Macaque to the Future

A revisit of the incredibly limited macaque boosting study.

The blogger who goes by “el gato malo”s latest floundering, incoherent Leaky Vaccine Disaster Affirmation-Fugue has me squarely in “can’t say something nice” territory so I won’t say— oh, uh… well, too late for that. Oops.

Ok, no, I let that one slip - but I won’t bend the reader’s ear too much with my thoughts on the (lack of) quality and (lack of) sincerity evident in the post in question, and stick to rebutting (yet again) the post’s “OAS is proven yet again!” conclusion.

For one thing, it seems irrelevant in any practical sense to point out moments that suggest the author in question is knowingly feeding his audience hot air in the guise of knowledge - it’s not like the audience is complaining, after all. They are reading (or paying) to receive a specific product; the author delivers:

worse, it means that this response becomes a primary evolutionary selector for the virus.¹ variants able to evade immunity without triggering a new adaptation will be selected for. rapidly. it’s not chance outcome that omicron was an OAS variant. it was the near inevitable outcomes of the selection pressure of antigenic fixation.²

When I read this, it provokes a visceral response. There are so many contradictions raised and novel assumptions implied by every sentence, that the universe’s failure to prevent me from reading the sentence constitutes an unacceptable insult - an insult for which the sentence’s author is at least partially responsible, as no one forced him to hit “Publish.”

But why should either the universe or this author mind whether I take offense? Indeed, neither should. It is important to let go of what you cannot control, otherwise you’ll never get through the day.

Meanwhile, anyone else who greets the above sentence with the same response as I has probably already learned that the author doesn’t engage thoughtfully with critiques in the comments, and no longer subscribes to the product. Ah, the wonders of sorting.

So let’s keep this one focused on the biology: No, OAS is not real.

Except when it comes to exactly what this study was attempting to examine.

Readers of this substack may be aware that I already offered terse notes on the macaque study last month, though buried at the bottom of a multi-part follow-up.³ And before we begin this more extensive revisit, we should address the question of why those original notes were so terse and out-of-the-way: This study is not worth discussion.

There were only eight boosted macaques, paired against eight unvaccinated controls, which means the controls (by not being vaccinated at all) cannot offer any insight into the effect of boosting (literally subject of the study) - and the controls do not even come into play for the portion being discussed at “el gato malo”s post anyway.

Gagne, M. et al. Fig. S1

Anyone using such a narrow, flimsy study design to claim “proof” (or even bare support) of claims as extreme as,

your [as in, billions of real-life human Covid-vaccine recipients’] immune response has ceased to be trainable⁴

should, I don’t know, look themselves in the mirror or whatever. A handful of monkeys in a lab setting cannot stand in for a real-life demonstration of the permanent dismantling of half the world’s immune systems. This is just… weird and pathetic.

(Edit, March 9: An accidental strawmanning. Although the quote is presented as written, I should have re-inserted a “with regard to SARS-CoV-2” in my follow-up characterization above, to match the more likely connotation in the context of the author’s post.)

So, why bother with a rebuttal at all? Good question. In fact, newer readers who want a better discussion of “OAS” and an examination of a study that fails to “proove” it, shouldn’t bother with this post. I recommend last month’s take-down instead, as at least some actual human participants were involved:

Original Antigroundhogic Sin

As for readers already familiar with my prior posts, you are likely becoming exhausted of the shtick where I dismantle the shtick of “proving” OAS by willfully misreading and/or misrepresenting studies simply by not willfully misreading and/or misrepresenting them. I hear you. I’m exhausted, too.

But if you’re some type of die-hard, Unglossed: The OAS Saga completist, then, fine - read on…

Obligatory Motte Acknowledgement

As acknowledged above, we are actually in the one realm where OAS is not an outright myth.

Since OAS, like any good bit of rhetorical fraud, is a motte-and-bailey argument, this disclaimer must always be made. Yes, if you vaccinate against A, then vaccinating against a closely-related antigen, A’, may not elicit a strong response.

And that’s it. That’s the one consequence of “imprinting”: That vaccination uses up the one chance to “trick” the recipient’s immune system into eliciting a strong humoral response, and there’s no undo button. Your vaccine recipient is going to have to take off the training wheels on their own.

But so what? There’s no relevance in terms of real-life infection. This is not 1960; immunity ≠ antibodies. When the vaccinated recipient is infected with a new variant, nothing “bad” is going to happen because they have related antibodies.⁵ That’s frankly idiotic.

Since the macaque study looked partially at antibodies alone, we might expect that in this narrow, idiotic realm, “OAS” passed with sailing colors.⁶ Eh, not really. Nonetheless, it should be clear that I am not trying to totally dismantle the results, or set the bar at “Zero Antibody Difference.” That’s a stupid place for the bar to be.

The bar is in the other portion of the study, which actually looked at how the macaques faired during an infection challenge.

The set-up

The authors had some monkeys sitting around which had already been double-dosed with the Moderna mRNA-1273 product against the classic, “patented” style spike protein of SARS-CoV-2.⁷

When “Omicron” (BA.1) made headlines and prompted Moderna to design a tailored “variant booster,” mRNA-1273.529,⁸ the researchers got it in their heads that their previously-vaccinated monkeys could be used as a magic 8-monkeys-ball to predict the success of Moderna’s Omicron booster in humans.

They got their hands on some of Moderna’s candidate product, and gave 4 of the 8 monkeys a half-sized 3rd dose of Moderna Classic - “mRNA-1273” - and the other half a similarly half-sized dose of “mRNA-Omicron” (-1273.529, but labelled “-Omicron” in the study text).

Note that at this point, the comparison is between 4 macaques which received a total of 250μg of mRNA for the spike model that this study will label “WA1,” and 4 which received 200μg of mRNA for the WA1 model and 50μg for Omicron. Clearly, the only reason the Omicron set could still have a WA1 bias is magic immune disablement!

As said above, this is not going to be worth our time.

The sample head-to-heads

Once the boosting was done, the authors collected swab and blood samples from the 1273- and Omicron-boosted teams, and compared them with samples among all 8 from before the boosters drove them apart. This is where things get messy.

As I mentioned in my prior comments on this study, there are two “immune outliers” in the pre-schism set. And there are two outliers in the 1273 team. Does this simply mean that the 1273 team got the two macaques who already had an exceptionally strong immune response to begin with?

Gagne, M. et al. Fig. 2 (cropped and annotated)

Purple dots are all 8 macaques together, before they were split into red and blue. Since the authors don’t split the “before” cohort into their corresponding boosters, there’s no way to tell which team got the two outliers. If the two “1273 outliers” are subtracted, meanwhile, it seems like the Omicron team… at least ties when tested for binding against Omicron, whereas they still flunk in the other variants.

Also note that results for Nasal IgG were reversed, which is funny. It’s almost as if this is a really small sample size, so that each “team” is really just four individuals with different biologies or something.

Again, I don’t want to belabor this point, because we are already fighting inside the motte to begin with. This is not where the actual “bar” for OAS is. This cannot tell us anything about outcomes in a real-life infection. This isn’t even an interesting question when trying to predict said outcomes, for anyone who has higher than a “Immunology 101, bro” understanding of immunology. This is just OAS trying to show us its cool action-figures in a closet that smells like transfected lab animals.

That said, a figure in the Supplemental Materials appears to confirm that the high-responders landed in the mRNA / red team, by normalizing all outcomes to each player’s corresponding Week 6 value:

Gagne, M. et al. Fig. S3

Look at that. OAS would insist that the Omicron-boosted team should still have just as high an expansion of “WA1+, Omicron-” reactive B Cells (relative to each primate’s individual Week 6 value) as the 1273 team. But they don’t. So the-thing-that-OAS-insists is actually, once again, refuted by these results.

The action-figure has fallen apart, and we haven’t even left the closet yet. The authors’ caption on this one rightly refutes OAS as well (emphasis added):

Figure S3 Expansion of memory B cells that recognize unique WA1 epitopes only occurs after homologous mRNA-1273 boosting […] Frequencies of memory B cells with indicated specificities as a percentage of total class-switched memory B cells (both S-2P-binding and non-S-2P-binding) were normalized to the corresponding frequencies from each individual NHP at week 6 post-immunization

Did the paper offer any other hint that the over-performance of the 1273-boosted team was, possibly, a result of drawing the two stronger players to begin with?

Yes. “El gato malo” literally shoves said hint in his readers’ faces. Turning to the blood samples, which were subjected to flow cytometry results to see how many B Cells bind both Omicron and WA1 spike protein:⁹

this is a scatter of memory B cell specificities post immunization and boosting. think of B cells as a recipe storage medium. they are not the antibodies, they are the cells that remember which antibodies to make and how to make them. it’s your immune memory. [No it’s not, it’s literally 8 random lab monkeys’ immune memories!]

these charts are a little tricky to read, so let’s walk through them: [Nice; language like that always sends my Intellectual Honesty Meter straight to 11!]

the scatters break into 4 quadrants. upper left are B cells specific to the Y axis variant. lower right are B cells specific to the X axis variant. the upper right are effective on both.

look what happens here. you can see fade from week 6 to week 41 and then a resurgence in week 43 (post a week 41 boost)

now look at how different the responses to omi [meaning, to WA1 and Omicron spike for the Omicron-boosted four] are vs [same for the four boosted with] traditional 1273.

(Note that “el gato malo” also includes part B, which compares Delta and Omicron spike response, which is strange, since there was no vaccination for Delta spike.¹⁰)

And so there it is, in all its alleged devastating glory. The Omicron boosted are clearly [incoherent, over-confident rambling that pretends to even understand why this supposedly verifies OAS]! Game over, you Covid-vaccinated suckers!

Perhaps you have already caught what the individual showing this figure as some kind of “proof” of OAS seems to have not noticed. If not, consider taking one more look at the version above, before scrolling onward.

And now:

Gagne, M. et al. Fig. 3

This is really just basic study interpretation and critical thinking best practice, here. When interpreting data, look at the whole picture, not just the part you think “confirms” your conclusion, or the conclusion asserted by the authors.

And if you want to rescue the results by comparing the relative increase on the WA1/Omicron axes, you will crash against the math for how much the Omicron boosted did not re-up their “WA1-only” response compared to the 1273 team ((.36/.11)/(1.63/.18) = .36, a 64% reduction in “WA1-only immune enhancement” for the Omicron-boosted).

Or, for a different approach, try holding the Week 6 and Week 43 plots side-by-side in your head for both booster-teams. Which team seems like, on Week 43, it has merely revived, and which “steered away” from it’s Week 6 WA1-centric response? So in what way was the mRNA-Omicron team “sinned” against at all?

The Omicron infection head-to-heads

now, what would have been REALLY interesting is to do this same study but use actual omicron virus instead of boosters and to then compare the B cell map in vaccinated primates vs those who were vaccine naïve.¹¹

Really? Even more interesting than just seeing how these two teams of boosted macaques do against infection with Omicron (BA.1), vs. an un-boosted or directly-Omicron-vaccinated set?

At all events, the authors did not offer their readers either wish.

Instead, they ran the BA.1 infection challenge with the two booster teams competing against each other and a set of 8 “blank” mRNA-injected controls.

To determine the extent of protection provided by a homologous mRNA-1273 or challenge virus-matched mRNA-Omicron boost following the two-dose mRNA-1273 immunization series, we obtained a new viral stock of [“actual”] Omicron, which was sequenced and confirmed to contain the canonical mutations present in the dominant [“actual”] Omicron sub-lineage BA.1.

Four weeks after administration of either boost, we [“actually”] challenged these NHP and 8 control NHPs with 1x106 [“actual”] plaque forming units (PFU) via both intratracheal (IT) and intranasal (IN) routes. The control NHP had previously been administered 50μg of control mRNA formulated in lipid nanoparticles at the time of boost and had never been vaccinated..¹²

Of course, anyone who already read “el gato malo”s post already knows this. To quote his discussion of the [“actual”] Omicron infection challenge results:

…

Oh, that’s right. He doesn’t mention that an infection challenge even occurred.

i wonder why [he] didn’t…?

As for what makes the choice to use unvaccinated controls frustrating, the result is that there is no way to know if boosting even made a difference in outcomes at all.

The authors started with 8 Moderna-vaccinated monkeys. Then they made a change to those 8 monkeys. Then they compared the changed monkeys with monkeys that weren’t like the before-change group. So what are they even measuring?

Regardless, both sets of boosted monkeys outperform the unvaccinated set (and BA.1 is mild in all of the monkeys anyway):

Oh, no!!! Boosting macaques works whichever way you do it!!!!! Humanity is doomed!!!!!!!

¹³

Update, March 9:

In a follow-up post, “el gato malo” extrapolates from his misreading of Gagne, M. et al. to a theory for how immune imprinting on a global scale could be responsible for Omicron and/or future super-escape-mutants (my words).¹⁴

My comments:

1. Obviously, all the linked substantiations for OAS are just prior complete misreadings of studies, including Gagne, M. et al.

2. The attempt to rescue OAS from the counter-example of flu vaccines, by suggesting that prior natural exposure insulates humanity from an OAS-effect for flu, is interesting (though he also seems to be trying to conflate immune senescence from aging as some kind of semi-example of OAS). But we should also notice the “quiet part out loud” aspect here: The author is acknowledging that there is no real-life impact to OAS in flu infections, and thus no precedent which supports expecting the same for SARS-CoV-2.¹⁵ It’s all a fever dream, premised on a profoundly obsolete understanding of immunity.

3. The weakness (nonexistence) of support for OAS is not fatal to the broader Monoculture Disaster Theory, anyway. In fact it makes more sense without OAS. Otherwise, there’s no accounting for why the Omicron wave stopped - if the Covid-vaccinated were just recalling the same-old antibodies, how did they avoid instant reinfection?¹⁶ And wouldn’t Omicron just stop evolving, since there is no new immune response to overcome? The Monoculture Disaster Theory is actually stronger in a model where immunity to each new variant is as tailored to that variant as possible.

4. Supposing widespread natural anti-spike immunity - in a hypothetical alt-Earth where there were no Covid vaccines - to be an iridescent quilt of pre-Omicron variant epitopes, you are still in a landscape that is favorable to Omicron (BA.1 and 2). Omicron gets around all prior anti-SARS-Cov-2 spike designs. The Covid vaccines are a superfluous element in this model of Omicron’s rise. (The Covid vaccine’s over-promotion of a single “design” also seems to be self-compensating by some mechanism, based on Röltgen, et al.’s interesting findings of higher RBD cross-reactivity.¹⁷) I don’t know what else to call the logical construction, “Because Covid vaccines made everybody only able to respond to one, outdated, version of the spike, we got a variant that can overcome responses to all previous versions” except contrived. Also RE Omicron:

   1. Non-spike-specific antibody responses are not covered by OAS. The controversy of whether the “breakthrough infected” are not generating normal levels of antibodies to N protein is still based on a single throwaway comment from October (which continues to be reprinted in the UKHSA reports to date), and would not be OAS anyway, since there’s no homology at play here (per OAS, nothing would stop you from vaccinating a spike-vaccinated person against the N protein).¹⁸ Otherwise, it’s an interesting question. But so is the entirety of how mucosal, resident T Cell, and innate immunity respond after breakthrough infection - the “goal” is that the Covid-vaccinated move beyond a purely humoral-immunity response, but there is no research available yet to decipher whether this is the case. However, precedent with other injected vaccines suggest that there will be some “immune correction” here, à la “natural boosting.”

   2. Supposing natural infection (in an alt Earth where there were no Covid vaccines) to have resulted in less spike-centric immunity, and greater mucosal immunity, Omicron is still favored, as it changes tissue tropism and thus evades resident T Cells left over from natural infection. The Covid vaccines are a superfluous element in this model of Omicron’s rise.

   3. What if the theory instead proposed that front-loading anti-spike immunity removed a pre-infection natural barrier that was preventing synchronized, global entry into the same infection cycle? Ah ha! Except… supposing the Covid vaccines to suppress innate immunity merely recycles vanden Bossche’s theory,¹⁹ and does not represent a new proposal. Moreover, Omicron becomes superfluous in this model of Omicron’s rise - Delta should have displayed a comparable scale of spread once antibodies waned in the summer. There’s a little wiggle-room for “innate immune disablement plus vaccine escape,” but, again, this are two different and pre-existing proposals, not based on OAS. The Monoculture Disaster Theory could be called a modified version of these two theories, in that case.

   4. The phylogeny of Omicron does not support a “waiting to strike” origin.²⁰

5. Overall, the Monoculture Disaster Theory is interesting, but needs more work. The presentation offered in yesterday’s post is mostly “Look, shiny.” Omicron and OAS are extraneous. It is especially unclear why Delta would not have become a “forever variant” per the theory if none of the Covid-vaccinated were developing better resistance to Delta (per OAS), so the theory works better with OAS removed.

6. At least “el gato malo,” in this post, isn’t subjecting readers to new misreadings of any studies.

Previously, in the OAS saga:

“Even-Steven.” (OAS is “proven” via generation of a more balanced immune response against Alpha or Delta after breakthrough infection.)

“Original Antigroundhogic Sin.” (OAS is “proven” via breakthrough blood samples taken too early for seroconversion, and an overhyped UKHSA comment.)

“Funeral for a Fact,” footnote 3. (OAS is “proven” because the boosters restore infection efficacy vs. Delta during the Omicron wave.)

“Darmok and the Spike Protein at Tanagra.” (OAS is “proven” when high pre-existing antibodies against coronaviruses… don’t correlate to severe outcomes in infection with SARS-CoV-2 in any way.)

1. Oh, no! Not a Primary Evolutionary Selector! Ahhhhhh!

2. “el gato malo.” “variant specific boosters fail to elicit variant specific response.” (2022, March 7.) bad cattitude.

which reviews:

Gagne, M. et al. “mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits comparable B cell expansion, neutralizing antibodies and protection against Omicron.”

3. See “The Grapes of Macaqueth.” Hopefully anchor links are working again; the key seems to be to not remove the query string.

4. (“el gato malo”)

5. Unless Dengue Fever, which is at times touted as the one “real world” affirmation of OAS (see “(Not) Coming Up”). But Dengue Fever is 1. Antibody Dependent Enhancement, and 2. A virus that is injected directly into the blood-stream (via mosquitos), which makes it incomparable to a respiratory or enteric virus.

There are, of course, other examples of ADE after vaccination, including an ancient example involving measles in the 60s (see Fulginiti, V. et al. (1967.) “Altered Reactivity to Measles Virus.” JAMA, Volume 202 (12) – Dec 18, 1967) but this has nothing to do with failure to mount a response against variants, since measles does not have (constantly antibody-evading) variants.

Other examples are the 60s RSV experiments, and prior animal coronavirus vaccine trials. ADE should not have been dismissed as a potential danger of the Covid vaccines; but ADE is still not OAS.

6. Leaving this one as I mis-wrote it. Sailing colors.

7. Not really patented. See “The Moderna patent controv.”

8. See https://investors.modernatx.com/news/news-details/2021/Moderna-Announces-Strategy-to-Address-Omicron-B.1.1.529-SARS-CoV-2-Variant/default.aspx

Yes, Moderna designed the Omicron Covid vaccine just as fast as the first one.

The Company has repeatedly demonstrated the ability to advance new candidates to clinical testing in 60-90 days.

9. Readers who want an explainer for flow cytometry may like “Flowcytometry Basics - Interpretation of Graphs | RAPID REVIEW !!!!” (youtube) (Watch out for the vintage stop the spread propaganda at the very start.)

For a thorough explainer on how to pronounce “macaque,” see “How to Pronounce Macaque? (CORRECTLY)” (youtube)

10. (Redundant) results for Delta/Omicron spike binding:

11. (“el gato malo.”)

If the reader is somewhat perplexed at why my critique takes such an acerbic tone, do take a stroll to the comments on his post. A sample. This is getting sickening.

12. (Gagne, M. et al.)

13. (link anchor)

14. “el gato malo.” “homogenizing herd level antigenic fixation.” (2022, March 8.) bad cattitude.

15. With a repeat of the Dengue caveat in footnote 5. I’m being evasive with the “evidence” for a real-world significance for flu as 1) it is always asserted, with no research support 2) an actual dive into the research reveals this to be another misreading. It is the rope I am still waiting for the proponents of OAS Disaster Theories to hang themselves on.

16. This critique is limited by the fact that most health authorities define cases as being a positive test that is at least a certain amount of time since a prior positive, often 90 days. This “prevents” instant reinfection by defining it out of existence. However, the naked eye would probably notice if the Omicron wave was still ongoing in places where cases are no longer officially doing the same.

17. See “Even-Steven,” which reviews Röltgen, K. et al. “Immune imprinting, breadth of variant recognition and germinal center response in human SARS-CoV-2 infection and vaccination.” Cell.

18. Discussed in “Original Antigroundhogic Sin.”

19. Discussed in “Neg.”

20. Due to Omicron showing signs of having evolved under constant, extreme high pressure either from B.1 or from a hypothetical common ancestor with the Wuhan strain - see “Omicron Origins.” (For which I still haven’t finished any of the additional illustrations!)