'Escaped From Lab' ≠ 'Genetically Engineered'

Tuesday, May 25, 2021

The idea that the coronavirus behind the pandemic may have escaped from a Chinese lab has resurfaced and is being discussed seriously.

Past news coverage of this possibility vs. current news coverage eerily reminds me of a couple of conversations I had some months ago, and it is worth observing the difficulties I had in light of the fact that the earlier coverage seemed utterly dismissive of the possibility while later coverage doesn't.

But before I go on, again observe my title: Labs study viruses that haven't been genetically engineered all the time, and I agree that this virus was almost certainly not genetically engineered. And as the article at this last link said (when it was written), one would need a smoking gun to link a lab with a virus outbreak. The Wall Street Journal may well have one: "Three researchers from China's Wuhan Institute of Virology became sick enough in November 2019 that they sought hospital care..."

This time last year, with the media establishment falling all over itself to break with history and not even use Chinese as a descriptor of this disease -- and Trump and some of his base ridiculously looking for the most nefarious explanation possible, it seems that escaped from a lab and was deliberately engineered became confounded.

Two examples: (1) My physician wife and I both both hold PhDs in biosciences. When I noticed this confusion and attempted to bring it to her attention, she initially thought I had fallen for the deliberately engineered notion, because so much coverage of the idea had equated it to escaped from a lab. I made it clear to her that that was not what I meant, and that the escape could have occurred from basic research, however unlikely. She conceded my point.

(2) Conversely, I had a conversation that went in circles for a long time with a sister-in-law, who is conservative, but became oddly defensive when I said that I thought that the idea that the virus was genetically engineered was a conspiracy theory. It took a while to realize that I needed to make clear the same distinction I had earlier, and that I was not calling her a conspiracy theorist just because she thought it plausible that the virus could have escaped from a lab.

Here's a relevant quote from the linked FiveThirtyEight article from about a year ago:

Image by CDC/ Alissa Eckert, MS; Dan Higgins, MAM, via Wikipedia, public domain.
According to a growing body of research, SARS-CoV-2 (the virus that causes COVID-19) is almost certainly a naturally occurring virus that initially circulated in bats then spilled into humans. But that hasn't stopped some from trying to find a more sinister origin. "It seems like such an extreme event that people are looking for an extraordinary explanation for it," said Stephen Goldstein, a postdoctoral researcher at the University of Utah who studies coronaviruses. No single piece of evidence has yet confirmed the virus' origin. But according to scientists, the evidence that does exist paints a consistent picture of a wild virus, not one that sprang from a lab. [bold added]
Notice how close we are to a false dichotomy. A natural virus one is studying can escape from a lab. Is "sprang from a lab" the same as escaped from a lab -- or does it mean created in a lab? Someone could not unreasonably read this either way.

Fast forward to a more recent piece on the subject that I highly recommend, by pharma-blogger Derek Lowe:
... I have to note that the actions of the Chinese government have not been characterized by the openness called for above. And as long as that is the case, suspicion will be hard to dispel. Their documented actions against Chinese physicians and scientists who spread early word of the pandemic do not inspire confidence, either. But at the same time, some politicians have also (for their own benefit) jumped at the chance to make accusations against the Chinese. This stuff has done nothing but sow fear, hatred, and confusion -- what was partly the plan on the part of the people promulgating it, of course. That's been in all directions, too, because there are many people who probably have refused to take the lab-leak idea seriously just because some demagogues and fools love it, too. This world would be a lot easier to understand if assholes were always wrong about everything, but that's not the case. To be completely even-handed about it, there are (for example) plenty of people in both the Trump administration and in the Chinese government that I put in that category. They can't both be right, though, can they? [bold added]
This is easy for me to see: I have noticed over the years, as someone who is neither a leftist nor a conservative, that people in either camp regularly confuse me with someone from the other camp.

I am open to the idea that the virus escaped from a Chinese lab. That possibility can have nothing to do with genetic engineering or malice by the Chinese. I am also comfortable saying, We don't know where it came from yet, and should investigate that question as thoroughly as possible. I agree with Lowe on that, whatever the answer and wherever the evidence leads. This doesn't make me a conspiracy theorist or a xenophobe, nor does it make me a fan of the Communist regime in China or of our own country's imitators in the media-government establishment, to borrow a few unflattering stereotypes that don't apply to me or to that great a proportion of other people, for that matter.

-- CAV

4 comments:

Anonymous said...

Hi Gus,

I thought the author of this article on the origins of the pandemic produced a tour de force of
epistemological consideration. I lack your credentials in the bio-sciences but it seemed,
to the best of my knowledge, to be well argued and worth one's time to read.

https://nicholaswade.medium.com/origin-of-covid-following-the-clues-6f03564c038

c andrew

Gus Van Horn said...

C.,

I recall the name and indeed Lowe mentions him. I either read part of or skimmed his article. Quoth the medicinal chemist:

"From here we get into a lot of details about the codons in the viral sequence, the presence of a furin cleavage site, similarities (and differences) between the current coronaviruse and the closest wild-type relatives. This Medium post by Nicholas Wade goes into many of these, but you should know up front that many virologists believe that he overstates the case (such as in the rarity of that furin cleavage site)."

I'm not a virologist, but I remember thinking that a lot of his argument hinged on the cleavage site, and that that, I believe, those do occur naturally.

Gus

SteveD said...

In vivo continuous evolution of genes and pathways in yeast | Nature Communications

A system for the continuous directed evolution of biomolecules | Nature

Origin of Covid — Following the Clues | by Nicholas Wade | May, 2021 | Medium

‘But blaming it on genetic engineering overstates the abilities of scientists, Garry said.’
Maybe in 2010 this overstated our abilities, but this is 2021. We no longer have to ‘genetically engineer’ a virus. We can evolve it in vivo instead. The links are to papers which describe systems for the continuous directed evolution of proteins. What is remarkable is that with these techniques (ICE and PACE are used in my lab group but for a different purpose) we do not even have to know what part of the viral protein binds to the receptor. We can learn that by looking at the end product; determine what part of the protein has changed. It is now a simple matter to take a protein which does not bind or binds very weakly to a receptor and using a continuous evolution system evolve it to make it bind tightly to that receptor or a different receptor (e.g., viral coat protein or toxin to a receptor).

There is no reason a lab working on viruses would necessarily use a known viral background. They could evolve an entire novel virus or just the viral coat protein and replace the original with the improved version by homologous recombination. Since the artificial evolutionary process mimics natural evolution, there would be no evidence in its sequence unless you had a complete record of all the closely related viruses in nature. This is called gain-of-function research and there is evidence the lab is Wuhan was working on this. (that was the basis of the argument between Fauci and Rand Paul in a recent Senate hearing).
Scientists are now taking the directed evolution hypothesis more seriously because they cannot find the predecessors (evolutionary links) of Covid19 like they found for MERS and SARS. It seemed to come out of nowhere with a high affinity for the ACE receptor, far more infectious than it should have been.

An artificial origin is at this point probably a stronger hypothesis for Covid19 than natural origin although neither hypothesis should be ruled out. The recent article by Wade lays out the evidence.

Finally, this sort of research is not necessarily nefarious. Gain-of-function research can tell us how a virus infects cells and what we learn can be used to find drugs or other treatments. However, it is dangerous for obvious reasons and requires extreme caution.



Gus Van Horn said...

Steve,

"We can evolve it in vivo instead."

Thanks for mentioning this (of which possibility I was aware), and elaborating on it/pointing to more information (which I did not feel comfortable doing). I recall (correctly or not) something like a virulent flu controversially being created with gain-of-function techniques amounting to hastened and directed natural evolution. This would NOT look like it was engineered.

That said, it is also helpful to know that -- as untrustworthy as the Chinese government has been -- the technique could have developed a virus like this even without the intent of developing it as a weapon, or even for a nefarious purpose.

This could explains both why -- if the virus is indeed not naturally-occurring -- there are no signs of the virus being engineered, and part of why it is important to learn, if possible, of a laboratory leak of the virus, if one occurred.

Gus