Probable Vaccine-Escaping Covid Variant Sequenced in Gauteng, South Africa and Spreading Rapidly; Press Underplaying Downside Risk

Not only is there a lot not to like about the new variant sighted in a cluster of cases in Gaunteng, South Africa, there is also not a lot to like about the handling of information about it. We held off from posting on this sobering development on Wednesday because we didn’t want to ruin your Thanksgiving.

One the one hand, the press in the form of a Guardian story was onto the sequencing of this variant a mere 36 hours after it was posted on GitHub and under discussion there. This evening, the media is giving it considerable coverage, apparently as the result of a press conference in South Africa on Thursday that admitted this variant, B.1.1.529, was widely spread in South Africa after its initial sighting in Gauteng.

One would like to see this speedy press reaction as refreshing departure from its prior tendency to not take notice of new variants, even ones ugly-looking enough to merit concern right out of the box. But as you’ll see, it appear more likely to be the result of serious concern at high levels, particularly now that the WHO is convening experts on Friday to determine if this new variant should be designated a “variant of concern.”

On the other hand, as we’ll soon see, even though the Guardian story and now other reports (fori instance, in the New York Times, Wall Street Journal and the BBC) took an alarmed tone, they are underplaying the downside. The account whose level of concern is closest to appropriately registering how bad this variant, quickly designated B.1.1.529 is is the BBC.

Even worse, the discussion among experts at GitHub was scrubbed and shut down (I know because I opened up the GitHub page apparently right before it was censored and so can see how it differs from the sanitized version). I am told this is not normal behavior at GitHub. One of the comments that was removed gave concrete reasons why B.1.1.529, just named Nu, looks like a train wreck.1 Is this deleted comment, which we have reproduced in our footnote, the sort of discussion among scientists that the officialdom is trying to hide?

This variant has the potential to be DEFCON Level-1 bad. It is so different from current variants that calling it a variant is a misnomer; it is more likely to be another strain and could even be SARS-Cov-3. Unlike the press, the experts on GitHub were discussing the implications in the summary statement, which remains unchanged:

As I asked GM:

I assume if it probably escapes monoclonal antibodies, it probably escapes vaccines too.

His response:

We don’t have direct studies on this variant, but based on the sequence, this is completely resistant to all monoclonals, and there is little doubt about it. So this is a kiss-the-vaccine-goodbye strain, that is correct.

My next question:

And am I correct in further assuming that its pretty fast emergence suggests it is competing effectively with and potentially out competing current variants?

This we do not know yet, but there is a worse possibility — that there will be no competition. This is just so antigenically distinct, that it may just as well circulate as its own separate strain that does not compete directly with Delta because there is no cross-neutralization and thus people infected with one are very soon after susceptible to infection from the other (just as COVID does not protect you from infection with OC43/229E/NL-63/229E and vice versa).

And Twitter is showing analyses and concerns similar to those censored on GitHub and articulated by GM:

If nothing else, Mr. Market has gotten wind of the this sudden variant emergence and is not taking well to it. Dow futures are down 400 points overnight and S&P futures are down 1.7%. That is actually tame in light of what is known now. The UK has already halted some flights from South Africa. But the US has nonstops to Atlanta and NYC from Johannesburg, and they have not been suspended yet, and likely won’t be until the early next week due to the Thanksgiving holiday. If so, this would be another testament to CDC incompetence. Why aren’t there provisions for emergency action when days can and do matter?

And underplaying the risk is wrong-headed at the stage when containment is still possible. Recall Nassim Nicholas Taleb’s warning in late January 2020, which was not heeded: that the downside of Covid-19 was that it could be a pandemic, and the risk was that of ruin. We may be at a January 2020 decision point again and will blow a second chance to do the right thing. That ought to be inexcusable, since by now we should know better.2

And if we collectively had any sense, we might have been able to prevent this. The immunocompromised make for great breeding grounds for new variants. The press did point out what the experts had been discussing, that this variant resulted from a protracted infection in an immunocompromised, likely HIV positive, individual (recall that HIV is widespread in South Africa). For instance, per the BBC: “This level of mutation has most likely come from a single patient who was unable to beat the virus.”

The “Kent” variant came from an area in the UK’s south, with high levels of poverty and drug abuse, and a large population of the immunocompromised.3South Africa has high levels of HIV and is thus an obvious hot spot for variant generation. Why didn’t the WHO trumpet the importance of sending vaccines to developing economies, targeting above all their HIV positive populations? Instead, all they did was bleat when the first world started launching boosters, that they should stop until 10% of the population of emerging economies were vaccinated. 10%? With no recommendation of prioritizing populations that could incubate variants That was tokenism, not a serious proposal.

But we may already be past that point:

The fact that the case came from Malawi means it has spread beyond the nations that have implemented travel bans. And note that the Israel cases were all in vaccinated individuals. Given that 4 million Israelis had gotten boosters as of early November, the odds are decent that at least some of these three were boosted too.

This “variant” was named quickly, as indicated, B.1.1.529, and now Nu. Before it had any label, GM had written quite a few e-mails about it. Cobbling them together:

This may well be the dreaded SARS-CoV-3 — but even if it is at all competing directly with Delta, rather than being its own brand new strain, it will have a gigantic advantage on immune escape in highly vaxxed populations.

This is a new variant from South Africa, with the following very large number of spike mutations:

A67V, Δ69-70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F

This is as BAD. And it has FCS mutations too.4

Because a fourth wave is starting in SA, specifically in Gauteng. And it started very rapidly and suddenly, i.e. it shows exactly the signs of something driven by a new variant.

They have only posted 7 sequences from Gauteng in the last couple weeks, and all 7 of those are this variant. So 7 sequences is very little sampling, but it is all consistent with this variant driving it, and those were not actually sampled from the same cluster, so it is spread quite widely there (which is also evident from the fact it was first reported from Botswana and was also caught in Hong Kong).

Gaunteng posted more sequencing Thursday morning, with another 44 sequences of this variant. So it does appear to be driving this outbreak, as opposed to a coincidence. And now the total is up to 77.

The press accounts have ritual “No reason to panic yet” statements like this one at the BBC:

There have been many examples of variants that have seemed scary on paper, but came to nothing. The Beta variant was at the top of people’s concerns at the beginning of the year because it was the best at escaping the immune system. But in the end it was the faster-spreading Delta that took over the world.

But this story to its credit does provide evidence that B.1.1.529 is spreading:

There have been 77 fully confirmed cases in Gauteng province in South Africa, four cases in Botswana and one in Hong Kong (which is directly linked to travel from South Africa).
However, there are clues the variant has spread even more widely.

This variant seems to give quirky results (known as an S-gene dropout) in the standard tests and that can be used to track the variant without doing a full genetic analysis.

That suggests 90% of cases in Gauteng may already be this variant and it “may already be present in most provinces” in South Africa.

The BBC is behind, there was a second case found in Hong Kong, and embarrassingly a transmission in a quarantine hotel due to the initial B.1.1.529 case wearing a mask with a respirator valve. But the next paragraph tries to dial down the worry level:

But this does not tell us whether it spreads faster than Delta, is any more severe or to what extent it can evade the immune protection that comes from vaccination.

Infection severity is indeed not known, but there is already troubling evidence of its transmissibility. Again from GM on Wednesday AM:

The R_t for Gauteng is 2.2 right now, which is huge

R_t is the current effective reproduction number. It represents the lower bound for R0. Recall that the RO for the Spanish flu has been estimated at 1.8. The R_t reflects the impact of any and all current interventions, including vaccination (South Africa is 24% fully vaccinated) and a high level of prior infection (seropositivity after the second wave was 60%, and South Africa has had a third). GM added:

We only really saw R_t of 3-4 in February and March 2020. The current massive surges in Europe exhibit R_t of 1.3 or so.

It’s an exponential, not a linear process

It is also notable it is around 1 or slightly above 1 in the other provinces. That gigantic difference screams that something different is happening in Gauteng.

Usual caveats apply — need more time to see how things play out, this could be a flash-in-the-pan aberrant event, etc.

But on the other hand the precautionary principle mandates that this is taken very seriously.

GM’s concern has been validated and then some. Look at how quickly B.1.1.529 has moved towards becoming dominant:

And the S-gene dropout validates his concern about vaccine escape:

So the proportion of PCR tests that shows that signature is rising vertically. Which means that the variant is taking over all throughout South Africa very rapidly.

It also makes B.1.1.529 easy to track without sequencing:

Other experts are quickly coming to grim conclusions:

The data comes in the first tweet came from from Tulio de Oliveira’s press conference in South Africa Thursday morning, where he confirmed that B.1.1.529 is spreading rapidly through South Africa:

And we are collectively about to pay for the eagerness of the officialdom to declare the pandemic over at every possible turn and put all their chips on a non-sterilizing vaccine, which is very useful at preventing worst outcomes of the current variants, but does little to prevent transmission of Delta due to its very high replication rate. Yet the authorities have been bludgeoning the public to get vaccinated, not to protect themselves and keep the medical system from breaking down, but as a confidence-builder, based on the inaccurate claim that the vaccines stop spread.

In the US, Biden administration systematically failed to support or actively denigrated all non-pharmaceutical interventions. It actively encouraged the vaccinated to abandon masks (positioning non-masking as proof of virtue). The CDC and WHO have been silent on ventilation and have actively opposing the aerosol theory of transmission. Even social distancing has been discouraged with Fauci recommending that the vaccinated carry on as if it were the old normal over Thanksgiving.

Now, when we need non-pharmaceutical interventions to hold the line until some sort of vaccine/treatment rescue arrives, they have all been systematically undermined and rendered dysfunctional by Biden’s vax only policy (a view embraced by the Democrat base and indeed taken as a marker of tribal affiliation).

By letting business drive public health policy with its quest for a “return to normal,” the entire last year was squandered, not just NPIs, but testing, contact tracing, international infection control standards, everything. We said this amounted operational to “Let ‘er rip.” B.1.1.529 may show us the true cost of that recklessness.

And where did the recent rounds of bad variants come from? This is three times – Kent, India, now South Africa – where the Anglo incubation reservoirs that capitalism creates have spilled over into waves of world-wide infection. China would be fully justified in never “opening up,” with obvious consequences for a “return to normal” in the supply chain.

Consider GM’s cheery advice (emphasis his):

Consider yourself fully unvaccinated from now on and go back to March 2020 precautions.

What happens when the great unwashed public works out that that is where they are, that their vaccine-conferred immunity is kaput even sooner than they expected, and regular boosting with the current vaccines may protect them against Delta, but not against B.1.1.529? What is going to be their appetite for taking two Covid vaccines and then their frequently boosters, even assuming that that a new mRNA vaccine can be developed rapidly? Remember that we already have riots in Europe right now the vaccine passports and lockdowns. What happens when you tell the vaccinated that they are no longer vaccinated at all? GM again:

Even the more formally educated true believers who have decided that it is all over because they got vaccinated don’t really understand anything about Class I/II/III neutralizing antibodies, NTD and RBD, what the Q493K+Q498R combination means, etc. stuff that is hidden in obscure papers that were never given the publicity of the “T cells give you lifetime protection” headlines.

Compliance will not be be there for more serious lockdowns, you can’t unring that bell…

Remember, as things appear now, B.1.1.529 is so different that it might not displace Delta but co-exist with it, meaning we may now have two pandemics underway.

And for the new one, minimal vaccine testing, for antibody response and then a new round of Emergency Use Authorizations, and then distribution, will easily take six months and longer is more likely. So the prospect of lockdowns is not crazy talk.

Now the one possible silver lining to this cloud may be that B.1.1.529 winds up being less lethal and/or generates less morbidity than recent variants. But we can’t pin our hopes on a lucky break.


1 Now you tell me, what is the basis for removing a comment like the one below? This comment is response to another remark, “We don’t know anything yet.”

We actually do — we have neutralization measurements for another RBD sequence with that many mutations, and it was completely resistant to all monoclonals.

WNY4 there had the following:


And that it should be so evasive is obvious just from the sequence anyway — we have multiple, often charge altering mutations in each of the key epitopes.

It does not have P681R, but why do we think P681R is the key to the universe? It was seen in many variants other than Delta, and those went nowhere, so clearly there is a context dependence. Who is to say N679K+P681H in this context is not sufficiently fit?

And this has both R203K and G204R, right in the same spot.

But most importantly, with very high certainty, this shows essentially zero cross-neutralization with Delta.

There was a measurement of the cross-neutralization of Beta with Delta serum, and the reduction was 34x (Delta on Beta was 12x). Which is huge.

But Beta has 3 RBD mutations and Delta has 2, 5 differences in total.

This thing has 15, one of them common with Delta.

What do you think the cross-neutralization is?

Is it even going to be competing with Delta other than through viral interference as opposed to just circulating as its own separate thing?

And it does not have to be competitive on raw transmissibility — if vaccination reduces Delta transmission by 50-70%, but there is a variant against which it only has a 5-10% effect, that variant should outcompete Delta in highly vaxxed and recently swept through areas, even if it is somewhat less transmissible (as long as it is not drastically less transmissible).

We had it bad enough in 2020 — lots of areas that already let it rip back then were infected at 70%+ levels.

2 But we have already blown the notion of a cordon, both via our priorities and our prior handling of South Africa. From GM again:

But in South Africa they are very pissed about the fact that after the appearance of B.1.351, much of the rest of the world tried to cordon them off so that it does not get exported (together with all the other nasty variants they have brewed). I’ve seen a lot of tweets from scientists from there complaining about the unfair treatment. And it really was unfair in a certain sense — Delta was freely exported from India for many weeks, while travel from South Africa was banned by many countries.

The problem is that right now, if you forget about the politics and the fairness of it, what has to be done is what was not done with China — ban all travel from all African countries in that region (South Africa, Botswana, Namibia, Lesotho and Swazilend as a bare minimum) and try to find, isolate and test everyone who has any connection to those countries anywhere else in the world. So that you at leas give yourself a chance to stop it before it takes hold everywhere. And, of course, a complete lockdown right now in those countries with elimination in mind. And all of the Pfizer pill supply goes there to clear the chronic infections. Needless to say, none of that is going to happen, and South African authorities will probably make sure it becomes pointless anyway by minimizing the problem for sufficiently long that it is already exported everywhere.

Which other governments will cooperate with, consciously or not, by also minimizing it, so that panic is not created.

And as this post shows, they are already trying to minimize it, when with a dangerous pathogen, the right reaction is to overreact first and dial it back later if better data says that’s not reckless.

3 Note it isn’t 100% certain that “Kent” did originate in Kent. The earliest sequences in the database date to New York, but there is some confusion on the reliability of those dates.

4 More detail for the technically-minded:

What is the significance of the FCS mutations?

So the key to Delta’s extreme transmissibility is the P681R mutation.

The original FCS was PRRAR, P being position 681. R stands for “arginine”, and arginine is a positively charged, basic aminoacid. So you have a string of Rs in there, and that’s how you form the FCS.

In Delta you change the PRRAR into a RRRAR, so it became even more basic, and that drove even more efficient S1/S2 cleavage (it went from 50% to 90%), which means more efficient infection of cells, and greatly increased cell-cell fusion. And this is one reason why it is so supertransmissible (one reason, the other is that it also seems to be much more efficient at packaging viral particles because of mutations in the N protein; which this variant also has, BTW).

However, other variants also had P681R (e.g. A.23.1 from Uganda/Rwanda) but those eventually disappeared. So clearly there is some context-dependence here.

But other successful (though not as successful as Delta) variants had P681H (Alpha/B.1.1.7 had that, and so does B.1.621/Mu). “H” stands for “histidine”, which is also a basic amino acid, but not as basic as arginine. So the thinking has been that P681H is just a poor man’s P681R.

More recent studies suggest that it might be a lot more complicated than this, and in fact P681H also enhances fitness through additional mechanisms (though Alpha and Mu are also much better at driving cell fusion than the ancestral variants, just not as good as Delta).

Anyway, in this variant we have N679K+P681H. So we have the P681H but we also have another positive charge replacing a negative charge very close by (the basic lysine K replacing an uncharged asparagine N), so together it might be better than P681H alone. Whether it is competitive with Delta, we don’t know, but it does not need to be

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  1. Samuel Conner

    to complete a thought in a prior comment (on the ‘disaster’ of disruptions to Thanksgiving travel),

    Orange is the new black, discomfort is the new disaster, and mass mortality is … the new normal.


    Thanks, Yves, for alerting us.

  2. DJG, Reality Czar

    Yes, thanks for this sobering assessment and its many details to contemplate. Thanks, too, for linking the public-health failures to the worship of business-as-usual. (The “shocked” analyses of the great resignation in the U S of A show the same level of business-worship and the same obliviousness to the symptoms in the form of years of mistreatment in the US, backed by labor law, of salaried and hourly workers.)

    It’s going to be a bumpy flight.

  3. PlutoniumKun

    As soon as I saw the tone of the science twitter sources I follow it was obvious that this was bad. And the uncharacteristically rapid reaction of the UK authorities yesterday confirmed it. This may not be worst case scenario (Sars 1 mortality rates would be), but its not far off.

    If the authorities had learned any lessons from 2020 it would be to shut down all international travel, right now. Not travel to South Africa, all long distance travel until it can be proven that it hasn’t spread beyond the known hotspots. If there are confirmed cases in HK, then there could be cases in any airline hub anywhere in the world. Needless to say, that hasn’t happened. We’ve learned nothing.

    At least the markets understand. Airline shares and oil prices are tumbling. Bye bye 2022.

    1. DJG, Reality Czar

      Moving very quickly here in Europe:

      Shutting down flights:

      L’Italia ferma da subito gli arrivi di chi negli ultimi 14 giorni è stato in Sudafrica, Lesotho, Botswana, Zimbabwe, Mozambico, Namibia ed Eswatini e la Commissione Ue annuncia che proporrà a breve una misura analoga, già adottata ieri dalla Gran Bretagna e Israele.

        1. BeliTsari

          Grave concerns about Guardian’s Panglossy claims that BioNTech can tweak NU vaccine along with efficacy of isolation, tracking of incoming travelers. Sounds like lies we’d been hearing as fliers rushed past TSA & immigration, trying to beat theatrics in ’20? If it’s been detected, in community spread cases from Belgium, Hong Kong, Israel (and Israel was reporting new strains in Europe, weeks back. I’m guessing it’ll be yet another repeat of NYC, putting on a show of useless Hygiene Theate; while CYA/ indemnification and blatant Catastrophe Capitalism feeding frenzies cascade exponentially? All they’ve learned, is how to lie, distract and hide the numbers.

        2. drumlin woodchuckles

          I remember hearing Fauci on NPR radio saying something like ” we don’t want to do any flight shutdowns until we have more data and can be sure”.

          I interpreted that to mean that Fauci wants to see flight shutdowns delayed until he can be sure that the newest mutant covid has successfully reached America and is spreading here.

      1. Alena Shahadat

        Switzerland closed yesterday for the same countries, plus Great Britain, Netherlands and .. Czech republic (??). People with long term stay permit or Swiss citizens have to quarantine for ten days. Others cannot enter. Except for Shengen citizens.
        The list:

        1. Alena Shahadat

          Saturday at midnight they said on Al Jazeera that one or two cases have been detected in Czech republic. I don’t have more information though.

    2. Louis Fyne

      Detected in Israel from a traveler to Malawi. Flight bans/quarantine already of southern Africa nations by Italy, UK, Germany, Japan.

      the speed at which the flight cancellations have started is evidence enough how dangerous this next wave will be

      1. PlutoniumKun

        According to the Guardian the case in Belgium was from someone who travelled from Turkey and has no connection to Africa.

        Also the Guardian is reporting that WHO is cautioning governments not to impose travel restrictions. Seriously.

        The World Health Organization has cautioned countries against hastily imposing travel restrictions linked to the new B.1.1.529 variant of Covid, saying they should take a “risk-based and scientific approach”.

        “At this point, implementing travel measures is being cautioned against,” Lindmeier told a UN briefing in Geneva. “The WHO recommends that countries continue to apply a risk-based and scientific approach when implementing travel measures.”

        Its so good to see that we are in safe hands.

        1. Louis Fyne

          Fauci publicly ruled out a travel ban between US and ZAR and is taking the WHO approach—wait and see.

          Good thing people are giving the Nu variant due process and applying “innocent until proven guilty beyond a reasonable doubt” to public health /sarc.

        2. JBird4049

          >>>The World Health Organization has cautioned countries against hastily imposing travel restrictions linked to the new B.1.1.529 variant of Covid, saying they should take a “risk-based and scientific approach”.

          Okay, wtf?

          Man, I feel like I am in some kind of hybrid Kafka-Helleresque novel. Where’s Hunter S. Thompson, Tom Wolf, or even Molly Ivins when we need them?

          This is so obviously delusional, as in an addict’s nuttiest delusions, as to be horrifically, darkly funny. These dudes are chasing the Normalcy Fairies so hard that they can’t see that cliff they’re running to.

            1. clarky90

              A senior citizen called her husband during his drive home.

              “Herman, I just heard on the news that there’s a car going the wrong way on Interstate 90, Please be careful!”

              Herman replied, “Darling, it’s not just one car. There’s hundreds of them!”

          1. Michael.j

            I am also very perplexed by suddenly changing the designation from nu to omicron. Is this medically based, or search engine based?

            1. Yves Smith Post author

              I think it was to save American officials and newscasters from being laughed at by the American Greek community (which is substantial in some cities) and around the world for inability to pronounce it properly.

              1. Angie Neer

                Unfortunately, it will take more than that to keep newscasters from saying laughable things. Today on public radio’s “Marketplace”, the host (a vacation sub, not the regular guy) giggled that “Omicron sounds like some sort of cartoon super-villian.”

                1. Cat Burglar

                  More like a cheap sports wristwatch. They should have taken time for some research, because I bet they violated somebody’s copyright.

                1. Raymond Sim

                  With this Greek letter thing they set themselves on a path to eventually naming a Covid variant after Xi Jinping?

                  Are we living in a novel?

              2. Tony Wright

                The “American Creek Community” . Briefly channelling Manuel from Fawlty Towers -Que?
                Sorry Yves, please enlighten this non- American as to the meaning of this expression.
                And on a more philosophical note: nothing like a lethal pandemic to reenforce my belief that a negative side effect of economic success in a country/society/empire is the survival of many incompetent and ignorant individuals who would not survive under more challenging circumstances.
                I have a sore neck from all the head shaking whilst watching on the news some of the dipshit behaviour of some citizens in many relatively priveliged, so-called first world countries.

                1. Yves Smith Post author

                  Looks like you had a vision fail. Greek, not Creek.

                  American Greek or Greek American, take your pick. There are a lot of Greeks in Boston, for instance. 1/3 of the restaurants, including many not specializing in Greek food, are run by Greeks. They is also a big mafia in academia in Boston.

        3. drumlin woodchuckles

          That’s because WHO wants to make sure the newest mutant covid has been introduced into every continent, in line with its Jackpot Design Engineering agenda.

          Proof? I don’t have any proof. I don’t need no steenkin’ proof!

          Logically speaking, what other reason would WHO have?

  4. cocomaan

    Any information on what kind of symptoms are present with this? I see a lot of data on transmission but not a lot of talk on what it does when it gets you.

    Lately people have been talking about the inverse relationship between transmissibility and virulence, I forget the name of the phenomenon. But I feel like Delta ran counter to that idea.

    1. Ahimsa

      My thoughts too.. if this is much more transmissible, then is it to be hoped that it is less virulent?

      1. GM

        No, the mechanisms that increase interhost transmissibility also increase intrahost transmissibility, thus it gets worse, not milder.

      2. Raymond Sim

        if this is much more transmissible, then is it to be hoped that it is less virulent?

        No! There has never been any basis for such hope regarding SARS-CoV-2. Anyone who has given you that impression was either lying or spouting wish-fulfillment fantasies.

        1. Yves Smith Post author

          GM has warned that the mystery has been that SARS-Cov-2 is so much less nasty that similar viruses and it therefore had plenty of potential to get worse.

          More generally, we have repeatedly pointed out that the idea that viruses evolve to be less lethal is an urban legend. SARS-Cov-2 has not been all that lethal (it does have pretty bad morbidity). If it had been, we would have gone down the eradication path.

          And modeling when Delta was becoming dominant showed that more transmissibility with the same level of mortality would produce more deaths than the same level of transmissibility and higher mortality. So even if B.1.1.29 is merely as lethal as Delta, we are still in a world of hurt.

        2. Ahimsa

          “There has never been any basis for such hope regarding SARS-CoV-2.”

          Well, this article from the Smithsonian discusses the varying bases for such thinking:

          Will the Coronavirus Evolve to Be Less Deadly?
          History and science suggest many possible pathways for pandemics, but questions remain about how this one will end

          The idea that circulating pathogens gradually become less deadly over time is very old. It seems to have originated in the writings of a 19th-century physician, Theobald Smith, who first suggested that there is a “delicate equilibrium” between parasite and host, and argued that, over time, the deadliness of a pathogen should decline since it is really not in the interest of a germ to kill its host. This notion became conventional wisdom for many years, but by the 1980s, researchers had begun challenging the idea.

          In the early 1980s, the mathematical biologists Roy Anderson and Robert May, proposed that germs transmit best when hosts shed a lot of the pathogen, which may often mean when they are quite sick. If you’re really sick, you are — the argument goes — shedding lots of virus, which makes it easier for the next host to pick it up. So virulence and transmissibility go hand in hand, until the germ gets so deadly it winds up killing its host too soon, and therefore can’t spread at all. This is known as the transmission-virulence trade-off…

          A second theory, developed by evolutionary epidemiologist Paul Ewald, which he calls the “theory of virulence,” suggests that, as a rule, the deadlier the germ, the less likely it is to spread. The reason: If victims are quickly immobilized (think of Ebola, for example), then they can’t readily spread the infection. By this thinking, if a germ requires a mobile host to spread, its virulence will, of necessity, decline. Like the older conventional wisdom, the theory of virulence recognizes that many germs will evolve less virulence as they circulate and adapt to the human population. But Ewald’s theory also proposes that germs all have their own strategies to spread, and some of those strategies allow the germ to maintain high virulence and transmissibility.

          However, I duly note Yves comment below:

          “…that more transmissibility with the same level of mortality would produce more deaths than the same level of transmissibility and higher mortality.”

          1. Yves Smith Post author

            Covid-19 is not all that deadly (morbidity is another thing, it’s quite bad and varied for a supposed respiratory infection) and peak virus shedding takes place for 2-3 days, usually a day or two before infection onset and that day and maybe a day after. The slide into viral pneumonia, if it occurs, is typically 5-7 days after symptom onset, meaning well after viral shedding. With any sort of treatment, death occurs at week 3 or later. In other words, viral shedding occurs so long before death that there’s no mortality-transmission tradeoff save maybe in those already at death’s door.

            Why these people use any thin basis for a cheery handwave rather than looking at relevant particulars is beyond me.

          2. PlutoniumKun

            I suspect a lot of people get confused between a virus evolving to be less dangerous and the host evolving to be more immune. Smallpox gradually became less dangerous over the centuries, but so far as I’m aware this had nothing to do with the virus – it was that it killed off all those more genetically vulnerable. When it first emerged it could kill 30% or more of a population, by the 19th Century it was just a very nasty and disfiguring infection that occasionally killed children. Humans evolved to accommodate smallpox, not the other way around.

    2. Mantid

      So many things and changes so fast. However, I understand that it’s hitting younger age groups in S. Africa. I won’t complain if I’m corrected. Be cautious and plan ahead.

    1. Yves Smith Post author

      GM is a scientist and a regular reader. He has a PhD in biology and a second degree in microbiology and is doing research at a big name institution you heard of.

  5. bold'un

    It will be interesting to see if the traditional inactivated whole-virus vaccines from China and India fare better against this variant than the spike-vaccines… The UK government may yet regret having cancelled its Valneva order!

    1. vlade

      more important, from the short term perspective, oil is down – a lot. NG is up though, so that’s a bit of a mixed thing.

      1. upstater

        Oil is mostly for going places, natural gas is for power generation and heating homes. Residential heating and electricity consumption will likely go up considerably if the public realizes the implications of B.1.1.529 and hunkers down on its own.

        Our county (population 470,000) remains blissfully ignorant with an 85% vaccination rate, despite Delta driving cases, hospitalizations and death higher than a year ago as B117 was ramping up. We never stopped using KN95s when going out; mask usage is now a small minority because almost everyone is “protected”.

        1. vlade

          Yes, but NG is also used for industrial uses, in fact, in the US, the NG industrial use is twice the residential. In the winter 2020-2021, NG use went down substantially IIRC (which was one of the drivers behind the low NG prices).

          So this would indicate that the markets expect transport to go south, but not industrial production. Which is a bit weird, as a lot of transport (that’s still there) is related to the industrial production.

          1. PlutoniumKun

            I guess that ‘if’ there is a logic to it, they expect this to hit airlines and travel, but that governments will do what they can to keep the overall economy going full steam. It might also be based on an assumption that demand for gas is less elastic as so much is used for electricity and base products like fertiliser.

            1. vlade

              Industrial demand on the NG is pressuposed by the ability of someone to operate the factory. If we have a massive CV3 wave, no workers = no production = no gas use. But we’ll see I guess.

    2. timbers

      Market falling? It won’t last. Dr Jerome Powell’s cure is better than no Covid at all – another free $3 trillion spent by the Federal Reserve to give to their rich friends.

      Mr Market will soar to every higher record levels the worse it gets, the more bad news there is the better, as long as Dr Jerome is free to hand out his miraculous cures.

      Sooner or later someone is going to realize we ought to have a Covid event at least every year or so.

      1. MonkeyBusiness

        I agree with this. Say tomorrow is the end of the world, the stock market will still continue to notch new highs.

        1. PlutoniumKun

          I’m sure they will prop up the overall stock market if they can, but I find it hard to see how airline and hotel stocks can avoid a calamity if this is as bad as it looks. This will devastate the 2022 travel season.

          1. Glen

            I can hear home prices going up in every unwrecked small town as we sit here mulling over our future.

            I think the Fed money injection is a good thing except they keep giving it to the exact same guys that should have gone broke and been gone in 2008.

          2. MonkeyBusiness

            What’s new? The government is going to take a big stake and right before the recovery, they will give every chance to the private sector to buy back the stake for cheap.

          3. lordkoos

            There will be more bailouts for large businesses. If this variant really takes off they might be forced to revisit pandemic unemployment benefits etc.

            1. Tony Wright

              And then watch out for the digital only US dollar, along with negative interest rates, taxation of every transaction, and maybe even an expiry date on d-dollars helicoptered into your account by Powell, Yellen & Co. to ensure that you spend or invest to keep the whole house of cards from collapsing.
              As Rahm Emmanuel famously said “ Don’t Let a Good Crisis Go to Waste”.

              1. drumlin woodchuckles

                If the DC FedRegime tries that, every person who can do so will withdraw cash from every place they can withdraw cash from and save a bunch of it for when the forced e-money omni-prison is fully built. People will use that cash for purchases on the Patriot Cash Market ( “black market”).

                Also, those who can will build up stockpiles of “alternate parallel currency trade-goods”). Standardized goods like several year worth of toilet paper for use as “barter currency” either by the roll or by numbers of sheets for tiny trades. Strong cheap liquor and hundreds of little bottles to contain little doses of it for little trades. Etc. Disposable razor blades . . . .

                Also, people will do as much work as they can in the Free UnMarket CounterEconomy, because why work for “money” which they try to tax and toll away from you as fast as you have made it? People will minimise their “paid work” in the Forced Market e-moneyconomy to the absolute minimum they can reduce it to without compromising their brute survival.

    1. vlade

      Belgian case via Turkey and Egypt. I’d say, it’s nu is well on its way out of SA, as there’s about zero chance that Middle East will test extensively enough (hell, we don’t..). So unless we get an international traffic lock-down again (unlikely to be fast enough, even if we do IMO), we’re past the “may spread” stage, and the question is only what’s the impact..

      1. PlutoniumKun

        I posted above but it disappeared – according to the Guardian, WHO is not recommending travel restrictions.

        The World Health Organization has cautioned countries against hastily imposing travel restrictions linked to the new B.1.1.529 variant of Covid, saying they should take a “risk-based and scientific approach”.

        “At this point, implementing travel measures is being cautioned against,” Lindmeier told a UN briefing in Geneva. “The WHO recommends that countries continue to apply a risk-based and scientific approach when implementing travel measures.”

        I’m beyond words.

        1. vlade

          “At this point, WHO is deemed to be not fit for purpose, having failed in a major way.”

          Does “risk based approach” mean “there could be a variant that’s more infectious than Delta that’s currently ripping through Europe, and ignores current vaccines, so let’s bring it on!”?

          Czech Rep just closed flights from all of Africa if I heard the news correctly.

          1. Basil Pesto

            hard to say if it’s reassuring or upsetting that, in pursuing their best interests, many governments are choosing to ignore *checks notes* the World Health Organization, ffs.

          2. Samuel Conner

            > so let’s bring it on!”?

            This suggests a “Wheel of Fortune” before-and-after puzzle:

            Scott Atlas shrugged

        2. Michael.j

          Sorry for being cynical, but it may very well be that the airlines & banks may be influencing WHO, due to booked non-refundable flights for Xmas travel. Remember, the fine print, “not fear of infection”, but actual probability of such. They still get to make the rules. Ka-ching!

  6. Kevin Smith

    Aris Katzourakis
    Polite notice: in Greek, ‘Nu’ is pronounced ‘Ni’ or ‘Nee’ (as in, the knights who say ni, not ‘new’).

    1. Return of the Bride of Joe Biden

      I don’t speak Greek.

      In my language, “Nu” is pronounced “Nuh” like “Duh.”

    2. IM Doc

      I can support this wholeheartedly. I am watching TV in the Doctor’s Lounge. It is being pronounced as “New” in Shiny “New” Car.


      It is like fingernails on a chalkboard.

      1. Samuel Conner

        nu is used a great deal as a superscript or subscript index in tensor notation. I suspect that nearly all physicists are saying it wrong, too.

    3. urblintz

      true this

      and Beta is pronounced “Veeta” (in Greek, the “b” sound is written as “mp” – β is more like the hybrid b/v sound of both consonants in Spanish: “no es el mismo tuberculo que ver tu culo” – the v’s and b’s are pronounced the same)

      and the “d” in delta is a soft “th” as in “then”

      1. Mantid

        Exactly. I’d hate to be a Greek as second language learner but English is pretty tough too. Enough! Ee noo gu huh?? And which witch is which? I’ll try to remember Nee. Thanks all.

        1. TimH

          So many place names in UK are not phonetic. And my teeth grit with ‘water’ pronounced as ‘ward-ter’. Then we have glottal stops, grumble whinge whine…

        2. flora

          Is the ‘gh’ pronounced like:

          ‘f’ , as in enough (enouf)
          ‘w’, bough (bow)
          ‘g’, as in ghast (gast)
          ‘g’ where the ‘h’ also signals a long vowel sound as in ghost (goest)
          or silent, as in dough (doe)

          / ;)

    4. Basil Pesto

      looks like it’s ‘Omicron’ now. Good news for the nu pronunciation purists, bad news for lazy punners the world over ?

      1. IM Doc

        Of note, to those with some skills with the koine?

        Does it appear we have skipped over “Xi” to get to Omicron?

        Was there a variant “Xi” that I somehow missed?

        I wonder why they would have skipped over “Xi”?

        1. Samuel Conner

          Maybe the State Department was concerned it would escalate international tensions to not pass over that spelling.

          1. Basil Pesto

            haha, yes, that was my thought when I read IM Doc’s post, ignorant as I am of the Greek alphabet. Not an unreasonable decision when you consider how unreasonable people are, in general.

          1. marcel

            “Nu” is ‘naked’ to several hundred million french speakers.
            “Xi” is the name of the leader of over around 1.5 billion people

            Both good reasons not to associate them anything else, I think.

        2. lyman alpha blob

          If they called it Xi, Trump would be saying “See, I told you it was the China virus” and nobody wanted to give him the satisfaction.

      2. PlutoniumKun

        When I first read that, I scanned it as the ‘Omigod’ variant, which somehow seems appropriate.

  7. Count Zero

    A travel ban for flights from South Africa to the Uk isn’t going to work. People are cunning. I remember last year’s travel ban from Brazil to the UK. A young woman was interviewed who had recently arrived from Brazil. As she blithely explained: she flew to Holland instead and then took an onward flight to London. Simple.

    Travel bans aren’t very effective, at least in the long term. You can’t seal off a territory permanently. Look at New Zealand. I suppose you can buy some time, weeks perhaps. But that virus will soon be in a bar or store or bus close to you.

    1. Basil Pesto

      Travel bans aren’t very effective, at least in the long term. You can’t seal off a territory permanently.

      This is a strawman, nobody wants to permanently seal off its borders, least of all NZ. Recall that NZ and Australia established a mutual travel bubble earlier this year when both countries had eradicated Covid. There’s no doubt that lockouts are an important tool in fighting covid spread (if they can be improved down the track with limited quotas and strong but humane bespoke quarantine facilities, even better).

      Selective travel bans can have more limited efficacy though due to the barn door/bolted horse problem. Although serious governments can obviously prevent the “add another stop” method of circumvention by providing more stringent border passport controls or some other means of travel history checks.

      1. ChrisPacific

        New Zealand borders are still ‘closed’ (i.e., subject to full MIQ) at present, a cause of much kicking and screaming. They are scheduled to begin reopening from 17 Jan, intially for fully vaccinated returning New Zealanders, and then any fully vaccinated travelers from April.

        If we are lucky there will still be time to reverse that decision if we get a sense of the severity of Omicron before then. Whether the political will and public mandate will be there remains to be seen.

        1. Tony Wright

          So far we have had to scrap four separate planned travels to NZ from here in Covid 19 free South Australia. Travel plan #5 sceduled for Easter is now looking precarious.

          1. The Rev Kev

            Get the timing wrong and you may find yourself trapped in NZ with the Australians borders closed. A coupla months ago there were about 45,000 Aussies in this position. At this point, I would guess Easter to be a bust. Sorry.

        2. Basil Pesto

          My opinion is that countries like Australia should be building bespoke quarantine facilities for repatriation at the very least, again, with the aim of making the experience as humane and pleasant as possible under the circumstances. Not sure if they are in NZ but I gather the Queensland facility will be complete in the first half of next year. I feel very badly for the Australians and Kiwis that want to repatriate but can’t (although, as a former expat, I think this gives us the chance to acknowledge that that sort of emigration is not without risks, that it’s not an endless festival of consequence-free overseas sojourns to try and ~find yourself~)

          1. GM

            The problem is that they abandoned elimination already.

            So it is very hard to make the argument for trying to keep the new variant out when the measures required to do that make no sense in isolation if you are planning to “live with” Delta in the same time.

            It is either back to eliminating Delta and shutting borders again as part of a reinstitution of the elimination policy.

            Or you will “live with” Omicron too.

            This is something that has been warned about by the few remaining sane voices for a very long time — unless you try to keep all COVID out, when the complete escape mutant arrives you will have neither the technical infrastructure nor the political capital to do what has to be done to prevent it from destroying you vaccines-only policy. Which has been falling apart already anyway. You also won’t even notice it in a sea of Delta.

            People who run testing labs are already saying that they are seeing S-gene dropout samples in the US.

            But guess what? Because there are 100K positives every day, a few dozen S-gene dropout samples are never noticed. And we had S-gene dropout with Alpha, so the assumption was probably that these are some Alpha infections that have still survived the Delta sweep. Nobody thought to preferentially send them to sequencing. And really, send them to who? There is no functioning centralized health department to organized surveillance or anything of the sort. This is a failed state we are talking about after all, not some communist hellhole.

            While if you are maintaining an elimination policy any COVID you see is COVID you try to stamp out immediately, so you keep all variants out.

            1. Raymond Sim

              …unless you try to keep all COVID out, when the complete escape mutant arrives you will have neither the technical infrastructure nor the political capital to do what has to be done to prevent it from destroying you vaccines-only policy. Which has been falling apart already anyway. You also won’t even notice it in a sea of Delta.

              And, till the complete escape mutant arrives you’re pretty much guaranteed explosive growth of any other variant that shows up with a nifty new trick or two. How long oh Lord, how long?

    2. Greg

      NZ was doing fine at keeping the borders relatively tight for a long time, until “business” decided to start kicking up a stink and forcing the politicians to “open us back up to the world!”. The entry of delta into NZ was a direct result of “opening up” via an Australasian bubble while NSW was out of control.

  8. Redlife2017

    I get to read the traders chatter at my firm and, yeah, they are all like – this is going to be fine. Let me give you a taste:
    * SA are quite sharp in terms of sequencing so I can’t help but feel they’re suffering at the hands of their own diligence here.
    *It also means that R estimates for Nu are probably way overstated at present
    * Also beware of the founder effect, where a new strain takes over very quickly while cases are low
    * All in all we need to watch carefully. Clearly some govs and markets are taking the panic early approach. [this is my emphasis] Could be a big opportunity to prepare for upside if global data upswing continues and Nu turns out to be a nothingburger.

    The cope is hard with these boyz.

    1. Mikel

      “SA are quite sharp in terms of sequencing so I can’t help but feel they’re suffering at the hands of their own diligence here…”

      I don’t see how someone could find comfort in that statement. That is the kind of diligence needed in times of pandemic. So he’s basically saying “I wish scientists would be half-assed so I can pretend nothing bad is happening.”

  9. Samuel Conner

    The thought occurs that, whether or not Nu terms out to be a major problem, antibody therapy in immunocompromised patients may require highest-possible containment measures. It kind of sounds like this is BSL-4 level risk. Are the hospital containment wards currently employed for this purpose sufficiently isolated?

    1. Raymond Sim

      I can’t recall if I’ve discussed this previously, but imo long-term infection in immunocompromised patients as the source of immunoevasive variants fails Occam’s razor. First we need to be able to dismiss ongoing mass circulation among young adult essential workers,

      Such circulation has the notable advantage of conserving or even enhancing traits required to be competitive at transmission.

      1. Yves Smith Post author

        You need to explain your basis for this view rather than make an assertion. Many experts have discussed precisely that, a long term infection due to an individual’s inability to clear the virus, as a cause of variant generation.

        This article describes a particular case of variants developing in an immunocompromised patient. This has been observed in the real world. It is not a theory:

        That Scientific American piece appears to be based on this Jama Network story, which states that the example they showcased is not an isolated example:

        The use of convalescent plasma, which has been restricted to very sick patients, was one of those not so hot ideas, it also promotes the evolution of variants:

        1. Raymond Sim

          There’s no doubt that persistent infection can produce a population of immune-evading virus within the unfortunate host, and of course whatever treatments are attempted will exert selective pressure. As you say, this is a documented phenomenon.

          My question is, “Would the virus need to be hiding in one body to find conditions conducive to such evolution?” And looking at Julia Gog’s “Simplest Model” for vaccine escape, my mathematical intuition is that with sufficiently high transmission in a sufficiently large population it would not. The Mixers, to use her terminology, would seem capable of fulfilling the role. Here’s a link to her discussing the subject:

          She’s specifically addressing the question of which parts of the population should be given priority for vaccination in order to minimize the evolution of escape variants, but the considerations apply to the evolution of immune escape generally.

          I would be delighted if others with the requisite math background (partial differential equations and vector analysis) would have a look at this. In my view the ‘Mixers’ collectively being the body in which immune evasion evolves provides a straightforward explanation for the dynamics of the pandemic to date. And as it happens, viral evolution during persistent infection doesn’t seem to be required.

          1. Yves Smith Post author

            Please see GM above. The authorities identified a case infected in 2020 which has been persistently infected that the RSA experts appear to think was the incubator.

            1. GM

              That is not correct, they have not found any such case

              What I said what that this is a B.1.1.X virus, and there has been no B.1.1 in a very long time; the closest sequence to this is from June 2020.

              So most likely the chronic infection started more than a year ago.

              Then sometime in August-September this year it hit the jackpot with the right additional mutations, from there it spread to other people, and it has since then been spreading very fast in South Africa starting in early October

              1. CanCyn

                Hit the jackpot where? In South Africa? Or somewhere else? She asked thinking about the Spanish Flu that actually started in the US. Impossible to know at this point?

              2. Yves Smith Post author

                Wellie, as far as I am concerned that is pretty close to what I said, save being unduly definitive as having identified a patient, as opposed to surmising from data that it was very likely a very longstanding infection in one patient.

                1. Raymond Sim

                  … surmising from data that it was very likely a very longstanding infection in one patient.

                  My point here is that so far as I can tell this surmise is mostly a matter of a lack of other explanations, and has the flaw of introducing an element the evolutionary dynamics don’t seem to require.

                  1. Yves Smith Post author

                    No, it is that this sort of long branched variant with many mutations has been previously observed n HIV positive patients. You keep denying the considerable history here. But the other cases didn’t add up to a more robust virus. Most variants don’t rise to getting any attention due to not making much/any difference in virulence.

              3. andrew

                Do you know whether there has been any human trials of the new Merck Covid 19 Pill in Southern Africa? The mode of action is supposedly to drive mutations in the viral mRNA. Could there be a link?

              4. Raymond Sim

                What I said what that this is a B.1.1.X virus, and there has been no B.1.1 in a very long time; the closest sequence to this is from June 2020.

                So most likely the chronic infection started more than a year ago.

                Replace “…most likely the chronic infection started more than a year ago” with “…most likely the virus had been circulating in a large poorly monitored population for more than a year.” and you’ve got my picture of what’s happening.

                1. Yves Smith Post author

                  Ahem, that is how most variants evolve. From GM via e-mail”

                  1. We see exactly that kind of evolution when we sequence the virus over time from chronic patients

                  2. The long branches are a common feature. Delta was the sole exception

                  3. There is a non-stop stream of weird variants from Southern Africa where most of the world’s HIV population is.

                  1. Raymond Sim

                    1. The fact that it’s how most variants evolve isn’t a counterargument. Assuming I’m right about the mathematical models, it amounts to conceding that parsimony is on my side, which I’m pretty sure was my original point.

                    2. Aren’t the long branches simply an indication of repeated replication in an environment relatively permissive to replication after mutation? Is there any feature of transmission in human populations we can point to that would lead us to conclude they can’t be sufficiently permissive?

                    3. Southern Africa, South Africa specifically, is where we would anticipate earliest detection of variants emerging after long sojourns in large, and largely unmonitored populations within a vast portion of Africa, regardless of the role played by HIV or any other factors.

                    Please note, I haven’t excluded a role for HIV, or indeed any mechanism that might exert selective pressure or speed adaptive mutation.

    2. Yves Smith Post author

      The post states that monoclonal antibodies almost certainly won’t work on B.1.1.529, see the long discussion in footnote 1, so I don’t understand this comment in light of that.

      And while we are on therapies, the wind just got taken out of one with respect to current variants. Via e-mail from the Covid brain trust:

      Merck said on Friday updated data from the study of its experimental COVID-19 pill showed lower efficacy in reducing the risk of hospitalization and deaths than an earlier interim analysis, cutting them by 30% in the study.

      The drugmaker released interim data in October showing a roughly 50% reduction in hospitalizations and deaths in 775 patients. The updated rate on Friday is based on data from over 1,400 patients.

      1. Samuel Conner

        The thought was “what can be done to reduce the likelihood that escape variants arising under future such therapies get released into the general population?”

        Presumably new antibody therapies will be devised to deal with the new variants that are not susceptible to the current therapies, and will be employed in therapy for immunocompromised patients.

          1. Greg

            I’ve seen a fresh round of anti-horse paste memes circulating among the enlightened liberals on facebook, perhaps a result of the disappointing trial results.

            1. ilpalazzo

              Horse paste is doing great so far as my bubble goes. In my trial of n=2 it’s been 100% effective.

  10. The Rev Kev

    It was always a matter of time before a new variant arose to supplement Delta and it was likely to emerge in a country which has nowhere near enough vaccines for its people. But what I never expected was something that amounted to a SARS-CoV-3. That was not on my bingo card that. That would put us back in February of 2020 in terms of protection. As it turned out, the best protection turned out to be what people managed to do themselves such as masking, social distancing, ventilation, etc. and not obeying everything that came out of the WHO or the CDC. Some of their advice was fatal. A word on that Gauteng mentioned here by the way. From Wikipedia-

    ‘Situated on the Highveld, Gauteng is the smallest province in South Africa. Though Gauteng accounts for only 1.5% of the country’s land area, it is home to more than a quarter of its population. Highly urbanised, the province contains the country’s largest city, Johannesburg, which is also one of the largest cities in the world. It also contains the administrative capital, Pretoria, and other large areas such as Midrand, Vanderbijlpark and the affluent Sandton.’

    So yeah, you are talking about places like Jo’burg with its concentrated urban population. How will it play out next year? Imagine a ward of people infected with Delta and all pretty sick. And then Nu comes in to do a clean sweep. Healthcare systems around the world have cracked under the strain already so how can they cope next year? People stepping outside their homes to clap and cheer is not going to do it. Time to prepare to batten down the hatches once more and lay in a supply of food stocks, mask, etc. Politically? It is going to be sheer chaos as I think that people will not be able to cope with this new variant. Forget about the Great Resignation. We will be seeing the Great Bail Out instead.

    1. GM

      it was likely to emerge in a country which has nowhere near enough vaccines for its people.

      The original chronic infection from which this developed happened in 2020.

      Quite possibly the person was vaccinated later but that only placed additional selective pressure

      This one isn’t on vaccine inequality, although that is indeed a problem

      1. Joe Well

        Maybe this is on inequality in access to HIV medications, including prophylaxis, and the world’s failure to throw everything it had at a vaccine or long-acting prophylaxis?

    2. Eric377

      I do not mean to sound callous, but the population is no longer the same as it was in February 2020. I do not see a generalized inability to cope with this variant as very likely. What does that even mean, really?

    3. chris

      With SARS-COV-2 passenging through domestic and urban animals, SARS-COV-3 was a foregone conclusion. I have to do inspections on mechanical systems in NYC on all kinds of buildings. I’ve been treating the basement areas, sanitary connections, and other places where rats frequent as hazardous/contaminated areas for months now because of the research from Missouri showing the suspected evolution of SARS in what’s assumed to be the rodent population in NYC.

      I had hoped we had more time. Seems like we don’t.

      1. Robert Hahl

        There are probably a lot more immune compromised humans in South Africa than there are cases of rats giving COVID to humans.

  11. Carla

    Well, this post gives a whole new meaning to “Black Friday.” Thank you, Yves, for not unleashing it on the national day of thanksgiving.

  12. Tom Stone

    Is it time to appoint Kamala as Sars Czar ?
    I know it’s morbid humor,but there will be some entertaining moments provided by the Biden administration and especially Dr Fauci.
    Hoocoodanode that Corona Viruses mutate?
    Especially amongst the immunosuppressed?

    Or maybe they’ll try calling it a nothingburger for a while,”There’s nothing “NU” under the Sun”…

    1. polecat

      U mean from her current stint as a demiCzar of cackling Gaslight??
      Of course the king title position goes to the Prime Gaslitian himself – St. Anthony the Pinched!

      Now where did I put my Bic …

  13. Brooklin Bridge

    What a wake up.

    It’s hard to imagine a country more poorly suited to deal with this, on any level, than the USA, if it is indeed what GM and others fear. All the tools necessary at hand, but they must make insane amounts of money or no one can have them. And this results in worse strains globally. Which we welcome with open arms because air line profits, business. Science is forced underground by the Truth Ministry. And so it goes.

    Just heard that even NPR is talking about this.

    1. tegnost

      Re NPR…
      Anything to get people to shop today and avoid the new strain!
      Glad I didn’t travel this weekend, I’d be stressing

  14. Louis Fyne

    Fauci in a sit-down with USA Today, Feb. 18, 2020, literally saying coronavirus risk is “low” for the USA.

    In other words, IMO the DC medical establishment plays PR spin-games like everyone else in DC.

    IMO Don’t expect anything different now. And if Nu is in HK it will be in JFK, it hasn’t already landed

  15. Mikel

    Best to just call it “Nu” or “B.1.1.529”.

    The speed of global travel today guarantees that by the time it is sequenced/discovered in a lab that it is already in other parts of the world. It’s already in the USA too.

    South Africa may just be the first to sequence it or report their findings.

    It’s really just a matter of waiting for more studies about how fast it spreads and how hard it hits.

    1. Mantid

      Yes, get with your neighbors and begin the trades. I’ll give you 2 jars of peanut butter for 20 rolls of toilet paper. For basics such as beans or rice,use 5 gallon, food grade buckets and screw top lids. Put in a few bay leaves or a wedge or two of cedar wood to keep the bugs down. Can last a couple years.

  16. David

    Just to add, if you didn’t know, that Gauteng is pretty much the centre of business and political life in SA, and Joburg is the country’s unofficial capital. It is a magnet for itinerant workers, economic migrants and foreign organised crime (the Nigerian mafia is strong there). Joburg airport is huge and modern and is a hub for pretty much the whole of sub-Saharan Africa. It has direct flights to most European capitals . All you need is one infected passenger on the way to Dubai and the variant will be in all over the world in a few days.

    1. vlade

      The belgian case came from Middle East (Turkey/Egypt). Chances are, it’s already starting to spread there a lot.

  17. Basil Pesto

    As breaking news about this variant dribbles out today, NC already has a long, informed and robust analysis, a couple of days in the making, ready to go. Truly outstanding.

    Meanwhile a trend I’ve noticed (I was first concerned about it a few months ago, but it seems to be picking up a bit of steam) is the gearing up of blaming the generation and proliferation of harmful new variants on – you guessed it – the unvaccinated. It’s the bottomless basket of deplorables that just keeps on giving.

    On top of that, today Australia’s health minister said it’s keeping an eye on this variant, but not to worry because (paraphrasing, far closer than I would like to be): “the broad-spectrum protection conferred by the vaccines suggests she’ll be right, mate”. Yay.

    But I think the real question on everyone’s minds right now, is this:

    Just how big is the Jewish community in Malawi anyway?


    1. Eris377

      The Lemba people of eastern central and southern Africa have traditions that they originated in Judea and migrated to Africa (including what is now Malawi), via Yemen. Genetic surveys do indicate substantial Semitic Y chromosome among the Lemba. They also have had cultural artifacts that suggest substantial Jewish influence. It is not so different really from the clearly Jewish Ethiopians, apart for the significant fact that Jewish religious practices remained current in Ethiopia to a much greater degree.

    2. Lois

      Yes I’ve already seen people on twitter today commenting that the unvaccinated caused this. No understanding of immunosuppressed people being incubators. UGH.

      1. saywhat?

        No understanding of immunosuppressed people being incubators. Lois

        It just occurred to me how that might happen.

        Suppose a successful overall mutation requires several previous individual mutations that, in themselves, add nothing to the survival of the virus, and in a normal immune system, would result in an increased probability of the mutant virus being culled. However, a weakened immune system might not do that with the result being a combined mutation that would overcome even a healthy immune system.

        It’s kind of like car repair: Neglected minor repairs will eventually result in problems that can’t be neglected.

        1. Tony Wright

          That sounds logical.
          What surprises me is the report I heard stating that this new variant has 32 separate mutations compared to the “wild” i.e. original Covid19 strain.
          To me, 32 in about two years represents a very high (unusually high) mutation rate compared to other viruses like Influenza.

  18. CostcoPizza

    Did we give up on a sterilizing vaccine?

    I know it’s fun to rag on the rags, but from a quick glance at a US morning ‘news’ show, they mentioned Nu twice on the scrolling ticker. Family that is not exactly Covid observant were aware of it yesterday too.

    1. chris

      As far as I’m aware there is no option for a sterilizing vaccine for an upper respiratory virus like this. whuch is why we dont have one for rhinovirus, influenza, adenovirus, and other coronavirus. Over many months of discussion on NC about all this… no one has said or shown anything to contradict that. That’s why Yves religiously stomps down on anyone mentioning things like “herd immunity” in the comments. Because it doesn’t exist for this virus.

      So if you’re aware of some authority claiming they have an option for sterilizing immunity to any strain of SARS, please do share.

  19. Carolinian

    If the new variant does take hold perhaps it will be time to admit that current policies and most especially universal vaccination with a flawed “vaccine” are “Covid theater” in the same way that the TSA is security theater. We will have to return to basic medicine and stop, as in the case of Ivermectin, censoring information that may be helpful. Fauci of course will be relegated to the retirement home he should already be in.

    1. polecat

      Things is is that those in Authority are now doubling down, as in what’s occurring in Austria .. well, the EuroZone in general, as well as the Antipodians .. sure to spread like we’ll, a virus .. only to triple, quadrupal into much moar death and chaos if not, uhh, ‘suppressed’ by the publics at large.

      And you know, if full non-liability for Big pHARMA wasn’t enough to convince many to not play this game of charade$ .. known early by those who were paying attention, than Pfizer’s request put forth to the F D A to lock in a Half-Century of ‘non-disclosure’ re. their efficacious NON-efficacious potents should be the tell that this is not about public health .. public hell, for sure! .. but not public health.
      And that’s not even taking into account the insidiously griftifying killing engine known as the PREP Act!

    2. ambrit

      Well, the ‘Kabuki’ nature of the TSA is pretty much common knowledge now, but it is still hanging on, bugging and pestering travellers to death at every step. I’ll suggest that the new “Politicised Medical Establishment” is of similar stuff. The laws of bureaucratic inertia and self-protection of turf are very active here. The “new” Medico-Political Complex will not just wither away. It will have to be killed first, and then rebuilt along different lines. No one, absent the “True Believers,” has any trust in the pronouncements of the “Official Version” of Public Health left. So, the problem becomes, how long can the Insular PMCs continue fuctioning in their bubbles while the world around them goes merrily to H—?
      I have a copy of Murnau’s “Faust” somewhere in the DVD piles. Time to give it a repeat viewing.
      Faust is pertinent to today. A ‘Man of Learning’ makes a Pact with the Devil, here, to stop a plague that is ravaging his town. Sound familiar? The only difference between the plot of the film and today’s “real life” is that, in the film, Faust finds redemption. Today’s Fausts seem H— bent on riding the “gravy train” clear on down into Avernus. The shame is that they will be taking so many of we ‘innocents’ along for the ride.

  20. Tom Stone

    This will be harder to blame on the unvaxxed, which is a plus.
    However,anyone who thinks this isn’t already in CA and New York is closing their eyes real tight.

    1. ambrit

      Watch the “It’s the Fault of the Unvaxxed” Big Lie be ramped up to 11 on the propaganda dial.
      We are dealing with Clinically Delusional Elites here.
      As a somewhat “disturbed” young man I used to know put it; “Crazy is it’s own excuse.”

  21. Lost in OR

    It’s interesting to me that non-vaccine pharmaceuticals are still not included in the typical list of public and individual intervention options. Other than the new Pfizer cash cow there seem to be few new options, studies, or discussions.

    I’ve been wanting to get IVM for a long time now. I do not have health insurance and am very healthy so interaction with the medical industry is rare and foreign to me. The FLCCC site has added more MD’s offering IVM assistance. However, as was my experience last summer, the wait times are long. The MD closest to me was happy to put me on their waiting list, Feb 1 being the first possible appt.

    So back I went to the FLCCC website and found this:

    You can use the toggles to find pharmacies that ship to your area and do NOT require prescriptions. The site also has advice for dealing with pharmacies refusing to fill prescriptions (as I have already encountered).

      1. Screwball

        A buddy of mine caught a case a month or so ago, then gave it to his wife. He knows where he caught it – a gathering where someone showed up who was sick and had symptoms. Not smart. He went to a local doctor here in a North Central Ohio town I call “Cornhole.” I call it Cornhole because we are rural farm country surrounded by corn. :-)

        The doctor prescribed the drug that cannot be named, to which I was shocked. Him and his wife were on it for a week. 70 bucks for a weeks supply. I’m not sure of the dosage. Not all the pharmacies would fill it, but I don’t know what chain did. They got better.

        I follow a well known guy on Twitter for stock market stuff who buys his overseas. He said a while back he put in an order and Mastercard cancelled his card and order, and then issued a new card. Strange. I have no reason to not believe him.

        It is much cheaper to buy from overseas. My last batch was about a buck a pill for 6mg tablets. Takes about 4-6 weeks.

      2. rowlf

        Vitamin D3 is available for horses too. (I just wanted to be ahead of the media.)

        Horses are given vitamins, y’all are not a horse.

        1. Raymond Sim

          My neurologist thinks I’m a horse?

          She does always have me doing a bunch of funny movements, kind of like dressage.

      3. Rob Dunford

        I already have two courses of IVM.
        I am doubling my Vit D dose to 8000IU + K2.
        I’m like a rattling pill box, with all the other supps I’m taking!

    1. ProNewerDeal

      I am also in the USA interested in doing the same, as per the FLCCC Prevention Protocol, say ordering IVM from a CAN pharmacy. At least while the prevalence is “elevated” at 7+/100K 7-day average of cases in my county. It is already above 30 & don’t guesstimate it getting below 7 until 2022-Mar at the earliest.

      Would love to hear of such a CAN or other international pharmacy reccomendation.

          1. ambrit

            You’re welcome fellow NCer. I heal pretty quickly, even for a geriatric geezer.
            Is it me, or are we seeing an increase in “short, offensive beasties that live under bridges” on the site lately? I wonder if NC is in the sights of a Hasbarist Organization, or are there just that many more “True Believers” wandering about unattended in the Infosphere today?
            Be safe!

  22. ChrisFromGeorgia

    Anyone else worried about ADE with this variant? Will the vaccinated possibly get it worse?

    Thank you Yves for great coverage on this on Black Friday which is more or less a holiday in the US.

    1. Raymond Sim

      Anyone else worried about ADE with this variant? Will the vaccinated possibly get it worse?

      Worse than the previously infected or those who’ve never had Covid?

      If you have some basis for thinking ADE is less likely in the previously infected than the vaccinated I would be very interested to hear it.

      1. saywhat?

        I would think “antigenic original sin” would be more likely with the vaccinated pumping out obsolete antibodies to just the spike while the previously infected might still have some useful antibodies that target the rest of the virus.

        1. ChrisFromGeorgia

          Having very little background in biology, my layman’s concern is the vaccinated have had their immune systems trained to respond to the spike protein from the original “Alpha” version, but now they have as you say “obsolete” antibodies vs. prior natural immunity that gives a deeper and better immune response (neutralizing antibodies.)

          I guess that would be more OAS than ADE. If this new variant evades the vaccines entirely, that would seemingly imply that the spike protein antibodies simply don’t get produced so maybe I was off the mark with the ADE speculation.

          1. Mantid

            A great analogy I heard is that the vaccines train your system to attack a specific spike protein, for example. Then that reference book is put on the shelf ready to go if a viral spike protein infects you. Then a new infection occurs, with a different spike pathway or mechanism. Your body grabs the reference book off the shelf and kicks out the good ol’ remedy. Trouble is, it’s ineffective. But the body is thinking, we got this. Well, after a couple days you realize you have the old edition of the book and it’s worthless. You are now days behind in the fight and are on the loosing side.

          2. chris

            Fellow Chris, some corrections to your post are needed.

            Any immune benefit gained from a vaccine, and any immune benefit gained from recovering after an infection, are both natural. There is no data to show that the immune benefit from a previous infection is any better than a vaccine response. What data we do have shows that the response from post infection can vary greatly from person to person and from experience to experience. The reaction from a vaccine is much more homogeneous. But either could be less than ideal depending on the person.

            The risk of targeting the spike protein, as opposed to all the other parts of the virus, was always that it doesn’t take much change in the virus to produce a different spike. The spike has been reported to be about 10% of the viral code. So it doesn’t take many different changes to alter the spike. One of the things that recovery from an infection gives you is resistance to the nucleocapsid of the virus as opposed to the spike protein. I haven’t seen any data to say that’s better or worse than the spike approach. It’s just different. So if the current vaccines are shown to be ineffective against Omicron, then it means the spike proteins that Omicron produces are not the same as the prior spike proteins so the antibodies from those spikes are not useful. But we don’t know much yet so we’ll have to wait and see. There are currently different vaccines mRNA in testing and production that focus on the nucleocapsid instead of the spike. Perhaps they’ll be ready soon and will perform well against Omicron?

            Lastly, we still don’t know what the correlates of protection for this virus are. We don’t know what mix of t-cell, b-cell, and antibody make up a successful response to infection. That’s one of the reasons people on NC and on podcasts like TWIV have been so skeptical of the boosters. There’s no evidence that temporarily boosting antibodies will give you a much improved result.

            1. Ahimsa

              “There is no data to show that the immune benefit from a previous infection is any better than a vaccine response.”

              I understood the weekly reports from Public Health England have been showing a difference in the immune response between vaccinated and unvaccinated, namely:

              ” (iii) recent observations from UK Health Security
              Agency (UKHSA) surveillance data that N antibody levels appear to be lower in individuals who
              acquire infection following 2 doses of vaccination. ”

            2. Yves Smith Post author

              We are very strict on disinformation and you are treading on VERY thin ice.

              And you have also made a series of assertions with no substantiation, starting with an opener that is abjectly false.

              I have objected to the use of the term “natural” because it inhibits neutral discussion of vaccine conferred versus infection conferred immunity. However, studies have overwhelming found infection-conferred immunity to be superior, if nothing else more durable. It also seems to confer immunity to a broader range of variants.

    2. Yves Smith Post author

      We haven’t even had enough rounds of infection with this probable new strain, let alone vaccination, to be talking about ADE. I’d worry about what the mortality/morbidity of B.1.1.529 first.

  23. Xquacy

    South Africa has high levels of HIV and is thus an obvious hot spot for variant generation. Why didn’t the WHO trumpet the importance of sending vaccines to developing economies, targeting above all their HIV positive populations?

    Need for clarification; don’t vaccines depend on a functional immune system to work? What possible difference could a vaccine make on an immuno-compromised individual?

    1. Yves Smith Post author

      You appear to be new here. I see you complained about your comment going into moderation, as if that was the result of a human decision about your comment. That is not how moderation works. I suggest you read our Policies.

      Asking a mere hour and a half after your comment went into moderation about it gets you off on a less than good start here. Complaining does not get us to act any faster. It eats up more of our resources and annoys the site adming.

      We are a thinly resourced site and even the MSM doesn’t liberate comments as quickly as you demand. We commit to only clearing comments in 24 hours to set expectations, although we usually are considerably faster than that. On top of that, we told readers that our main comments DJ was on holiday through and including Sunday so clearing the mod queue would be on an even slower schedule

      Your question amounts to an assignment, which is not something we view favorably here. Why don’t you use a search engine, rather than force me to substantiate what is generally known?

      Vaccines of all sorts are very much recommended for HIV positive and other immunocompromised individuals precisely because they are particularly vulnerable. However, live virus vaccines are not recommended for them.

      The fact that their immune systems are weaker and they can therefore have a weaker response to the vaccine does not render them unproductive. Older people have weaker immune systems too yet they are exhorted to get vaccinated.


  24. LawnDart

    Biden owns this.

    How long until the White House makes a statement to the public with regards to the Nu-flu? (I know it isn’t, but heck, it’s catchy… (LD hangs heads in shame, promises to look into vasectomy– enough, dad.)).

    I think that the White House might pull a Willie Brown and dump this load into Kamala’s lap– nobody likes her anyway (except maybe Hillary Clinton, if she actually was capable of holding warmth and affection for another in her heart).

    If the Commander in Chief has any marbles clicking together, it might be a damn fine time to check-out on a Section 8 (blame dementia, which no one will doubt) and quickly pass the bag.

    Time to head to the grocery store to lay in a few large bags of dog food (I don’t own a dog) and a lot of hot sauce.

    1. Raymond Sim

      I think that the White House might pull a Willie Brown and dump this load into Kamala’s lap …

      Dude, you’re just being gross.

      1. ambrit

        This is just a demonstration of the “high esteem” in which we hold our dear Veepette. Thinking about Veepette, I would much prefer to see Smurfette in the Veep’s office. At least Smurfette is more than a one dimensional character.
        As for the ‘Relationship’ between Harris and Brown, well, I have heard that the Veep one Christmas sent Willie a copy of the “Kamala Sutra.”

      2. CitizenSissy

        Sexist and gross, TBH. Not a fan of hers, but the appearance of a roaring, virulent mutation (which is certainly here already) was just a matter of time. Way too much pressure to return to “normal.” This’ll be with us for a very long time.

        1. Yves Smith Post author

          Harris deserves the sexist treatment. She got where she is 100% due to being Willy Brown’s mistress. She has no accomplishments of her own. Brown even warned her not to run for President! She only polled IIRC 2% in her home state in the 2020 primaries.

          And I hate to say it, I know many professional women with big boobs. They wear bras that are on the Valkerie breastplate level to somewhat reduce prominence and greatly reduce movement. If you watch Harris, her jackets are cut to emphasize her zaftig-ness and she wiggles all the time, making it hard for even a straight woman like me not to notice her breasts. Has to be way worse for straight men.

          1. Raymond Sim

            It feels weird to be on this side of the discussion, but I’m uncomfortable normalizing (not terminology I often employ) the imagery used.

            My position is pretty paleo – we men are swine, and we should be encouraged to watch our mouths when speaking of women, even women who sleep with Willy Brown.

            1. Yves Smith Post author

              Women who have gotten where they are the hard way deeply resent people like Kamala Harris. Or worse, women who were sexually harassed at work and got no upside. Women like Kamala encourage men to think that women want to trade sex for advancement and make life hell for the rest of us.

              1. Raymond Sim

                Like I said I’m pretty paleo on this. To my way of thinking women who sleep their way to the top are probably the second biggest obstacle to real progress for women, and they should be shamed for it.

                But men are the biggest obstacle, and regarding women as things to dump loads in seems to be a lot closer to our default setting than I wish it was. To my mind insulting Kamala in that way is likely to have the unintended consequence of encouraging men to think all women are like Kamala.

                An aside: You’ve had me noticing female helplessness in drama for a while now. It really is appalling. In fact it seems close to being fetishized. What the heck is wrong with us?

                1. Yves Smith Post author

                  Thanks for noticing re the crime show stuff. Now that I am in a room with that sort of thing regularly, it is appalling. They don’t even run away, they just scream. Only women cops and foxy ninja girls get to fight back.

              2. Fiery Hunt

                Thank you, Yves!

                My mother dealt with corporate America for the better part of 40 years…and to call out the women who used sex to advance, well, damn, that’s real strength.

                And true feminism.

    2. MonkeyBusiness

      It can be worse. What if Biden gets the virus just like Trump did? Say the worse were to happen, Kamala becomes Commander in Chief, and McKinsey boy, Pete B might have to kiss his presidential aspirations goodbye.

    3. Lambert Strether

      > Biden owns this.

      I imagine when Biden gets back from Martha’s Vineyard we’ll have a decision on air travel in a few days. Meanwhile, the direct flights from SA will continue, good job.

      1. petal

        There once was a man from Nantucket….
        EXCLUSIVE: Scranton Joe ups his game! President ‘rents’ his billionaire private equity ‘friend’ David Rubenstein’s $30M Nantucket compound for Thanksgiving – where a rock on the front lawn reads ‘I’d rather be working’

        Update on flights: BREAKING NEWS: Biden bans travel from EIGHT African countries from Monday in bid to stop new Omicron super-mutant variant – hours after Fauci said it was too soon – as UK and Europe halt flights in fear of worst COVID strain yet

        Snip: “The policy does not apply to American citizens and lawful permanent residents. As with all international travelers, they must still test negative prior to travel, the White House said.

        Further details on what new restrictions will be imposed on non-US citizens and green card holders are expected to be announced imminently.”

      2. CitizenSissy

        With all due respect, previous bans were easily evaded; fliers from redlisted countries flew to a favored nation, then to the US.

        1. lambert strether

          This ban also does not apply to US citizens, who should obviously be quarantined. (IIRC, the Belgian case was symptomatic after eleven days.)

        2. Yves Smith Post author

          No, it depends on how stringent the ban was. Plenty of countries had selective bans plus strict quarantines for all arrivals from abroad.

          Please don’t Make Shit Up here, it’s a violation of site Policies. More of this and you will be put in moderation.

    4. Glen

      The other aspect of this that we are just not dealing with: America’s health care system.

      It’s perfect for maximizing profit, at everything else like actually providing healthcare, dealing with a pandemic- we are on the road to disaster. What can we do?

      Forgive student debt – especially doctors, nurses, all healthcare related.
      Free college, especially doctors, nurses, all heath care related.
      Get profit out of health care.
      Get prepared for the long haul in health care.

  25. Code Name D

    I am wondering how Biden will jump at this. He has invested so much into his vaccine mandates, what will he do when they are now pointless in the face of Nu? The first law of Neo Liberalism is that Neo Liberals never make mistakes. So Biden will have “no choice” but to triple down on a policy that was doomed from the begining.

    I wonder if talk of Nu suddenly becomes “conspiracy theory” by the PTB because it makes the vaccine look bad and gives fuel to the anti-vax movement. I also wonder how the punitive measures against vaccine hesitant (read Trump Voters) “Trump Voters” will be perceived when the consequences fall on everyone again?

    Nu is going to completely upend the official narrative. And as we already know, the narrative always wins when confronted with the facts.

    I need to buy more popcorn for this one,.

    1. Louis Fyne

      IMO, we should be happy that Nu broke over Thanksgiving as Biden is in Nantucket, DC health establishment are home, sympathetic news editors are not in the office too—so there is little spinning of the actual facts.

      The “News Narrative” probably would have been totally different in US media if this happened when decision-makers were all in the office.

  26. philnc

    There are a large number of repos on dealing with COVID-19 related data and analysis. Do we have the URL for the one being referenced here? Thanks.

    1. philnc

      Think I found it, Looks like the comment would have been attached to issue #343 ( Git history isn’t immutable, same for issues posted to a repo (or gists). In general many software maintainers can get prickly about what they consider runaway discussions in issues (which are ordinarily used for identifying and responding to specific bugs in the subject software). But it looks to me like data dumps and extended discussion are quite common in the issues of this particular repo.

  27. carpediem

    This thing seems to be evolving exactly as this belgian scientist Bossche has been predicting for some time now.
    I wish GM could take a look at his theory and share his thoughts for the working class here.

      1. flora

        It also took place in a high HIV/AIDS country where many people have compromised immune systems. Did that make a difference? Did the size of already immuno-compromised cohort on anti-retro virals medications have anything to do with this viral mutation? There are so many unanswered questions.

      2. carpediem

        I absolutely dont tout him.
        But he doesnt seem like a selfpromoting crackhead, motivated by money imho.
        I read his blog and things he says make sense to the uninitiated.
        When I look for some critique of his thoughts all I can find is demeaning attacks on his persona.
        That is why I hoped to see an independent expert’s take on his thought.

        1. Yves Smith Post author

          You are touting him by attributing his position on vaccination to this variant without any evidence and in fact counter-evidence (low vax rate in SA).

          are making clear that you exhibit the cognitive bias known as halo effect, of seeing people as all good or all bad. Taleb made the point that if presented with two surgeon who had excellent reputations, one who was precise and well spoken, neatly tailored, with a well ordered office versus one who was fat in a messy office who talked with a heavy Queens accent, the latter would be the one to use because the first one was benefitting reputation-wise from hewing exactly to stereotypes of “accomplished professional.”

          And as for affect, go read Barbarians at the Gate. Kravis and Roberts, two of the most money motivated men in the world, had the RJR board eating out of their hand, thought they were wonderful unassuming men…and found out otherwise after the deal was done.

    1. Raymond Sim

      My two cents on Bossche: His arguments appear to proceed from axioms about the evolution of immunity which I’m not sure apply to the current situation. That said, the potential undesireable consequences of mass vaccination amidst mass transmission are all too obvious, and we’ve ignored them.

      In any case the fact that variant was first described in South Africa and is only just recently spreading there makes for good odds that it evolved somewhere else on the continent – it’s so heavily mutated that had it developed in South Africa the process would have been noticeable. Unless of course it did jump into the population from an immunocompromised person already pretty much fully formed. In either case, as others have noted Bossche’s concerns about mass vaccination aren’t likely relevant, the drivers of this variant’s evolution would have been natural immunity and/or medical treatments.

  28. Dave in Austin

    Three questions for the more technically informed:

    First, the 30 or 32 changes in the spike protein is very unusual. Might this mean the B.1.1.529 is an example of rapid mutations in a rarely tested population? Or is there another good hypothesis?

    Second, Ivermectin is widespread in Sub-Saharan Africa and my guess is that is part of the reason this very poor part of the world has been spared the worst of Covid. I caught one reference that suggested that Ivermectin may be less useful against .529 (sorry, can’t remember the source), and the strain is less well treated by monoclonals. Is this the new reality?

    Third, the high R values and the very high viral load reported out of I think Hong Kong are very troubling. Are there more recent reports (as in “today”) out of the scientific community on this?

    Yves, et al: Sorry for your lost weekend/vacation.

  29. Susan the other

    Thanks for this rundown. I wasn’t sure I was getting the sequence right. Was this Nu one the same as the one from the Congo or another? So it looks like it is the same but it isn’t from the Congo, it’s from SA. Which does not surprise me.

    1. Brian Beijer

      Thanks for bringing this up Susan the other. I’m also a little confused by this. It seems to be the same strain I read about on here a month (?) ago… maybe longer, maybe shorter. Working 11 hours a day really messes with one’s sense of time. If I am right about the time frame, then governments worldwide have had plenty of time to gather whatever information is available about Nu. That they chose to allow the press to announce it now, seems like they know it’s already in a theater, bar, restaurant, etc near you. This might also explain the hesitation in closing international travel, except for a few who are going through with the theater of just restricting flights from SA. As previous commenters have noted, that won’t change anything. The time to call for a full travel shutdown would have been weeks ago. They already made their choice not to. Can’t let a lil’ ol’ pandemic interfere with holiday profits.

    2. Yves Smith Post author

      No, it does not “look the same”. As you can seem from the discussion it has as ton of variants in one variant, including the S-gene dropout. It is not the same. It was first sighted with only 7 cases sequenced in SA.

  30. LawnDart

    CNBC talking-head just dismissed cancelling flights between USA and currently know affected countries as “ineffective”, “would only slow the spread by a week or two” and that best policy is to ensure vaccines get to where they are needed.

    Press underplaying downside risk

    Oh yeah, Yves and Co. right on the money once again– thank you.

    But to be more charitable to the MSM talking-heads and our (s)elected misleadership, I’m sure that these statement regarding the Nu will be noble lies made with only the purist intentions.

      1. LawnDart

        Hey, Fauci is going to retire some day, and this young doc is from Haa-vaahd…. …so were he to be Fauci’s successor, maybe we could refer to him as a mutated variant..?

        While he obviously isn’t a reader of NC, at least he did mention that masks and ventilation were helpful. But yeah, way too gung-ho on these magic-bullet vaccines.

  31. Jason Boxman

    Maybe it’s so obvious I’ve missed it, but I’ve looked and cannot find a link to the GitHub project in question. Is it cov-lineages? Someone added an issue: B.1.1 decendant associated with Southern Africa with high number of Spike mutations.

    That issue was closed by rambaut of the CoV-lineages org because understandably it is a work tracking ticket, not for general discussion. This is not atypical of GitHub projects in my experience.

    Or is this some other GitHub project?

  32. JBird4049

    Now that I understand that the current vaccines are likely near useless with the latest variety, can anyone tell about the home testing kits? Are they effective with the latest variant/strain?

    1. ambrit

      Good question. I can well imagine our corrupted Elites ‘approving’ seriously defective home test kits for purely financial reasons. (Those home test kits have not been made free to the public yet, as far as I can see. Ka-thunk!)

      1. JBird4049

        Just mandate them like with the vaccines only with the users having to pay for them like with Obamacare. Problem solved.

      2. Carla

        Actually, since late August/early Sept., the state of Ohio has made rapid home tests for Covid-19 available free to anyone who asks at public libraries throughout the state. Some of the libraries have recently run out but I think the state is going to replenish the supply.

      3. Basil Pesto

        It is a very good question but

        I can well imagine our corrupted Elites ‘approving’ seriously defective home test kits for purely financial reasons.

        huh? this kind of automatic cynicism does nobody any favours, and doesn’t really have anything to do with the question. This variant emerged only a few days ago.

        Moreover, whether the tests are paid for by the end user or by the state, the manufacturers are still getting paid (see: vaccines).

        1. ambrit

          I base this part of my cynical world view on the initial roll out of the Covid test materials to the hospitals, et. al. back in 2020. It was seriously bungled by the CDC.
          Opinions vary, so YMMV:
          I too once wanted the world to be run by loving, caring, Philosopher Kings. So far, about all I have encountered in control of the ‘Public Sphere’ are amoral grifters.
          One of the biggest challenges for my generation is in coming to terms with the fact that Meritocracy is a sham.
          I cannot deny your point about the medical manufacturers being paid for their peoducts. However, this is a direct result of the Capitalist economic system at work. Now, if the State was to nationalize the drug makers….
          You see the conflict of interests here.

    1. cnchal

      An excrementitious video if I ever saw one. MSNBC viewers are told the unvaccinated are the problem, over and over and what was the point of having a talking head on that says nothing.

      Listening to these two venal twerps will dumb the viewers down to worse than uninformed, by misinforming them. Covid theater indeed. The third twerp says nothing so I have no opinion on him.

      By the way, what is the point of limiting travel to several African countries when obviously it should be from?

      Still Flying = Total Fail. But I repeat myself, since Feb 2020.

      This is year two of a ten year grind.

  33. Bart Hansen

    This news will be especially tough on health care workers who are already stressed. Teachers also.

    1. ambrit

      Yes. Expect to see hospitals closed and schools also closed as this ramps up. Closed not necessarily by policy but from lack of trained help being available.

      1. chris

        The possibility of lockdowns again will cause most people in suburbia to break out in hives. I honestly don’t know what we’d do if we had all our kids home again. We’ve gone most of the fall without any COVID scares. Our local schools have been handling this great. But the problem with a change in the virus like this is we’ll lose local control and it won’t matter whether we think we can handle it or not. Also, if it is as aggressive and virulent as feared, we can’t be sure we know how to handle it.

        I can’t imagine how wrecked all of our public institutions will be from another series of lockdowns. I can’t imagine we’ll have many public schools left if the teachers bail again. Having no staff for certain activities is certainly possible. It’s already happening in other places. And to think of the damage we’ve done to these kids… we’re going to have a cohort of broken people in a few years.

        I’m rambling but the thought of going through the helplessness of watching the pandemic crash into us again, again because of our incompetent leadership, and having to do so much more for my family, my community, my company, again…it’s not quite a slit the wrist moment. But it’s on that spectrum. Time to pour another drink.

        1. ambrit

          Try to see the “silver lining” in the approaching storm clouds.
          The school system has already been failing children for decades. Ever since the “teach to the test” mantra became official policy, schoolchildren have been trained not to think. Just learning and repeating pre-selected “answers” to “questions” will get you a good “grade.” It does not mean that you actually understand how anything works. You play within a ‘
          system.’ A ‘system’ created by someone else, for their own reasons, pursuing their own goals. One does not learn how to create one’s own systems, to serve one’s own ends.
          This is not education; this is ‘training.’
          Finally, do not take it out on yourself. If the bad decisions that result in our present and future maladies are the work of others, then think on methods for slitting their wrists, not your own.
          Stay safe! Community starts at home.

  34. Anony

    Some trivia: South African’s don’t often refer to their country
    as SA – it is either RSA (the republic of) or .ZA (Zuid Afrika).

    On the topic of immune escape: Gauteng, the province where
    the Omicron cluster was detected, has just come
    out of heavy Delta wave (so The Rev Kev’s projection for
    2022 is out of date). This suggests that the antibodies
    binding to Delta might not do that much for Omicron.

    This is also quite possibly the reason for Omicron
    being discovered there – researchers encountered
    an unexpected and unexplained uptick in Covid numbers,
    prompting them to look a bit harder. Of course luck
    favours the prepared – the research teams there
    are capable, in possession of good sequening kit and
    know how to use it.

    I would not be surprised if Omicron arose somewhere
    else completely, and just got detected in Gauteng.
    The vast number new of mutations could be explained
    by an unknown population outside RSA, whether
    nearby in Zimbabwe or at the other ends of
    Africa be it in Senegal or Egypt.

    This does suggest that blocking flights from
    RSA might already be too late. This is not to say
    that quarantining international flyers is a bad
    thing – if I were in charge that would be the
    case for any international arival anywhere. Pets
    have always been quarantined – if your dog has to
    do it, you should too.

    Finally I have a theory why the WHO is so reluctant
    to ban international air travel: WHO staff are probably
    among the most frequent of fliers – one day in Geneva
    at a conference, the next day in Canada to lobby for
    funding and the next week in the DRC to worry about
    Ebola. This means that blocking flights is unthinkable
    for them, even if it is a sensible course of action.

    1. MarkT

      I’m from SA and always refer to SA as SA, as does everyone else that I know. I haven’t heard RSA used since the 1980s.

  35. Gregory Etchason

    The only question you can ask at this point is. How many times do the “authorities” get to get it wrong. Fauci “Travel bans are possible. We need more information”. NO Tony stop the travel NOW and then sort it out. Oh forbid someone may loose some money with a travel ban.
    If Omicron is what it appears. Error on the side of caution should be the plan. Pfizer stated it would take 2 weeks to see if current vaccines are effective. Or if not another $100 billion please for a new vaccine.

    1. Synoia

      It’s Christmas.

      SA Industry shuts down over Christmas, and many return to their birth places for the Christmas break

      The Namibia and Zimbabwe borders are relatively sparsely populated, but many from Zimbabwe have migrated to South Africa, and could spread the disease north.

  36. AlexS

    So.. if this thing is as bad as it is being touted to be… How can it be that the RSA’s raw case numbers for 2021-22 are trailing the numbers for 2020-21 (so far) by a decent margin? I mean their cases per mil are 16 vs 44 on this date last year. If you adjust for testing levels, it looks even less dangerous – wish that I could embed graphs here but no dice. However, it is the time of year when RSA gets a big seasonal spike. I’d say that something is not lining up here.

    1. skippy

      The drama here is were fighting evolutionary escape across a geographical/climatic variables whilst ideology gets in the road and for some reason some seem rusted on about letting it play out and let the card fall where they may for political/ideological advantage alone.

      Raw data at this moment is weak yet at the same time it needs to be reconciled with the known potential and how that effects risk assessment. Per se NC has offered more than a few links on that subject and has been borne out with the passage of time.

      I said long ago on this blog on financial matters that risk was absurdly structured because it inverts manifold when it hits a tripwire. Why does this happen you ask, well ideology refuses to accept anything outside its framework or the devotion too it.

  37. The Rev Kev

    Just to show you that every cloud has a silver lining. Biden had all sorts of problems the past few week with out of control fuel prices forcing him to get a number of other countries to tap their strategic reserve to save old Joe’s bacon. Well with this new variant, oil prices have crashed as mentioned above so perhaps that will be one less problem on his plate-

    1. megrim

      Now if covid could just forgive all those student loans and raise the minimum wage, we’re getting somewhere!

      1. The Rev Kev

        Here is an idea. So last year, colleges in America collected the fees from their students and then turned around & cancelled in-person classes ‘due to the pandemic’ and sent those kids to do their classes through Zoom instead. It was quite a racket for those college admins and I have no doubt that if there is a major ‘Omicron wave’™ next year that they will do the same to those kids. But when you stop and think about it, a student can Zoom in from anywhere. So what if this time around, some highly accredited institutions overseas in the UK, Germany, China, etc. offer the same courses and accreditation of them when those students finish their courses? If accreditation is already recognized for those institutes, what happens then? Yeah, those kids aren’t going to those campuses but they aren’t going to the ones in the US either.

  38. MonkeyBusiness

    We certainly need more data …………

    “The first South African doctor to alert the authorities about patients with the omicron variant has told The Telegraph the symptoms of the new variant are unusual but mild.

    Dr Angelique Coetze said she was first alerted to the possibility of a new variant when patients in her busy private practice in the capital Pretoria started to come in earlier this month with Covid-19 symptoms that didn’t make immediate sense.

    They included young people of different backgrounds and ethnicities with intense fatigue and a six-year-old child with a very high pulse rate, she said. None suffered from a loss of taste or smell.”

    1. Yves Smith Post author

      This is fake news. From GM via e-mail:

      Hospitalizations in Gauteng Province are up, and they are up by a proportion of the cases from last week (accounting for the week-long delay between cases and hospitalizations) that might even be larger than the hospitalization ratio seen previously.

      And most of the current cases are young people, so it would get a lot worse once it has spread to the older cohorts too.

      More importantly, nothing in the sequences suggests it is milder, exactly the opposite.

      This is just the usual tactic of getting ahead of the situation and making sure that the first thing that people hear is what you want them to hear, because they don’t pay attention after that and are stuck with that impression. It was masterfully done early on with “it is just like flu”, “only old people die”, “you will be immune for life”, etc. lies, and has been applied again and again later on.

      Actual data:

      Last week is missing — currently they are slightly below 800, but they will pass that tomorrow. So we have a 5-6 times increase in hospitalizations in 3 weeks.

  39. Bricky

    I’ve been reading this morning that early indications are that the Omicron variant is “unusually mild”. If this were true, if it were mild and also very easily spread, not only would be it be good news, it would be great, amazing news. In this scenario, Omicron would function as a free, mandatory vaccine that would outcompete everything else and end the pandemic.

    However, I think I tracked down an article with more direct information on the original source of this “unusually mild” scenario:

    It seems that Omicron was not unusually mild, but unusual in its symptoms and also mild. Further, the Pretoria doctor quoted has only seen it in young healthy adults and children. Of course it will be mild with that sort of population, as all covid variants have been during this pandemic. The question is if it will be mild for older people, and people with comorbidities. So far there is no indication of that, and based on the symptoms listed by the doctor among his young and otherwise healthy patients, I don’t think so.

    Another thing, there seems to be a widespread sense in SA that being so diligent and forthright has been their undoing, so I will personally be cautious about “it’s not that bad” stories coming out of there from now.

    1. Yves Smith Post author

      I believe they were also making that claim with Delta early on, that it might be milder (not “unusually mild” though). More generally, the Torygraph is not a great source for science reporting.

      To your point, the average age in the RSA is 27.6 years v. over 38 in the US.

    1. ambrit

      Otherwise known as “The Heartland” or “The Homeland.” Not to be confused with “Lebensraum.”

  40. Fubar.N.Wass

    “The new virus was detected on four foreign nationals who had entered Botswana on the 7th November 2021, on a diplomatic mission,” said Botswana in a statement. The four diplomats tested positive for COVID-19 on November 11 and genomic sequencing confirmed the variant on November 24.”

    Given the timeline November 7-11, did the Diplomats catch the virus in Botswana, catch it in transit to Botswana and incubate it while in Botswana before being tested leaving Botswana, or catch in at their place of origin and then incubate it in Botswana before being tested while exiting

  41. Eric377

    Just curious if people think the possible vaccine escape is for all vaccine types or mostly for mRNA? I know mRNA specifically targets the spike protein, but do the other vaccines have a broader target spectrum to elements that the omicron might not have mutated so much? Would a booster of J&J be smart for those on Pfizer or Moderna?

    1. andrew

      I read somewhere that the main Chinese vaccine was a dead copy of the whole virus (i.e. a traditional vaccine) and not mRNA or DNA virus vector. The effectiveness of the Chinese vaccine though has reportedly been low, but that depends on who you listen to.

      Happy to be corrected if I am wrong.

      1. Jack Parsons

        So, it is very possible that we will see a head-to-head competition between traditional vaccines and the new mRNA technology, with respect to variants.

        I wonder how well Sinovax and Sputnik will do?

        1. Yves Smith Post author

          This “variant” is so different, with so many fixed mutations, that calling it a variant is a misnomer.

          The experts are already saying that prior infection will not confer any immunity to Omicron. That means existing killed virus vaccines will fail too.

  42. Mtnwoman

    Fyi, The current rapid tests should pick up omicron.

    So says, @michaelmina_lab
    Epidemiologist, Immunologist, Physician. Discuss vaccines, immunity, infectious diseases, public health strategies out of COVID19.

    1. PlutoniumKun

      Worth noting of course that both South Korea and Japan have caught their cases at the airport, so they have a chance of stopping it. Nothing that efficient in the US or Europe. The Dutch reacted chaotically and the UK didn’t even try.

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