

        Thanks.

        So how similar is the nearest COVID19 relative that also infects humans? And the next nearest, etc?

        And how dissimilar is this year’s flu from last year’s, etc?

        Is there a handy chart of viral similitude somewhere?

    • gcochran9 says:

      Because he’s got some motive for lying, and isn’t the sort of guy who’s into telling the truth and shaming the Devil. It isn’t hard to imagine possible motives, but I don’t know enough to guess his.

      Ask ” why?” too much and you’ll probably go crazy.

  8. j says:

    After an year in quarantine because of that tropical horseshoe bat, I wonder if massive deforestation and extinction of mammalian species is so evil. Maybe it is defensive. It is crazy to legally protect dangerous species like cobras and vipers, they should be exterminated like malaria-carrier Anopheles.

    • dearieme says:

      Yeah, kill ’em all. God will know his own.

      • LOADED says:

        Both of the preceding comments are the stupidest things Ive ever read. Wow. Just wow.

        • dearieme says:

          They are what are technically known as jokes. When your school reopens you could ask one of the teachers to explain.

        • LOADED says:

          I mean I hope so. Otherwise theyre completely nonsensical and counterproductive to what would be called human decency.

          • j says:

            I was NOT joking. Where human had settled, everywhere, they fought a life-or-death war against parasites and predators. Wolves, for example, were totally eliminated in Europe. In Antiquity, the Greeks eliminated all the lions and other predators of their cattle. Agricultural pests are exterminated, city cockroaches and rats are killed by the billions. African farmers kill elephants that graze their crops. Sentimentalism is a luxury only possibly from a totally secure place, and humanity is not yet there. I was for protecting (poisonous) desert scorpions, too, till one stang my daughter.

            • Coagulopath says:

              Sorry about your daughter.

              Bur realize that natural systems are complex and optimized, and changing stuff can have bad consequences.

              In 18th century Prussia there was a fad of “scientific forestry”, where natural forests were logged and replaced with high-lumber-yield Norway spruce, planted on a rectangular grid. It caused the ecosystem to collapse: important creatures lost their habitats/food sources, the soil didn’t recycle nutrients correctly, plant diseases spread everywhere, etc.

              • gcochran9 says:

                Europe and most of America have enjoyed drastic ecological alternations. The Ice Age ended, the paleoIndians killed off the megafauna, white settlers cut down most of the forests.

                And now we do fine. The stuff about how everything goes to pot if we eliminate passenger pigeons, or the Carolina Parakeet – that’s not true.

              • gcochran9 says:

                Natural systems are not optimized.

              • j says:

                “…and changing stuff can have bad consequences”.
                I understand and respect your concern, but that is not my way. It is not Homo sapiens’ way.

            • Smithie says:

              Sometimes, I think it would be good to eliminate the gnats that bite humans. There aren’t that many (species). But, then again, the woods would most likely fill up with annoying urbanites.

        • Kilo 4/11 says:

          If those are the stupidest things you’ve ever read, you need to read more.

          • LOADED says:

            Are you being legitimate here? Do you not understand how stupid your comment is? This is crazy. I have no hope for humanity.

            Fix the human population or continue to see degeneracy go unchecked. These are the only two options we are left with.

          • LOADED says:

            You must be really dumb my man. Did you just tell me to read more so I can find more stupid things people are saying? That is beyond my scope of understanding at this point.

            Incomprehensible stupidity should be met with the sword honestly.

  9. LOADED says:

    Viruses of the human mind exist as well and I hope theyre eradicated from the general public. In reality that is the most conscientious decision anyone could ever make!

    I am fortunate to have lived the life I have. Every single individual may interpret this differently but that is because i have supreme empathy!

  10. Sterling Sorbet says:

    I see Moderna is working on another vaccine aimed at the South African variant. Is this going to turn into lockdowns and a continual game of chasing after mutations the next few years?

  11. Coagulopath says:

    Europe and most of America have enjoyed drastic ecological alternations. The Ice Age ended, the paleoIndians killed off the megafauna, white settlers cut down most of the forests.

    And now we do fine. The stuff about how everything goes to pot if we eliminate passenger pigeons, or the Carolina Parakeet – that’s not true.

    “We lived through it before” could be used as an argument in favor of a lot of things – like Russian Roulette. There have been big failures of government attempts at ecological changes: cane toads come to mind. It seems like it’s easy to screw up, with irreversible consequences.

    We’re not talking about draining some swamp or killing some rare animal. Bats live everywhere, and they’re important for all kinds of stuff.

  12. dearieme says:

    “They failed in an important aspect of their job.”

    It has just occurred to me that in many American accents that would be pronounced as “They failed in an important aspect of their jab.” Ha!

  13. M says:

    I have a good friend who’s intelligent, who early on believed COVID was a danger, but then got on the flu-bro train. Since, then, he’s been consistently against any restriction; 1,5m, lockdown, masks, curfew, even cleaning etc, and telling me old ppl shd just stay home. He now thinks less of me, because, in his eyes, my fears are bigger than my rationale shd be, based on statistics for COVID.

    He believes the real danger is governments enforcing lockdown and unhealthy masks. We should all lose weight instead (which isn’t a bad idea for most, btw). Same with UK variant: he thinks this is just more fear created by virologists and governments officials for selfish purposes.

    We’ve seen over 2M deaths globally, with the most severe anti-virus restrictions in history ever, and he still believes COVID is totally irrelevant and harmless. Tbh, I’m starting to think he has a character flaw. What else can it be, if you genuinely don’t care for so many people dying earlier than ottherwise would?

    • gcochran9 says:

      He’s a loon. I know plenty of them.

      • j says:

        You may know plenty but not all of them. In my country, whole cities are in open rebellion against government orders, refusing vaccines; they believe that only god can help them.

      • Grégory Lielens says:

        Or he’s young(-ish), and impacted strongly by the measures, economically or otherwise. Young people risk much less. In addition, young (males at least) have lower physical risk aversion. Maybe a loon, or another risk/benefit structure than yours. Remember when the boomers where the selfish loons refusing to limit energy use?

        • gcochran9 says:

          He’s a loon. if there was a widespread real problem that didn’t threaten me personally, I might pay it no never mind, I might ignore standard precautions – but I wouldn’t say that it didn’t exist.

          • Grégory Lielens says:

            Fully agree. That’s the honest way to do it. However, in modern western politics looking selfish is a very bad way to advance your agenda, so you need to pretend to care, play your own victim card and hope it trumps the others, or say there is no problem.

            • gcochran9 says:

              I doubt if that guy was a professional politician. More likely, just a loon – not someone that lies to others for Machiavellian reasons, rather someone that lies to himself.

    • Coagulopath says:

      I have a good friend who’s intelligent, who early on believed COVID was a danger, but then got on the flu-bro train.

      We all have that friend, I think.

      A lot of people are pathological contrarians: they need to feel like they’re smart and clued-in and not one of the sheep. A year ago, when everyone thought the virus was no big deal, they thought it was bad. Now that everyone’s taking it seriously, they believe the danger’s overblown.

      In theory we could manipulate their psychology to prosocial ends. “Big government wants YOU to leave your room a mess and to never refill the ice-cube tray in the fridge!”

      • M says:

        Yes, he’s very contrarian. Always the most extreme version of everything.

        I guess it’s time to take a break from some people. At least, until this all blows over. But, even still, I won’t forget this. You learn somebody’s true nature in hard times.

        • Grégory Lielens says:

          Amen to that. People opposing the measures will remember the delations, the travel bans with 1 day-notice, and other lockdowns too I guess….

  14. dearieme says:

    You can’t go far wrong telling people to wash their hands – just consider the people you see in public loos who don’t bother. Distancing might well help too. Stopping sizeable public gatherings where people would shout or sing at each other also seems a reasonable move.

    What I don’t understand is the certainty – in either direction – about masks.

    “A year ago, when everyone thought the virus was no big deal, they thought it was bad.” Yep, that’s me.

    “Now that everyone’s taking it seriously, they believe the danger’s overblown.” That’s not me. I mean, the danger in people’s minds clearly is overblown for healthy people below 60 or even 70. But there are many people not in those categories who are in danger.

    My main complaint, though, is that people don’t take it seriously in the only way that matters i.e. intellectually seriously. There’s still far too much “I feel that …”, too much “How can you even say that?”, and too much lack of evidence. For instance, is there any conclusive answer to the question of whether asymptomatic people can be a major source of spread? Has any government made an evidence-based case that its lockdown has saved more lives – or perhaps more relevant, more Qualys – than it will cost?

    • Craken says:

      “the danger in people’s minds clearly is overblown for healthy people below 60 or even 70.” I think there is evidence for significant risk of long term health damage in this group of younger, healthier people. Have you seen any studies showing that this is not so? What I’ve seen is all over the map, often with methodological problems–but none of it’s reassuring on this point. The best show 10% suffer long term effects; the worst (a small German study) showed signs of cardiac damage in 75% of Covid cases. I’m disinclined to dismiss this issue just because the evidence is currently ambiguous. When a huge percentage of the human population is being infected by a novel pathogen, a more precautionary stance is needed.

      • Grégory Lielens says:

        10% of which group? intensive care survivors? Intubated or not? hospitalized? I live in Belgium (Covid Ground Zero), with quite a few friends who had the Covid. I can not see how 10% of covid case suffering long term effect can be right, if we are talking about all cases…Or those effects are subtle enough that there are not perceptible. It’s possible of course, especially for cardiac effects, but I find it doubtful…
        You can say it’s the “living in war zone” or fatigue effect, but frankly, after being quite worried in the beginning (I follow this blog, so I was informed in advance), one year later I am not worried anymore, except for my mom and her friends. For my generation (early 50) and the next ones, I am not anymore.

        • Craken says:

          The UK has something called the “UK Covid Symptom Study,” which is an ongoing study-via-app that has an extremely high level of participation (3 million people). It shows 10-20% of Covid patients still have symptoms a month after diagnosis and 5% 2 months after. These are not just hospital patients, although it’s likely that they’re self-selected to some degree, which would increase those percentages. These are people reporting symptoms; no account is taken of cryptic disease processes in this study. Yet, many different viruses cause many different cryptic diseases, which sometimes only manifest years after initial infection. This is a known unknown.

      • dearieme says:

        10% of what? Of hospitalised cases? Of symptomatic cases that have tested positive? Surely not of all cases, since asymptomatic cases go largely uncounted (as far as I know).

        “a more precautionary stance is needed”: this is meaningless. Do you wish to be cautious about the damage done to people by lockdowns or cautious about the damage done to people by Covid? Whichever you choose please explain why the interests of the other group should be ignored.

        • Craken says:

          The rulers haven’t even bothered with the precaution of clearly informing the general public about the unknown risks of long term damage. This risk hasn’t even gotten through to regular readers of Westhunt, like you. But, even if people were informed, there remains a need to balance individual and state interests. If there is a substantial risk of incapacitating 5-10% of adults for life, the state has an interest in preventing this outcome. Fellow citizens also have an interest in preventing this expense.
          The primary problem with lockdowns is that the financial hit is too concentrated. The government could have compensated for this, but seems to have done a poor job of it, at least in America. A temporarily reduced level of that abstraction called GDP is of little consequence in itself. Mismanaged distribution is the problem. Proper lockdowns, like China’s, can be fairly brief. It’s not as though Western governments lack the surveillance/enforcement capacity to do more or less what China did. But, they choose to deploy their power against political enemies instead of against the pandemic.

  15. j says:

    The Chinese imposed a brutal quarantine and think they defeated the corona epidemic. But take notice, Krakken, that 1.5 billion Chinese are corona-virgins, have no experience with this novel virus, and no protection. In the meanwhile, the COVID is mutating land getting more effective in infecting and rapidly killing people. The South African variety is a vast improvement on its original self. I sincerely hope that the American natives meeting Europeans scenario will not be replayed. As always, the Brits reacted most effectively, in their comic and muddling way they exposed the population to the virus and Oxford created some kind of vaccine.

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