Fast and Furious Omicron New Variants Defy Explanation, and Don’t Bode Well for Future Either

As readers may have worked out, scientist GM, whose observations via e-mail and in comments we have often hoisted into posts, is on the pessimistic end of the spectrum of Covid prognosticators and yet (or maybe due to that) has been early and very accurate. For instance, he was one of the first to notice the data from Israel in July 2021 showing a marked falloff in Pfizer vaccine protection 5-6 months after the jab. GM was also immediately on top of Omicron, that its many mutations on the spike would mean close to total evasion of prior protection (whether via vaccination or prior infection) and therefore potentially rapid spread.

Thus it isn’t at all good when developments surprise GM on the downside. As we’ll soon discuss, the speed of emergence of Omicron variants has surprised him in a bad way. Mind you, many of them are different enough that they should have gotten their own Greek letter, but that degree of truth in advertising would conflict with the party line that Covid is over.

But GM was also a bit disconcerted by the results from large-scale study using VA data, now out as a preprint, on Covid reinfections (we have additional links on it in Links). It does confirm what GM had warned about from the very outset, that getting Covid has a health cost, and those costs add up and maybe even multiply the more times you contract Covid. However, as he remarked:

I actually have doubts about the precise numbers — they are much much worse than I expected at this stage, and some things in the way this was done look kind of sloppy and should be hopefully sorted out in review.

But one important aspect of it is that this looks at different metrics from previous studies — previously reinfections were scored on hospitalization and on death being written as COVID on the death certificate. And those showed some protection on first reinfection (but already worsening on the second).

Here they look at the various sequaelae and at all-cause mortality for a larger period of time post infection.

And if true this is what reveals the real damage even at the first reinfection.

Also, reminder that the bulk of these reinfections are Omicron, i.e. the least dangerous version so far. Presumably it would have been much worse without all those S2 mutations.

When Pi [the next major variant] hits one can expect a total disaster — billions of people are right now accumulating preexisting conditions that are setting the stage for the grim reaper to take them when the next big antigenic shift happens.

P.S. Again from South Africa, this is what it might look like:

Note that this is still a first-gen variant — it is classified B.1.1.488.

This one was sampled in April but only posted three days ago, so if it was going to be what becomes Pi, it would have perhaps taken over by now (though of course Delta was first detected many months before it exploded so one never knows).

But the fact that these kinds of variants are popping up again and again means that Pi is coming. Probably sooner than later…

IM Doc asked GM if these Covid variants could be the result of animal reservoirs. As you can see, GM finds that none of the likely causes of mutation are sufficient to explain the rate of variant emergence. Needless to say, that is not a good picture. From GM:

Nobody knows for sure.

The Omicron origin becomes more and more mysterious with every new iteration. None of the possibilities explains it well:

1. A single chronic infection that has produced all of BA.1-5 and then transmitted them forward over a period of 4-5 months between October and January. I guess it’s not impossible, but how likely is that?

2. It is not a single individual, but a community of people, most of whom are immunocompromised, where the virus has been bouncing around repeatedly, accumulating mutations, and then leaking out of that community. This is actually not that implausible. Think of how we used to have leper colonies not that far along even in the West. Perhaps in South Africa they have some places where they send people with HIV to live out their days, and those places don’t have all that much contact with the outside world, which explains why the virus leaks only from time to time. Doesn’t necessarily have to be a place specifically for people with HIV, what would also work is some rural locality that is isolated and out of the way, where few people go regularly, and where many people have HIV. Gauteng actually does fit the bill — remember those famous photoalbums of rural poverty from the early 90s, with the very famous photo of the “inbred twins”:

That was in what was then Western Transvaal, which later became the North West and Gauteng provinces.

But such a scenario imposes the strict requirements that the rural locality in question has a lot of immunocompromised people and is isolated. Which is a rather unique situation.

3. Some rodent species in South Africa got the virus and it has been circulating there, making the reverse-reverse zoonotic jump from time to time. This is again a highly unlikely situation though, because BA.1, 2 and 3 appeared all at the same time, and then BA.4/5 also appeared at the same time. And if there is widespread transmission in rodents (or some other animal) you would not expect to see multiple related lineages making the jump at the same time. It’s just not very likely.

Animals are a problem for another reason — we are talking huge amount of mutations here, and we have only seen that in immunocompromised humans. So then the question arises regarding how is it that the virus accumulated so many mutations in whatever animal population is the reservoir? Because I am betting a lot of money that the percentage of immunocompromised individuals in wild animal populations is much much much lower than it is in the human population. In the human population they survive because modern civilization can shield and support them. Out in the wild they are dead very quickly. Also, rodent populations aren’t as huge in size as people think, and rodents are physically much smaller than humans, so at best there has been ~1/100th of the viral replication that has happened inside humans in those populations.

The NYC wastewater studies (the one with the many more and super highly divergent sequences that they found in the year since the original paper) do not bring any clarity either. That problem about how so many mutations appeared so quickly applies there too.

But we have added complications.

First, the concentration of these extremely divergent viruses in wastewater is very high. Much higher than could be reasonably expected that a single individual could shed. Yet in the same time if those lineages were being transmitted widely, that would be picked up by patient surveillance sequencing, as crappy and patchy as the coverage is. But they are only found in wastewater.

This would suggest rats.

But, the second problem is that if it was circulating in the rats, one would expect those viruses to be widely circulating within the city, and to be sweeping the way they do in humans. We don’t see that though — they see the super divergent sequences usually only in individual watersheds, and they see a lot of diversity. No sweeps (other than whatever circulates in humans at that time, which always dominates the signal).

Third, you can measure how much rat RNA there is in those samples, and in some of them there is none, even though there is lots of divergent SARS-CoV-2.

So it remains a mystery.

P.S. Given how important this is, one would think that we would be doing the following:

1. Mass population-wide testing of the whole population in South Africa during the periods in between waves, then sequencing of all positives, in order to identify the chronic infections and figure out what is brewing. It would cost quite a bit of money, but it is a drop in the bucket compared to the damage that has been done and will be done.

2. Someone would actually go down in the sewers in NYC (and all other major cities around the world) and sample the rats, mice and other fauna, in order to conclusively identify any possible reservoirs. Combined once again with mass testing of the human population.

Again, it’s a lot of money at first glance but it’s a trivial amount in the grand scheme of things, and especially given how $50-60 billion just got sent to Ukraine without any hesitation for the Russian artillery and missiles to target practice on.

Naturally nobody is doing any of that.

Needless to say, the failure to investigate is very likely to make bad outcomes worse than they need to be. And it make the regular hectoring of China for keeping infections down look even more deranged as the US seems determined to remain a Covid disease reservoir.

Print Friendly, PDF & Email

128 comments

  1. Roger Blakely

    Someone around here pointed out that we no longer hear talk about herd immunity. Every day in the Water Cooler Lambert posts the CDC map transmission map glowing red from coast to coast with a sliver of blue and yellow up the middle.

    We don’t have a narrative for the future. Every spring we get to pretend that COVID-19 will go away if we ignore it. And every summer the South lights up as people take refuge in air conditioning. Once we get to Halloween, the official start of the holiday season, it’s on like Donkey Kong. And once we get to Christmas, all hell breaks loose.

    It is hard to remember, but Omicron came at us on Thanksgiving Day. We did not start crawling from the wreckage until April.

    I don’t know. Maybe COVID-19 will go away if we ignore it. That seems to be our only plan at the moment.

    Reply
    1. GM

      The math is simple — if immunity lasts a year, on average there will be 0.25-0,3% of the population infected every day.

      If people stay positive for 10 days, at any given moment 2.5-3% of the population will be infected.

      In reality it is not going to be uniform, there will be waves and quieter times.

      But the floor can be very high.

      This is exactly what we see in the UK — they dismantled much of the surveillance infrastructure but there is still ZOE and ONS and the results have been quite startling — it hasn’t gone below 1M infected at any given moment ever since the winter 2020-21 lockdown and the post-vaccination reopening.

      And it was 1M when Delta was dominant — once Omicron arrived, the floor has been 1.5M. Or 2% of the population.

      At any given moment, as the baseline…

      So in the UK if you find yourself in a gathering of 100 people, there is only a slightly more than 10% chance nobody is positive.

      And that’s life from here on.

      So the map will be red most of the time. Provided that someone is still publishing the map…

      Reply
      1. Objective Ace

        if immunity lasts a year, on average there will be 0.25-0,3% of the population infected every day.

        What is this based on?.. It sounds reasonable–I’d just like to be prepared when I’m inevitably asked

        Reply
        1. albrt

          It looks like just treating a day as 1/365 of a year, on the assumption that you will get it again pretty quickly after your year of immunity is up.

          Reply
          1. playon

            Somehow I was under the impression that immunity was not lasting that long – wasn’t it revealed that Omicron does not provide much if any immunity from the variants? Either way it looks like we are F’d given the current non-response from western governments. The Chinese will inherit the earth…

            Reply
            1. Anthony G Stegman

              I recall reading that an infection with an Omicron variant provides at best roughly 90 days of immunity. Some are being reinfected within weeks of prior infection. As they say, your experience ay vary. Stay vigilant.

              Reply
            2. Mucho

              Yes, I also remember reading this, seeing Omicron reinfections less than a month after the first (Omicron) infection. Where does the 6/8 months figure come from?

              Reply
      2. Kris Alman

        Mutagenicity is a key variable and there are various means by which evolutionary pressures create favorability for the virus to escape the immune system, especially in immune compromised individuals. Some speculate that vaccines administered widespread during a pandemic does so.

        But what about antivirals?

        Searching google scholar, I found this article:
        Molnupiravir and Its Antiviral Activity Against COVID-19
        https://www.researchgate.net/profile/Huahao-Fan/publication/358657960_Molnupiravir_and_Its_Antiviral_Activity_Against_COVID-19/links/624bb67321077329f2f37ad4/Molnupiravir-and-Its-Antiviral-Activity-Against-COVID-19.pdf

        And these passages stood out:
        Remdesivir, another nucleoside analog, is the first approved antiviral treatment against COVID-19 (https://www.ema.europa.eu/ en/human-regulatory/overview/public-health-threats/coronavirus- disease-covid-19/treatments-vaccines-covid-19#remdesivir- section). Compared with molnupiravir, remdesivir would not cause mutations of RNA.

        ANTIVIRAL RESISTANCE
        SARS-CoV-2 is a single-strand positive-sense RNA virus with a genome generally characterized by high error rates, high viral yields, short replication time, and abundant homologous and nonhomologous recombination (84). Therefore, ‘viral swarms’ consisting of different genomic mutant populations with different degrees of fitness are generated, which can rapidly develop drug resistance while maintaining overall viral fitness, posing a great challenge to the development of broad-spectrum antiviral drugs (54).
        Currently, few studies are focusing on the resistance of SARS- CoV-2 variants to molnupiravir.

        Reply
        1. Kris Alman

          And I don’t find this passage reassuring:

          The recommended dose for molnupiravir is 800 mg (four 200 mg capsules) taken orally every 12 hours for five days, so it is unlikely to bring long-term pressure on the virus to induce drug-resistant variants. However, the generation of drug-resistant virus strains needs long-term and close monitoring. One solution to reduce drug resistance is “cocktail” therapy. The combined effect of molnupiravir and favipiravir has been studied and needs to be verified by more clinical trials (75). However, whether combination therapy will lead to more side effects is also a question that needs to be considered.

          Reply
          1. Yves Smith Post author

            This is an important point. Our Covid brain trust also worried about that.

            From GM on December 1:

            https://twitter.com/michaelzlin/status/1465781477736521736

            This is about how molnupiravir will create variants by accelerating viral evolution while not killing the virus.

            Curiously, Gauteng was one of the places where they trialed it. That does not change the fact that the branch is very long and dates back to 2020. So if this was indeed a chronic infection, it probably started there. But what if this was an HIV patient that someone tried to cure with the drug and that gave it the final mutagenic boost? We will never know…

            From GM on May 23, the icing on the cake, it doesn’t even work!

            https://www.bmj.com/content/377/bmj.o973

            Molnupiravir reduced the risk of hospital admission or death by 52% versus placebo in the interim analysis but raised risk by 35% among patients subsequently evaluated.4 There was no clear explanation for this substantial disparity in treatment effects between the interim and final phases. Molnupiravir showed no overall benefit over placebo for resolution of covid-19 related signs and symptoms.5

            Reply
  2. Tom Stone

    Oh, shit.
    Anecdata, a week ago no one close to me had tested positive, in the last few days five people I know have.
    Including my Daughter’s fiancee’.
    The bars and restaurants are packed, concerts are happening and maybe 10% are still wearing masks.

    Reply
    1. Eric Anderson

      More anecdata.
      Up here in (extremely) rural N. Idaho, my wife reports that 7 of her U.S. Forest Service colleagues have tested positive in the last week. The agency has been sending fire resources from all over the U.S. to the fires in the desert southwest. These aren’t the Pulaski motor fire fighters, but GS-7+ staff and line officers who provide administrative support functions on the big Type I and Type II fires. They work in close proximity in mobile trailers and big tents and such.

      The agency had some pretty locked down Covid SOPs until about 3 mo ago, then, poof — everything’s fine. Go back to work as normal — conveniently timed of course with the summer work season. Fortunately, my wife seems not to have contracted it again — she got it about a year ago and her symptoms were loss of taste and smell for 3-4 weeks. Says she still doesn’t have them back completely.

      My son and I have, to my knowledge, not contracted it. However, I suspect we’re of the asymptomatic nature due to O- blood. I was around a bunch of these folks, prior to them testing positive for an outdoor retirement party recently. Now, blowing and hacking yellow/green phlegm w/two negative rapid tests spaced a couple days apart after symptom onset. I don’t trust them though and will be heading in for PCR today.

      Reply
      1. Petter

        Type O blood – everyone oneof my sister’s three children and their spouse got it, including seven grandchildren, all except my brother in law. He’s type O.
        I got Delta, last November and still haven’t got my full sense of smell back.

        Reply
        1. kareninca

          My 79 y.o. mom finally caught it a couple of weeks ago – she is double vaccinated, once boosted, but not careful. She has type 0 blood..

          Reply
        2. redleg

          My vaxed type-O father died from delta last year. He wasn’t asymptomatic. Sorry to derail this train of thought.

          Reply
      2. Anthony G Stegman

        I attended the Golden State Warriors championship parade. There were tens of thousands of celebrants packed closely along Market Street. I’d estimate that less than 1% were wearing masks. It remains to be seen if the parade turns out to be a super-spreader event. The BART trains were also packed, though the majority of riders were wearing masks as masks are still required on BART.

        Reply
        1. Eric Anderson

          It’s another world up here in the “American Redoubt.” Throughout the entire pandemic you would never see more than 10% of the population masking. Still the lowest vax rates in the entire U.S. Across the board, not just covid. I would not be surprised to learn that N. Idaho is in the end determined to, in fact, be a backwater Guateng reservoir like IM Doc is alluding to.

          Reply
          1. drumlin woodchuckles

            Would the low population and far-apart dispersal of many of the people there be a mitigating factor on the lower and slower spread side?

            Dare one hope for such?

            Reply
            1. Eric Anderson

              It seemed to take a long time to reach us in the beginning due to the restrictions. But now? I feel based on the number of people I know reporting through word of mouth that we’re at a peak. Like I said about the US Forest Service up thread … people travel and the world shrinks fast. See, for example, Sun Valley/Ketchum during the peak of the pandemic … huge numbers.

              Reply
    2. curlydan

      I went to a retirement party/happy hour for a friend yesterday at a restaurant (high ceilings in the location at least). 30 people there. I was the only one masked with my 3M Aura N95. I felt kind of like a freak, but that’s the only way I was going. I did remove the mask to make a brief speech about my friend.

      We almost all work at home, but in my small work group of 5 people, one guy had it last week, and one lady had it this week. Disheartening. It was 100 degrees yesterday where I am, so there was no way to have the party outside.

      Reply
    3. Jason Boxman

      Not really surprising; The pandemic was “over” back in December 2020 in Somerville, as far as I could tell based on Davis Square restaurant activity, and the same in Raleigh, NC at that time. At that was really lacking was the lifting of what few restrictions were in place. So many Americans never recognized it as a pandemic, and the rest decided vaccination meant it was over.

      Not a recipe for success. The bill will come due.

      Reply
    4. playon

      In my social circle quite a few people are getting sick or have been ill with COVID (including myself and my wife), they are mostly older folks, 60s & 70s, along with some some friends in their 30s. From what I can tell we are in the middle of a big wave, yet when I go out perhaps 10% are wearing masks. I view our government in the USA as criminal for the neglect of public health.

      Reply
      1. antidlc

        “I view our government in the USA as criminal for the neglect of public health.”

        I do, too. So much suffering, so much death, so much sickness.

        I am absolutely livid at their negligence. And for what? Because the Biden administration thinks that it will help them in the midterms if everyone pretends COVID is over?

        I don’t think that will play well. I have read numerous accounts of people who are shocked, ABSOLUTELY SHOCKED. that they caught COVID even though they were vaxxed and boosted. I don’t think they are going to be happy with the Democrats come election time.

        Reply
        1. Lee

          “I don’t think they are going to be happy with the Democrats come election time.”

          Alas, as ever was, our choices continue to be between tweedledumb and tweedledumber.

          Reply
          1. drumlin woodchuckles

            They and we will need a whole new political party devoted to containing and then eliminating covid.

            Maybe it could be called the Stop And Reverse Covid Party.

            Of course parties and politics itself could be irrelevant and obsolete in America. People who take covid seriously can hopefully recognize eachother in public by wearing serious masks. If people without masks ( for whatever reason) decide to harass the covid cautious for their serious masks, the covid cautious can say something like ” Its a condition of my bail” or “its a condition of my parole” or anything to discourage further conversation and contact. If thats not enough to keep the Zombie Karens away, perhaps pepper spray, bear spray, etc. to make the covid spreaders keep their distance.

            Coupled with maximum feasible avoidance of superspreader or even spot-spreader venues, events, gatherings, etc.

            Reply
          2. Tony Wright

            Here in Australia, we have just had a Federal Election and, for the first time ever, Green and Teal Independent candidates got over 30% of the Lower House vote and 14 of the 151 seats. We have a preferential system, not first past the post, so the arithmetic is a bit complicated.
            This is the first time since Federation that votes for the two major parties, Liberal/National and Labor, have been more or less equalled by independents and “minor” parties. And this despite the best efforts of the ranting Murdoch syncophants on Fox “News” and at News Ltd.
            This moderately seismic change in the political landscape here is widely attributed to public concern regarding woeful climate change policies, lack of effective anti-corruption measures/structures and inadequate attention to issues of importance to women.
            Prior to this latest election the conventional wisdom was that the deck was stacked so far in favour of the two major parties that it was almost impossible for third party or independent candidates to succeed.
            Point being, just because things always have been so doesn’t mean they have to stay that way, perhaps even in the USA. If things get bad enough, the peasants will revolt.
            Pitchforks anyone?

            Reply
      2. neo-realist

        Maybe some blame should go to the 90% not wearing masks. The president and the government can’t make idiots take the necessary protective measures if they want to live in denial or dislike the inconvenience.

        Reply
        1. drumlin woodchuckles

          But the president and the government lied on purpose about masks ” not being necessary” anymore after widespread vaxxing. Do you really think 90% of people are idiots? I think it is more likely that 10% of people are psychological “conspiracy theorists” . . . like me.

          And remember, its not a conspiracy “theory” if it happened. Or if it is happening right now as we watch.

          Reply
          1. Hickory

            I sadly disagree. Whether a person considers something a theory or fact depends on what that person knows. Your fact may be their rampant unfounded speculation if they refuse to investigate / listen.

            Reply
            1. drumlin woodchuckles

              I wish I could sadly disagree with my own self. But when 90% of people are behaving like functional idiots on a major issue or problem, it can’t be innate idiocy anymore. It is the result of very careful Mass Idiocy Design Engineering by various powerful Brainwar Actors.

              The Government and establishment were flooding the zone with sh!t from their end even as the Trumpanons were flooding the zone with sh!t from their end.

              And the government and its spokestrolls were flip flopping their own positions over and over and over again, as well as trying their hardest to suppress the obvious fact of coronavid’s airborne-ness for long enough to get that suppression printed into the brains of the trusting Mass Middle Majority.

              So I can’t write it all off as innate idiocy.

              But sadly, the Mass Design Engineered Idiocy is all around us. ” You’re soaking in it” as Madge the Palmolive Lady might would have said.

              So the best that we the non-idiotized minority can do is mask proudly and learn how to recognize eachother and share knowledge and information among ourselves and then . . . . cautiously . . . . to anyone who seems ready to learn and apply the knowledge.

              And we will just have to accept with a heavy heart that Darwin will take all the rest.

              Unless we have an undeniable Pearl Harbor Moment, followed by a Storming of the Bastille followed by a Russian Civil War where the covid caution side eliminates the covid zombie side (including all the Fauci Svengalis who sent the zombies here) from political and health infrastructure power, presence and existence.

              Reply
    5. Hazelbrew

      More anecdata.
      I am on day 8 of covid. First four to five days were awful. 38.5c temp, cough,sore throat, aches , fatigue, very mucusy, etc. Spent most of first few days asleep. I am now just left with the runny nose and fatigue. 12 hours sleep a night and a top up of 1-2 in the afternoon is essential. And I’m not doing much. Watering the plants for 10-15 minutes? Yes going to need a lie down after that. I never thought that waking up tired was a thing. I do now.

      All from a new office opening work event. 70-100 people together for a few days to the week.
      All double jabbed and boosted, and all asked to confirm with negative LFT before taking part, and reconfirm each day before coming in. Three didn’t make the event,, testing positive before the week itself. And with good cross ventilation in some parts of the building.

      But it still got us. Roughly 10-12 I think testing positive after the event, taking it home to the US and Canada from London. Me and two others on day four. Others by the weekend. :(. Our very own little superspreader event

      Reply
  3. Rob

    Gauteng Province encompasses the single largest metropolitan sprawl in South Africa, including the metropolitan areas of Pretoria and Johannesburg, not mention Soweto, and other surrounding townships/residential areas, so cannot in any sense be described as a place ‘insolated and out of the way’.

    Reply
      1. Thuto

        I’m not sure what you mean by this, I live in Gauteng and my hometown is in the Northwest so I travel regularly between the two provinces, I agree with Rob here. Even the area “immediately to the west of Gauteng” can hardly be described as “isolated and out of the way”, in fact you’d have to travel beyond my hometown of Mahikeng (about 300km from Johannesburg) to start encountering communities you could describe as such. Even then most people in these communities have never even been to Gauteng or had contact with people from there (which protected these rural areas from being ravaged by Covid during the height of the pandemic).

        The second remark I want to make is that SA doesn’t have a place where people with HIV are sent to live out their days, the ARV dispensing coverage is wide enough that infected persons generally live anywhere they want.

        Reply
        1. GM

          I did not say that I know there are such places, I said that hypothetically there might be, but it would have to be a very special situation.

          Regarding the rural places, what you describe does fit the scenario I am proposing — it doesn’t have to be a suburb of Pretoria, but needs to be in the very general vicinity, so that when it spills over the first major population center the virus is detected in is GP,

          I have no idea where exactly that place is or could be, this is why I am saying they need to make some effort to find it, but nobody wants to do that, for a long list of reasons.

          Reply
    1. John Emerson

      Those photos are unconvincing. Flatten the ears, give them better haircuts, and get them to smile and you wouldn’t automatically assume that they were defectives. That sort of genetic science had a lot of agendas.

      It may be that their monstrous appearance is a sign of actual serious defects, but being funny-looking doesn’t mean anything.

      Reply
      1. GM

        That photo gets taken out of context a lot, I made a bit of a mistake by sending it, but I wanted to link the larger context it comes from to something well known.

        Reply
      2. playon

        Perhaps you should read the link above the photograph which goes into some detail about the twins and their lives. “Flattening the ears”, is that a surgical procedure?

        Reply
    2. drumlin woodchuckles

      I thought these photographs were supposed to have been taken in the “Platteland”. Is that the same thing?

      Reply
  4. MT_Wild

    Makes me wonder about chronic and latent infections in wildlife. Most of what you hear about is particulary lethal outbreaks that cause die-offs and get noticed.

    There is limited background surveillance of known circulating wildlife diseases done by USDA, for things like rabies, avian influenza, and some feral swine diseases, but limited in scope and focused on seroprevevalence. But if we were a serious country and wanted to do this there are existing national and state level wildlife disease programs that could do it.

    Just looking around this morning I found this on hepatitis in wild rats in Europe and Asia. Up to roughly 25% of wild rats were found to have HEV-C RNA. Obviously not HIV, but maybe the idea of host pools of immunocompromised wild animals is not that far fetched. As a bonus, the article mentions the potential role of wild boars in interspecies transmission between rats and humans.

    https://www.frontiersin.org/articles/10.3389/fmed.2021.726363/full

    Reply
  5. Basil Pesto

    2. Someone would actually go down in the sewers in NYC (and all other major cities around the world) and sample the rats, mice and other fauna, in order to conclusively identify any possible reservoirs. Combined once again with mass testing of the human population.

    Again, it’s a lot of money at first glance but it’s a trivial amount in the grand scheme of things, and especially given how $50-60 billion just got sent to Ukraine without any hesitation for the Russian artillery and missiles to target practice on.

    Naturally nobody is doing any of that.

    Ha, not only that but last month I remember Lee Fang, one of the left-libertarian covid goober journalists, mocking the notion of China as a relentlessly competent and efficient society…… on the basis of a 20 second Tik Tok clip of a couple of Chinese workers swabbing crabs – presumably in service of animal reservoir surveillance.

    Of course, in the grand scheme of things he and his ilk are irrelevant, but it gives you some sense of the grim intellectual situation generally: people trying to understand and react to covid through their political prejudices and predilections and tribes, without understanding – apparently without being able to even countenance – how utterly ignorant they are, and lacking in meaningful (and, indeed, journalistic) intelligence: looking at such a clip and thinking “hahahaha look at these backward idiots” and not “hmm. that’s peculiar. Why are they doing that? Are we? What am I missing here?”. Follow that line of questioning and you’d probably stumble upon one of the great journalistic stories; as GM has argued, if people understood what was being done to them, there would be blood in the streets.

    Who knows though, maybe it’s a “there but for the grace of god” situation and I’d be thinking along the same lines as him if I hadn’t been an NC reader. So, for that, thanks.

    Reply
    1. ChiGal

      link? I have a high opinion generally of Lee Fang’s investigative reporting. one of the few decent people left at the Intercept.

      Reply
      1. Basil Pesto

        Here you go

        It’s no reason to throw the baby out with the bathwater re: Fang; doubtless he still does good work. It’s just a worrying indicator of trends in groupthink/epistemology/reason generally*, including in a journalistic clique that has more than a little self-regard about being better-than-mainstream. Generally true: the mainstream sucks, and Covid is no exception. But merely viewing a complex scientific issue as a dichotomy (made inevitable by the inane “left-right” civic tribalism, which is a classification so diffuse as to be meaningless), and taking what is, superficially, an anti-mainstream position (Covid is a nothingburger now thanks to vaccines; ongoing concerns about Covid are liberal safetyism gone mad; masks are dumb and bad; China is literally insane; all is for the best in the best of all possible worlds) with no or weak evidence to support that position will, in this case, ultimately just prove to be an example of cutting off your nose to spite your face

        * to be fair, I think this is also an inevitable consequence of public health’s failure throughout the pandemic, discussed at length on NC in the past 2.5 years. If these institutions cede their trustworthiness, then bullshit will proliferate in the face of unreliable civil guidance and general uncertainty.

        Reply
        1. podcastkid

          Both post and reply pretty dern on point, Basil. Too tired to think of another phrase, so I’ll use Limbaugh’s. Fang used to be cutting edge. Very cutting edge. And maybe still is on everything else. But there are too many reporters and “analysts.” They’re all out there going with whatever niche contagion [you have begun here on a thesis that should get more coverage]. Sadly just to survive. About 99% of’em should be CNAs instead (we would still have enough…enough from the MICIMATT tribe alone, who’ll be the last looks like to switch over to something constructive). This includes the offbeat podcasters (but you see in my mind the ones I listen to are not offbeat, ha!). I respect Snowden’s opinion, though, that China was too rigid in some respects [“official” Russia policy seems a little that way too]. At least China had gone some miles forward before they did a few overkills. Quashing discussion of bat lady of course was wrong throughout…it’s not just a lady. It’s probably a lot bigger [involving US too]; and we won’t know how big for a long while. I make the guess mostly just blind, stupid, unquestioning inertia…vs actual depopulation agenda.

          I don’t know anything about facilities in the North West and Gauteng provinces. Nothing. So, there may be pockets of ignorance, but I don’t know about them. There even might be “labs” for all I know, and if there are pockets of backwardness, poverty, and unknowingness, there might not be much local resistance (to any kind of facility). It would seem “labs” run poorly might explain “multiple related lineages making the jump at the same time”? IOW facilities trying to do what GM is suggesting must be done right. Whatever were the conditions conjectured, though, they’ve been mentioned in a vague way. This is why the twins were a bad choice. The argument’s not detailed, and if it hints that there are pockets of extreme ignorance in this area…what bearing does that have on humans-there-were-not-asking-questions-when-rats-picked-up-so-many-lineages? (I don’t see much discussion in the US about what could happen near US sewage treatment plants) If there are no labs in these provinces, then people there might be touchy about claims that regional ignorance alone explains the twins plus covid taking off inordinately. But GM may have been vague on purpose. I can see a reason for that. Anyway, I wish the photo would be removed, so I could share this thing. That said, of course I feel I owe GM and a couple others a ton.

          Reply
    2. PlutoniumKun

      What a lot of people fail to realise about China is that the active public health response (as with so much else) is very localised, albeit based on firm (if vaguely worded) instructions from above. Local officials have to guess from often gnomic announcements what is expected of them and balance that up with all the usual local political and economic considerations. Hence various responses can range from highly competent and humane, to comical and very cruel. So you can find evidence for anything from extreme Chinese efficiency to extreme Chinese stupidity and cruelty if you look for it, and despite the Great Firewall, there are plenty of clips out there to prove whatever your priors are about China.

      There appears to be a huge internal argument in China over Covid – and it seems to be as much based on which Beijing camp you belong to as much as a scientific or public health argument. And there is the usual business vs science argument. A peculiarity of China it seems to me is that while doctors in general have a very low status, public health in general is taken seriously as part of the ‘deal’ between Party and people is that peoples lifestyles should be on an upward trajectory. They’ve even been surprisingly successful lately at dealing with the awful air quality in most cities.

      Reply
      1. Basil Pesto

        I saw Naomi Wu on twitter make a similar point about the variable localised nature of the response recently, comparing Shenzhen (where she lives) to Shanghai. See this thread too.

        I’m sure you don’t need me to tell you that flashing contextless 60 second video snippets is, or should be, pretty weak tea as far as convincing propaganda goes, generally speaking. Yet it seems to do the trick. One wonders how many brief video snippets one could use to make the United States look like a complete civic basket case (or any country for that matter, except maybe Andorra or Luxembourg and the like).

        It remains a pretty open question which way China will go in the next 5 years. Who really knows what the thinking is in the party. I hope they can hold on as long as possible because they’re the only source of hope in an otherwise bleak landscape at the moment, as far as I can see.

        Reply
        1. GM

          We will see where we will be by the time we get to Sigma.

          Then we will know who had the right approach.

          Right now mortality is low because boosters are still holding somewhat while even BA.4/5 still isn’t as bad as even Alpha was.

          But we did see a lot of severe reinfections in early and mid-2021 in South America, Africa, Iran and India, it’s just that nobody directly recorded them as such due to the very limited testing there.

          It’s highly doubtful the bulk of the Delta wave in Iran wasn’t reinfections, and that was much worse than anything prior to that. The estimates were for attack rates up to 250% in some areas. Then they got nearly everyone eligible vaccinated and shortly after that BA.1 hit and infected most people yet again.

          So the average Iranian right now has two doses of vaccine from 9 months ago on top of two infections followed then by a BA.1 infection 5 months ago.

          No wonder cases and deaths are so low. But it is not going to last. It’s delusional to think there isn’t a very high chance of going back to the situation from the Delta wave within the next 2-4 years the latest, perhaps even sooner.

          Reply
          1. Susan the other

            So, dumb question here: why don’t we attack the virus itself? Why can’t we do accelerated “gain of function” procedures on all the spike protein variants, in the lab, until they wear themselves out. The Peter Principle. And then take these pooped-out viruses and inoculate the rest of the viruses. Neutralize them all. Is something like that even poss?

            Reply
        2. PlutoniumKun

          Yes, Wu, for all her (very adorable) eccentricities, is one of the very few China based sources who try to tell things relatively independently (although you have to bear in mind that she will be aware that her account is closely monitored and her access to western social media, and hence her living, will be cut off in an instant if she overstepped the bounds). The same applies for westerners in China who try to be fair (Michael Pettis for example), and you always have to read between the lines sometimes.

          Unfortunately, as with so much else, commentary in China has devolved into simplistic arguments which are equally stupid whether they are pro or anti. China is very big, very complex, with lots of shades of right and wrong, genius and stupidity. Decision making is incredibly opaque (I suspect its almost equally opaque to all but the most insider of insiders) and I’m not sure anyone outside Xi’s inner circle really knows what the calculations are around covid. It may be based on a rational assessment of the health risks to the population, or it may simply be inertia tied to Xi’s belief that he can’t be seen to backpedal having nailed his mast to keeping China clear.

          Since my first visit to China in the later 1990’s I’ve been largely a bear about China’s prospects, and I’ve been almost entirely wrong so far. But it is undeniable that there is a potential perfect storm about to hit China’s economy (housing, debt, over-investment, low productivity growth, bad demography) and I’m not sure they have the tools to deal with it. But as I’ve said, I’ve been wrong before many times. Nobody really knows what will happen if it is perceived that the CCP has ‘failed’ in its implied contract with the population.

          Reply
          1. Raymond Sim

            China’s failure to implode like a proper advanced economy worked a slow-moving but profound change in my attitudes about economics.

            I think my awareness of it is what prepared me to benefit from NC.

            Reply
          2. digi_owl

            The one thing China has, it seems, is that their leadership is willing to take the money men to task in order to save the nation.

            This in sharp contrast to USA and EU, where the monied get bailed out time and time again even as their antics place the overall economy in an ever more precarious situation.

            Reply
            1. Basil Pesto

              two other salient differences, imo, are:

              1. general lack of austerity policy.
              2. a relatively less powerful rentier overclass

              Perhaps that is my wishful thinking/bias projected onto an analysis of why China is continuing to contain this successfully. But they strike me as important factors.

              Reply
              1. PlutoniumKun

                It depends on what you mean by austerity. Like all countries that have adopted an export model of development, Chinese policy is based on permanently suppressing internal demand for products. Chinese personal consumption is significantly below the GNP PP figures indicate it should be. From the point of view of the average Chinese person, that is permanent austerity.

                As for a rentier overclass, China has been very astute in preventing the type of billionaire class arising that is crushing the west, but a country where a huge proportion of the population have their personal life savings tied up in empty apartments is not exactly a healthy model either. China is a nation of landlords without anyone paying rent (the ‘profit’ comes from rising values).

                With privatization of existing public housing and massive provision of private housing mainly in the ownership sector, China has transformed itself from a country dominated by public renters to one of the countries with the highest rate of homeownership within a very short span of just two decades. Today China is a country of homeowners with more than 90% of households owning homes (87% in urban and 96% in rural China) (Clark, Huang, & Yi, 2019). At the same time, more than 20% Chinese households own multiple homes, higher than many developed nations (Huang et al., 2020). This achievement is particularly impressive and is in sharp contrast to the recent decline of homeownership rate in the U.S., Western Europe and other developed countries.

                Reply
                1. Basil Pesto

                  Thank you for the further background and I defer to (and appreciate!) your China knowledge. I also do recall reading here over the years that private debt held in China is dangerously high. I do wonder if those landlords have enough power, or think they do, to have a say in SARS2 policy. I expect many would be bringing some form of pressure to bear, but compared to the oligarchic pressures in the US?

                  re: austerity, my line is rather glib, to the extent that it risks being stupid: it’s no surprise (to me) that a country that just got on with building a massive HSR network in, what, 20 years? Isn’t too worried about the “cost” (setting aside the dubious economics of this calculation, typically pushed by the likes of FT, Bloomberg and the like) of containment. Although I assume cost issues become a bit more nuanced when you get down to the local government level.

                  Reply
          3. GM

            I see that argument about “bad demography” a lot.

            In reality it is the exact opposite — they will have managed to halve their population by the time the resource crisis really hits to the point of societal collapse elsewhere, and to have done that through peaceful and organized means.

            It’s still not a guarantee order there will be no disaster, but it’s certainly a much better situation than the one e.g. south of the Himalayas.

            A 70-year old can still work and be productive in a lot of areas.

            But you can’t magically conjure food and energy for hundreds of millions of young people and then effectively keep them from rioting when the realization sets in that there is not enough for everyone.

            The one-child policy is an extremely rare example of a government looking far ahead and taking decisive measures to avert catastrophe.

            Reply
              1. PlutoniumKun

                The natural collapse in birth rates seems pretty much inevitable in the Asian (Japan/ROK/Taiwan) model of development. The pressures on young women in the workforce is brutal and makes having more than one child very difficult.

                The only way to create a more stable population is not by ‘letting’ people have more children, but by having more family friendly workplaces and support for people with families. But there is a very strong ideological and cultural set of obstacles for this across Asia, not just in China.

                Reply
            1. PlutoniumKun

              The main problem is not a drop in the number of people – thats a good thing. The main problem is the rapidity of the transition. China is going to go from a ‘young’ country to an ‘old’ one very fast and with little evidence of preparation.

              Add in cultural issues – in China people tend to see it as ‘normal’ to work incredibly hard for 20-30 years and then retire relatively early when your children take up the load. If you think telling the French that they can’t retire early is hard, try telling 500 million Chinese.

              Reply
        3. digi_owl

          That has begun to frustrate me a lot of late.

          Media keep treating Russia and China like some singular blob where all dictates come from Moscow and Beijing. But they are internally not that different from USA, only they do not market the individual “states” as hard as USA does.

          Reply
  6. DRFRANK

    I am curious about the case being made that the virus will mutate in highly vaccinated populations into something that not only has the high rates of infection that are already being seen, but also a high rate of morbidity. Clearly, the vaccines have been effective in suppressing virulence, but not infection rates. Will virulence return at some point, especially among the vaccinated? I don’t know how to evaluate this argument.

    The main proponent of this view is Geert Vanden Bossche, a voice from the periphery whose priors are hard for me to evaluate, to say nothing of his science.

    see https://www.voiceforscienceandsolidarity.org/videos-and-interviews/second-call-to-who-please-dont-vaccinate-against-omicron

    Reply
    1. OnceWereVirologist

      It’s nonsense. A sentence like “If we are now going to vaccinate against Omicron, we are going to take away this window of opportunity for the population to generate herd immunity, thanks to freeing up our innate antibodies.” doesn’t make a lick of sense. Omicron doesn’t generate persistent lifelong immunity any more than any other variant. Nor does going unvaccinated and getting a “natural” infection make the slightest difference to that fact. As to the specific contention : “By doing mass vaccination against Omicron, we may be putting enough immune pressure on viral infectiousness to give variants that are capable of entering into the cell through an alternative receptor – to give them a competitive advantage.” A natural infection will produce an antibody response directed at antigens on the spike protein, too. It’s the exact same selection pressure either way. Some of the variants we have already seen emerged in primarily unvaccinated populations. Further : “Such a situation is in fact, a textbook example, for how you provoke antibody-dependent enhancement of the disease.” This is not unreasonable. But if ADE were a factor in COVID morbidity we should know it by now given how many people have been infected multiple times. And again if COVID developed this ability (not impossible, as it has been seen in laboratory studies with SARS) then it could just as easily happen in an unvaccinated person.

      Reply
      1. Basil Pesto

        This very weird conceit about the apparent invincibility of the “natural” human immune system has proliferated in the last couple of years.

        And again if COVID developed this ability (not impossible, as it has been seen in laboratory studies with SARS) then it could just as easily happen in an unvaccinated person.

        Yes, and if/when it happens, GvdB will simply say “I told you so” circumstantially, without actually coming close to proving his argument at all.

        Reply
        1. OnceWereVirologist

          Having further read the website, in answer to the question “What is going on in India? Why is the pandemic there so aggressive although they haven’t been vaccinated?”, I found the following “I presume that there has been massive spread of the virus amongst asymptomatically infected people. Asymptomatic infections fuel spread of more infectious Sars-CoV-2 variants due to increasingly frequent re-exposure of previously infected subjects experiencing suppression of their natural antibodies as a result of suboptimal S-specific antibodies (Abs).” So now it’s not only vaccinees but asymptomatic people who are problematic. The implication is that you have to get properly sick if you want a proper “natural” immune response. But if non-vaccinated asymptomatic people also produce suboptimal antibodies that promote the spread of new variants hasn’t he completely invalidated his main thesis : i.e. that vaccines are bad because they produce suboptimal antibodies whereas natural infections don’t.

          Reply
    2. Raymond Sim

      I haven’t delved into Geert Vanden Bossche’s analysis in detail, because he appears, at first inspection, to be operating with a set of false axioms, whether these are ever explicitly stated, or merely tacit I do not know. I’ve actually been quite curious about it, but the need to triage the stuff I use my limited brain energy on has kept me from investigating further.

      In case anyone’s interested, I think his errors are likely as follows:

      1. He invests innate immunity with excessive coping powers*, and fails to allow for the possibility that the virus might find selective advantage in ever-increasing ability to overcome innate immunity (The damn thing does seem to be evolving in this direction btw.).

      This would be a natural way to go wrong if, as I suspect,

      2. He assumes that the pathogen and host populations are divided into subgroups that are more isolated from one another than they actually are. This is a big deal because it amounts to assuming that while local extinctions may occur, universal** extinction is unlikely. It’s the constraint that penalizes attack on innate immunity sufficiently that the virus is unlikely to continue enhancing this capacity indefinitely. Needless to say, air transport makes this error so severe as to be risible. Hence my as yet unsatisfied curiosity as to what the guy is actually thinking.

      * ‘Coping’ in this sense could mean stacks of corpses in the parking lots where the refrigerated trailers used to be. I don’t think Vanden Bossche minces words about this, but I have the impression lefty whisper-down-the-lane may be obscuring it.

      ** 100% universal extinction might indeed be unlikely, but if you think a scenario where China and Cuba are the only technologically advanced nations still functioning ten years from now is fantastical, your ‘thinking’ is grounded in your emotional needs, not the facts available to us.

      Reply
  7. Holly

    Fascinating and disturbing.
    I suppose there is no end to what we will do to keep up the illusion that all is well and profits must continue.
    Sadly, I don’t think this virus will just go away because we want it to. With nearly 8 billion on the planet we will soon dredge up another zoonotic to replace it anyway.

    Reply
  8. Onward to Dystopia

    The worst case of covid to happen to anyone close to me was just a few weeks ago to a friend of ours. He said it was literally the worst thing he’s experienced since dealing with withdrawals from meth addiction. I have no idea what that’s like, but in any case, he’s doing okay now.
    What stuck out to me here was this, “When Pi [the next major variant] hits one can expect a total disaster — billions of people are right now accumulating preexisting conditions that are setting the stage for the grim reaper to take them when the next big antigenic shift happens.”
    I mean, I still pay attention to this stuff, I try to take precautions, but I don’t expect any kind of lockdowns, financial aid, etc. People would have to be dropping dead in the street like a Romero film. COVID is simply inconvenient to American’s screwing each other over for a dollar, and that trumps everything else — so you’re on your own, folks.

    Reply
    1. BeliTsari

      That’s just it. Our recent 3rd acute infection (BA.2.12.1? PCR, but not sequenced) kicked our ASS! We’ve picked up a pretty standard array of cascading PASC symptoms, in 2 1/2 years. BUT, Rochelle still calls them, “preexisting comorbidity” and is trying through equally corrupt media & academia, to re-cast long COVID as uppity essentials’ psychosomatic malingering, so Harris can incarcerate indentured gig-serfs into fire-jumpers, line-cooks or replacement HCW, care-givers, eviction/ collection-app peons or teachers? Balrog, to hit as Broadway unmasks?

      Reply
    2. chuck roast

      So far I have avoided the plague…I think…unless I have been asymptomatic without knowing it. Even with GM, IMDoc and the rest of the NC brethren chirping and trying to figure it out, I’m still doing the Sgt. Schultz defense. The only thing I am pretty sure of is that a coronavirus is a cold virus. Decades of getting a cold in the spring and a cold in the fall have re-enforced that there is very little recourse for me. And the only thing that I am absolutely sure of that there is no public health only a medical cartel. Well and truly family-blogged.

      So, I got two J&J shots in the belief that an adenovirus was preferable to being an mRNA lab rat. I put a bit of povidone-iodine in an OTC nasal spray and blast myself with it when I come home from my limited social rounds. I’m a geezer and can deal with it. If all the USAian kids aren’t developing serious and permanent cases of PTSD they are not paying attention. I’d feel badly for them if they didn’t spend all their time lookin at their hands. So, they are not paying attention. Maybe there is hope for them in a bass ackward kind of way.

      Reply
      1. Mike

        Wish I had gone the J&J route, I chose the mRNA lab rat route. 2nd shot kicked my butt big time, booster shot changed things in me… I thought I was going to die after taking that. For some time after words felt like my heart would explode out of my chest, I stopped working out almost entirely. Granted I am an N=1 it still makes it very believable for me that all the drama of heart attacks in professional athletes could be from the shots. I’m sure living at 9000 feet doesn’t help though.

        Though tied up in all of this is that long covid presents its own risks though it also seems the vaccines could pose additional and possible unacceptable risk in young people, but filtering the signal in the noise with all of the information out there is a tall order for us plebs.

        Reply
        1. Onward to Dystopia

          Same here — I got two mRNA vax. First was fine, but the second laid me up in a dark room feeling like hell for over a day. I just never went back for a third, and hey maybe I should have, but I’m sure there’s more people like me who just have an aversion to doing it after that experience, some never got around to it others intentionally avoided. I was a mix of the two. I wondered how much worse a THIRD shot would be, and I’m not working right now so I can lay around and recover, but not everyone has that option.
          And now it’s been so long, over a year since covid shot #2 that I have no idea what another one would accomplish — is it still a booster at that point? Or am I just starting over from scratch? Are these vax even targeted at these new variants? (No.)
          I know my friend had at least two mRNA vax, because I actually went with him and got my first shot when he got his second — like usual I was procrastinating — not sure if he had a booster or not, but he got really sick. I think I’ve had covid twice (but not certain) first was pre-vax and both were fairly mild, loss of smell both times and drowsy. The vax experience was rougher.

          Reply
      2. eg

        My immune system has been on a carnival ride. I had AZ first, but Canada stopped administering it, so my second shot was Moderna. Then at Christmas I got Pfizer as my booster.

        The reaction to AZ was unpleasant for about 36 hours starting at T+12 hours. I had minimal to zero reaction to my mRNA shots.

        Reply
  9. Samuel Conner

    I wonder if the large dataset underlying the new study could be mined or massaged to answer a question that might get people’s attention and motivate them to take NPIs seriously:

    How many months does the first CV infection knock off your life expectancy?

    What is the life expectancy decrement for each subsequent infection?

    —-

    Answers like these would put the official “you’re on your own — make your own risk assessments and adopt the precautions right for you” policy posture in stark relief.

    “Yeah, I want to live life like it used to be, and this is how many years of my lifespan I am willing to surrender (and how much additional illness I am willing to embrace) in order to get back to ‘life as normal’.”

    That is what they are asking us to do.

    Reply
    1. Mikel

      I’ve come to the conclusion that no form of entertainment is worth the chance. That is what is largely being “life as normal”. Entertainment.
      “Here we are now
      Entertain us…”

      Reply
      1. antidlc

        “I’ve come to the conclusion that no form of entertainment is worth the chance. ”

        I reached the same conclusion. How i miss live theatre and opera. I get brochures in the mail (used to be a season ticketholder) and stare at them longingly.

        And it’s so dang hot that any outside activity is pretty much out of the question.

        Reply
    2. Michael G

      A very interesting idea. But I suspect it will be a case where there is a large difference between mean and median. There may be a clear difference in average life expectancy, but the average person will show far less effect.

      Reply
  10. Ghost in the Machine

    I wonder what happened to the much touted ‘plug and play’ ability of mRNA vaccines for new variants.

    Reply
    1. Basil Pesto

      technically, this could have been doner much sooner than it has been (I’ve seen reports of an Omicron update for Moderna for August 1 in Australia. But it’s for BA.1, lol. day late, dollar short).

      Operation Warp Speed was stopped by Biden admin, and self-funding the update timeously costs these companies money. I assume their profits have otherwise gone to C-suite, dividends and the like.

      Reply
      1. Greg

        Are the mass manufacturing supply chains as hot swappable as the updated mRNA designs?

        I’ve wondered this, since in theory a new mRNA vaccine is as advertised, super fast to build, but we haven’t seen any in the wild. Implies something else is up.

        It doesnt seem like it would just be cost in the design phase, because fast ≅ cheap, in knowledge work. So that implies cost due to retooling somewhere in the supply chain. Or somewhere else.

        Reply
  11. Michael G

    I have wondered why experts don’t give more consideration to recombination. Surely the easiest way to acquire a large number of differences would be via simultaneous infection with COVID and an established coronavirus? Occasionally one of the resulting recombinants could be a super strain.

    Reply
  12. Susan the other

    I think doctors are trying to impart this message to patients without causing too much alarm. I went in for my yearly last week and my doc popped into the room wearing a snug mask; she stayed always at least 6 feet away from me. About 20 minutes. In the course of our conversation she said she thinks docs will be wearing masks for a long time. She implied years. Because there are so many epidemics always circulating. She was careful not to say that Covid was unstoppable, etc. But she made sure I understood the value of a good mask for the duration.

    Reply
    1. Raymond Sim

      Susan, are you by any chance in or near Davis California?

      Doctors with their heads screwed on right are more precious than rubies.

      Reply
    2. Petter

      I was admitted to the hospital with pneumonia a couple of weeks ago. None of the physicians or nursing/support staff were wearing masks, not even the nurse who administered a PCR test.
      Government ministers refer to the pandemic as being in the past. The Public Health Institute is saying, not so fast, as they expect the B5 variant to hit come fall and are lobbying to get funding restored.
      — We are all corpses on vacation (Eduard Limonov)

      Reply
  13. IM Doc

    I view my most important job as a physician to be education of my patients. To tell the truth as I see it at all times and to give my commentary on the current data based on experience. I took to doing this on this site earlier in this pandemic because I could not see that was happening too often in the media landscape.

    As such, I will give this update on where we are in my practice with just today’s numbers, which I will be discussing with inquiring patients today.

    My staff and I maintain a spreadsheet daily of what we are seeing. No one in officialdom seems to care about this type of on the ground data – but I think one day it will be very helpful for those learning about what happened during this pandemic. Every morning I am given a condensed top line list of the patients with COVID that were encountered the day before.

    Right up front, I work in one of the most vaccinated counties in the USA, >80% vaccinated – >60% boosted. The surrounding areas where a good number of my patients come from is at best 50% vaccinated.

    Yesterday, I had 45 COVID patients evaluated by me or my staff. More than 50% of these were from 2 different superspreading events, one a wedding, the other a performance. Out of these 45 patients, one was completely unvaccinated, 17 were double vaccinated, 9 were vaxxed with one booster and 19 were vaccinated with 2 boosters.

    The very concerning thing to me is how many of these were reinfections. Of the 45 patients, 37 were reinfections, and 11 of those have just been within the last 6 weeks.

    This is right in line with what I have been seeing for the past few weeks and it is also right in line with what is reported in this paper. Reinfections are becoming more and more frequent – and the patients, vaccinated or not, are getting sicker with each episode.

    First of all, the majority of these patients at this moment in time are not all that sick. But some of them really are quite ill. 12 from yesterday to be exact.

    Much has been made of Simpson’s paradox in our national media the past few weeks in an attempt to explain away all these infections and reinfections in the vaccinated. It is a very complicated statistical concept, but in general it basically is this – I work in a >80% vaccinated area so I would expect >80% vaccinated patients. Therefore, we are good. THIS IS EXPECTED. The writers of these articles know nothing of medical statistics and this is profoundly misleading. It is making people much more comfortable than they really need to be.

    It is absurd to invoke Simpson’s paradox in this situation for 2 reasons –

    a) Simpson’s paradox has never been invoked in a vaccine situation to my knowledge – not one time. This goes back to the sterilizing vs non-sterilizing issue. We would just not even see patients at all if the vaxxes were sterilizing. Simpson’s paradox is perfectly appropriate to discuss in medical therapy for heart disease, etc.. For vaccines, it is completely inappropriate.

    b) Much more important – June 21st of 2021 – I had 2 COVID patients – in a much less vaccinated environment – June 21st of 2022 I had 45. This is important if you assume some seasonal variation. YOU SIMPLY CANNOT HAVE THIS LEVEL OF DIFFERENCE and invoke Simpson’s paradox

    What these writers and news outlets are doing is very dangerous – and is giving the vaccinated a sense that they are bulletproof. WE ARE ALL GOOD – MEDICAL STATISTICS TELL US THIS WAS EXPECTED – EVERYTHING IS GREAT. This is not a good message. It is not based in reality.

    My education bullet points to my patients—— This is very serious. Your vaccine status is giving you zero protection from catching and transmitting this virus. We have no idea what these frequent infections can do to you, but my sense is it is not good for you. PLEASE PLEASE do not depend on this vaccine to protect you from infection. Take every precaution you can. There is evidence that it may protect you from severe illness, but even that seems to be not as solid as it was before.

    And I go back to what I have been saying all along. Get healthy, get your a1c down, get your waist size down. Eat well. Sleep well. Enjoy good times with your family. Get out in the sun. De-stress. Get going on the VIT D and ZINC. Please please be careful.

    Everyone here – I would say the same to you – please be careful.

    Reply
    1. Samuel Conner

      Is there some way, within the medical payments system, to prescribe the wearing of N95 respirators and bill that to insurance? To my simple-minded way of thinking, N95 respirators employed for this purpose qualify as “medical devices”; are they covered by any insurance? Given the cost to insurers of COVID-induced hospital stays, I would think that the insurers would be falling over themselves to encourage their use, and would gladly pay for them.

      The counsel to take all available precautions is essential, but me thinks it would help to lower the barrier a bit if it were possible to actually issue medical “orders” that specific NPIs be implemented.

      Reply
    2. Raymond Sim

      I think about the bias towards the vaccinated among your patients requiring treatment a lot. I don’t see any plausible way of accounting for it that isn’t very bad news.

      I’ve probably said it before, but the worst case scenario I come up with is that it’s socioeconomic in origin – a host of perverse influences have led to wealthier, more educated vaccinated people tallying up reinfections faster, and since number of infections is a discrete variable, initially the consequences are dramatically disproportionate in that group. It’s worst case because eventually it embraces the whole population.

      But now there’s this discussion of ‘imprinting’ …

      Whatever its causes I think this phenomenon you’re observing is probably of great importance, and it’s good to know you’re documenting it, and as my wife the virologist likes to say “Making it science.”

      Reply
      1. Basil Pesto

        Thank you both.

        I must say when I was reading about the ‘imprinting paper’ that came out last week, it very much reminded me of IM Doc relating the disproportionate number of vaccinees he’s observed at his work needing care, something that he’s been describing for about 1-2 months now, if memory serves.

        I’m a bit too dumb to be able to tease out the imprinting issue and its implications much further so I’ll leave it to the actual scientists. Only to say, yes, it does strike me as worrisome.

        Reply
      2. flora

        I don’t see any plausible way of accounting for it that isn’t very bad news.

        Well, sadly, I think “very bad news” is not to be dismissed out of hand at this point.

        Reply
    3. GF

      IM Doc,

      A couple people in comments above mentioned Type O blood in passing and that the two individuals who have Type O did not get the infection others in their group did. Does having Type O blood make one less likely to be infected?

      https://www.nakedcapitalism.com/2022/06/fast-and-furious-omicron-new-variants-defy-explanation-and-dont-bode-well-for-future-either.html#comment-3743038

      https://www.nakedcapitalism.com/2022/06/fast-and-furious-omicron-new-variants-defy-explanation-and-dont-bode-well-for-future-either.html#comment-3743080

      Reply
      1. IM Doc

        I have never read, seen or listened to any compelling evidence that blood typing has any kind of prognostic role in COVID infections.

        Therefore, no this has not been routinely tested. It would be simple enough to do a database search and see in our EMR because that is a lab that is immutable once done.

        Reply
    4. ChrisPacific

      My education bullet points to my patients—— This is very serious. Your vaccine status is giving you zero protection from catching and transmitting this virus. We have no idea what these frequent infections can do to you, but my sense is it is not good for you. PLEASE PLEASE do not depend on this vaccine to protect you from infection. Take every precaution you can. There is evidence that it may protect you from severe illness, but even that seems to be not as solid as it was before.

      I’ve followed NC enough that these statements all seem self-evident to me (and with the reinfection study linked here, assuming it’s approved for publication, we now have some evidence for the ‘not good for you’ hypothesis). The fact that it’s so far at odds with the public sentiment is an indictment of policymakers around the world.

      Reply
    5. SocalJimObjects

      “Get healthy, get your a1c down, get your waist size down. Eat well. Sleep well. Enjoy good times with your family. Get out in the sun. De-stress. Get going on the VIT D and ZINC.”

      I have a sweet tooth, so I find it impossible to get through an entire day without consuming some sugar. But, ever since Covid began, my BMI has gone down from 30.5 to the current 24.9. That took almost an entire year by the way. I walk at least 3 miles every morning going up and down a sloping hill near my place, and I watch my calories intake like a hawk. I don’t like drinking soda, but would eat a very small slice of cake or some bread with filling as afternoon snack every day (I have as sweet tooth after all). I have also been consuming 5000 IU of Vitamin D and 1000 ml of Vitamin C every day for the last 2 years. I don’t think I am super healthy, but I am trying to get better. I am now very slowly working up to adding 100 squats and 50 push ups a day to my daily exercise routine.

      Because of my weight loss, all my clothes now look baggy on me, but I am not fashion conscious so I haven’t bought a new wardrobe. Because I try to walk everywhere, on occasion I do find it annoying that I have to keep pulling my pants up after a couple of steps here and there :)

      Reply
      1. Yves Smith Post author

        Congrats! Losing weight and keeping it off takes discipline!

        Have you tried very sweet fruits as an alternative to cake, like ripe mangoes and pineapple? I think they have a similar glycemic index but are less calorie dense. A really good mango is delish.

        Reply
        1. SocalJimObjects

          Thanks Yves. I love mangoes and pineapples, but for some reason I don’t find them as “satisfying”. It could all be psychological. I have broken some bad habits, but I am not ready to give up on the rest yet :(

          Reply
          1. PlutoniumKun

            Congratulations on the weight loss, it sounds like you have a healthy balance.

            I think its important to recognize that the ‘satisfaction’ sugary foods give us is from insulin spikes. If you hit your body with too much sugar you get a dip in insulin a couple of hours later, which needs more sugar to bring it back up again, hence the feeling of ‘satisfaction’ when that sugar hits your bloodstream. It is literally an addiction that works the same on our body as opiates or nicotine. Its this effect which makes us feel we ‘need’ a snack at 11am and 4pm to get us to lunch or dinner.

            Its not just a case of the amount of sugar you consume, but the speed it hits your body. For example, if you drink a healthy smoothie with fruit, it can affect your insulin levels the same way as a sugary soda if you drink it fast – but if you take your time with it and sip it over half an hour or more, it has a much lesser effect and so is less likely to provoke a desire for something sugary 2 or 3 hours later.

            it sounds hard core, but I’ve found great benefits from occasional fasting for 5 days (building up from one day fasts to get your body used to it). If you eat very healthily for the few days after a fast I find it resets my tastebuds and I find less food, and healthier food, more satisfying. When I went on long bike rides I used to think I needed regular sports drinks or sugary snack infusions to keep going – now I find I can cycle happily most of the day on a ‘normal’ diet. I may not be particularly fast, but I think adopting your metabolism to tick over at a steady natural pace (even when exercising hard) can give great long term benefits. When I find myself craving too much food I’ve found that homemade protein shakes are very effective at suppressing appetite (I mix pea protein with some walnuts, raw chocolate and frozen blueberries).

            If you check out Dr. Brad Stansfield on YT and twitter, he gives some very solid advice and seems very open minded (unlike most, he isn’t trying to sell a lifestyle). Nutrionfacts.org is heavy on the vegan messaging, but also sound on the science with lots of great information.

            Reply
            1. SocalJimObjects

              Thanks. Yeah, in the past I was definitely a much bigger sugar addict. Soda and alcohol have never been my thing, so for me it’s always been sugar in processed foods.

              Speaking of insulin spikes, during my “glory” days when I was giving myself a generous helping during meal times, I would often experience a “crash” afterwards. I am however glad to say that those days are behind me. The thing is, my fasting blood sugar level is around 105, which I think means I am prediabetic. So yes, my weight is now at a level that’s considered healthy (borderline) according to BMI, but in actuality I still have a lot of work to do if I want to get healthier.

              Wow, occasional fasting for 5 days is probably something I will never be able to do, but 1 day a week is probably doable. Thanks for the suggestion!!! I’ll also checkout Dr Standsfield’s videos.

              For me, the thing I’ve learned is that when it comes to weight loss, I am more of the slow and steady type. Gradual small changes and consistency is what worked for me.

              Reply
              1. Noone from Nowheresville

                @SocalJimObjects

                If you can make your own bread and desserts, you can do a lot to control the sugar hits.

                On desserts, I use about 1/3 of what’s called for on the sugar. You won’t get the punched in the face sugar hit. But after 3 or 4 bits you will notice it.

                I’ll also use maple syrup or molasses in place granulated sugar when it makes sense.

                I started baking my own bread. I replace flour with things like flaxseeds, chia seeds, amaranth, scottish oats, nuts. Whatever alternatives happen to be onsale which might add more nutrition to the mix than only plain flour. I occasionally use molasses to create a starter. Gives the bread more caramel color and flavor. A little goes a long way.

                Smoothies are wonderful! I highly recommend them as well. My base starts with water and I add measured sodium (I monitor this also don’t eat many processed foods so not getting the hidden sodium). Flip from veggie based one day to fresh fruit based another. Add a little not from concentrate juices as well. Mostly water though. I also like to add dried or fresh chili peppers to the fruit or veggie mix. A little chili in whatever form goes a long way. Seems to wake up the palate and get the blood pumping.

                A leisurely one in the morning can really set the day off right.

                Reply
    6. eg

      My 16 year old son has had 4 respiratory infections in the past 6 months (maskless schools; occasional gym attendance; working in a McDonalds). Thanks to our troglodytic provincial government he hasn’t been eligible for PCR testing during this period. We have attempted use of the rapid testing kits several times (all results negative) but I am suspicious of our competence to administer them correctly. I find it difficult to believe that none of these episodes were due to Covid.

      Fortunately neither my wife nor I have been infected, but the more often he is the greater our chances of contracting it from him.

      We are less than impressed with the public health response in Ontario, to say the least.

      Reply
    1. Yves Smith Post author

      Yes, this was also a topic among our Brain Trust. And it’s not just an issue for men. An endocrinologist I saw years ago had a pet peeve that women outside elite athletes (who might natively be high testosterone and need to show their history) are pretty much never tested for testosterone, it’s a pricey test. He said that 1/3 of the women on anti-depressants are low testosterone and getting their test levels to normal would in most if not all cases clear it up.

      No one is gonna look at testosterone impact in women when it’s important for them too.

      Reply
  14. Dick Swenson

    My wife and I received both Pfizer shots in early Spring 2020, and both boosters as soon as they were released. We became positive on 5 June, quarantined until 10 June, and were still positive until 12 June. My wife volunteers at a local hospital and was required by the hospital to wear a properly fitted N-95 mask until advised otherwise if she wanted to continue her volunteer work. Everyone inside the hospital is required to do so, positive or negative.

    We have had a slowish recovery, indicated by fatigue, but otherwise asymptomatic.

    What lessons can we learn? Personally, I believe the vaccine mitigated our symptoms, and I believe that PROPER masking mitigates transmission.

    I also strongly support most of the discussion above about how “personal care physicians” should discuss Covid with their patients. Honesty and simplicity are always to be preferred. I am 84, my wife is 70.

    Reply
  15. Raymond Sim

    The Omicron origin becomes more and more mysterious with every new iteration.

    Ain’t it the truth? I wish heard it acknowledged more often.

    How about circulation in a resistant human population? If I’m not mistaken the genetic heritage of Southern Africans includes contributions from some lineages rarely seen elsewhere. Perhaps including ancient hunter-gatherers who often sheltered in caves, or even at times utilized cave-dwelling bats as a food source?

    Reply
    1. Lee

      Recently there have been a couple of papers looking into the possibility of genetic factors determining susceptibility or resistance to Covid.

      The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies PNAS

      “…Based on previously identified inborn errors of type I interferon (IFN) immunity (9), the COVID Human Genetic Effort (10) has shown that type I IFN immunity is essential for protective immunity to respiratory infection with SARS-CoV-2 (11–14). We have reported that inborn errors of Toll-like receptor 3 (TLR3)-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in a small subset of patients (14)…”

      The major genetic risk factor for severe COVID-19 is inherited from Neanderthals Nature

      “Abstract
      A recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A separate study (COVID-19 Host Genetics Initiative)2 comprising 3,199 hospitalized patients with coronavirus disease 2019 (COVID-19) and control individuals showed that this cluster is the major genetic risk factor for severe symptoms after SARS-CoV-2 infection and hospitalization. Here we show that the risk is conferred by a genomic segment of around 50 kilobases in size that is inherited from Neanderthals and is carried by around 50% of people in south Asia and around 16% of people in Europe.”

      Only two major populations, sub-Saharan Africans and Northeastern Asians, generally lack Neanderthal heritage.

      Reply
      1. Yves Smith Post author

        This study was published in 2020 and therefore on wild type. It’s irrelevant now. Wild type used ACE-2 + TMPRSS2 to enter cells. That combo is found disproportionately in the aveoli, which is why under wild type many got viral pneumonia and the ones who died did so by having their lungs over weeks turn into goo. Omicron uses only ACE-2, which is all over the body.

        Reply
  16. Joe Well

    New variants are yet more reason to explore sterilizing nasal sprays like Sanotize, since they aren’t specific to evolving features on the virus like particular spikes.

    I’ve tried Sanotize and it is as tolerable as any other nasal spray.

    Reply
    1. Joe Well

      Recent clinical study (not peer-reviewed):

      “Among the 203 participants who used NONS [Nitric Oxide Nasal Spray, generic name for Sanotize], 13 tested positive (6.4% infection rate). Of the 422 in the control group, 108 participants tested positive (25.6% infection rate), a statistically significant difference from the treatment group (P<0.0001)."

      Why is this not being reported all over the place?

      Reply
  17. ChrisPacific

    Thank you for the reinfection study. I’ve been looking for evidence-supported results on the effect of reinfections, and in particular whether each reinfection is a new roll of the dice for long Covid. I see the authors avoid venturing an answer to that question, but point out that every reinfection (up to the third, which presumably is the most we have good data on) adds negative outcome risk independently of the previous infections. That sounds an awful lot like a Yes to me, albeit a provisional one. The author does avoid attempting to quantify the risk from reinfections, merely claiming that it exists, and that could make a big difference in the result. We’ll need more data to be sure, which will come with time.

    It’s at the point now where it’s impossible to completely avoid risk (if you’re a parent of school age children, at least) so I think my strategy will be to lower it as much as possible and get Covid as infrequently as possible. Since most of humanity have apparently volunteered to be guinea pigs and test the reinfection hypothesis themselves, that should give some warning of what I and my family can expect.

    Reply
  18. Traveller5678

    The Omicron origins are even more murkier when you read this story about how it was originally detected first in four diplomats in Botswana. Botswana has still not completely identified where they came from or stated their travel itineraries before arriving in Botswana – https://www.nytimes.com/2021/12/03/world/botswana-diplomats-omicron-europe.html

    As for myself – I had my first bout of covid at the beginning of May, unvaccinated, with what I assume to be BA2 according to sequencing reports in my state at the time. I am in my early 40’s, normal BMI.

    My symptoms were a 102 degree fever for one night, followed by 2.5 days of a sore throat, followed by another 3 days of runny nose and head being stuffed up. Briefly lost taste and smell for two days but it all came back within a week. Also had a cough of course. No fatigue or lingering symptoms that I’m aware of. Unlike a regular cold and flu – all the symptoms were completely separate from each other separated by a good 6-8 hours.

    Do I hope this gives me some immunity to sub variants of BA2? Yes. Will it, only time will tell really?

    I think IMDOC has mentioned before this is more similar to the russian flu pandemic of the 1890’s – in which waves of illnesses came back every year for 5-10 years before it finally faded away into endemic background noise due to most of humanity’s immune system having encountered it multiple times.

    Reply
    1. Basil Pesto

      I think IMDOC has mentioned before this is more similar to the russian flu pandemic of the 1890’s – in which waves of illnesses came back every year for 5-10 years before it finally faded away into endemic background noise due to most of humanity’s immune system having encountered it multiple times.

      It’s an interesting historical hypothesis (the ‘OC43’ hypothesis) but imo the evidence is too circumstantial to be relied upon to predict outcomes for the SARS2 pandemic. The latter seems sufficiently sui generis so as to evade neat comparison with previous human-afflicting pathogens, and my understanding is that SARS2 is sufficiently different from OC43 genetically so as to make such comparisons a bit difficult.

      GM has used avian IBV coronavirus and its natural history as a more likely SARS2 analogue, which certainly makes me hope the OC43 comparison is more likely! But we should take nothing for granted.

      Reply
  19. mike

    1. Mass population-wide testing…

    2. Someone would actually go down….

    (My add): 3. World-wide surveillance and auditing (or out right bans) of biolabs making artificial modifications to viruses. We still all know there is a great possibility that Covid came from a lab. Like many other technologies in this world, just because we can doesn’t mean we should, it is a Pandora’s box. At this point the premise/logic behind search for new viruses in the wild as well gain-of-function research has no merit. Traditionally they have sold us on early detection and understanding of a virus as a means to know of our future “what-ifs”. When you think about how Moderna can sequence covid and tailor a mRNA vaccine in 48 hours, knowing a genetic sequence in advance helps you by what… 1 day? Considering they still took 6 months to ram through on testing and efficacy you can see the gain of 1 day for having programs of gain-of-function or wild animal monitoring doesn’t help us much. And it certainly doesn’t help us much when you realize the cause of the pandemic could very well be the G.O.F. research in the 1st place. For my non M.D. brain the risk analysis proposition for the virus research taking place makes no sense. It is maddening that they are only expanding on these programs:

    https://www.usaid.gov/news-information/press-releases/oct-5-2021-usaid-announces-new-125-million-project-detect-unknown-viruses

    USAID ANNOUNCES NEW $125 MILLION PROJECT TO DETECT UNKNOWN VIRUSES WITH PANDEMIC POTENTIAL

    Reply
  20. THEWILLMAN

    Everyone talks about if the original Covid is from a lab. Omicron is from the original variant (not Delta) and just popped up out of no where and is defying all expectations – has anyone considered that Omicron was intentionally released as a less lethal and more contagious variant to end the lockdown portion of the pandemic?

    I’ll put down my tin foil hat now. Thanks for continuing the amazing analysis on this as it progresses.

    Reply
      1. Yves Smith Post author

        No no no. We went through this at the time. It is almost certainly the result of a protracted infection in an immuno-compromised individual. It has a massive numbers of changes on the spike. The reason it was so contagious is the massive number of changes = immune escape. Its success was due to the public having largely dropped all non-pharmaceutical interventions due to the vaccines, like flying on airplanes, going to parties, not masking.

        Reply
  21. kareninca

    It looks like a majority of people with long covid don’t actually clear covid from their bodies:

    “We analyzed plasma samples collected from a cohort of PASC and COVID-19 patients (n = 63) to quantify circulating viral antigens and inflammatory markers. Strikingly, we detect SARS-CoV-2 spike antigen in a majority of PASC patients up to 12 months post-diagnosis, suggesting the presence of an active persistent SARS-CoV-2 viral reservoir.” (https://www.medrxiv.org/content/10.1101/2022.06.14.22276401v1)

    So it is thought that they may have an active viral reservoir.

    That being the case, why couldn’t they be the source of the countless variants? Wouldn’t they be just as good a prospect as immune compromised people? Their bodies are constantly trying to fight it off, too, and failing. And there are a lot of people with long covid.

    (this is a preprint, but the authors are at Harvard medical school so presumably they know how to test for spike antigens)

    Reply
    1. Skunk

      Kareninca,

      Not sure if you saw this link previously posted in NC. An hour long, but incredibly informative and well done.

      https://videocast.nih.gov/watch=45296?jwsource=twi

      A couple of key points:

      1) Findings of viral replication in the brain, with mutations occurring in the brain rather than the respiratory tract.
      2) Ability of the virus to “hide out” in various tissues without activating the immune system or causing inflammation
      3) Ability of the virus to infect a wide range of tissues in the body without any changes in the spike protein

      Reply
  22. drumlin woodchuckles

    Here is an individual who reports having a job interview cancelled on the spot because he wore a mask to the interview.
    https://www.reddit.com/r/self/comments/vi6r2m/i_was_just_denied_a_job_interview_because_i_wore/

    If indeed this happened as reported, the person who cancelled the interview is definitely a functional malicious-covid-spreader in spirit if not in technical fact. How should people like that have their power to prevent covid control taken away from them and how should they be punished and destroyed in public to discourage others just like them from doing the same?

    Reply

Leave a Reply

Your email address will not be published. Required fields are marked *