The origin of COVID: Did people or nature open Pandora’s box at Wuhan?

[Opti]

Word on the street is that it was a pangolin called Dennis.

[Herainestold]

It went from bats to an intermediate animal host and then to humans in the wet market.

It seems that we still haven't figured out what animal served as the intermediate host.

Unless I missed that somewhere which is quite possible.

[Bird on a Fire]

It went from bats to an intermediate animal host and then to humans in the wet market.

It seems that we still haven't figured out what animal served as the intermediate host.

Unless I missed that somewhere which is quite possible.

Raccoon dogs seem a strong contender. They're a known SARS-CoV reservoir, and the earliest cases were apparently in an area of the market selling them. https://www.scmp.com/news/china/science ... e-pointing

Unlikely we'll ever know for sure, as China is keeping the environmental samples hushed up.

It's a bit concerning, as raccoon dogs are farmed (for fur), meaning this isn't simply a case of people eating funky exotic wildlife: it's the interaction of funky exotic wildlife with poor animal husbandry, which is much commoner (and growing) on a global scale.

[Herainestold]

The next step would be to trace the provenance of the racoon dogs and try to find the location where they were infected by bats.

[Bird on a Fire]

I'd be surprised if China hasn't already done so.

[shpalman]

The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic

https://doi.org/10.1126/science.abp8715

[Woodchopper]

tl;dr looks like strong evidence for Covid-19 having been created in a lab.

Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2

Abstract

To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident. The genome of SARS-COV-2 contains a peculiar pattern of unique restriction endonuclease recognition sites allowing efficient dis- and re-assembly of the viral genome characteristic of synthetic viruses. Here, we report the likelihood of observing such a pattern in coronaviruses with no history of bioengineering. We find that SARS-CoV-2 is an anomaly, more likely a product of synthetic genome assembly than natural evolution. The restriction map of SARS-CoV-2 is consistent with many previously reported synthetic coronavirus genomes, meets all the criteria required for an efficient reverse genetic system, differs from closest relatives by a significantly higher rate of synonymous mutations in these synthetic-looking recognitions sites, and has a synthetic fingerprint unlikely to have evolved from its close relatives. We report a high likelihood that SARS-CoV-2 may have originated as an infectious clone assembled in vitro.

https://www.biorxiv.org/content/10.1101 ... 8.512756v1

Some commentary: https://twitter.com/ballouxfrancois/sta ... XvySBntEFA

[Woodchopper]

tl;dr looks like strong evidence for Covid-19 having been created in a lab.

Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2

Abstract

To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident. The genome of SARS-COV-2 contains a peculiar pattern of unique restriction endonuclease recognition sites allowing efficient dis- and re-assembly of the viral genome characteristic of synthetic viruses. Here, we report the likelihood of observing such a pattern in coronaviruses with no history of bioengineering. We find that SARS-CoV-2 is an anomaly, more likely a product of synthetic genome assembly than natural evolution. The restriction map of SARS-CoV-2 is consistent with many previously reported synthetic coronavirus genomes, meets all the criteria required for an efficient reverse genetic system, differs from closest relatives by a significantly higher rate of synonymous mutations in these synthetic-looking recognitions sites, and has a synthetic fingerprint unlikely to have evolved from its close relatives. We report a high likelihood that SARS-CoV-2 may have originated as an infectious clone assembled in vitro.

https://www.biorxiv.org/content/10.1101 ... 8.512756v1

Some commentary: https://twitter.com/ballouxfrancois/sta ... XvySBntEFA

Popular science summary: https://alexwasburne.substack.com/p/a-s ... sars-cov-2

Thread by the author: https://twitter.com/washburnealex/statu ... XvySBntEFA

[Bird on a Fire]

It's a compelling thread.

I'm having a go at the preprint. It's a very methodological argument, so commentary from anybody who doesn't regularly assemble viral genomes, preferably with experience of Golden Gate Cloning, is worthless.

But the nuts-and-bolts is comparing the (first reported) Wuhan genome with two datasets: one of wild-type coronaviruses, and another set of viruses known to have been constructed using Golden Gate Cloning.

If I were trying to reject the hypothesis that the Wuhan coronavirus resembled a wild-type coronavirus, I would want to make very sure I had a representative sample of wild viruses, especially as the wildlife trade is implicated here. I would have a figure showing where my samples came from (1) around the world, making sure I had decent coverage of Africa and SE Asia as well as China, and (2) in terms of host phylogeny: I want to see a lot of pangolins and mustelids in there.

They just say that they've got 72 of them. The actual list, like the list of constructed viruses they used, isn't in the MS nor the supplementary materials. It is on the authors' github. Is that normal in virology?

"Literature reviews from our search were read and examples of coronavirus infectious cDNA or BAC clones mentioned were included." Maybe cite the reviews?

The main "gotcha" plot - and you should always have one - is Figure 2, where they compare properties of the Wuhan virus with the wild distribution. They generate "the wild type distribution of the longest-fragment length is estimated by digesting a wide range
of non-engineered CoV genomes with a large set of endonucleases." Obviously that distribution is very sensitive to input data, which they're coy about. In the methods it turns out they generated it by "digesting a broad range of natural coronavirus genomes in silico with a comprehensive set of restriction enzymes" but they don't cite the software or the enzymes. Does that matter?

Plus they've drawn a red box, which on Twitter they said is the ideal zone for constructed viruses, but don't explain in the legend what it is at all. It's just there, waggling its eyebrows. And they don't put the Wuhan virus on it till Figure 3, but much smaller in an inset? It's like a twitter thread rolled into a preprint. Is repeating figures normal in virology?

I'm honestly not sure if these are problems with the underlying argument, or I'm just in thesis-editing mode. But the MS seems to spin a lot out of doing stuff with big data, without explaining much about what the data is, what they're doing or why they're doing it. Remember when ENCODE launched?

Or maybe these are authors outside academia (hard to tell from the affiliations if any of them are virologists), and I'm unfairly judging the writing style when it's all solid. Not a Scobey.

Looking forward to hearing from somebody who really knows what they're talking about.

[Chris Preston]

Looking forward to hearing from somebody who really knows what they're talking about.

Most of your questions are well thought out. Most of the things you point out are not normal in papers. This paper struck me as more a fishing exercise looking for a signal that could be associated with a lab construct and then declaring anything they found as proof. However, my knowledge of the methods used is slim.

As for the authors, cancer researchers and a mathematical modeller who claims they are "fixing science".

Bruttel has previously claimed that the Omicron variant was created deliberately. The argument in that case was an argument from incredulity. He claims it could not have occurred in an immunocompromised individual, because they don’t make antibodies. This argument is complete nonsense. People who have high viral titres will have higher numbers of variants. Variants that can evade immunity are most likely to first occur in such people, but selected when transferred to other people.

Washburne has an association with the Brownstone Institute - of Great Barrington Declaration fame - where he has written criticising masking and COVID-19 vaccines.

I am not being filled with confidence here.

[Millennie Al]

Bacteria can acquire DNA from other bacteria. Can viruses do it also? If so, maybe engineered DNA sequences in one (natural) virus might have been picked up from another (engineered escape) in nature.

[Chris Preston]

Bacteria can acquire DNA from other bacteria. Can viruses do it also? If so, maybe engineered DNA sequences in one (natural) virus might have been picked up from another (engineered escape) in nature.

A lot of transfer of genes between bacteria is through plasmids - small circular pieces of DNA. Virus do not do this.

Virus can swap genes, but it requires the same cell to be infected with multiple viruses.

[Bird on a Fire]

Also AIUI they're analysis genome-wide patterns rather than individual genes, so transfer wouldn't account for the claimed patterns.

[Bird on a Fire]

A couple of threads I've come across taking issue with the methods and findings:

1) "the “unusual” sites are all *exactly* found in natural bat coronaviruses"
https://twitter.com/acritschristoph/sta ... 3416969216

2) Apparently, standard cloning methods (including those used in Golden Gate Assembly) result in the the restriction enzyme sites being removed. Which would seem to blow their whole method (spotting restriction enzyme sites) out of the water.
https://twitter.com/Friedemann1/status/ ... 0902048768

"Therefore, if proposed mechanism of synthetic SARS-CoV-2 generation is by engineering BsmBI/BsaI cut sites for ligation assembly then the synthetic, full-length product should no longer have *any* of these RS present."
https://twitter.com/santiagokique/statu ... 4745655296

3) Issues with the proposed null distribution: "Also...the only distribution of fragment lengths where the longest would be an "outlier" in their "null distribution" would be the scenario where both enzymes are used to generate 6 total fragments...but most assembly methods to my knowledge rely on a single cutter per reaction"
https://twitter.com/santiagokique/statu ... 7192485888

A similar study that's already been peer reviewed (which used a single cutter) found that "SARS-CoV-2 does not contain peculiar RS or other markers": https://www.nature.com/articles/s41598- ... 64-6#Sec16

4) "so deeply flawed that it wouldn’t pass kindergarten molecular biology" - loss of BsaI and BsmBI happens very frequently, often with synonymous SNPs
https://twitter.com/K_G_Andersen/status ... 8740219906

5) The exact same devious “silent mutations” exist in RpYN06. (This thread was a discussion with the authors before the preprint was posted)
https://twitter.com/zhihuachen/status/1 ... 9527977986

Francis Balloux has deleted his account, btw.

Looks increasingly like a fishing expedition from cranks.

[Grumble]

I like the idea of kindergarten molecular biology

[Grumble]

We all know biology is basically just colouring in anyway

[Woodchopper]

Thanks Bird and Chris for all your feedback. The methods etc are way beyond my capabilities so I'll remain an interested spectator.

Here's an Economist article which summarizes some of the points made in the discussion on the preprint. I'll copy and paste it as its available via archive.org anyway.

A new paper claims SARS-CoV-2 bears signs of genetic engineering
But it has yet to be peer reviewed. And others strongly disagree

Astring of about 30,000 genetic letters were all that it took to start the nightmare of covid-19, the death toll from which is likely to be more than 20m. Exactly how this story began has been hotly contested. Many think that covid-19’s emergence was a zoonosis—a spillover, as so many new pathogens are, from wild animals, for it resembles a group of coronaviruses found in bats. Others have pointed to the enthusiastic coronavirus engineering going on in laboratories around the world, but particularly in Wuhan—the Chinese city where the virus was first identified. In February 2021 a team of scientists assembled by the World Health Organisation (who) to visit Wuhan said a laboratory leak was extremely unlikely. However, this conclusion was subsequently challenged by the who’s boss, who said ruling out this theory was premature.

Two recent publications appear to have bolstered the case for a natural origin connected to a “wet market” in Wuhan. These markets sell live animals, often housed in poor conditions, and are known to be sites where new pathogens jump from animal to human. Early cases of covid-19 clustered around this market. But critics counter that there are so many missing data about the epidemic’s initial days that this portrait may be inaccurate.

The opposing idea of a leak from a laboratory is not implausible. The accidental escape of viruses from labs is more common than many people realise. The flu epidemic of 1977 is thought to have started this way. But an escaped virus does not imply an engineered virus. Virology labs are also full of the unengineered sort.

Research such as that done in Wuhan offers a number of ways for a virus to leak out. A researcher on a field trip could have picked it up in the wild and then returned to Wuhan, and so spread it to others there. Or someone might have been infected with a wild-collected virus in the laboratory itself. But some argue that sars-cov-2 could have been assembled in a laboratory from other viruses that were already to hand, and then leaked out.

Into this fray comes an analysis from an unlikely source. Alex Washburne is a mathematical biologist who runs Selva, a small startup in microbiome science based in New York. He is an outsider, although he has worked in the past on virological modelling as a researcher at Montana State University. For this study, Dr Washburne collaborated with two other scientists. One is Antonius VanDongen, an associate professor of pharmacology at Duke University, in North Carolina. The other, Valentin Bruttel, is a molecular immunologist at the University of Würzburg, Germany. Dr Washburne and Dr VanDongen have been active proponents of an investigation into the lab-leak theory.

The trio base their claim on a novel method of detecting plausibly lab-engineered viruses. Their analysis, published on October 20th on bioRxiv, a preprint server, suggests sars-cov-2 has some genomic features that they say would appear if the virus had been stitched together by some form of genetic engineering. By examining how many of these putative stitching sites sars-cov-2 has, and how relatively short these pieces are, they attempt to assess how much the virus resembles others found in nature.

They start from the presumption that creating a genome as long as that of sars-cov-2 would mean combining shorter fragments of existing viruses together. For a coronavirus genome assembly they say an ideal arrangement would be to use between five and eight fragments, all under 8,000 letters long. Such fragments are created using restriction enzymes. These are molecular scissors which cut genomic material at particular sequences of genetic letters. If a genome does not have such restriction sites in opportune places, researchers typically create new ones of their own.

They argue that the distribution of restriction sites for two popular restriction enzymes—BsaI and BsmBI—are “anomalous” in the sars-cov-2 genome. And the length of the longest fragment is far shorter than would be expected. They determined this by taking 70 disparate coronavirus genomes (not including sars-cov-2) and cutting them into pieces with 214 commonly used restriction enzymes. From the resulting collection, they were able to work out the expected lengths of fragments when coronaviruses are cut into varying numbers of pieces.

The paper, which as a preprint has received no formal peer review, and which has not been accepted for publication in a journal, will be picked apart in the coming days—as well it should be, for this is the way that science works. Early reactions, though, have been deeply divided. Francois Balloux, a professor of computational systems biology at University College London, said he found the results intriguing. “Contrary to many of my colleagues, I couldn’t identify any fatal flaw in the reasoning and methodology. The distribution of BsaI/BsmBI restriction sites in sars-cov-2 is atypical”. Dr Balloux said these needed to be assessed in good faith. But Edward Holmes, an evolutionary biologist and virologist at the University of Sydney, said that every one of the features identified by the paper was natural and already found in other bat viruses. If someone were engineering a virus they would undoubtedly introduce some new ones. He added, “there are a whole range of technical reasons why this is complete nonsense.”

Sylvestre Marillonnet, an expert in synthetic biology at the Leibniz Institute for Plant Biochemistry, in Germany, agreed that the number and distribution of these restriction sites did not look quite random, and that the number of silent mutations found in these sites did suggest that sars-cov-2 might have been engineered. (Silent mutations are a result of engineers wanting to make changes in a sequence of genetic material without making changes to the proteins encoded by that sequence.) But Dr Marillonnet also said that there are arguments against this hypothesis. One of them is the tiny length of one of the six fragments, something that “does not seem logical to me”.

The other point Dr Marillonnet makes is that it is not necessary for the restriction sites to have been present in the final sequence. “Why would people introduce and leave sites in the genome when it is not needed?” he wondered. Previous arguments in support of the possibility of a lab leak have stressed that a manipulated virus would not need to have any such tell-tales. However, Justin Kinney, a professor at Cold Spring Harbor Laboratory, in New York, said that researchers have created coronaviruses before and left such sites in the genome. He said the genetic signature indicates a virus ready for further experiments and said it needed to be taken seriously, but warned the paper needed rigorous peer review.

Erik van Nimwegen, from the University of Basel, says there are only small scraps of information and it is “hard to pull anything definitive out of that”. He adds, “one cannot really exclude at all that such a constellation of sites may have occurred by chance”. The authors of the paper concede this is the case. Kristian Andersen, a professor of immunology and microbiology, at the Scripps Research Institute in La Jolla, California, described the pattern, on Twitter, as “random noise”.

Any conclusion that sars-cov-2 was engineered will be hotly contested. China denies the virus came from a Chinese lab, and has asked for investigations into whether it may have originated in America. Dr Washburne and his colleagues say their predictions are testable. If a progenitor genome to sars-cov-2 is found in the wild with restriction sites that are the same, or intermediate, it would raise the chances that this pattern evolved by chance.

Any widely supported conclusion that the virus was genetically engineered would have profound ramifications, both political and scientific. It would put in a new light the behaviour of the Chinese government in the early days of the outbreak, particularly its reluctance to share epidemiological data from those days. It would also raise questions about what was known, when, and by whom about the presumably accidental escape of an engineered virus. For now, this is a first draft of science, and needs to be treated as such. But the scrutineers are already at work.

https://web.archive.org/web/20221022130 ... ngineering

[Woodchopper]

I do though take issue with this though.

Francis Balloux has deleted his account, btw.

Looks increasingly like a fishing expedition from cranks.

As mentioned on another thread scientists have been withdrawing from social media because they've been the targets of personal abuse (Balloux may be another example). This is a problem for everyone who wants to follow the research. It would be good if we could discuss a scientific paper without making negative comments about the authors.

[Woodchopper]

Here's what I assume is one of the at the recent papers on a natural origin:

Summary
Evidence suggests pandemic came from nature, not a lab, panel says
New report takes sides in debate over COVID-19’s origins
https://www.science.org/content/article ... panel-says

Original paper
Pandemic origins and a One Health approach to preparedness and prevention: Solutions based on SARS-CoV-2 and other RNA viruses
https://www.pnas.org/doi/full/10.1073/pnas.2202871119[/quote]

[Bird on a Fire]

As mentioned on another thread scientists have been withdrawing from social media because they've been the targets of personal abuse (Balloux may be another example). This is a problem for everyone who wants to follow the research. It would be good if we could discuss a scientific paper without making negative comments about the authors.

That's fair. My apologies.

[Bird on a Fire]

Here is a curated collection of threads and tweets rebutting a preprint that made the rounds, illustrating the many ways in which the study is problematic.

https://twitter.com/flodebarre/status/1 ... 8015831040

[bob sterman]

Not sure why this falls to the Department of Energy but...

Covid-19 likely emerged from laboratory leak, US energy department says
https://www.theguardian.com/world/2023/ ... department

[bolo]

Not sure why this falls to the Department of Energy but...

Covid-19 likely emerged from laboratory leak, US energy department says
https://www.theguardian.com/world/2023/ ... department

DOE runs a network of 17 national labs that do R&D on a wide range of topics not limited to energy, including things like genomics and bioterrorism countermeasures. They also have lots of experience dealing with highly classified intelligence, e.g. related to nuclear weapons design and testing. And as well as working for DOE itself, the labs do work on behalf of other agencies like DOD and DHS. So it's not outside their lane to opine on this question, though I haven't looked at their analysis at all so I won't claim to know whether it's any good.

[bolo]

For some reason all the headline writers have omitted the part of the DOE analysis that says it has "low confidence" in its conclusion.

[bob sterman]

For some reason all the headline writers have omitted the part of the DOE analysis that says it has "low confidence" in its conclusion.

FBI has made its own assessment and has "moderate confidence" in lab-leak theory.,,

https://edition.cnn.com/2023/02/28/poli ... index.html