In defense of a natural origin of Omicron, this study describes the remarkable evolution of SARS-CoV-2 during convalescent plasma treatment of an immunosuppressed patient for 3-4 months; the mutations also reduced sensitivity to neutralizing antibodies: https://www.nature.com/articles/s41586-021-03291-y
We know that there is a large immunocompromised population in Africa and that Covid-19 is rampant there. We also know that most hospitals, regardless of country, don't have the resources to track the evolution of SARS-CoV-2 in their immunocompromised patients. So it's not unexpected that a variant like Omicron could have evolved over an entire year in an immunocompromised individual before finally infecting others.
If there is any evidence that a lab in the region was serially passaging SARS-CoV-2 in neutralizing antibodies/patient serum, then I'd say there is something to go on for a potential lab origin. But at the moment, there is not even circumstantial evidence pointing to this happening in Africa. Maybe setting up a secure channel for whistleblowers with evidence of the above would be the most productive approach.
The above is not to say that I don't think there needs to be much more transparency and accountability from scientists working with pathogens. https://twitter.com/Ayjchan/status/1468582694007279616
> Omicron COVID was in Italy as early as 2021-10-13 – 7 weeks before alarm from South Africa.
> per upthread, Italy also where SARS-CoV2 immune-escape gain-of-function variants bred, since 2020, in less-than-max-biosecurity labs.
https://twitter.com/gojomo/status/1473471612112441344
(IANA biologist)
> Omicron COVID was in Italy as early as 2021-10-13 – 7 weeks before alarm from South Africa.
7 weeks before the alarm, but only 10 days before in retrospective sampling, and even less in other places in Africa.
Saying it appeared in Italy but somehow it spread in Southern Africa first goes against normal epidemiological dynamics, especially given how contagious Omicron is. The chances are it started where the first cluster is detected, not where the first retrospective case is detected, because the possibility of it escaping in Italy, flying to SA, and somehow staying dormant in Italy while giving SA a head-start is extremely unlikely.
I 1st learned of the referenced Italy antibody-escape gain-of-function paper via an HN post which appeared almost concurrently with the first reports of the (not-yet-named) Omicron variant: https://news.ycombinator.com/item?id=29359125
As Twitter user @Vbruttel has pointed out (https://twitter.com/VBruttel/status/1466930489026093056), similar published research was done in Durban South Africa, which has at most a BSL-3 lab.
This is not to say either of those are the origin; just that this kind of research seems pretty common: within the capability & interest of many labs, who cheerfully report their creation, via selective pressure, of immune-escape variants in published papers.
Consider this: days after the successful sequencing of Omicron, similar cases were reported in dozens of countries, having arrived there just before or just after the announcement. We know, that it's "just before," because references are being kept and re-analyzed in those cases, and none of the countries with the resources for genomic surveillance has any data on earlier strains in the phylogenic tree.
It is simply very unlikely (not impossible, but if you're in London and hear hoof beats, it's probably a horse, not a zebra), that Omicron could have developed over 33 N and a superset of S mutations without ever popping up in any surveillance. South Africa, especially, is a key surveillance player. They're often much more granular than even European key players like the UK, Germany, or France.
A strain with this level of infectivity doesn't linger in one hospital. From the looks of the genome, that part (infectivity) would have developed before immune evasion. Having a highly infective strain evolve would ring alarm bells in labs the world around.
I guess it's pretty non debatable that Omicron started its World Dominance Tour in October or November 2021. To get there, it had to undergo a massive sequence of events making it as far removed from α.7 as it is. So we can state, with some certainty, that it evolved in isolation and broke free shortly before being discovered.
If we now consider the possible origins, wild zoonotic, single origin immune compromised, or accidental leak from research, the latter doesn't sound so improbable anymore. Again, horse, not zebra.
Sounds much like the "missing link" gotcha that creationists loved to deploy.
Is it likely that this infected person would not have started any detectable cluster this whole time? How do you explain the ratio of functional vs silent mutations?
Yeah I agree with the going undetected too unless they're potentially asymptomatic (in which case why should we ever expect to find/treat them).
All leading to the same response of you can't control highly transmissible virus(vurii) once they have infected a large amount of the population. (aka a 0 covid strategy is self-defeating)
Fair enough. So is the hypothesis that this immune compromised person in SA was given a lot of antibodies over a long period of time, creating enough evolutionary pressure to create highly mutated forms of the virus? Such a person might end up with a highly mutated virus that is resistant to existing antibodies. Fair enough.
That explains one of the four weirdnesses, and leaves three unexplained. Where are all the missing silent mutations (Weirdness 2)? If someone is followed medically and receiving all these treatments, did no one around them ever get sick with an intermediate variant? (Weirdness 1)? And what about the mouse-related mutations? (Weirdness 4) Did the viruses in the immune compromised person develop those mouse-related mutations independently?
I find the "immune compromised person" hypothesis not a very parsimonious or compelling one, although if you can steelman it further, I'm all ears.
But you know what they say, even a person who makes money by telling obvious lies about science is right twice a day, so we should probably evaluate this from first principals as if it wasn't coming from a professional serial liar.
The only question is why we didn't observe some steps on the way. And as you say, poorly monitored infections of the immunocompromised can easily explain this. It hardly seems necessary to posit nefarious secret labs when COVID is constantly spreading among billions of people, a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas.
How do "poorly monitored infections of the immunocompromised" explain weirdnesses 2 and 4? (Referring to the blog post under discussion)
Did the blog author "posit nefarious secret labs"? Not that I'm seeing. There are labs all over the world doing things with SARS-CoV-2, probably for what they believe to be legitimate reasons. "Nefariousness" and "secrecy" is not in the article. "Nefariousness" and "secrecy" are not part of the hypothesis.
"a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas": Contrary to people's seeming stereotypes about "Africa," South Africa monitors SARS-CoV-2 really well. The hypothetical immunocompromised person in Alina's discussion would not be someone untreated in some remote village, unnoticed for a year and a half. No, to get that level of immune evasion, Alina must be talking about someone who was being treated medically, with fancy treatments, and being monitored for a very long time.
Well, for one thing: My first question is "Who is it? Who is this person who received all the convalescent plasma and all the different monoclonal antibodies for a year and half, in well-monitored South Africa?"
But even if we don't know who this hypothetical person is, there are other problems:
That person apparently never infected anyone else. And...that person in a year and a half never had any _intermediate_ viruses that infected anyone else either, to account for the gaps in the phylogenetic tree. And...that person had a set of mutations that you might expect to see in a humanized mouse (Weirdness 4).
You see, then, that while this is all "possible" it's not very parsimonious. I think we do better to begin with parsimonious hypotheses and try to test those and rule those out.
The lab leak is a parsimonious hypothesis -- but instead, mainstream people, for whatever reason, are portraying it as so far-fetched as not to merit consideration -- they would dismiss it, rather unscientifically, as if the hypothesis were really wild and not meriting consideration, like "Space aliens from planet X did it." Then, instead, they put forward hypotheses that are in fact way more far-fetched because they don't account for the data neatly, like "it was an immune compromised person" -- but the set of circumstances in which that would be true, while kinda-sorta possible, is much more unlikely than the circumstances of "lab leak."
The failure of the scientific community to address this really makes no sense to me.
"[Edited, 5 Jan 2021, to add: Many people have been confused about the statement about delta, so I must have worded it poorly. I’m not saying delta originated in a lab leak. I’m saying delta escaped from a lab late in 2021 where it was being used in research. It’s an example of a research-related lab leak.]"
The fact that developed countries are hoarding vaccines, essential medications and are willing to let it go to garbage than to send it to those who need it there isn't helping either.
> https://www.taiwannews.com.tw/en/news/4371212
> https://www.taiwannews.com.tw/en/news/4382708
Neither of these have nearly enough evidence or support for such a massive claim (the second doesn't even mention delta), as far as I can tell, and I can find no other reputable sources that make a similar claim. Heck, I can't even find un-reputable ones that mention this.
Am I missing something? I'm not going to continue with the article if this is how flimsy the sourcing is.
So what's the point? 1,000,001 people have Delta instead of 1,000,000? No. The point is to show that Covid infections are indisputably already happening in labs. And if there is a GoF lab that creates a new variant, it logically follows that it is possible for that new variant to escape. So instead of the not-so-bad 1,000,001 vs 1,000,000 Taiwan scenario, you could have a disastrous 1 vs 0 scenario.
And assuming there are currently thousands of labs studying covid, even with a low leak rate there could be some leaks. But of an already existing virus, so not so bad.
The author is saying that there was a lab leak involving delta, not that delta originated via a lab leak.
The latter claim would indeed be a red flag, but the former is just describing a very well-documented event.
Sorry, the hysteria on HN is ridiculous. At least read the damn thing and try to be objective about it.
> the hysteria on HN is ridiculous.
"Hysteria"? How do you get hysteria from my response? Because I asked for citations for what I thought was an extreme claim?
> At least read the damn thing
I did. Reading it was a pre-requisite for posting my response, which cited specific links he included.
> and try to be objective about it.
Asking for high quality sources was my attempt to be objective.
--
Edit: Actually, you know what, I take it back. If you write a sentence like this, it's on you if it's misinterpreted:
"For example, we know that the delta variant of SARS-CoV-2 leaked out of a lab in Taiwan in late 2021."
Heck, I'm not even sure it wasn't the author's intent at this point.
We should note you're talking about covered up lab leaks where all of the participants are conspiring to keep it secret because of convoluted motivations. It doesn't "stand to reason" that this happens at all, let alone is the normal case that we should all assume.
"[Edited, 5 Jan 2021, to add: Many people have been confused about the statement about delta, so I must have worded it poorly. I’m not saying delta originated in a lab leak. I’m saying delta escaped from a lab late in 2021 where it was being used in research. It’s an example of a research-related lab leak.]"
Some of the other points made in this article were mildly compelling to me (though I don’t know enough on this topic to be able to poke holes) but that delta claim and lack of convincing data to back it up doesn’t help with credibility.
Regardless, there is nothing actionable about any origin theory aside from "be mad at some unnamed scientist" or, as some of these conspiracy-theory vendors would prefer, "be mad at science in general."
So, what is the call to action here? Stop researching gain of function entirely?
Yes, this was very explicitly stated. And this is nowhere near the first call to do so (a lot of very respected scientists were calling for a stop to GoF research before the pandemic).
Whatever claims GoF research had beforehand of helping w/ pandemic preparedness have evaporated, because none of the successful responses to the pandemic (vaccines, antivirals) have relied on GoF research whatsoever. It appears to a high risk with no reward.
Neil deGrasse Tyson sums up the scientific approach as follows: "Test ideas by experiment and observation. Build on those ideas that pass the test, reject the ones that fail. Follow the evidence wherever it leads. And question everything." Cosmos (2014).
Why is that approach considered so anathema when it comes to hunting down the killer of millions of people?
This is what motivates conspiracy theories and scientific discoveries alike. It's even true about flat Earth kids, however misguided they may be.
The "so what?" is always an after thought, and often is irrelevant to the goal of simply finding something new.
To be clear: I see no evidence that Omicron is even a second lab-leak, much less that it's part of a sinister plot. My point is that there are immediate geopolitical implications, in addition to the scientific and public-health implications you have highlighted.
The majority of the the piece goes to arguing exactly that. What's the counter?
To the person you're quoting's benefit, there is evidence given, but it doesn't convince them. That's all they are saying.
Yes
> We need to make efforts to stay informed about what’s happening with these viruses and the status of GoF research. We need to tell our friends and families, to use whatever platform we might have, big or small, to promote the end of this research. We need to get this in the public eye, so the public can demand change. We need to demand change, and not take no for an answer.
I'd say it's this:
> We need to decide whom to believe: the people with a lot to lose and their not-very-parsimonious or plausible-sounding explanations, which receive almost all the media attention; or the people with expertise and parsimonious explanations who don’t have a dog in this fight.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC416634/
I’m genuinely surprised this (and similar articles) don’t have greater citation counts.
So maybe respiratory diseases, no matter how dangerous they currently are should be heavily restricted to labs that can handle them, and then have international monitors at each of them with strict reporting rules not tied to any organization like WHO or UN or whatever, they are just there to report lab leaks no matter how small.
(on a serious note: the answer is, the scientists don't have to know about a leak for it to have happened, the important part is that they don't want to know. That is, China prefers if this question goes unanswered.)
Not saying it's true, but I don't think "they couldn't keep this a secret" is a particularly compelling rebuttal here.
When looking at a large sampling of data across an entire population, we would expect to see a gradual accumulation of point mutations over time. And very rarely, some larger insertion or deletion event. None of this is new. We had all the tools to do this for over two decades. I was using Perl for bioinformatics 15 years back.
So given the assumption that we would see a gradual accumulation of point mutations over time, if we see any big changes appear out of the blue, that's a flag to investigate more closely at what happened. That's not "creationism" of any sort. Given that the point mutations give a very clear fingerprint, we can immediately find the most closely-related genome, which is why it was found to match a sample collected in early 2020. That completely breaks our expectations of it missing a whole 12 months of natural accumulation of point mutations. We might not sample perfectly--we might occasionally see two or even three point changes because we failed to sample those intermediate states. But to have a jump spanning dozens of changes--that's just not matching our existing expectations, particularly when we tracked nearly every Delta change.
Now that might be real. But the probability of that being natural is very, very low. Almost nonexistent. But the chances that this was stuck in a freezer and pulled out, skipping over those 12 months of mutation-gathering while frozen in a tube, are unfortunately a much more likely possibility.
They might simply have been lost in the crowd or not even noticed, depending on where they were posted. How carefully have we studied the variants in animals?
> Suppose, then, that every bacterium that has ever lived contributes one mutation before its demise to the history of life. This is a generous assumption; most bacteria pass on their genetic information unchanged, unmutated. Mutations are the exception. In any case, there have evidently been, in the whole history of life, around 10^40 bacteria—yielding around 10^40 mutations under Axe’s assumptions. That is a very large number of chances at any game. But given that the odds each time are 1 to 10^77 against, it is not large enough. The odds against blind Darwinian chance having turned up even one mutation with the potential to push evolution forward are 10^40x(1/10^77)—10^40 tries, where your odds of success each time are 1 in 10^77—which equals 1 in 10^37. In practical terms, those odds are still zero. Zero odds of producing a single promising mutation in the whole history of life.
One quoted thread was from "Tony VanDongen, an associate professor of pharmacology and cancer biology at Duke"
Seems like a reasonably valid opinion from someone with a clue. He's addressing specifically why Omicron is weird, and doesn't look like a normal evolution of COVID-19.
Another is from "Scott Ferguson, a PhD in pharmaceutical sciences and a postdoc at the Harvard Center for Systems Biology".
3rd and 4th are: "Phillip Buckhaults, Ph.D., is a molecular biologist and cancer geneticist at the University of South Carolina" and "Valentin Bruttel, who received his PhD in 2016 at the University of Würzburg (Germany) where he studied tumor immunology, autoimmune diseases, and development of biologicals"
A key diagram used is a Phylogenetic Tree from Science.
Looks like a collection of valuable scientific info, collected to support an opinion. Not saying it proves COVID came from a lab leak, but it's not just random speculation. Seems like a pretty valuable discussion to me.
Wouldn't you want to know if a disease impacting billions of people looked inconsistent with a naturally evolved virus? The scientist involved mention possible other explanations, poor models, etc. But do seem to lean towards a likely explanation of artificially tweaks to get omicron.
But more importantly, it's well reasoned. It's not "wild speculation". It's learned speculation based on history, opinions of experts, and independent sources, synthesized with deduction.
I understand the reflex to push back on claims of conspiracy. I find the mainstream meme conspiracy theories (flat earth, 9/11 was an inside job, etc) to be somewhere between laughable and terrifying. But this is a unicorn among conspiracy theories: both the initial conditions are plausible (that this was an accident, of a kind that has happened before, not a nefarious pre-planned event with dubious benefit), and the conditions of the conspiracy are plausible (the set of people with positive knowledge of a given leak would be quite small, and their incentives to keep it secret would be strongly aligned).
Asking valid questions, though. Is that better to bury one's head in the sand?
I'm not sure I buy the lab leak theory -- and certainly not solely on the basis of the information presented in this article alone -- but I do believe it's worth further investigation.
And we know lab leaks do happen; safety processes in even highly-regulated labs seem to be severely lacking. Calling attention to that, as well as the dangers of gain-of-function research (especially when considered in context of poor safety processes) is IMO critical.
At least this person has a reasoning and stands behind it, that's heads and shoulders above the tactics of those who want to bury this.
The author argued in section "weirdness 1" that the phylogentic tree implies the omicron strain is directly related to an ancestor genome from Spring 2020. I have the following concerns:
the tree is based on https://nextstrain.org/ , a database initially introduced in 2018 [1]. This is a great data source. However, for COVID, nextstrain naturally bias towards the more viable biosamples. In other words, COVID strains in wild animals such are going to be underrepresented, if represented at all. And if so, the large sequence divergence is surprising but not a direct indication of lab leak. The author can supply with a rough overview of sequencing sources of nextstrain to counter this. Or better, it would be good if the author can compare with, or cite existing literatures, phylogenetic trees of other epidemics and demonstrate that the sequence divergence is much larger than what we would expect from wild animal reservoir.
"weirdness 2" has a stand, but it should be accompanied by silent/functional mutation ratios in other COVID strains since synonomous mutation could be not entirely silent if translation efficiency is affected (correct me if I'm wrong).
Briefly on one other point, "weirdly it's exactly mice, not other animals": we use mice as lab animals for a reason. They are somewhat similar to human in terms of physiology. Therefore we can expect that they could be more prone to COVID infection, aren't we?
editted to add one more sentence: from a peer review aspect, this blog is beyond terrible and I'd probably have 10 major conerns listed if it comes in as a PR.
[1] https://academic.oup.com/bioinformatics/article/34/23/4121/5...
As a GoF researcher you don't want to cull 'silent' mutations because those are a major source of building blocks for useful mutations.
In a virus, most nucleic acids have multiple, layered, and unknown functions - it's much much harder to assign any given nucleic acid as "silent", and be confident that that is the case from an evolutionary perspective.
As another posted, it's a good hypothesis that's straightforward to test statistically against all of the other variants. But on its own, it's not necessarily convincing here that the S/NS ratio is particularly concerning (and as above, doesn't speak to how directed evolution works either).
There are at least 2 other possibilities:
* The virus could have stayed alive in an immunocompromised person for months and accumulated mutations there.
* The virus could have jumped to animals (e.g. mouses), accumulate mutations, and jump back to humans.
I'm an immunologist and molecular biologist, though I currently work on software-related things. I've worked in class 3 facilities in a medical school as a PhD and a postdoc. I've seen a fellow PhD student infect themselves with a tropical disease. I've seen my fair share of good and bad working practices. Scientists are not infallible, they are human. They make mistakes, they get sloppy, and they lose attention. The unfortunate reality is that lab leaks are commonplace. Most you never hear about because the consequences are minor.
Given the poor track record of labs worldwide to practice good biosafety, the real question here is whether we should have a complete worldwide ban on gain-of-function research. Is the risk really worth the benefit?
Over time, we'll gradually learn the real truth of the origins of all of the variants as we get more data, but attempting to suppress discussion of genuine avenues of investigation is about as anti-scientific as you can get. Please reconsider your attitude.
Also, everything that's unpleasant to consider isn't a 'conspiracy'. Labs have performed gain-of-function experiments that create nastier viruses fairly regularly, often proudly publishing their work. Those same kinds of labs, while they always try not to, sometimes leak dangerous disease-causing agents - typically by infecting a researcher who then infects others in the community.
So the speculated chain of events doesn't even require any malice – just known-to-happen events cooccuring at an inopportune time.
And how can "armchair detective work" like this be "dangerous"? Hackers love to engage in armchair detective work! Unless there are reckless accusations placing potentially innocent people in danger – not at all true of this article – there's no grounds for suppressing good faith discussion, at least not in any culture that values open discussion of ideas, including even suspect ideas, to confirm/refute/improve them.
"Conspiracy stuff" means baseless, hand-wavy claims. While the author's hypothesis may turn out to be false, my reading of it suggests that the argument is made in good faith, and is supported by data. It may not be the right interpretation of that data, and the conclusions may be incorrect, but I don't consider this "conspiracy stuff".
Regardless of whether or not any of this turns out to have been one or more lab leaks, we need to keep talking about it, in an evidence- and data-based manner. We still have no idea where this virus originally came from, and we need to continue to explore all reasonable options until they are ruled out, or another option is proved to be true. You may not think a lab leak is reasonable, but I think that's short-sighted, and certainly hasn't been ruled out as an option.
The meat of the speculation is a scary looking graph plotting genetic delta from the origin. Here’s a more objective plot from the Wikipedia entry: https://en.m.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant#/...
Notice anything? Looks like Gamma and others have similar genetic distances without other mutations.
Sensational blogging is pretty sensational. That’s about it.
This sentimental reminds me of a talk given by a government bomb expert where a naive student asked “why do we allow the ingredients for bombs to be sold in store, shouldn’t we ban them all?”
The answer of cause is that if we do that, then we suddenly don’t have gasoline, orange juice, basic electronics, fertilizer or even just basic sanitation products available anymore, but of cause anyone who wanted to make a bomb would still be able to do so easily.
If it really is the case as pitched that 1000$ gets you a virus that will bring down nations, why on earth would we leave the field only to bad actors? Would that not just make it ever so more important that such researched happened openly and under well funded, strictly controlled conditions so we know what to expect and so we can start to develop plans for counter measures for when the next 9/11-like fanatic driven attack comes along?
I'm also surprised gain of function research has not been banned, the risk is far too high
A New Scientist article from two weeks ago suggests two other hypothesis for the evolution of omicron: that it either evolved in a single immune-compromised person, or that it jumped to an animal population and then jumped back: https://www.newscientist.com/article/2302268-how-did-the-omi...
I've been following COVID news the same way I do the weather during tornado season. That is to say, consistently and with an effort at personal awareness, but I'm hardly an expert. Yet I'm aware of several other "parsimonious hypotheses" which the author is not, and, worse, they apparently consider their own ignorance as evidence.
However, this actually made the article less credible to me, as this make me feel the article's purpose is to build a narrative and try to discredit everyone else, not to fairly evaluate all theories equally.
One thing I have been feeling about internet is there are too many experts on it, so one can always find enough quotes that support ones theory. However, as a reader, it's become impossible to determine whether particular expert should be trusted.
In the paper that the article links about mutations in an HIV patient (https://www.medrxiv.org/content/10.1101/2021.06.03.21258228v...)
There is a figure 1 and the left side (A) which shows a maximum-likelihood phylogenetic tree. If you examine this tree, you can see that the highlighted piece is based off a recent (to the HIV patient's case) variant.
On the other hand, the linked article (https://bprice.substack.com/p/lab-leak-20) has a tweet by Jonatan Pallesen showing a tree for Omicron. This tree shows that Omicron is based off of a variant from a surpringly long time ago. This alone is bizarre.
That combined with the lack of silent mutations is extremely suspicious. I'm not saying this is concrete evidence or anything, but its very strange and doesn't appear to line up with a natural course of evolution
https://www.nytimes.com/2021/10/14/science/bat-coronaviruses...
A sad state of affairs indeed.
*EDIT* it looks like it didn’t actually get deleted. When I went to edit the post my edit wouldn’t take and it said the post was deleted. But I am still seeing the post, so I think it’s “there” at least..
Substack is becoming YouTube for text at this point.
Sure, the tinfoil hat crowd will likely take things like this and run with them in all the wrong ways. But that's going to happen regardless, and that's just the price of living in a society where we can and should be able to discuss ideas freely, even ideas many of us may vehemently disagree with.
I'm also unclear how such researchers could come to the conclusion that it is less dangerous and more contagious with humanized mice considering it is the result (AFAIU) of it contaminating and replicating in the airways rather than the lungs. I'd be curious for someone more informed than me (an ecologist with very superficial understanding of viruses and studies in mice), but if I'm correct that lung vs. airway contamination isn't quite replicable in humanized mice vs. humans, intentional "alter and release" seems dubious.
Not that I'd put such a plan past some people...
I don't doubt that the Hong Kong protests were a major problem for the CCP and that COVID allowed them to implement a series of restrictions and laws to stop protests. I also don't doubt the very real possibility of a lab leak in Wuhan (in fact, given how the CCP have responded, I find it very likely).
What I do doubt is that this virus was released to combat the Hong Kong protests. If it was on purpose, it was a huge self-inflicted wound, as the CCP's inability to contain the virus has made them look weak internally and externally. It's hugely crippled their own economic growth which was set to overtake the US, which has now been set back at least 5-10 years based on projections (if they are to be believed).
If I were an evil regime, I would probably fake terroristic plots from the protestors and then respond to them heavily. There were plenty of other options available too, such as "starving out" the protestors (a tactic I believe they employed).
What's more likely is that the CCP are very good at utilizing the current situation to serve their own means. They are surprisingly bad at it though and seem to completely misunderstand how they are perceived on the world stage.
It may be a case of aligned incentives. A new virus occurs (even CCP does not know whether it is lab-leaked), and it is allowed to exist for some time (doctors arrested for spreading rumors). Definitely prefer incompetence to malice here, but maybe a decision was made to "sit back and assess" while the problem grew more serious.
Faking terroristic plots and blaming protesters is old hat, and the outcome of cracking down on the free territories while you still have the #2 Navy in the world are predictable. Hong Kong is not alone in desiring independence, and Beijing is not willing to lose face. A re-run of Tienanmen Square was starting to look inevitable. What if instead of that well-trod path of war, they chose to boost the poll numbers by allowing a crisis to occur and saving the day?
The cost of an economic slow down, well it's a risky calculus, but if the pandemic becomes global, they will not be left that far behind the competition. In fact, a totalitarian regime may be better-able to enforce health mandates and become productive again sooner.
What's more, USA was also dealing with a kind of dueling rebellion between BLM and Trump-Forever types. Perhaps the two agreed that the world needed a cooling-off.
/tin-foil
Likewise, it's not that there's compelling evidence of a lab leak (now or in 2019/2020). It's that we're sort of left with it by process of elimination. For example: if Covid-19 came from an animal population (eg via Wuhan wet markets) then why hasn't that population been found? The sources of SARS and MERS were, I believe, found relatively quickly.
Just like we shouldn't just accept the prevailing theory of MH370's disappearance as fact and we should continue to look for the plane and hopefully factually establish what actually happened, we shouldn't take the "lab leak" hypothesis as fact. Extraordinary claims require extraordinary evidence.
As for the articles claims about Omicron origins... I really don't know. I'm certainly no virologist so can't speak to the mutations. That's an odd-looking graph though.
I'm also wary of drawing conclusions from anything to do with statistics, just because it's so easy to make a mistake. My favourite example is the long-running idiocy about "natural immunity" being better than a vaccine. This is based on comparing two populations: vaccinated and unvaccinated. Except... those populations aren't equivalent. The vaccinated group includes people who would've died without the vaccine (and thus are more likely to have comorbidities). Those people are dead in the unvaccinated population.
there's a great deal of compelling evidence for alpha leaking from a lab; e.g. the director of the WIV publishing papers about introducing furin cleavage sites, which have otherwise never been detected in coronaviruses, into bat coronaviruses in the years leading up to the pandemic. if anybody has not read the nicholas wade essay in the bulletin of atomic scientists from last year that was mentioned briefly in the linked piece, i strong recommend it: https://thebulletin.org/2021/05/the-origin-of-covid-did-peop...
> But it took nearly 15 years and extensive animal sampling to find a closely related virus in bats.
It's a great deal of throat-clearing for a one-sentence argument from ignorance. Alina Chan has pointed to a more plausible alternative in this comment https://news.ycombinator.com/item?id=29789480
Although the claim that there's little chance for Omicron to have developped resistance to antibodies in an immunodepressed patient (that is without antibodies) needs to be adressed to.
I would love to see a reasonable fact-based response to the article that actually take into account the points being made.
Incorrect. She claims four supporting lines of evidence and does not label any one of them as the "main" argument. The NS:S ratio is just the second of four presented. She is throwing everything at the wall and seeing what sticks, because she lacks the expertise to evaluate how strong any one of her arguments is.
> So you are actually making a false presentation of her argumentation and I believe this is called... slander ?
No, it's not called slander. I just didn't see it when scrolling through this poorly organized and low-information blog post to extract the 1-2% of text that contained novel or interesting claims. Honest mistake.
If we want to talk about this silent/non-silent ratio seriously, we need to look at the data a little more carefully and not just trust some random Twitter person's guesstimate. There is at least one other random Twitter person who doesn't agree with the ratio presented in the OP. This second person does a transparent calculation citing an authoritative source, so it's a lot higher quality claim than the first random Twitter person: https://twitter.com/TheBrettRGM/status/1471317205014900739
If you look at the counts of non-synonymous and synonymous mutations for each variant listed at https://covariants.org/variants, you will see that all variants have a very high NS:S ratio. So either the entire evolution of the virus is being guided by mad scientists in secret labs, or we armchair virologists are over-interpreting the NS:S ratio.
> Although the claim that there's little chance for Omicron to have developped resistance to antibodies in an immunodepressed patient (that is without antibodies) needs to be adressed to.
Immunocompromised people don't lack antibodies.
I think there is ample evidence at this point that this person is not an expert and the arguments made are probably much less strong than they may sound to a layman.
Given the current state of biotech, it is not possible to just edit the viral RNA achieving the desired clinical result, but is entirely feasible to keep applying minor edits and measuring the propagation rate in different tissues in vitro, effectively optimizing it to be more transmissible and less lethal. The snapshot of the phylogenetic tree, showing how Omicron "branched out" mid-2020 highly supports this assumption.
It is also quite obvious that an endeavor like this would be against all written rules and norms and would face backlash of epic proportion even if it wouldn't backfire, so it's safe to assume we won't hear an official confirmation of this theory from any of the governments.
[0] https://www.the-scientist.com/news-opinion/omicron-propagate...
But something tells me that "oops we created a dangerous virus now we need to seize more control" offsets that risk to the governments of the world.
As the article states, we should be clearly weighing the benefits of gain-of-function research against its risks. It seems like that was the intent of the 2014 funding ban in the US, but we never actually did that work, and that's horrifying. And if the some/many/all of the benefits of GoF research can be realized through other means, even if those means are more difficult or costly, we should probably just do that anyway.
We know that the virus is likely to continue to mutate in the wild, on its own - and that the virus in the wild has upended our way of life with great economic costs. Is this a viable path way to introduce widespread natural immunity? Omicron introduces mutations with extremely high contagious properties but very mild virulence. In one swoop, you expose vaccine-hesitant and developing nations to a virus they're likely to survive, help inoculate them against future mutations and outcompete the dominate strains such that the human race is somewhat protected against future infections.
In effect, you kind of "undo" the original mistake.
If the piece hinges on getting this pretty basic element wrong, how wrong is it about some of the more sophisticated analyses?
Immunocompromised people, in order for their "omicron" to develop resistance to the various treatments available (the monoclonal antibodies) must have been exposed to those treatments. If they were exposed to those treatments, they were being followed medically. If they were being followed medically, and receiving long-term treatments, it's then odd that they didn't infect a single other person in a year and a half.
On the other hand, there's the somewhat bigoted implication that "oh there are a lot of remote people in Africa that don't come in contact with anyone else." Well, then how did their omicron develop resistance to all the fancy treatments?
Either it's an immune compromised patient who never came in contact with anyone else, and the specific resistance to monoclonal antibodies, which they never received, is not explained.
Or it's an immune compromised patient who received intensive treatments for a long time, in which case the lack of any intermediate variants ever being documented is not explained.
S/he didn't say immunocompromised people don't have antibodies.
S/he says mice don't have human antibodies, so if the "mouse hypothesis" is correct, how did the mice, unless they were lab mice, get the immunity to all these human treatments?
> The last two coronavirus outbreaks took around fifteen years to understand.
Is it possible that because these diseases had less impact, less people worked on them? It seems like virtually every scientist in even a tangentially related field is working on Cov-2. Not to mention that we have made significant improvements in technology even over the last decade.
I am not saying that this proves or disproves your comment, but couldn’t it be said that more people, resources and technology could get us answers faster in 2019? Especially if we are building of research and knowledge we have acquired over the preceding 2 decades?
Animal antibodies would work just fine to put selective pressure on the virus.
This author presumes every major VoC stemmed from a lab leak. From the wild strain to Delta to Omicron. This is sensationalist, unsubstantiated claims with weak supporting evidence.
"LEAKED GRANT PROPOSAL DETAILS HIGH-RISK CORONAVIRUS RESEARCH The proposal, rejected by U.S. military research agency DARPA, describes the insertion of human-specific cleavage sites into SARS-related bat coronaviruses."
https://theintercept.com/2021/09/23/coronavirus-research-gra...
"Lab-Made? SARS-CoV-2 Genealogy Through the Lens of Gain-of-Function Research"
https://yurideigin.medium.com/lab-made-cov2-genealogy-throug...
"RaTG13 – the undeniable evidence that the Wuhan coronavirus is man-made"
I think there is ample evidence at this point that this person lacks expertise in virology, and the arguments they make are probably much less strong than they may sound to a layman.
The important thing is that mutations occur at a certain rate per virus per unit time. If you have an isolated population that's sequenced infrequently then (1) that strain will appear to evolve more slowly as there's a smaller population capable of mutating, and (2) once that strain is sequenced it's going to look far from what you've seen already since you haven't been tracking the intermediate mutations in this population.
The S/N ratio can be analyzed in terms of a random walk in high dimension. Variance in these walks grows over time (in terms of distance from origin, i.e. number of mutations), so the discrepancy doesn't seem super far from what's plausible under the null hypothesis. Perhaps someone can do the math on that.
The hypothesis merits further investigation, but the strength of the evidence presented here really requires some complex statistical analysis to determine if innocuous explanations fit. The analysis is far more complex than I would expect an epidemiologist or virologist to apply in the course of their work.
I'm lost, who is the author? Without names and credentials this just looks like some kind of covid fan fiction or something.
this is becoming the new russiagate
