The lead author of Proximal Origin wrote this in slack on April 17, a month after the letter had been published in Nature Medicine:
"Okay, so about the current news. Is there any reason to believe that they might be onto something, or is it all smoke and mirrors? Eddie Holmes - any insights on the China side? The main things from my perspective:
1. Bioweapon and engineered totally off the table
2. If there is no engineering and no culturing, then it means that somebody magically found a pre-formed pandemic virus, put it in the lab, and then infected themselves. The prior on that vs somebody coming into contact with an animal source infected with the virus is as close to zero as you can get. Humans come into contact all the time with SARS-like CoVs, but the likelihood of somebody finding exactly that pandemic virus and infecting themselves is very very low (make no mistake - if they did find that pandemic virus. then they would get infected if they grew it in the lab - but the likelihood of them finding it in the first place is exceedingly small (or so one would hope - otherwise, good luck World avoiding future pandemic).
3. But here's the issue - I'm still not fully convinced that no culture was involved. If culture was involved, then the prior completely changes - because this could have happened with any random SARS-llke CoV of which there are very many. So are we absolutely certain that no culture could have been involved? What concerns me here are some of the comments by Shi in the SciAm article ("I had to check the lab" etc) and the fact that the furin site 1s being messed with in vitro. Yes, it loses it but that could be context dependent. Finally, the paper that was shared with us showing a very similar phenomenon (exactly 12bp insertion) in other CoVs has me concerned...
I really really want to go out there guns swinging saying "don't be such an idiot believing these dumb theories - the president is deflecting from the real problems" but I'm warned that we can't fully disprove culture {our argument was mostly based on the presence of the O-linked glycans - but they could likely play a different role... We also can't fully rule out engineering (for basic research) - yes, no obvious signs of engineering anywhere, but that furin site could still have been inserted via gibson assembly (and clearly creating the reverse genetic system isn't hard - the Germans managed to do exactly that for SARS-CoV-2 in less than a month)."
And:
"Shi didn't do any GOF work that I'm aware of - but GOF work isn't the concern here. She did A LOT of work that involved isolating and culturing SARS-like viruses from bats (in BSL-2) and that's my main concerning scenario (we cite several of those in the paper - if you have a look at those original publications, it's definitely concerning work, no question about it - and is the main reason I have been so concerned about the 'culture' scenario)."
I don't think much more needs to be said. The above messages are self-explanatory.
Also, in the accompanying press release from Scripps, Kristian Andersen says:
“These two features of the virus, the mutations in the RBD portion of the spike protein and its distinct backbone, rules out laboratory manipulation as a potential origin for SARS-CoV-2.”
In that April slack conversation, the lead author expressed strong, persistent concern about a lab cultured virus that had adapted and become pandemic-ready through that process. Lab culturing = lab manipulation.
Authors have taken their names off papers for much less.
Yes, there is much more evidence. My medium blog also cites the Chinese CDC in early 2020 and the China-WHO joint report, both of which corroborate the fact that case definitions used in Dec 2019 to mid-Jan 2020 required a link to the market or at least that the patient had to be admitted to a hospital near the market or live in the neighborhood of the market.
"In the first days of the epidemic in Wuhan, cases were identified on the basis of clinical features, including fever and acute respiratory symptoms, radiology and epidemiological features. An association with the Huanan market was identified among some of the earliest recognized cases and, for a short period until mid-January 2020, exposure to the Huanan market was included in the case definition. It rapidly became clear, however, that there were cases without a link to the Huanan market, and this element of the definition was dropped a few days after being introduced (Annex E3)."
On the unlinked cases - if you read my medium post, it explains that even the cases with no connections to the market had been identified with ascertainment bias. Local investigators had searched hospitals and the neighborhood near the market for cases even if they had no link to the market.
On your 2nd point, I've clarified that it was not a rewording but a removal of both claims of dispositive and incontrovertible evidence from the preprint. This means that peer review flagged both of these strong assertions in the manuscript and the authors had to remove both of them.
You state below that the requirement for cases to be linked to the market was removed after only a few days. Is it possible that all 120 "unlinked" cases were in fact identified within those few days?
Removal of a claim of "dispositive" evidence isn't weakening the case; there could be further incontrovertible evidence that would make the present evidence no longer dispositive.
By the time the case definition requirement for a link to the market was removed (Jan 18, 2020), nearly 200 cases had been confirmed. This is not including the number of cases that were suspected/clinically diagnosed.
The 174 cases with onset in Dec 2019 considered by Worobey et al. include both confirmed cases and clinically diagnosed cases. Therefore, most, if not all, of these cases had been identified using the criteria that the patients had to either be linked to the market or, if unlinked to the market, have been identified at hospitals near the market or in the neighborhood of the market.
Re: weakening of their claim, not only did Worobey et al. have to remove these instances of unscientific language, but they also had to insert a new study limitations section and this clarification in their article:
“However, the observation that the preponderance of early cases were linked to the Huanan market does not establish that the pandemic originated there.”
"Study limitations" is standard language in epidemiological papers, so that's not a surprise, nor a condemnation.
Further, to my knowledge it is known that "case zero" (i.e. the zoonotic event) did not occur at the Wuhan market, specifically because there was already sequence divergence in early cases.
However, that doesn't prevent the market from being the main source of the outbreak. There's no evidence for any other source.
Here is my evaluation of a recent Science Magazine publication, "The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic".
The updated epilogue now discusses three significant new developments since the publication of the hardback that are being hotly debated in the comments here. The first was the discovery of a virus in a bat in Laos that is slightly more similar to SARS-CoV-2 than the virus studied at the Wuhan Institute of Virology; but both are still not the progenitor of the pandemic. The second is detailed information about how prominent western virologists, who had privately thought the virus was likely manipulated in a laboratory, began to instead tell the public that no lab-based scenario was plausible. The third is a trio of conflicting studies about whether the Huanan seafood market was the site of a natural spillover of the virus from animals to people or just the site of a human superspreader event in December 2019.
As with the hardcover, half of our earnings from the book have gone/will go to charity.
2. Does the available evidence lean towards a market origin?
Some experts have asserted that there is dispositive evidence that the virus jumped from animals to people at the Wuhan Huanan market. However, their analysis failed to take into account the realities in the early days of the pandemic. Without access to the methodology and actual data collected by investigators in Wuhan, their interpretation unfortunately falls prey to ascertainment bias. Please see this thread for details: https://twitter.com/Ayjchan/status/1499794942012579843
At the moment, US intelligence, the WHO SAGO advisory group, and many top virologists and experts find both natural and lab origin hypotheses plausible and deserving of investigation. The evidence does not lean so strongly towards one hypothesis or the other that we can assume one as the default truth.
3. Can scientists manipulate and genetically engineer naturally found viruses without leaving a trace? In other words, can the genome of the virus tell us its recent history?
We describe the seamless genetic engineering capabilities developed in the years leading up to the pandemic in VIRAL. Due to advanced technologies, it is no longer always possible to use the genome of a virus to distinguish between a natural pathogen vs one that has spent time in a laboratory. Even top coronavirologists, including Ralph Baric who collaborated with the Wuhan scientists, have said that the only way to know is to look at the Wuhan lab records. You can also read my twitter thread: https://twitter.com/Ayjchan/status/1493733086089121794
Even the presence of the furin cleavage site insertion that is unique to the pandemic virus and is indeed what makes it a highly infectious pandemic virus is not “dispositive evidence” of either a natural or lab origin. Please see our peer-reviewed analysis here: https://academic.oup.com/mbe/article/39/1/msab327/6426085
4. Why does the lab leak hypothesis encompass so many different scenarios by which research activities could lead to the emergence of the pandemic virus?
A natural spillover hypothesis also encompasses several different scenarios, e.g., bat direct transmission to people in natural habitats, bat to people in markets, bat to farmed animals or wildlife to people in nature, at farms or market, etc.
This doesn’t mean that a natural or lab origin are insinuations. It just means we are lacking so much key evidence that it’s not possible to pin down an exact mechanism by which the virus emerged in the Wuhan human population.
5. Does finding close relatives of the pandemic virus in bats, e.g., in Laos, mean that its origin is natural?
No, because viruses that escape from labs were also ultimately derived from nature and we know that scientists in Wuhan had been collecting viruses from across 8 countries (China and SE Asia) where the closest relatives to the pandemic virus have been found. Please see the graphic in this tweet: https://twitter.com/Ayjchan/status/1522117270612451335
6. Is there anything to do about finding the origin of Covid-19 now? Isn’t it a dead end? And is that why interest is waning?
There is plenty to do to investigate the origin of Covid-19 using sources and data that exist outside of China. Please see a recent peer-reviewed letter in PNAS: https://www.pnas.org/doi/10.1073/pnas.2202769119
It is very surprising to me that these feasible routes of inquiry have not been explored more than 2 years into the pandemic.
7. Have infected animals on sale at the Huanan market been found? Was there any evidence that SARS-like viruses were circulating in the Wuhan animal trading community before the emergence of Covid-19?
8. Regardless of the origin of Covid-19, shouldn’t the focus be on making sure there is more oversight and regulation of current and future pathogen research?
I agree and wish that we didn’t need to prove the origin of this pandemic to motivate scientific leaders to better regulate risky pathogen work. I have been dedicating efforts to this cause since last year and hope to be able to share some exciting news later this year.
thank you for doing the work that some others are seemingly afraid to touch! There are many fair-weather scientists, but researchers who consider all credible leads and data, no matter the popularity or political implications of the results, are much rarer.
I have two questions:
1. There were genome sequences removed from the 'Sequence Read Archive', at the request of Chinese scientists.¹ It was later portrayed by US authorities as something that commonly happens. As a layperson I'm curious if that's true and it's a regular occurrence that researchers in another country ask for data to be deleted from the archive. That seems odd.
2. In case you read Chinese, do you know about that Wuhan Institute of Virology job ad where they were looking for a researcher to study coronaviruses in bats, which was posted on their website a few weeks before the outbreak became known? I saw this myself in the very early days of the pandemic, possibly before people in the West were even aware that there was a serious outbreak in Wuhan. At the time I didn't think much of it, but then 2 or 3 days later they first deleted that ad, then the whole board and when I visited today I found their entire website has been completely reworked. Have you seen this and do you know if it was saved anywhere? Not that the job opening itself seemed suspicious and it's well known this sort of research was done there, but I just found it odd they would try to hide it.
1. The deletion of published data is thankfully not something that commonly happens, but it is not against the rules of the NCBI database. Scientists who deposit their data into the database have the right to ask for that data to be taken down even if it has been published. That's why there is a concern that some scientists may have used this mechanism to delete original data with early Covid-19 sequences in it. Some scientists have called for NCBI to please allow them to search through deleted or suppressed data for these early Covid-19 sequences, but they have not been granted permission. Please see Vanity Fair's report on this: https://www.vanityfair.com/news/2022/03/the-virus-hunting-no...
2. I have seen an archived version of that job posting but, like you said, it didn't surprise me that they were looking for more coronavirologists - the Wuhan Institute of Virology does have one of the world's largest (if not the largest) bat coronavirus hunting programs. The website being revamped kind of goes into speculative territory - maybe it was just time to upgrade the site or maybe they did it to avoid negative attention. The more disturbing thing to me is that they did not share their pathogen database (taken offline in Sep 2019) despite a pandemic happening. The database was meant to help inform pandemic response, but when a real pandemic happened, the database could not be found anywhere. None of their collaborators, including in the US, have seemed to be able to provide a copy.
> At the time I didn't think much of it, but then 2 or 3 days later they first deleted that ad, then the whole board and when I visited today I found their entire website has been completely reworked. Have you seen this and do you know if it was saved anywhere?
Regarding your answer to 8, how important is gain of function research in the virology eco-system, is there sufficient reason amongst the powers that be within the discipline (that is, well-known researchers, leaders of departments or labs, funders and program managers, etc) to be wary of a funding cut for this research that they might be biased in dismissing the idea of a lab leak?
My analogy is in particle physics, the idea of supersymmetry is incredibly popular amongst the super start researchers, heads of parts of CERN, funding agencies, etc, that very few in the field are willing to admit the lack of evidence for supersymmetry at the LHC is in fact a crisis for the field after how many billions have been spent on the supercollider. My question is, is gain of function that important or popular in the field of virology? Why can't they just admit it's dangerous and chuck it, will enough of them suffer if they were to do so?
The vast majority of virologists are not working on gain-of-function research or with potential pandemic pathogens, but this type of research has some very influential backers who control significant sources of funding in virology and infectious diseases. This makes it very awkward and professionally risky for virologists to say that the top leaders in their field advocated for research that might have caused this pandemic and taken millions of lives globally.
National Science Advisory Board for Biosecurity (NSABB) has been reconvened this year to review US government policies on dual use research of concern (DURC) and research with enhanced potential pandemic pathogens (ePPP/P3CO).
Their public meeting is available here: https://videocast.nih.gov/watch=44823
Please also see my thread on it:
https://twitter.com/Ayjchan/status/1499035660627419139
Based on these sessions and the history of the NSABB, I'm not confident that they will recommend measures to make this type of research more transparent or even safer.
The elephant in the room, as far as support for GOFROC (gain of function research of concern) goes, is Fauci. Several leading biologists (Marc Lipsitch, David Relman and others) have argued for years that the risk/reward ratio for GOFROC is too high to justify it. But it had to go all the way to Obama for Fauci to change course. Obama imposed a 3-year moratorium from 2014-17, which was lifted soon after he left office.
https://www.washingtonpost.com/opinions/a-flu-virus-risk-wor...
To me the fact that top officials in both the US and China have a likely interest in not investigating lab origins goes a long way to show why this hasn’t been done. And why no other country can get the ball rolling on it, these are the two most powerful countries in the world.
IMO it’s likely no one knows where this virus came from right now. but it could well be a lab, but anyone who could potentially investigate this theory absolutely does not want to in case it turns out it was.
It's even worse. If you look at that Lancet Letter scandal, you'll find for example Christian Drosten as a signatory, who was the expert with the most influence over the German government until recently.
Even after the Daszak conflict of interest was discovered, despite the declaration of no conflict of interest, none of them ever retracted it or even apologized. Even more, it was later revealed the letter had actually been authored by Daszak himself, as the pretend lead author Charles Calisher himself admitted. Calisher is a long retired professor born in 1936 who at this point may or may not understand what's going on. To his credit at least he told the truth when journalists questioned him. It looks like Daszak used his name to distract from his authorship. The strategy worked too, at first.
What's shocking is that none of them have faced any consequences.
Shocking and depressing. It was a gross abuse of the trust that society places in scientists. What is astonishing is that the conlicts of interest of the authors would have been clear with a simple Google search. Yet, no newspaper thought of doing that! More likely, they took a decision to not pursue that angle.
I agree. Australia was one of the few countries which called for an investigation of all possibilities and the reaction from China was swift and furious. For most countries, concerns about trade and geopolitics outweigh everything else.
The US (and I would add France, which built the BSL-4 lab in Wuhan) has additional reasons not to investigate, as you said.
Not long after Australia pointed the finger at China, it emerged that Australian Government Labs had been doing gain of function research on bats ...
If the bar for proof of guilt is "swift and furious reactions" then by the playground court rules; "whoever smelt it, dealt it" and "whoever said the rhyme did the crime"
Ah of course I am parotting disinformation from the CCP, not quoting from statements made by the Chief Executive of Australia’s national science agency, CSIRO.
Perhaps your aggressive rebuttal was a sign of your guilt and complicity in the global pandemic.
Though your link doesn't quite say that, there are strong advocates of GOFROC (Doherty, Subbarao and others) at the Peter Doherty Institute, Melbourne. Moreover, one of the leading Australian virologists, Eddie Holmes, is a long-term collaborator of WIV and other Chinese institutes. But these facts by themselves are not indicative of guilt or complicity.
What has been missing is an independent investigation of both possibilities (lab related and zoonotic spillover).
The baffling reluctance of the US and China to call for such an investigation is very disturbing. However, to talk about guilt is premature at this stage.
Hey Alina, thanks for contributing so much to the discussion.
One thing that always made me balk was this interview on CCTV which shows researchers collecting bat samples (feces etc) while seemingly skimping on PPE and admitting to getting bit by the wild animals and having a clear skin reaction all the way back in 2017 [1] - Do you have any comment on that in particular? Supposedly these are researchers from the Wuhan Institute of Virology but all I have to go by on that notion is some news from Taiwan and the New York Post, since I don't speak Chinese this video is a little harder for me to personally verify...
Hi Jamal,
Yes, there is quite a bit of evidence (photos and interviews of the scientists) showing that the virus hunters in Wuhan did not always wear appropriate protective equipment while hunting for potential pandemic viruses in remote areas. We describe this and provide citations in VIRAL (will be on page 127 in the paperback). In any case, even with full PPE, you can get bitten or exposed to animals and their pathogens. Accidents happen, especially in an uncontrolled environment, e.g., a cave swarming with millions of live bats that you're trying to catch and sample.
Nice, I am a voracious book reader so I'll keep my eye out for your title.
I definitely support your push for getting gain of function research reconsidered, I can't imagine anything but nefarious ends to that kind of thing whether or not it is the culprit behind what we've all gone through over the past couple of years.
Hej Alina! Thanks for being open with having an economic interest in this topic being dragged out into the open again.
> It is very surprising to me that these feasible routes of inquiry have not been explored more than 2 years into the pandemic.
It's not too surprising to me. International diplomacy works like this. With a more general picture in mind, specific topics often need to be swept under the rug. Otherwise international relations between any two countries would be constantly in shambles and we'd long have seen WW3, WW4 and WW5.
Note that I'm not advocating for any of this hush-hush. I'd also like to know what happened. But that's just not how international diplomacy works. In this particular case, if WHO wants continued support from China, then you need to carefully balance what and how you criticize. Nobody is helped if China leaves the WHO or next time doesn't even tell anybody that a pandemic is coming for fear of being bullied for this kind of thing. I'm sure the responsible bodies (lab people) will learn their lesson and be more careful going forward. That's the only thing we can hope for nonetheless. It's unrealistic to think China would be punished and all their labs shut down. This won't happen.
Hi,
My perspective is that, if the pandemic started due to the virus hunting program which was a very international collaboration (US, China, several European, African, Asian, Middle Eastern countries), then it's not really a China-specific thing. It could just be that China is so much further along in their virus discovery and characterization pipeline (as the scientific literature points out) that unfortunately they were the first to leak one of these pandemic level viruses either found in the wild and sent to the lab or created in the lab during the process of characterization.
I don't think that a country should be singled out for punishment for having a lab accident (unless it can be demonstrated that they do not have proper biosafety protocols and accountability mechanisms in place; a case of reckless negligence). But I do think there should be new international agreements and penalties for suppressing information about an emerging outbreak, e.g., transmissibility of the virus, its genomic sequence, number of cases and geographic spread etc., and costing other countries time in preparing to respond to the outbreak.
My question has been the same, ( apology if this was already answered ) why do we accept Dec 19 as the starting date, when we have evidence that partial Wuhan lock down due to "lung disease" started in November when Wuhan blocked International ( but not national ) flight to Wuhan airport.
I am going to ignore the WeChat evidence for discussions on WuHan "lung disease" in October and prior since those could be fake. But surely flight schedule cant be made up?
Is there any evidence of a link between sars-cov-2 to other previously known viruses that the Wuhan lab might have had in its possession? Could there be a plausible candidate virus that might have escaped from the lab? Was any of this data public prior to the pandemic?
We cover this quite extensively in our book. I also have a manuscript that will soon be in peer review describing the relationship between SARS-CoV-2 and other known viruses. None of the publicly disclosed viruses could have plausibly been the progenitor of SARS-CoV-2.
However we now know that when news emerged of a novel SARSrCoV with a novel cleavage site causing an outbreak in Wuhan… scientists in Wuhan did not tell us that they were working with 9 of its closest relatives, linked to mysterious pneumonia cases, and that they had been collecting 1,000s of unpublished high-risk samples from animals & humans across 8 countries, with a clear roadmap for synthesizing consensus SARSrCoV genomes and inserting novel cleavage sites into novel SARSrCoVs. Their database meant to inform pandemic prediction & response remains inaccessible.
This is Alina Chan, one of the co-authors of Viral: The Search for the Origin of Covid-19.
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.
First detection is an indicator of that, when it was first detected, not a guarantee that it was first there. Only a very small fraction of RT-PCR positive samples are sent for sequencing under normal conditions.
> 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.
But Italy, hit extremely hard by early waves, and now with a much-higher vax rate than South Africa, could more easily miss a rising wave of mild cases in already-immune that don't seek treatment. There are plenty of factors in all directions, and only very spotty variant surveillance most places.
Thanks for referencing my tweet - & asking some questions I would!
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
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.
Another thing that the blog post appears to be unaware of is that the absence of samples showing the step-by-step evolution towards omicron doesn't mean that this didn't happen. A lot of places in the world don't have the resources to do covid testing and genomic surveillance.
Absence of evidence is not evidence of absence, yes. But take another look at the phylogenetic tree. Those are huge gaps. See also this article describing how good South Africa is at spotting and sequencing variants."The reality is that southern Africa is a top international powerhouse of COVID-19 surveillance."
https://www.businessinsider.com/how-southern-africa-detected...
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.
But, the point is it was growling so fast you wouldn't expect it to show up in other places until the "knee" of the exponential showed up there as well. SA being just a couple of weeks ahead is a lifetime for Omicron.
100% agreed. Again, this is a possibility, not a certainty. But I'd be loath to dismiss it, just as I am not willing to dismiss a reservoir origin. In the end, the author does make a good point: we need mandatory disclosures of GoF research and a general ban on GoF financing of labs who aren't working in full disclosure mode.
Ideally, we should not have this discussion because the GoF leak is impossible. Sadly, as secretive as this research is, as much money as we funnel into labs in China and Russia, and as reluctant as oversight authorities (such as the WHO) are to even consider leaks, the best response would be a general ban on GoF and GoF financing.
There is a belief that Omicron originated in South Africa, but some growing evidence that it was present elsewhere earlier, but only either detected or first identified early on in South Africa.
And even if they did do genomic analysis - it's entirely plausible the results are sitting in a hospital database somewhere instead of uploaded to the international gene surveillance repository.
Plausible, yes. If the data exists, it should be made public. The article still mostly just makes a hypothesis and makes the argument that this is something that should be seriously investigated, not that the author has determined without a doubt that this is a lab leak.
Sure - but what are the chances that whichever hospitals did the sequencing even know they're in possession of the intermediate data? The OPs' method of "just asking questions" is really bad science and feels a whole lot like the God of the Gaps argument style that Creationists are so fond of using.
I'm not sure the best way to judge the quality of a scientific argument is whether it 'feels like good science.'
While the author is obviously only scratching the surface in an article targetted at non-scientists, the several PhDs he cites make decent arguments that are based on a little more than feelings. It would probably be more in line with the ideal of 'good science' to actually investigate the possibilities presented than dismiss them from emotional associations.
It is a worrying trend that the way science feels is increasingly more important than the actual evidence (or lack thereof). One could even describe the current attitude towards science outside of scientitific institutions as religious.
And the reason not all of these spread fast is obviously that one mutation (or combination) impacts the spread rate more than the 30+other mutations in isolation...
Although after enough conversations I've found this too needs spelling out in plain English...
The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa?
Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps.
> The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa?
You're pointing out distinctions that do not make any relevant or substantial differences to the argument.
> Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps.
With lack of information, ideas that have the less assumptions and concepts tend to be true than their counterparts who require many possible sub-hypotheses and concepts. GoF happen and lab leaks happen and the genetic histogram and the genes makes make this hypothesis the more likely one. The opposite require many hypothetical actors (mouses, immunosuppressed patients, back and forth between geographically distant places and all the combinations thereof) to account for it "hiding" since spring 2020.
> especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons.
Nobody blamed nobody here. GoF research happens everywhere.
> Give the science time and we might start to fill in the gaps.
Science is not beholden to your worldview. Filling the gaps is part of the scientific method, by the way.
All I'm saying is that my bias is towards this virus being a natural phenomenon and I think waiting for the full context will settle the case. Jumping to conclusions on the basis of flimsy evidence mainly serves political agendas. We simply will not know for a long time, months or years, where Omicron came from and that's uncomfortable, but we have to sit with that.
If you DO want to get conspiratorial, you can watch this 2001 Bush administration pandemic simulation where China blames the US for a smallpox lab leak. It's pretty amusing to me to watch the US administration astounded by their luck of COVID-19 first being identified in China try to flip the script on their simulated exercise. My feeling is this Omicron theory is trying to breathe life back into the original lab leak theory by proxy.
I don’t understand how natural origin is your “bias” while everyone else is “jumping to conclusions”. There’s a lack of conclusive evidence for either scenario. And politics aside, SARS has leaked before resulting in deaths… no conspiracy required!
That's true Delta leaked in Taiwan, but that was a preexisting natural strain. Smallpox's last fatality also was a lab leak. However, most gain of function experiments use test harasses that can't infect humans or can't replicate. It's not impossible, but it's hard to have any conclusion at all at this early date with very little evidence.
The virus is infecting so many people and changes so rapidly that a natural explanation will not be surprising in the least. New variants have been expected. I think people are surprised at how bad the new variants have been, but anyone following the scientific literature wouldn't be taken completely off guard.
You seem to have caught some memes which don't make you see things rationally.
> The opposite require many hypothetical actors (mouses, immunosuppressed patients, back and forth between geographically distant places and all the combinations thereof) to account for it "hiding" since spring 2020
If you ever implied that closeness of outbreak of the Wuhan variant to the Wuhan lab the same should make you incredibly suspicious about this being a lab leak, since there is such lab nearby. So it would require an actor in another country to "breed" this variant and import it into South Africa/have agents spread it world wide and someone funding and green lighting what would a be case of international bio terrorism or even bio warfare.
As for accounting for those factors. Africa is an incredible diverse places with Nomads and hyper dense slums, with untreated large scale AIDS and healthcare systems as South Africa has and also a poorly understood and explored flora and fauna.
Does it seem that implausible that some combination of immuno compromised tribes/rural human and animals caught the old variant and didn't interact with the new variants from western civilization for less than two years? I don't think so.
As for the low number of silent mutations. I can not imagine how the lab leak theory would account for that, if it was designed why would there a low number of silent mutations and not an average number or none and if it was due to GoF why would a lab environment have less silent mutations then a "natural" one?
AFAIK we have almost no data on variants in some African capitals let alone people in rural/tribal areas or surveillance of animals. Maybe along its evolutionary it was a variant that has an advantage in sparsely populated areas so we didn't notice a large part of its history because it wasn't competitive in cities with other variants.
There are many possible explanations but the lack of lab is kinda blow for a lab leak theory and your political goal of less GoF-Research is only compatible with a lab leak and not any other form of lab caused (philanthropist/evil government developing and releasing this variant) explanation.
Gaps can appear if there are (1) missing data or (2) a big change such as a transposition or elision event. Neither are the case for our coronavirus data. For (1) we have a good random sampling of the population as a whole so it is exceedingly unlikely we would not see intermediate changes and for (2) the overall structure has not changed dramatically--we are looking at the accumulation of point mutations over the course of 18 months. So while gaps can and do occur, we would not expect this to occur naturally in the situation we are observing today with coronavirus.
Gaps also appear because evolution is not a smooth process, and once in a while a large number of mutations are selected for. We see the same type of pattern even in vitro. Moreover, mutations are not always well described by gaussian processes: the rate of mutation can be seen as having a fat tailed distribution.
Mutations has to be incremental because most mutations are not viable or doesn't provide any reproductive gain. Having multiple functional mutations all at once happening in a very short amount of time and being naturally selected in big enough number of infections is very very improbable.
> mutations are not always well described by gaussian processes: the rate of mutation can be seen as having a fat tailed distribution
I'm sorry if I have to be blunt, but you have no idea of what you are talking about.
Sure and if it had arisen in Europe then those questions would have to be asked. But it's a safe assumption that very little analysis is happening in southern central Africa. It doesn't seem that outrageous that a parallel line has been percolating there for quite some time and only recently gained a mutation or two that allowed it to shoot to stratospheric levels.
Even in Europe I wouldn't find it all that difficult to believe. We see the same sort of pattern, qualitatively speaking, even in well controlled in vitro experiments.
"Omicron could have evolved over an entire year in an immunocompromised individual before finally infecting others"
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?
Evolution experiments in the lab mimic natural evolution. The ratio of functional vs silent mutations has also been used to characterize the evolution of viruses under natural selection.
According to the blog post that we are commenting on, there is a strange ratio of silent to functional mutations. How can this be accounted for if it was a natural course of evolution?
Without looking more at the variants themselves and just going by the numbers in the post, it’s entirely plausible. It’s not likely, but plausible.
Mainly because we are talking rare events. If the level of success is 33/3.5 (9.42), we’d expect that 4 (or less) silent variants would happen with a probability of ~ 0.042 (Poisson X <= 4). So, a bit more than a 4% chance. But with millions of people infected, this ratio of S/NS variations would still happen at a pretty high absolute number.
Anytime you look at numbers like these, remember with a big denominator, even rare events are expected to happen.
If it was the case that the absolute number mattered, we would be able to sample different "Omicron-like" variants and observe various ratios such as 33N/10S, 33N/15S, etc. mutations. But according to the data presented, we don't: We only see a single (kind of) Omicron, the one with (about) 33N/4S mutations, presumably spilling over by a single event, so I don't see how your conclusion follows.
There are two different (and independent) forces at play here: mutation and natural selection.
The question is, given a known ratio of 3.5 NS/S, what is the likelihood that there would be only 4 non-silent mutations in any random strain (like omicron)? What the mutations are is irrelevant to this question. (I will use mutations and variants interchangeably below, but both mean a single change in the genetic code for the virus).
Because we are dealing with integer counts, you can’t really have 3.5 mutations. You can only have 1, 2, 3, etc. So, 3.5 is just the average of all ratios. When dealing with count data like this, the Poisson distribution is what you use. When you have 33 non-silent mutations, you could have 1, 2, 3, etc silent mutations. We’d expect to see 9.4 (33/3.5), but you can’t have 0.4 of a mutation, only integers. There is a specific probability associated with each possible value (1,2,3…), and that can be calculated using the Poisson distribution.
You are most likely to see 9 or 10, but all other values are also possible. To calculate how likely you are to see exactly 4 silent variants, you use the Poisson distribution. Again, we will expect that the rate should be 33/3.5 silent variants.
In R, you’d do:
dpois(4, 33/3.5)
[1] 0.02647255
So, if we had 33 nonsilent variants, we’d expect to see exactly 4 silent variants 2.6% of the time. To put this into context, the most likely number of silent mutations is 9, which is expected only 13% of the time.
We normally think in terms of “how likely is it that we’d see 4 or fewer mutations”, so we re-run the test for 0:4 and add them up:
sum(dpois(0:4, 33/3.5))
[1] 0.04211515
Which is how I got a probability of 0.042. And which answers the specific question — if we see 33 non silent mutations in a strain, how likely is it that we would be 4 or fewer silent mutations in the same strain? 4.2% of the time.
Given these numbers, I’d say it is plausible that you’d see this ratio of NS/S mutations occur naturally. It would be rare, but still somewhat expected to occur.
Now this says nothing about what the mutations are, or why the omicron strain is so prevalent. This is where natural selection takes over and this combination of mutations is out competing all others.
I was not taking an issue with the calculation of the 4% chance, but rather with this phrase: "But with millions of people infected, this ratio of S/NS variations would still happen at a pretty high absolute number."
I thought you were implying that since this was a 4% chance happening over millions of infection events, it was a virtual certainty, and thus the 4% factor made this highly probable. To which I counter argued, the 4% chance matters and should be accounted as a factor in a "natural vs lab leak" model, because everything seems to point that "a variant as infectious as Omnicron appears" was a single event.
It is a virtual certainty that a 4% likely event would occur given the millions of people that have been infected (and the subsequent mutations occurring within each of them). But that doesn't have anything to do with omicron specifically... and I certainly don't intend to suggest a correlation between NS/S and infectiousness. Mutations have a certain rate, but the events themselves are random.
I guess a different way to say this is -- It makes no sense to use the NS/S ratio as a rationale to claim that omicron was a lab-leak. The 33/4 ratio should be rare, but not unexpected. If you were going to claim that, the absolute increase in mutations would be a more compelling argument, but again, there are plausible reasons for how that could occur in the wild too.
We have very incomplete sampling data, so looking at a single strain and determining risk, or likelihood, is very difficult.
The sequence of mutations leading to Omicron is a one-off. Presumably, if there were a thousand variants with the same N mutations as Omicron, you'd see ratios like the ones you describe, but there's only one Omicron. The previous poster is pointing out it's plausible (~5% chance) that the path Omicron took has only 4 S mutations.
More simply, I don't think people tend to remain infected (and infectious) for a whole year (not saying they can't just that this seems a farcical assumption)
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)
The mouse theory is interesting .... because omicron is more benign - one of the problems we have with covid is that because of all this modern medicine saving lots of lives (not enough though sadly) there's not a lot of evolutionary pressure to make things more benign.
But if omicron has been in a wild mammal population without vaccination or hospitals then there might be more evolutionary pressure to become more benign.
It's worth noting that some vaccines in the past have been 'live' vaccines - essentially viruses that get passed around with a sniffle or two but no more harm. This actually what we all hope omicron would be .... I can't see why we shouldn't give the virus a bit of a help along .... the right lab leak might be just what we all need
The Nature article you mention says, "These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals."
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.
The other author of her book is Matt Ridley, the climate change skeptic.
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.
That assumes the origin is Africa, but it could have just risen to prevalence there. We know the original COVID-19 was spreading around the world when at the time we thought it was mostly China. It needs only a 12-hour plane ride to get to the other side of the planet.
Thank you for visiting HN, Alina! And I agree, natural evolution seems to make more sense. It's natural to wonder about lab-driven adaptation before COVID was unleashed on the human race... but once it had the entire human race to run its own "gain-of-function experiments", a lab hardly seems necessary anymore.
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.
"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.
You misread that - there is no claim that delta was initially released by a lab, rather a the known fact that a lab studying delta had an accident. Read the links the author provided.
The claim wasn’t that Delta originated from a lab leak but rather that Delta happened to leak from a lab (after the point that it existed in the wild). Additionally, the phylogenetic points from the article would suggest that Delta is of natural origin
"[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.]"
> We know that there is a large immunocompromised population in Africa and that Covid-19 is rampant there.
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.
Thanks for the book, alina. As a former molecular biologist (who worked on non-pathogenic enzyme gain-of-function projects) when the details of the virus came out I looked at it and immediately thought, "huh, that's exactly what I would have done", caveat I wasn't a virologist, of course, but I felt like I was being gaslit for being told that there was "no way" it could have been a lab leak. I know that I am not the only molecular biologist who felt this way. In no small part due to your work I think it's being taken more seriously, and maybe this is selfish in the context of the crazy situation going on worldwide but I feel 'less crazy'.
> I felt like I was being gaslit for being told that there was "no way" it could have been a lab leak
Can I say, as someone also looking at this somewhat dispassionately, how upsetting it is that the discourse on this issue has shifted from "It was a lab leak!" (to which strong replies absolutely were "There's no evidence"), to "It might have been a lab leak", now to "People were unfairly treated on the internet for saying it was a lab leak".
I mean, it's been two years now, and there's still no evidence beyond the kind of circumstantial stuff detailed by Chan and Ridley (I have the book but haven't read it yet, though I've seen most of Chan's public posts on the subject so I'm pretty sure I know the arc of what's in it).
And it seems like everyone has basically conceded that. But instead of just admitting we'll never know with certainty (and that natural evolution remains the most probable origin), everyone wants to talk about meta stuff instead?
It’s important to have a meta conversation because the media and social media were actively hindering discussion (censoring) that examined the lab leak hypothesis.
One can’t have an honest investigation if one major avenue is shut down.
But... we're literally discussing a book written on the subject. It wasn't censored. Neither were discussions here on this site, where lab leak arguments were very popular.
Are you really sure you aren't confusing controversy (the fact that an opinion can be a minority one with which most experts disagree) with suppression?
Just because suppression wasn't successful doesn't mean it wasn't attempted. And the attempt itself, by leading Western scientists who attempted to forestall any discussion and gaslight dissenters with accusations of anti-Chinese bigotry and scientific ignorance, is to me an even bigger story than covid's actual origins.
The government continued to investigate the lab leak hypothesis from the very beginning. The fact that some scientists tried to paint it as anti-Chinese bigotry (and some of the accusations clearly were) did not stop this. There's very little there there.
Social media actively censored such discussion and Google also manipulated autocomplete, etc. The WHO and CDC dismissed the theory at the time. The CCP actively scrubbed data which would affect the effectiveness of any subsequent investigation.
2. Facebook ham-fistedly censored conspiracy theory posts that the virus was man-made and later realized that they were also censoring actual lab leak discussion and fixed their policy.
3. Google turned off autocomplete because most of the autocompletions were crazy conspiracy theories. People could still search for whatever they wanted.
None of this stopped actual investigation of the lab leak hypothesis, which you claim could not have happened due to Facebook's actions.
I mean, the reality also is that there were in fact serious attempts to unleash bigotry instead of focusing on response. That is reality of what happened too. Huge reason why people painted it as anti-Chinese bigotry is that such a thing played a huge role in Trump response. Renaming Covid-19 to Chinese virus while downplaying need for tests and such was exactly that.
There was no suppression, quite tyje opposite: the lab leak hypothesis has been pusjed again and again, often with 'convenient' timing.
Now for scientists there is no point discussing this without any concrete element. Sure, a lab leak or even an artificial origin of the virus are potential hypotheses but then people need to find evidence, and the more far-fetched the hypothesis the stronger the evidence needed before keeping mentioning it (or writing books...)
Currently I don't think there are any material element so the reasonable and scientific thing to do is to work on finding the origin of the virus and only then to discuss facts.
Lancet CORRESPONDENCE| VOLUME 398, ISSUE 10309, P1402-1404, OCTOBER 16, 2021
The authors associated any alternative view with conspiracy theories by stating: “We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin”. The statement has imparted a silencing effect on the wider scientific debate, including among science journalists.
Edit: to add context: the authors of that letter didn’t disclose their conflicts of interest and mischaracterized the cited genomic research which hadn’t and still hasn’t found a wild match.
Daszak’s story began falling apart last November when the non-profit group US Right to Know published emails gathered through a freedom of information request that showed he had orchestrated the Lancet statement without disclosing that he was funding Shi Zhengli through grants from the National Institutes of Health (NIH). Daszak’s credibility took a further hit this June when Sachs published an essay that called for an independent investigation of the pandemic’s origin and charged that both China and the NIH should be transparent about virus research, including “gain-of-function” studies that make viruses more transmissible and virulent.
"not a natural origin" is not simply a lab leak, it's claiming that the virus is artificial and engineered.
I don't believe that there are any elements to support this claim at the present time. To keep bringing this claim up to 'discuss' it is therefore not scientific and might be considered FUD or conspiracy theory indeed.
Open research and science does not mean giving all claims equally. As said, the more extraordinary the claim the more solid the evidence. A claim backed by nothing has no place in publications. This is not "suppression". In fact, what you've quoted shows the opposite: the claim is pushed by dubious means.
It’s like saying, after Snowden released his trove of documents, what government secret data collection? look, here’s what Snowden showed us, it’s not secret!
We need open discussion at all times not only after we “get permission”.
When we had the ricin incident in the 2000s people openly discussed the possibility of a lab insider being the source any it wasn’t censored by the media.
When the establishment media and big tech puts forth extreme concerted effort in using whatever underhanded techniques it can to attempt to slander and undermine you and your ideas, calling you every name in the book, associating you with "undesirable" groups of people, putting "debunked" labels next to the things you say, de-platforms, cancels, the whole nine yards... and its followers lap up that behavior, and engage in it themselves on discussion websites and social media, and even in real life, but you can still technically talk about it on the far corners of the web or if you're in a group of people you're sure think like you think, sorry but that is absolutely 100% still a form of censorship.
The lab leak theory was never treated by the establishment as "a minority opinion with which most experts disagree", it was ridiculed and attacked, thereby effectively changing much of the public psyche against it. The damage was done. The government doesn't have to force a website to delete a post mentioning the lab leak theory in order for something to be considered censorship. Otherwise you're playing the semantics game - and losing at it.
> It’s important to have a meta conversation because the media and social media were actively hindering discussion (censoring) that examined the lab leak hypothesis.
> One can’t have an honest investigation if one major avenue is shut down.
The problem is that to my understanding the lab-leak discussion was (and still somewhat is) dominated by raving mad conspiracy lunatics[1] or instances trying to inflict racism. I fully admit that someone should seriously research that hypothesis (I fully assume there are some serious folks doing just that), but it is also difficult to blame media trying to keep the raving mad in check, even if some sensible arguments are thrown with the bathwater. (Besides, I am not sure if public discussion has anything substantial to add before there is some conclusion on the matter)
[1] As this is somewhat heated discussion, I think I need to emphasize that I definitely do not imply that all who doubt lab-leak are raving mad. If you think I do, please breathe and read again.
The really odd part of the meta conversation is that the “pro lab leak” folks are complaining they were stripped of nuance, but claim they were told it’s impossible or it’s crazy to think it could’ve been a lab leak. That might have been their subjective experience of people apparently not taking them seriously, but I have never actually seen this position held by an authority. What are we supposed to do, send military-escorted scientists into Wuhan to swab every inch? And what if that came up inconclusive, as it certainly would?
The “anti lab leak” position has always been 1) we don’t know, 2) it’s not the most important question right now, and 3) we probably will never know.
The people complaining about lack of nuance are proving their own inability/unwillingness to grapple with nuance.
That is absolutely not true. Don't you dare try to rewrite history. The anti-lab-leak position has included claims like "it's racist to say that china lab leaked the virus". At best, the "official" anti lab leak position has been framed by the lancet article. Go read that and tell us if that position is as neutral as you claim.
Yeah this is another view I see commonly expressed and have found no evidence ever coming from an authority. The Lancet letter (effectively an op-ed), for example, mentions race exactly zero times. It does somewhat recklessly affiliate these theories with conspiracy theories, but it’s worth remembering that they were responding to actual conspiracy theories like the virus being a bioweapon purposely released. This is an actual theory of conspiracy for which there continues to be no evidence. Scientists were getting death threats on this basis.
And again, the Lancet letter itself points to the then-current body of evidence, which people can contribute to or refute via their own publications (this is how science works).
They weren't responding to any body of evidence. There was zero at that time, on either side. They were trying to get out in front and head off what they thought was something reasonable people would include in their consideration of origins.
They had no evidence either way but knew that they had a lot to lose, and fired everything they had.
The letter didn’t blame racism, the letter cited several genomic analyses that actually had already been conducted by that point, and to my knowledge that letter didn’t disrupt any research into the virus’s origins. Open to seeing evidence otherwise though.
You're twisting my words and deflecting from my point. To clarify: The letter did not call it racism, other people did. This is verifiable in many places.
And we’re to take some commentators (Twitter users? TV personalities maybe?) calling it racist as evidence of what would certainly be the largest scientific suppression campaign ever conducted?
The Lancet article was opinionated. It may have been wrong. I still don't see how that constitutes suppression or cancellation or censorship (and certainly not an accusation of racism). There were people within the scientific community who disagreed (Chan is one). There just weren't many of them.
Holding an opinion contrary to an expert consensus isn't a state of persecution.
The Lancet letter came about to imply there was an expert consensus, when there was not yet one. It was driven by the exact people who would know best that a lab origin was plausible, saying loudly that it was not.
That's not suppression, though. It's just disagreement. I understand that you personally believe that the Lancet authors were acting in bad faith. But you surely agree they had the right to author that letter, right? You just... disagree.
That's the way things are supposed to work. Maybe science is wrong sometimes, and people argue. And eventually we come to consensus.
I have to say: it sounds like you're the one on the pro-suppression side here (arguing that the Lancet shouldn't have published that letter). Am I wrong?
I don't blame the Lancet for publishing it. They had no way of knowing it was not what it seemed. They should have maybe looked for the conflicts of interest a bit harder, and it is to their credit that they encouraged Daszak to write a correction later.
Everyone should be heard. Unfortunately the intent of that original letter was to pre-bias against opposing viewpoints, before they got to be heard.
> the intent of that original letter was to pre-bias against opposing viewpoints
Isn't that the same thing as saying the intent was "persuade" the reader? How is it different except in the sense that they managed to persuade people to believe something with which you disagreed?
You're right. It's highly suspicious, but it's just that and the problem is that the lab leak theory has many ramifications that are net negative for everyone: was it intentional, was it preventable, was it modified to test bioweapons, was it financed by France (yes, in France, we're not so hot about discussing our own little responsibility in building that lab).
I think if it was a clear-cut case of manipulation screwup, and that some people in China know today for sure that it was, we'll know eventually when we care less. If nobody, even close to the lab in China, knows for sure, then we probably won't investigate more just in case we'd discover with horror we killed all these people.
Btw I don't think the French should feel so bad, by my understanding they did the right thing, or as best as they could: once they reviewed the construction of the building they refused to sign off on the bsl certification and no french researchers were sent to the institute (or maybe it was just one). I suppose they could have raised a bit more of a stink about it, but it was a different era, one when diplomacy with china was still a net win-win for everyone.
I'm looking forward to reading your book. As a former microbiologist / biochemist with a fair amount of knowledge about what is possible in terms of gain-of-function research, and with a fair amount of experience reading technical research papers and a long-standing interest in both environmental and infectious microbiology and virology, the discussion of origins of the virus in the literature really seemed shady during the first six months of the pandemic.
In particular, the early flood of 'data' about potential links to pangolins and a supposed bat-pangolin cross-breeding event, which was discredited pretty quickly, indicated that someone was trying to muddy the waters. Past natural outbreaks involving these kinds of cross-species jumps (MERS and camels for example) had a a long-term natural history, they didn't just appear wholly formed out of the blue, and the natural reservoirs were quickly identified[1, 2]
The failure to identify any such natural source of the virus within six months despite intensive searches really put the Wuhan lab leak theory back on the front burner, and the fact that the Lancet and Nature op-eds proclaiming a 'natural source' were organized by those linked to providing U.S. funding to the Wuhan lab was another huge red flag. When it became clear that the funds sent to Wuhan were intended to continue a branch of research (gain-of-function with respiratory viral pathogens) that the U.S. government had severely restricted in 2014[3], well...
Clearly both some elements of the US government's academic funding wing and of the Chinese government have a deeply vested interest in not allowing an open and independent inquiry into the actual source of the pandemic. This only encourages future similar outbreaks - as it really seems that there may be literally hundreds of wild-type animal viruses that can be turned into human pathogens by selective modification of their cell-surface-protein binding capabilities via techniques such as CRISPR etc. International bans on this kind of research (including an inspection regime as with nuclear non-proliferation treaties) really make sense.
"The failure to identify any such natural source of the virus within six months despite intensive searches really put the Wuhan lab leak theory back on the front burner"
We have had to look for the reservoir animal for Ebola for decades before having a viable candidate. On that scale six months is a very short time.
The failure to identify a natural reservoir does throw a lot of doubt onto the 'wet market-origin' theory, since some close variants should have existed in some of the animals there and none were found. If on the other hand the virus was one collected from a remote location and transported to the lab for further study and possible modification, as part of a well-intentioned research effort, and then accidentally escaped (by infection of lab techs, visitors, etc. most likely), that would be an understandable situation.
It doesn't, really. All it takes is a single individual animal to carry a virus. The assumption that all of the individuals of a species harbor the virus is faulty, it could well be a small fraction of a rare animal, in fact the difficulty of locating the reservoir is strong evidence for that.
Sticking to Ebola for the moment: even though there were major suspicions that a species of bat was responsible for Ebola it took a very long time to identify which species and how Ebola managed to transit the continent and to pop up in different places.
Reservoir animals can be very hard to determine with certainty. Note also that the reservoir animal itself need not have been present in the wet market for this to have worked, it is enough that a pig or some other suitable amplifier host got infected which then passed it to humans. In that case too, you'd see a small number of animals, possibly even a single individual, carry live virus. And given the nature of the wet markets you can be pretty sure that any such evidence was erased before COVID even had a name.
Until there is hard evidence for a lab leak I will chalk it up to a possibility, but a remote one. And if and when the reservoir animal is found I'm sure that too will be discounted by the proponents of the lab leak theory, who seem to have their bullet-proof fix already in the works: in that case the claim is that the virus was first sampled from an individual of the reservoir animal species and moved to the lab from where it leaked.
So we likely will never see the end of that, but that doesn't mean that any of it is true. Which is a problem with many conspiracy theories, they tend to be inherently un-falsifiable which allows them to stick around forever. The way in which one of the authors of the book effortlessly integrated new knowledge that invalidated the premise of the book into an altered version of the same - instead of admitting they got it wrong - is a very nice example of that.
They did detect virus on the ground in the market. It seems there were wild animals in the market illegally that were all removed before the scientists got there. There was also a lot of wild animal farming in the Wuhan area which would be quite a likely candidate and which wasn't tested at all probably for political reasons. It had been encouraged by Xi and so would have been embarrassing if they found that to be the cause.
"Okay, so about the current news. Is there any reason to believe that they might be onto something, or is it all smoke and mirrors? Eddie Holmes - any insights on the China side? The main things from my perspective:
1. Bioweapon and engineered totally off the table
2. If there is no engineering and no culturing, then it means that somebody magically found a pre-formed pandemic virus, put it in the lab, and then infected themselves. The prior on that vs somebody coming into contact with an animal source infected with the virus is as close to zero as you can get. Humans come into contact all the time with SARS-like CoVs, but the likelihood of somebody finding exactly that pandemic virus and infecting themselves is very very low (make no mistake - if they did find that pandemic virus. then they would get infected if they grew it in the lab - but the likelihood of them finding it in the first place is exceedingly small (or so one would hope - otherwise, good luck World avoiding future pandemic).
3. But here's the issue - I'm still not fully convinced that no culture was involved. If culture was involved, then the prior completely changes - because this could have happened with any random SARS-llke CoV of which there are very many. So are we absolutely certain that no culture could have been involved? What concerns me here are some of the comments by Shi in the SciAm article ("I had to check the lab" etc) and the fact that the furin site 1s being messed with in vitro. Yes, it loses it but that could be context dependent. Finally, the paper that was shared with us showing a very similar phenomenon (exactly 12bp insertion) in other CoVs has me concerned...
I really really want to go out there guns swinging saying "don't be such an idiot believing these dumb theories - the president is deflecting from the real problems" but I'm warned that we can't fully disprove culture {our argument was mostly based on the presence of the O-linked glycans - but they could likely play a different role... We also can't fully rule out engineering (for basic research) - yes, no obvious signs of engineering anywhere, but that furin site could still have been inserted via gibson assembly (and clearly creating the reverse genetic system isn't hard - the Germans managed to do exactly that for SARS-CoV-2 in less than a month)."
And:
"Shi didn't do any GOF work that I'm aware of - but GOF work isn't the concern here. She did A LOT of work that involved isolating and culturing SARS-like viruses from bats (in BSL-2) and that's my main concerning scenario (we cite several of those in the paper - if you have a look at those original publications, it's definitely concerning work, no question about it - and is the main reason I have been so concerned about the 'culture' scenario)."
I don't think much more needs to be said. The above messages are self-explanatory.