If the vaccine is not causing the variants, why do vaccinated people appear to have a greater probability of being infected with variants? Large population-wide studies have shown this effect.
This evidence cannot override evidence that directly speaks to 1) where Greek letter variants come from and 2) whether the virus evolves in the wild. 1 does not show any relationship to the vaccine (the 2020 Greek letter variants appear before wide release; the Omicron family has molecular markers of a not-wild origin), 2 continues to show that the virus doesn't evolve much in the wild, not more now than it did in 2020.
Even setting that aside, "negative variant efficacy" isn't intrinsically suggestive of anything besides "some Wuhan efficacy." So when Omicron came out a lot of substack writers started showing relative infection rates without even seeming to understand that this was actually just showing that the (very very recently) injected still had resistance to Delta (https://unglossed.substack.com/p/funeral-for-a-fact#footnote-3). So you definitely could say that the vaccines created a favorable landscape for Omicron BA.1/2 versus Delta: But that doesn't change the fact that Omicron was made in a lab. Just like you could compare some Monsanto plants with some natural plants and see one do better against bugs or whatever (I am not a farmer); that doesn't mean the bugs "caused" the Monsanto genes except in an abstract, human intention sense.
In that case, what would explain why heavily mRNA vaccinated countries saw large spikes in cases around December 2021 (like Korea, Japan and most of western Europe), while India and African countries didn't exceed their earlier peaks? Does that mean that some of the lab variants were explicitly designed to be more infectious to mRNA vaccinated people?
"Earlier" peaks in lockdown-ed countries correspond with lower post-wave seropositivity than African / Central Asian countries. Whereas waves subsided at 10-20% seropositivity in lock-down-ed areas, they subsided in 30-70% in non-locked-down areas. So "more-than-earlier" in the lockdown-ed countries is not actually as big as "more-than-earlier" in non-locked-down countries.
What would be truly impressive is if low-vaccine countries like India, Russia + Romania + other slavic countries, due to just having had Delta waves, were resilient against Omicron. But they weren't. So even without the vaccine Omicron was rampant.
Korea and Japan never had lockdowns, so I wouldn't consider them lockdown-ed countries. It's quite striking to look at the graph of covid cases since 2020 in Japan and Korea vs India; Japan and Korea both see peaks orders of magnitude higher post-vaccine, while India never sees peaks exceeding its mid-2021.
I'd argue that Romania and other slavic countries (excluding Russia) don't make as good a comparison as India (which did not use mRNA vaccines at all), since even though they were relatively unvaccinated, they still had a double digit percentage of the population mRNA vaccinated. Given how dramatic the case rate increased in Japan and Korea post vaccine, even just 1/5th of that increase would still result in a larger rate relative to the previous peak.
Unfortunately my IRL distractions are rendering me a poor interlocutor. So the question of whether the Omicron family demonstrates anything about whether the vaccines "cause variants" is again subject to the limitations above. 1, they have clear molecular evidence rendering any kind of natural evolution from wild Wuhan-family virus improbable. Lab origin the least improbable explanation. So I just want to make sure that's still on the record when discussing the more nuanced hypotheticals about what (absolute or Wuhan-relative) negative efficacy and population trends would imply if the origin was actually in question.
Regarding population trends, it's a question of whether the vaccine is required to explain what happened. Well, east Asia was functionally "immune" to the Wuhan strain for reasons we don't understand. For all we know it could be due to microbiome, maybe even from natto bacteria, which break down Wuhan spike. If anyone knows it's probably whoever designed Omicron. You can speculate the vaccine caused a change here but without an "unvaccinated East Asia" control group, speculation is all that is. But Hong Kong at least is a good falsification of negative Omicron efficacy on a within-population level. The unvaccinated elderly got hammered, if we are to take the CDC's word for it https://www.cdc.gov/mmwr/volumes/71/wr/mm7115e1.htm
This isn't to fully answer your points; at the moment I am multitasking.
This was more disturbing than anything I've read in the past two years. The evil of tinkering endlessly with the virus probably in hopes of making something more lethal, and the psy-ops possibilities make me feel sick.
Actually never trusted van den Bossche at all, mainly because of the look in his eyes. (I could have used logic, but I'm pretty good at reading faces.)And his predictions of imminent viral takeover because of vaccination kept not coming true.
NO COMMENT on the eyes, haha. I don’t know which, if any of the Leaky Vaccine Evolution crew are ops - they could all be unintentional supporters who are just intoxicated by the premise of some Garden-of-Eden-fable type of biology. Or the whole thing really is emergent; obviously either possibility makes the opposite possible as well.
Brian, you are a treasure. My little monthly subscription doesn't convey my appreciation enough; if I had a million bucks it would be yours 🙂.
When this subject has been finally been wrung out (🙏 ), I hope you'll continue with your substack including other subjects as you used to do before the scamdemic took over.
why can't it be a combination of a little of everything?
lab created. lab accidental release, lab deliberate release., vaccine evolutionary pressure, natural evolution? depending on which particular variant a person is talking about?
What I claim / argue is that there is simply no evidence of vaccine-induced evolution. You (as in a hypothetical substack writer) can say it is happening, fine, I won’t bother you. But if you assert there is evidence, I disagree. As Peter details, the 2020 Greek variants precede the vaccine wide release, and Omicron has clear molecular evidence of a lab origin. When you therefor don’t include the mutations that these variants “ship”/come with, the virus isn’t actually evolving faster now that it ever was in 2020. It remains relatively static.
Additionally, vaccine-effected evolution makes specific predictions depending on if you are using a “Immune escape” model or an OAS model. Immune escape depends on infection efficacy staying in tact. But once the vaxxed started getting and transmitting Delta there was no way for them to exert selection / bottleneck pressure on it. OAS in comparison implies that pressure turns off. In other words if Delta was the escape variant, the vaccinated cease to put pressure on it. How can they push Delta if they “can’t make Delta immunity.” That leaves various shell game models where pressure happens absent selection which I do not find lead to any coherent predictions.
Delta appeared before vaccines were rolled out. So that rules out vaccine pressure. All of the main pre-December 2022 variants appeared before the vaccines.
Omicron is derived from B.1'ish. Or perhaps more neutral is of origin unknown (Brian and I slightly disagree on details) but not an evolution of Delta or other early variants. What is key is it underwent huge amount of evolutionary pressure, then forked into (at least) two which each also had enormous evolutionary pressure, but were during these pressure periods never seen in the wild ever anywhere. Then magically both appeared at the same time in the wild. Lots of mysteries, but whatever caused its evolution, hence wasn't in the wild under vaccine pressure.
I don't know why Brian feels there is a continuous release, but I may just misread his words. But regardless there is however evidence of a summer/early fall 2019 release or leak (Wild type and Brian believes also B.1), and then possibly a second (Omicron BA.1 + BA.2 twins) somewhere late 2022. Within each there are multiple possibilities based on intend and what exactly was leaked. Also the actors (if any) and intend may not be the same for both these events. But vaccines seem to have either way virtually no effect on these two major events.
RE continual, it’s just something I don’t want to rule out 100%. At least before Omicron, I’m not would-want-to-bet-my-life-on-it convinced that the virus was good enough at sustained transmission to just “virus” *edit: as in the phrase “virus gonna virus” where it is assumed that SARS-CoV-2 wasn’t impacted by mitigation. Once again was on the way out door while typing this one
Given that a computer sequence can be added to a viral backbone - and that GMO RoundUp Ready crops can spread the RoundUp Ready genes to super weeds - why would we not expect that a computer sequence stuck on a very mutatable coronavirus, might not also mutate?
Yes, variants seem to be being used as a fear-demic media tool, but that is a different story.
A lot of this comes down to an assumption that all "pathogenic" genomes are naturally going to evolve in response to human efforts to kill the pathogen. But in fact, that's not a guarantee. Bacteria anti-biotic resistance for example is not driven by "evolution," it's driven in a lot of cases (if not all) by plug-n-play genes from plasmids and viruses (phages) that confer extra hardiness, that were always in the bacteria's "app library" all along.
Then we consider RNA viruses:
1 We have been immunizing against polio for decades and decades, it hasn't evolved to resist our effort to eradicate it.
2 Same for measles.
3 Ah, but flu - well, actually, as far as our limited observation has shown, flu usually drops in from avian reservoirs that have almost no evolution goin on, the spike protein runs out of evolutionary "moves" a few decades after crossing into humans, and that spike protein just goes away, replaced by a different species of spike from the unchanging avian reservoir. So flu can't actually "escape" human immunity either. It can just delay being relegated back to the avian reservoir.
So for RNA viruses I don't think there is any precedent to assume 100% that coronavirus would mutate to escape immunity. It might, it might not. So then when we look at nextstrain and consider what the Wuhan virus seemed to be doing in 2020 and 2021, there is no evidence that it was trying to mutate much. And if other RNA viruses don't mutate to escape immunity, then the fact that this one doesn't seem to do so (out in the wild) should be taken at face value.
From there, the argument becomes whether the greek letter variants are proof that wild immune escape does happen or, as I would argue, exceptions to the rule which must therefor be considered unnatural creations.
Omicron already reverted back to a form that escapes the jabs. It is part of the RNA species nature to readily Lego-block themselves into different forms for different environments within the body. Read the quasiswarm info by @Harvard
Regarding "Omicron already reverted back to a form that escapes the jabs" does this refer to Omicron not stemming from Delta or any known circulating genome after B.1? That, itself, is evidence that it was made in a lab from a DNA<>virus "stock" template with the B.1 mutations in it.
As I put it in Omicron Origins, I don't want to actually propose that viruses can't do really surprising things that we can't explain, just instead to look at the question according to the "rules" that science normally uses for inferring genetic origins. These "rules" do not allow a conclusion that Omicron was somehow hiding and evolving in the Delta swarm.
True, Omicron is non-typical. ... an oddly coincidental older strain suddenly became prevalent as it can bypass the jab antibodies. Was it a GOF release to try to mitigate the chimeric spike release/escape?
I don't know the motives. My guess is that it wasn't meant/realized that it included two majorly different virus phenotypes (BA.1 vs BA.2/4/5), so whether it was supposed to be virulent or mild it was a backfire.
Yes, I get that. But what about all the bloody variants/mutations/there are hundreds of them..not all named...but are you saying that everyone of them is a lab release?
No, these are post-release progeny. If SARS-CoV-2 is a tiger clan in a zoo being re-released into the wild, then there is a release in late 2019 (either "Wuhan" model, or B.1, or "Wuhan" then B.1, the picture here is muddy but I am leaning toward just the first one). Then a year later the zoo releases some more tigers that evolved in the meantime and these displace all the previous progeny from the 2019 tiger, these are the late 2020 Greek letter variants. Then another year and the zoo releases some more tigers, these are the Omicron family. Again they displace the previous progeny. If there is any other releasing going on my guess is it would still be of the "model" released in the end of the previous year. The updates don't ship until October. I don't personally have a bet on whether it will happen again this year, I'm not actually a mind-reader.
Wow. This is mind boggling. But just as probable as anything else...
Just read this am that Covid 19 was sent to a lab in Ukraine in November of 2019 I think...before it even had that name...
I am definitely Alice in Wonderland, and can believe six impossible things before breakfast.
Can I ask...what is the intent behind all the releases? Scientific curiousity? Let's see what this one does? And do they never think that maybe it might not be such a smart idea, unless they already have the antidote to any future strain combo???
While I agree that there are plausible scenarios by which variants of the SARS-COV-2 virus can be lab engineered, it strikes me as a leap of logic to argue exclusively for lab engineering to the exclusion of natural evolution.
Given that subvariants of Omicron are now the latest doom strains out there, it seems there is a certain arbitrariness to the assigning of Greek letters, which means there is a certain arbitrariness to assuming which variants are lab engineered.
The Omicron "scrabble" variants don't bear the hallmark of being parachuted in from unclear mutation chains. So there isn't anything actually special about them except:
1 - they are being given funny names; but so were the "bird variants" of late 2020 that no one remembers anymore.
2- They do seem to reflect more "hotness" in their RBD hotspots than previous. But this is not surprising since anti-Omicron natural immunity is now at a peak that anti-Wuhan / Delta immunity never reached. This is just down to the Omicron family being a lot fitter at spread than the Wuhan line ever was. So the Wuhan line never showed any convincing signs of immune escape outside of the "parachuted" arrival of the greek letter variants. (Instead, hotspots seemed related to functional fitness).
Now, you could obviously say that there are loads of "evolutionary leap" sequences even going back to early 2020. But these never spread. The "bulk" of the B.1 cloud in the nextstrain map was always pretty inert, as were the clouds for Alpha and Delta. In every case when a variant "parachutes" in it's way above the mutation trend and then drifts along at the same slope as the trend. I think if I could look at nextstrain right now the Omicron swarm would be finally showing an uptick but like I said that's natural immunity at work. So if natural evolution is the trend, then by definition it isn't a good candidate for the greek letter variants because they all pop in way above trend. Or you could attack this argument by saying that "goes on to spread successfully or not" isn't a meaningful way to distinguish noise leaps from not-noise leaps. But really the other leaps (the dead ends) could just be the rare bad reads that pass QA.
"The Omicron "scrabble" variants don't bear the hallmark of being parachuted in from unclear mutation chains."
Is that a "knowable" metric? Do we really understand viral evolution so well that we can make such a claim?
This is not a question that is necessarily limited to SARS-CoV-2 or coronaviruses or even viruses in general. There is a body of thought within evolutionary biology that posits evolution occurs not through an incrementalist process but through "evolutionary leaps"--and there is a countervailing body of thought that insists those "leaps" are merely gaps in the evolutionary history.
While it is challenging to our human understanding of the world to be confronted with such "leaps", which we are if we posit a natural origin for Alpha, Delta, and particularly Omicron, the occurrence of such leaps is not necessarily proof of artificial origin, as such occurrences are found time and again throughout Earth's biological history. The challenge of Omicron is a challenge that has been found throughout the fossil record for a whole host of species.
This is not to say that Omicron or any of the other Greek alphabet variants are synthetic in origin, nor is it to say that they are not synthetic in origin. This is to ask the question "how can we KNOW they are synthetic in origin?" That a phenomenon is possible is not intrinsic proof that said phenomenon is.
So what I mean by this is that when you go to nextstrain and into clock view, every "cloud" of dots is the same angle, and the 2020 greeks and Omicrons just start as being "dropped" above this angle (ignore the diagonal trend line as this incorrectly maths in the drops that don't match any actual trends). So the scrabble variants are just part of the same cloud trend, they aren't "dropping" in above it or making it curve higher. The "claim" here in question is merely that this is what is visible in nextstrain. The scrabble variants are just like previous "cloud dots" that didn't get special names, or that did get names that we forgot about anyway (the bird variants).
Also as in my comments to Markael, I am not arguing that leaps are "ruled out." But given that "wild" SARS-CoV-2 and the Omicron family have molecular evidence of lab origin, the observer has to make a call here one way or the other and I think lab origin for the 2020 Greek crop is more likely than coincidental evolutionary leaps, especially given little apparent change in the evolutionary landscape in fall 2020 as I mention in the linked post.
For myself, I specifically refrain from making the call one way or the other. From the epidemiological perspective, lab origin is mostly irrelevant. Once a pathogen is in the wild, it's in the wild, and the virus will proceed to virus the same as anything else.
Lab origin questions are extremely important for understanding the mendacity and duplicity of our self-anointed public health "experts", but for contending with the spread of an infectious pathogen, not so much.
As I have long considered your analyses as among the most thoughtful, original, and impartial, I am a bit saddened to see you making some assertions here that I don't think can be rationally justified.
"This is not “more evidence that SARS-CoV-2 came from a lab.” It is more evidence that SARS-CoV-2 is a proprietary product."
I'm surprised that no one thought to do an RE site analysis before. It is however worth noting that the authors apparently chose BsaI/BsmBI for their analysis precisely *because* these chopped the SARS-CoV2 genome into synthetic-looking fragments - not because they had solid evidence that the viral engineers used these two enzymes. Exactly what sort of p-hacking type bias this decision might introduce is at least worthy of consideration - i.e. if we were to choose the ~25-50 RE's most commonly used for IVGA and were to run such a fragment/count length analysis on viral genomes for all of them, how anomalous would be BsaI/BsmBI pattern for this virus truly appear to be? Or, in other words, what proportion of naturally-occurring viruses would appear as an equivalent outlier for *some* combination of REs commonly used in IVGA?
In answer to your second sentence, would not merely removing one restriction site be enough to generate an anomalous pattern here? I've done a lot of RE-based genetic engineering in my earlier career path (gene insertions/deletions/promoter replacements in cyanobacteria) but no actual IVGA. I think much stronger evidence would be required to claim that this virus is a truly synthetic, IVGA-based "proprietary product."
"The synthetic origin paper shows what a farce it is to even care about the question. All the greek letter variants, from Alpha to the Omicron family (and a few suspicious sequences that never caught off the ground, from Central America and the US) should be considered lab-designed updates to the original DNA<>virus SARS-CoV-2 platform."
Again I think you are going too far here and postulating too much synthetic editing and lab release without evidence. The BA.1 and BA.2 lineages have sufficient genetic difference that some unusual explanation (IVGA, mouse serial passage, long residence in an animal reservoir, etc.) is required to explain their appearance. Maybe also BA.5. Most of the other variants display exactly the evolutionary pattern and mutation rate that one would expect from a novel RNA coronavirus adapting to a human population that is simultaneously developing immunity.
The naming of these variants is entirely arbitrary and has almost nothing to do with their degree of genetic divergence. Alpha was a very small mutational step from the wild-type. I find it interesting that the rate of new variant naming is more directly proportional to the level of fear the narrative-controlling forces are attempting to instill. Thus we had the whole Greek alphabet in 2020-early 2021, but during the "vaccines are safe and effective" period we had a level of diversity exceeding all previous variants contained under the name "Omicron".
Now they're inventing new designations again and ramping up the fear (to convince people to get the bivalent booster? to distract from vax injuries?) and we've got the BE, BY, BQ, XBB, etc. appearing in the news despite the fact that on e.g. NextStrain mutation charts these are only small incremental changes from the current circulating variants.
“We also argue that our checklist for IVGA is best viewed as one test.” - reflects my shoot-from-the-hip interpretation. Certainly some very dazzling maths used to demonstrate unlikelihood of false discovery, I’ll say!
"would not merely removing one restriction site be enough to generate an anomalous pattern here?" - This might be N/A after your other comment below, if you are no longer disagreeable to the paper's conclusion that there was a construct before the "wild" virus. Still I would note that removing one restriction site cannot create shortness of longest fragment. The shortness has to either be architectured or emerge randomly. Which goes back to the false discovery question that is discussed in the other sub-thread. *edit: This did not address the question of "what if the shortness is already there." In which case a virus can accidentally place itself in the quadrant of interest by just randomly removing X number of sites as long as it does so without creating a new longest segment. So actually this is a tricky math problem but essentially devolves to "few wild coronaviruses are going to be in the right quadrant."
"Most of the other variants display exactly the evolutionary pattern and mutation rate that one would expect from a novel RNA coronavirus adapting to a human population that is simultaneously developing immunity." This is discussed in my reply to both Kust and Depew above. There should, I argue, be no "assumption" of mutation rate given other RNA virus precedents. We should take the rate in nextstrain without the greek variant insertions (both before and after) and see if it predicts their insertion; it doesn't. (Unfortunately this is impossible to discern in nextstrain anymore). True, the vanilla versions of Alpha and Delta weren't radical in absolute terms but they still were above trend both before and importantly after. Maybe Delta was accelerating a bit in the end.
You could say "well this doesn't rule out natural evolution" but I am not trying to make a rule-out argument here. I am arguing that when we stop assuming without basis that the virus is going to evolve this much on its own, then different interpretations of the evidence become natural.
I am also not taking the greek-naming thing as creating a reality that prima facie demands an explanation. As my post alludes to, there were some unnamed variants that have the same very-informally-measured "too-different-ness" that appeared at the end of 2020 and in other geographies than the greeks (example, https://jamanetwork.com/journals/jama/fullarticle/2776543 in California).
Here again I may need to revisit the language in the post. If these cases are more borderline than the Omicron family then, even if they support conclusions about "wild" SARS-CoV-2 and the Omicron family, more nuanced language might be appropriate.
Finally, "The BA.1 and BA.2 lineages have sufficient genetic difference..." is essentially a litigation of my Omicron Origins argument. Well, that argument is only as good as it is, at the end of the day!
2. The Omicron sibling lineages represent a second lab release following serial passage in mice.
I'd say 90% on that, the shoe fits.
3. The virus was *designed* using in vitro genome assembly, rather than merely edited with genetic engineering.
I'm maybe 50% convinced after this paper. It's possible that IVGA is simply the easiest way to alter viral genomes these days, even if the adjustments (like furin cleavage site insertion) may have been relatively minor genome-wide.
4. The original virus *and most of it's named variants* have been orchestrated lab releases of engineered rather than evolved changes.
That's a radical claim that requires radical evidence, far in excess of anything presented here, and frankly your willingness to give voice to it leads me to question your reasoning. I'd say <1% chance on that, but I will continue to read your analyses and see if you can convince me.
We have never tracked the sequence-and protein-level evolution of a virus with this degree of detail before, so in many cases we may not have the necessary controls to distinguish engineering from evolution.
Accepting this claim necessarily begs the question of *why* someone(s) would be continually "updating" the virus in minor ways that create new waves of infection and immune evasion (mimicking what occurs naturally with the flu and other respiratory viruses) but don't appear to function as either an effective bioweapon or an effective attenuated-virus vaccine. The absence of a satisfactory answer to that question also leads me to assume natural-evolution-following-multiple-lab-leaks/releases until strongly proven otherwise.
That's all fine as regards my argument that "vaccine is not making variants" anyway. The 2020 crop of greeks is a superfluous part since these preceded mass roll-out.
RE 4, I would note (what I forgot at some point, a few months ago, and finally just remembered) that this wasn't even originally my observation. Trevor Bedford flagged the 2020 greeks as aberrant a year ago https://unglossed.substack.com/i/41820377/saving-private-mrnayn. His explanation was natural immune pressure; JJ Couey advanced the theory that it was the vaccines (trials?). I still think both are implausible because of the timing.
But, yes, you could still reject that the "parachute" effect demands any explanation in the first place by saying that evolution can't be ruled out. Regarding Bedford's math you could say "it's just math" (though, if I had to guess, what is really going on is he is looking at nextstrain and seeing what it is saying with the naked eye, like I do (before it became unreadable over this summer)). Regarding how certain we should be not to assume natural evolution, that's a complicated epistemological question giving that we are combining biology with ongoing human crime. I don't think humanity should use a "beyond scientific reasonable doubt" standard on this one. If this means I have introduced a distracting, superfluous element into my argument about "Leaky Vaccine Evolution" being an op, so be it. I might still edit on a comment about the 2020 greeks being before the vaccine though.
Lastly, regarding theory of mind for any hypothetical "they," I am ambivalent. My assumption for one thing is that no one can possibly know how a modified SARS-CoV-2 is going to behave in the wild in advance. The hypothetical they has to release the change to know what it is. So either they know this, in which case the only possible certain outcome is the media reaction and promotion of more injections, or not know this, because they are so full of hubris as to think lab results predict reality. In which case who knows what they are trying to achieve.
The only thing I'll say in closing is that I'm personally not at all surprised by the speed with which this virus is changing. Given the sheer scale (~10 billion virions per infection, 4+ billion global human infections plus other animals), the baseline error rate, and the fact that evolving immunity is continuously shifting the fitness landscape, the rate of change is not intuitively surprising to me aside from the "missing links" between the wild type clade, the BA.1 clade, and the BA.2-4-5 clade.
It's possible that if I had Trevor's level of knowledge or had put your level of time and thought into investigating this, that I would see the red flags in terms of improbable indels or amino acid transitions. But there is always the risk of thinking we understand natural processes and their limitations better than we actually do, and thereby filling the apparent gaps with malicious human intervention when doing so aligns with our broader narrative.
Whether it's the shots driving evolution or natural immunity, well, it's immunity in aggregate and I don't think we have any way of decoupling that to isolate the specific effects of the shots, with which I believe you would agree.
I am too short of time to tackle the full comment! RE “ Exactly what sort of p-hacking type bias this decision might introduce is at least worthy of consideration” I would say off-hand that the clustering of previous published synthetic covs in Fig 3 supports the rationale and moves the evidence into whatever the statistical term I forget is for when you decide the observed outcome in advance: previous synthetic cov’s decided which rs sites were of interest.
Looking more closely, I think their Figure S2 satisfies my first critique in terms of examining the degree of anomaly relative to *all* commonly used combinations of restriction enzymes.
I would still say that this is:
--very strong evidence of a lab origin and some level of RE-based genetic engineering.
--moderate evidence of in-vitro genome assembly and a fully synthetic design.
--very weak evidence that this is a "proprietary product" (as opposed to the usual gain-of-function viral engineering) and that subsequent variants have been "new releases" of this synthetic design.
So, still without having got to the rest of your OP:
It sounds like you are more agreeable to agreeing [edit: typing in a car; but I will just leave that in] that this is evidence that the "wild" sequence was preceded by a DNA construct. So the argument becomes whether that fact is evidence that it was (A) also a designer product as opposed to (B) a DEFUSE-style accident in accordance with the "approved dissent" narrative. Additionally, the question becomes whether my language is inaccurately ruling out (B) as opposed to emphasizing (A) over (B), with the only negation of (B) being that I am not calling this "more evidence" for it. So I'll think about whether the language needs to be a bit more nuanced there.
To elaborate, a lack of a DNA construct fingerprint would actually be "more evidence" of (B) relative to (A). It would mean, "ok, we know it was from a lab because FCS, but it still could have been some sort of mixup because it never clearly passed a construct stage until after release."
Hiya, SARS is not being edited in labs or vaccines, at least, there is no evidence for that.
It's being edited in computers!
https://georgiedonny.substack.com/p/x-ray-crystallography-and-3d-computer
Jo🙏🏽
If the vaccine is not causing the variants, why do vaccinated people appear to have a greater probability of being infected with variants? Large population-wide studies have shown this effect.
Hi,
my theory is that they are not being infected, but that their detox mechanisms are disrupted https://georgiedonny.substack.com/p/why-are-the-jabs-causing-death-by
Jo
This evidence cannot override evidence that directly speaks to 1) where Greek letter variants come from and 2) whether the virus evolves in the wild. 1 does not show any relationship to the vaccine (the 2020 Greek letter variants appear before wide release; the Omicron family has molecular markers of a not-wild origin), 2 continues to show that the virus doesn't evolve much in the wild, not more now than it did in 2020.
Even setting that aside, "negative variant efficacy" isn't intrinsically suggestive of anything besides "some Wuhan efficacy." So when Omicron came out a lot of substack writers started showing relative infection rates without even seeming to understand that this was actually just showing that the (very very recently) injected still had resistance to Delta (https://unglossed.substack.com/p/funeral-for-a-fact#footnote-3). So you definitely could say that the vaccines created a favorable landscape for Omicron BA.1/2 versus Delta: But that doesn't change the fact that Omicron was made in a lab. Just like you could compare some Monsanto plants with some natural plants and see one do better against bugs or whatever (I am not a farmer); that doesn't mean the bugs "caused" the Monsanto genes except in an abstract, human intention sense.
In that case, what would explain why heavily mRNA vaccinated countries saw large spikes in cases around December 2021 (like Korea, Japan and most of western Europe), while India and African countries didn't exceed their earlier peaks? Does that mean that some of the lab variants were explicitly designed to be more infectious to mRNA vaccinated people?
"Earlier" peaks in lockdown-ed countries correspond with lower post-wave seropositivity than African / Central Asian countries. Whereas waves subsided at 10-20% seropositivity in lock-down-ed areas, they subsided in 30-70% in non-locked-down areas. So "more-than-earlier" in the lockdown-ed countries is not actually as big as "more-than-earlier" in non-locked-down countries.
What would be truly impressive is if low-vaccine countries like India, Russia + Romania + other slavic countries, due to just having had Delta waves, were resilient against Omicron. But they weren't. So even without the vaccine Omicron was rampant.
Korea and Japan never had lockdowns, so I wouldn't consider them lockdown-ed countries. It's quite striking to look at the graph of covid cases since 2020 in Japan and Korea vs India; Japan and Korea both see peaks orders of magnitude higher post-vaccine, while India never sees peaks exceeding its mid-2021.
I'd argue that Romania and other slavic countries (excluding Russia) don't make as good a comparison as India (which did not use mRNA vaccines at all), since even though they were relatively unvaccinated, they still had a double digit percentage of the population mRNA vaccinated. Given how dramatic the case rate increased in Japan and Korea post vaccine, even just 1/5th of that increase would still result in a larger rate relative to the previous peak.
Unfortunately my IRL distractions are rendering me a poor interlocutor. So the question of whether the Omicron family demonstrates anything about whether the vaccines "cause variants" is again subject to the limitations above. 1, they have clear molecular evidence rendering any kind of natural evolution from wild Wuhan-family virus improbable. Lab origin the least improbable explanation. So I just want to make sure that's still on the record when discussing the more nuanced hypotheticals about what (absolute or Wuhan-relative) negative efficacy and population trends would imply if the origin was actually in question.
Regarding population trends, it's a question of whether the vaccine is required to explain what happened. Well, east Asia was functionally "immune" to the Wuhan strain for reasons we don't understand. For all we know it could be due to microbiome, maybe even from natto bacteria, which break down Wuhan spike. If anyone knows it's probably whoever designed Omicron. You can speculate the vaccine caused a change here but without an "unvaccinated East Asia" control group, speculation is all that is. But Hong Kong at least is a good falsification of negative Omicron efficacy on a within-population level. The unvaccinated elderly got hammered, if we are to take the CDC's word for it https://www.cdc.gov/mmwr/volumes/71/wr/mm7115e1.htm
This isn't to fully answer your points; at the moment I am multitasking.
Doesn't it suggest the variants are there before they get infected with them?
This was more disturbing than anything I've read in the past two years. The evil of tinkering endlessly with the virus probably in hopes of making something more lethal, and the psy-ops possibilities make me feel sick.
Actually never trusted van den Bossche at all, mainly because of the look in his eyes. (I could have used logic, but I'm pretty good at reading faces.)And his predictions of imminent viral takeover because of vaccination kept not coming true.
Thanks again for your reporting, it's unique.
NO COMMENT on the eyes, haha. I don’t know which, if any of the Leaky Vaccine Evolution crew are ops - they could all be unintentional supporters who are just intoxicated by the premise of some Garden-of-Eden-fable type of biology. Or the whole thing really is emergent; obviously either possibility makes the opposite possible as well.
Brian, you are a treasure. My little monthly subscription doesn't convey my appreciation enough; if I had a million bucks it would be yours 🙂.
When this subject has been finally been wrung out (🙏 ), I hope you'll continue with your substack including other subjects as you used to do before the scamdemic took over.
Thanks (as always)! If there is still a power grid / internet / etc, I intend to keep the project going.
why can't it be a combination of a little of everything?
lab created. lab accidental release, lab deliberate release., vaccine evolutionary pressure, natural evolution? depending on which particular variant a person is talking about?
What I claim / argue is that there is simply no evidence of vaccine-induced evolution. You (as in a hypothetical substack writer) can say it is happening, fine, I won’t bother you. But if you assert there is evidence, I disagree. As Peter details, the 2020 Greek variants precede the vaccine wide release, and Omicron has clear molecular evidence of a lab origin. When you therefor don’t include the mutations that these variants “ship”/come with, the virus isn’t actually evolving faster now that it ever was in 2020. It remains relatively static.
Additionally, vaccine-effected evolution makes specific predictions depending on if you are using a “Immune escape” model or an OAS model. Immune escape depends on infection efficacy staying in tact. But once the vaxxed started getting and transmitting Delta there was no way for them to exert selection / bottleneck pressure on it. OAS in comparison implies that pressure turns off. In other words if Delta was the escape variant, the vaccinated cease to put pressure on it. How can they push Delta if they “can’t make Delta immunity.” That leaves various shell game models where pressure happens absent selection which I do not find lead to any coherent predictions.
Delta appeared before vaccines were rolled out. So that rules out vaccine pressure. All of the main pre-December 2022 variants appeared before the vaccines.
Omicron is derived from B.1'ish. Or perhaps more neutral is of origin unknown (Brian and I slightly disagree on details) but not an evolution of Delta or other early variants. What is key is it underwent huge amount of evolutionary pressure, then forked into (at least) two which each also had enormous evolutionary pressure, but were during these pressure periods never seen in the wild ever anywhere. Then magically both appeared at the same time in the wild. Lots of mysteries, but whatever caused its evolution, hence wasn't in the wild under vaccine pressure.
I don't know why Brian feels there is a continuous release, but I may just misread his words. But regardless there is however evidence of a summer/early fall 2019 release or leak (Wild type and Brian believes also B.1), and then possibly a second (Omicron BA.1 + BA.2 twins) somewhere late 2022. Within each there are multiple possibilities based on intend and what exactly was leaked. Also the actors (if any) and intend may not be the same for both these events. But vaccines seem to have either way virtually no effect on these two major events.
i am also guessing there were animal trials even before the human trials started.
another lab leak that was associated with vaccine animal trials?
according to wiki delta was first detected in India late in 2020.
notice the date of the headlines out of India:
"India's first coronavirus vaccine 'Covaxin' to start human trials this week
By - TIMESOFINDIA.COM
Created: Jul 8, 2020, 11:24 IST"
https://timesofindia.indiatimes.com/life-style/health-fitness/health-news/indias-first-coronavirus-vaccine-covaxin-to-start-human-trials-this-week/articleshow/76848297.cms
RE continual, it’s just something I don’t want to rule out 100%. At least before Omicron, I’m not would-want-to-bet-my-life-on-it convinced that the virus was good enough at sustained transmission to just “virus” *edit: as in the phrase “virus gonna virus” where it is assumed that SARS-CoV-2 wasn’t impacted by mitigation. Once again was on the way out door while typing this one
Given that a computer sequence can be added to a viral backbone - and that GMO RoundUp Ready crops can spread the RoundUp Ready genes to super weeds - why would we not expect that a computer sequence stuck on a very mutatable coronavirus, might not also mutate?
Yes, variants seem to be being used as a fear-demic media tool, but that is a different story.
A lot of this comes down to an assumption that all "pathogenic" genomes are naturally going to evolve in response to human efforts to kill the pathogen. But in fact, that's not a guarantee. Bacteria anti-biotic resistance for example is not driven by "evolution," it's driven in a lot of cases (if not all) by plug-n-play genes from plasmids and viruses (phages) that confer extra hardiness, that were always in the bacteria's "app library" all along.
Then we consider RNA viruses:
1 We have been immunizing against polio for decades and decades, it hasn't evolved to resist our effort to eradicate it.
2 Same for measles.
3 Ah, but flu - well, actually, as far as our limited observation has shown, flu usually drops in from avian reservoirs that have almost no evolution goin on, the spike protein runs out of evolutionary "moves" a few decades after crossing into humans, and that spike protein just goes away, replaced by a different species of spike from the unchanging avian reservoir. So flu can't actually "escape" human immunity either. It can just delay being relegated back to the avian reservoir.
So for RNA viruses I don't think there is any precedent to assume 100% that coronavirus would mutate to escape immunity. It might, it might not. So then when we look at nextstrain and consider what the Wuhan virus seemed to be doing in 2020 and 2021, there is no evidence that it was trying to mutate much. And if other RNA viruses don't mutate to escape immunity, then the fact that this one doesn't seem to do so (out in the wild) should be taken at face value.
From there, the argument becomes whether the greek letter variants are proof that wild immune escape does happen or, as I would argue, exceptions to the rule which must therefor be considered unnatural creations.
Omicron already reverted back to a form that escapes the jabs. It is part of the RNA species nature to readily Lego-block themselves into different forms for different environments within the body. Read the quasiswarm info by @Harvard
Ah - I address quasiswarm in Omicron Origins (https://unglossed.substack.com/p/omicron-origins-part-1) for example with Oral Polio Vaccines, you actually have a genetic bottleneck at work where they de-attenuate virtually on day 1 (https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(20)30574-6). So we should be skeptical that the apparent relative stasis of SARS-CoV-2 in the wild is hiding potential leaps back to some unseen "T-1000" potential.
Regarding "Omicron already reverted back to a form that escapes the jabs" does this refer to Omicron not stemming from Delta or any known circulating genome after B.1? That, itself, is evidence that it was made in a lab from a DNA<>virus "stock" template with the B.1 mutations in it.
As I put it in Omicron Origins, I don't want to actually propose that viruses can't do really surprising things that we can't explain, just instead to look at the question according to the "rules" that science normally uses for inferring genetic origins. These "rules" do not allow a conclusion that Omicron was somehow hiding and evolving in the Delta swarm.
True, Omicron is non-typical. ... an oddly coincidental older strain suddenly became prevalent as it can bypass the jab antibodies. Was it a GOF release to try to mitigate the chimeric spike release/escape?
I don't know the motives. My guess is that it wasn't meant/realized that it included two majorly different virus phenotypes (BA.1 vs BA.2/4/5), so whether it was supposed to be virulent or mild it was a backfire.
Interesting. There had been speculation that it was a White hat release to try to mitigate the CoV viruence.
Yes, I get that. But what about all the bloody variants/mutations/there are hundreds of them..not all named...but are you saying that everyone of them is a lab release?
No, these are post-release progeny. If SARS-CoV-2 is a tiger clan in a zoo being re-released into the wild, then there is a release in late 2019 (either "Wuhan" model, or B.1, or "Wuhan" then B.1, the picture here is muddy but I am leaning toward just the first one). Then a year later the zoo releases some more tigers that evolved in the meantime and these displace all the previous progeny from the 2019 tiger, these are the late 2020 Greek letter variants. Then another year and the zoo releases some more tigers, these are the Omicron family. Again they displace the previous progeny. If there is any other releasing going on my guess is it would still be of the "model" released in the end of the previous year. The updates don't ship until October. I don't personally have a bet on whether it will happen again this year, I'm not actually a mind-reader.
Wow. This is mind boggling. But just as probable as anything else...
Just read this am that Covid 19 was sent to a lab in Ukraine in November of 2019 I think...before it even had that name...
I am definitely Alice in Wonderland, and can believe six impossible things before breakfast.
Can I ask...what is the intent behind all the releases? Scientific curiousity? Let's see what this one does? And do they never think that maybe it might not be such a smart idea, unless they already have the antidote to any future strain combo???
You and Katherine Watt are doing THE MOST IMPORTANT WRITING on EARTH right now
Flattered to be compared to Watt. I am much less skilled than her at moving my "work" from out of my brain onto the page, haha.
While I agree that there are plausible scenarios by which variants of the SARS-COV-2 virus can be lab engineered, it strikes me as a leap of logic to argue exclusively for lab engineering to the exclusion of natural evolution.
Given that subvariants of Omicron are now the latest doom strains out there, it seems there is a certain arbitrariness to the assigning of Greek letters, which means there is a certain arbitrariness to assuming which variants are lab engineered.
The Omicron "scrabble" variants don't bear the hallmark of being parachuted in from unclear mutation chains. So there isn't anything actually special about them except:
1 - they are being given funny names; but so were the "bird variants" of late 2020 that no one remembers anymore.
2- They do seem to reflect more "hotness" in their RBD hotspots than previous. But this is not surprising since anti-Omicron natural immunity is now at a peak that anti-Wuhan / Delta immunity never reached. This is just down to the Omicron family being a lot fitter at spread than the Wuhan line ever was. So the Wuhan line never showed any convincing signs of immune escape outside of the "parachuted" arrival of the greek letter variants. (Instead, hotspots seemed related to functional fitness).
Now, you could obviously say that there are loads of "evolutionary leap" sequences even going back to early 2020. But these never spread. The "bulk" of the B.1 cloud in the nextstrain map was always pretty inert, as were the clouds for Alpha and Delta. In every case when a variant "parachutes" in it's way above the mutation trend and then drifts along at the same slope as the trend. I think if I could look at nextstrain right now the Omicron swarm would be finally showing an uptick but like I said that's natural immunity at work. So if natural evolution is the trend, then by definition it isn't a good candidate for the greek letter variants because they all pop in way above trend. Or you could attack this argument by saying that "goes on to spread successfully or not" isn't a meaningful way to distinguish noise leaps from not-noise leaps. But really the other leaps (the dead ends) could just be the rare bad reads that pass QA.
"The Omicron "scrabble" variants don't bear the hallmark of being parachuted in from unclear mutation chains."
Is that a "knowable" metric? Do we really understand viral evolution so well that we can make such a claim?
This is not a question that is necessarily limited to SARS-CoV-2 or coronaviruses or even viruses in general. There is a body of thought within evolutionary biology that posits evolution occurs not through an incrementalist process but through "evolutionary leaps"--and there is a countervailing body of thought that insists those "leaps" are merely gaps in the evolutionary history.
https://phys.org/news/2005-05-evolutionary.html
While it is challenging to our human understanding of the world to be confronted with such "leaps", which we are if we posit a natural origin for Alpha, Delta, and particularly Omicron, the occurrence of such leaps is not necessarily proof of artificial origin, as such occurrences are found time and again throughout Earth's biological history. The challenge of Omicron is a challenge that has been found throughout the fossil record for a whole host of species.
This is not to say that Omicron or any of the other Greek alphabet variants are synthetic in origin, nor is it to say that they are not synthetic in origin. This is to ask the question "how can we KNOW they are synthetic in origin?" That a phenomenon is possible is not intrinsic proof that said phenomenon is.
"Is that a "knowable" metric? Do we really understand viral evolution so well that we can make such a claim?"
Related to my latest reply to Markael below, I just remembered that the relevant property of the 2020 greek variants that I call "parachuting" was observed by Bedford himself last year, https://unglossed.substack.com/i/41820377/saving-private-mrnayn
So what I mean by this is that when you go to nextstrain and into clock view, every "cloud" of dots is the same angle, and the 2020 greeks and Omicrons just start as being "dropped" above this angle (ignore the diagonal trend line as this incorrectly maths in the drops that don't match any actual trends). So the scrabble variants are just part of the same cloud trend, they aren't "dropping" in above it or making it curve higher. The "claim" here in question is merely that this is what is visible in nextstrain. The scrabble variants are just like previous "cloud dots" that didn't get special names, or that did get names that we forgot about anyway (the bird variants).
Also as in my comments to Markael, I am not arguing that leaps are "ruled out." But given that "wild" SARS-CoV-2 and the Omicron family have molecular evidence of lab origin, the observer has to make a call here one way or the other and I think lab origin for the 2020 Greek crop is more likely than coincidental evolutionary leaps, especially given little apparent change in the evolutionary landscape in fall 2020 as I mention in the linked post.
For myself, I specifically refrain from making the call one way or the other. From the epidemiological perspective, lab origin is mostly irrelevant. Once a pathogen is in the wild, it's in the wild, and the virus will proceed to virus the same as anything else.
Lab origin questions are extremely important for understanding the mendacity and duplicity of our self-anointed public health "experts", but for contending with the spread of an infectious pathogen, not so much.
As I have long considered your analyses as among the most thoughtful, original, and impartial, I am a bit saddened to see you making some assertions here that I don't think can be rationally justified.
"This is not “more evidence that SARS-CoV-2 came from a lab.” It is more evidence that SARS-CoV-2 is a proprietary product."
I'm surprised that no one thought to do an RE site analysis before. It is however worth noting that the authors apparently chose BsaI/BsmBI for their analysis precisely *because* these chopped the SARS-CoV2 genome into synthetic-looking fragments - not because they had solid evidence that the viral engineers used these two enzymes. Exactly what sort of p-hacking type bias this decision might introduce is at least worthy of consideration - i.e. if we were to choose the ~25-50 RE's most commonly used for IVGA and were to run such a fragment/count length analysis on viral genomes for all of them, how anomalous would be BsaI/BsmBI pattern for this virus truly appear to be? Or, in other words, what proportion of naturally-occurring viruses would appear as an equivalent outlier for *some* combination of REs commonly used in IVGA?
In answer to your second sentence, would not merely removing one restriction site be enough to generate an anomalous pattern here? I've done a lot of RE-based genetic engineering in my earlier career path (gene insertions/deletions/promoter replacements in cyanobacteria) but no actual IVGA. I think much stronger evidence would be required to claim that this virus is a truly synthetic, IVGA-based "proprietary product."
"The synthetic origin paper shows what a farce it is to even care about the question. All the greek letter variants, from Alpha to the Omicron family (and a few suspicious sequences that never caught off the ground, from Central America and the US) should be considered lab-designed updates to the original DNA<>virus SARS-CoV-2 platform."
Again I think you are going too far here and postulating too much synthetic editing and lab release without evidence. The BA.1 and BA.2 lineages have sufficient genetic difference that some unusual explanation (IVGA, mouse serial passage, long residence in an animal reservoir, etc.) is required to explain their appearance. Maybe also BA.5. Most of the other variants display exactly the evolutionary pattern and mutation rate that one would expect from a novel RNA coronavirus adapting to a human population that is simultaneously developing immunity.
The naming of these variants is entirely arbitrary and has almost nothing to do with their degree of genetic divergence. Alpha was a very small mutational step from the wild-type. I find it interesting that the rate of new variant naming is more directly proportional to the level of fear the narrative-controlling forces are attempting to instill. Thus we had the whole Greek alphabet in 2020-early 2021, but during the "vaccines are safe and effective" period we had a level of diversity exceeding all previous variants contained under the name "Omicron".
Now they're inventing new designations again and ramping up the fear (to convince people to get the bivalent booster? to distract from vax injuries?) and we've got the BE, BY, BQ, XBB, etc. appearing in the news despite the fact that on e.g. NextStrain mutation charts these are only small incremental changes from the current circulating variants.
This twitter thread from one of the authors allays most of my methodological concerns:
https://twitter.com/WashburneAlex/status/1583483075819843584
“We also argue that our checklist for IVGA is best viewed as one test.” - reflects my shoot-from-the-hip interpretation. Certainly some very dazzling maths used to demonstrate unlikelihood of false discovery, I’ll say!
Ok, the rest of the comment!
"would not merely removing one restriction site be enough to generate an anomalous pattern here?" - This might be N/A after your other comment below, if you are no longer disagreeable to the paper's conclusion that there was a construct before the "wild" virus. Still I would note that removing one restriction site cannot create shortness of longest fragment. The shortness has to either be architectured or emerge randomly. Which goes back to the false discovery question that is discussed in the other sub-thread. *edit: This did not address the question of "what if the shortness is already there." In which case a virus can accidentally place itself in the quadrant of interest by just randomly removing X number of sites as long as it does so without creating a new longest segment. So actually this is a tricky math problem but essentially devolves to "few wild coronaviruses are going to be in the right quadrant."
"Most of the other variants display exactly the evolutionary pattern and mutation rate that one would expect from a novel RNA coronavirus adapting to a human population that is simultaneously developing immunity." This is discussed in my reply to both Kust and Depew above. There should, I argue, be no "assumption" of mutation rate given other RNA virus precedents. We should take the rate in nextstrain without the greek variant insertions (both before and after) and see if it predicts their insertion; it doesn't. (Unfortunately this is impossible to discern in nextstrain anymore). True, the vanilla versions of Alpha and Delta weren't radical in absolute terms but they still were above trend both before and importantly after. Maybe Delta was accelerating a bit in the end.
You could say "well this doesn't rule out natural evolution" but I am not trying to make a rule-out argument here. I am arguing that when we stop assuming without basis that the virus is going to evolve this much on its own, then different interpretations of the evidence become natural.
I am also not taking the greek-naming thing as creating a reality that prima facie demands an explanation. As my post alludes to, there were some unnamed variants that have the same very-informally-measured "too-different-ness" that appeared at the end of 2020 and in other geographies than the greeks (example, https://jamanetwork.com/journals/jama/fullarticle/2776543 in California).
Here again I may need to revisit the language in the post. If these cases are more borderline than the Omicron family then, even if they support conclusions about "wild" SARS-CoV-2 and the Omicron family, more nuanced language might be appropriate.
Finally, "The BA.1 and BA.2 lineages have sufficient genetic difference..." is essentially a litigation of my Omicron Origins argument. Well, that argument is only as good as it is, at the end of the day!
I don't fully understand what you're saying here.
I see a variety of claims being made.
1. The virus came from a lab.
Almost 100% at this point.
2. The Omicron sibling lineages represent a second lab release following serial passage in mice.
I'd say 90% on that, the shoe fits.
3. The virus was *designed* using in vitro genome assembly, rather than merely edited with genetic engineering.
I'm maybe 50% convinced after this paper. It's possible that IVGA is simply the easiest way to alter viral genomes these days, even if the adjustments (like furin cleavage site insertion) may have been relatively minor genome-wide.
4. The original virus *and most of it's named variants* have been orchestrated lab releases of engineered rather than evolved changes.
That's a radical claim that requires radical evidence, far in excess of anything presented here, and frankly your willingness to give voice to it leads me to question your reasoning. I'd say <1% chance on that, but I will continue to read your analyses and see if you can convince me.
We have never tracked the sequence-and protein-level evolution of a virus with this degree of detail before, so in many cases we may not have the necessary controls to distinguish engineering from evolution.
Accepting this claim necessarily begs the question of *why* someone(s) would be continually "updating" the virus in minor ways that create new waves of infection and immune evasion (mimicking what occurs naturally with the flu and other respiratory viruses) but don't appear to function as either an effective bioweapon or an effective attenuated-virus vaccine. The absence of a satisfactory answer to that question also leads me to assume natural-evolution-following-multiple-lab-leaks/releases until strongly proven otherwise.
That's all fine as regards my argument that "vaccine is not making variants" anyway. The 2020 crop of greeks is a superfluous part since these preceded mass roll-out.
RE 4, I would note (what I forgot at some point, a few months ago, and finally just remembered) that this wasn't even originally my observation. Trevor Bedford flagged the 2020 greeks as aberrant a year ago https://unglossed.substack.com/i/41820377/saving-private-mrnayn. His explanation was natural immune pressure; JJ Couey advanced the theory that it was the vaccines (trials?). I still think both are implausible because of the timing.
But, yes, you could still reject that the "parachute" effect demands any explanation in the first place by saying that evolution can't be ruled out. Regarding Bedford's math you could say "it's just math" (though, if I had to guess, what is really going on is he is looking at nextstrain and seeing what it is saying with the naked eye, like I do (before it became unreadable over this summer)). Regarding how certain we should be not to assume natural evolution, that's a complicated epistemological question giving that we are combining biology with ongoing human crime. I don't think humanity should use a "beyond scientific reasonable doubt" standard on this one. If this means I have introduced a distracting, superfluous element into my argument about "Leaky Vaccine Evolution" being an op, so be it. I might still edit on a comment about the 2020 greeks being before the vaccine though.
Lastly, regarding theory of mind for any hypothetical "they," I am ambivalent. My assumption for one thing is that no one can possibly know how a modified SARS-CoV-2 is going to behave in the wild in advance. The hypothetical they has to release the change to know what it is. So either they know this, in which case the only possible certain outcome is the media reaction and promotion of more injections, or not know this, because they are so full of hubris as to think lab results predict reality. In which case who knows what they are trying to achieve.
That's all fair.
The only thing I'll say in closing is that I'm personally not at all surprised by the speed with which this virus is changing. Given the sheer scale (~10 billion virions per infection, 4+ billion global human infections plus other animals), the baseline error rate, and the fact that evolving immunity is continuously shifting the fitness landscape, the rate of change is not intuitively surprising to me aside from the "missing links" between the wild type clade, the BA.1 clade, and the BA.2-4-5 clade.
It's possible that if I had Trevor's level of knowledge or had put your level of time and thought into investigating this, that I would see the red flags in terms of improbable indels or amino acid transitions. But there is always the risk of thinking we understand natural processes and their limitations better than we actually do, and thereby filling the apparent gaps with malicious human intervention when doing so aligns with our broader narrative.
Whether it's the shots driving evolution or natural immunity, well, it's immunity in aggregate and I don't think we have any way of decoupling that to isolate the specific effects of the shots, with which I believe you would agree.
I am too short of time to tackle the full comment! RE “ Exactly what sort of p-hacking type bias this decision might introduce is at least worthy of consideration” I would say off-hand that the clustering of previous published synthetic covs in Fig 3 supports the rationale and moves the evidence into whatever the statistical term I forget is for when you decide the observed outcome in advance: previous synthetic cov’s decided which rs sites were of interest.
Will read the rest shortly!
Looking more closely, I think their Figure S2 satisfies my first critique in terms of examining the degree of anomaly relative to *all* commonly used combinations of restriction enzymes.
I would still say that this is:
--very strong evidence of a lab origin and some level of RE-based genetic engineering.
--moderate evidence of in-vitro genome assembly and a fully synthetic design.
--very weak evidence that this is a "proprietary product" (as opposed to the usual gain-of-function viral engineering) and that subsequent variants have been "new releases" of this synthetic design.
So, still without having got to the rest of your OP:
It sounds like you are more agreeable to agreeing [edit: typing in a car; but I will just leave that in] that this is evidence that the "wild" sequence was preceded by a DNA construct. So the argument becomes whether that fact is evidence that it was (A) also a designer product as opposed to (B) a DEFUSE-style accident in accordance with the "approved dissent" narrative. Additionally, the question becomes whether my language is inaccurately ruling out (B) as opposed to emphasizing (A) over (B), with the only negation of (B) being that I am not calling this "more evidence" for it. So I'll think about whether the language needs to be a bit more nuanced there.
To elaborate, a lack of a DNA construct fingerprint would actually be "more evidence" of (B) relative to (A). It would mean, "ok, we know it was from a lab because FCS, but it still could have been some sort of mixup because it never clearly passed a construct stage until after release."