Thread by @Ayjchan

Since 🧵s on furin cleavage sites (FCSs) are now in fashion, I thought I should do one too.

The S1/S2 FCS insertion in SARS2 (the covid-19 virus) is super interesting because this unique feature is (1) not found in other SARS viruses, and (2) enhances the virus' infectiousness.

There is precedent of such an S1/S2 FCS appearing in other more distantly related coronaviruses. There is also precedent of such an S1/S2 FCS being inserted into SARS virus.

https://twitter.com/Ayjchan/status/1266805310313967617

Indeed, the first scientist who inserted an S1/S2 FCS into the 2003 SARS virus was interviewed post-covid and said “there is no way to know whether humans or nature inserted the site.” nature.com/articles/d4158…

That was also my opinion back in May 2020, and remains the same one year later today:

https://twitter.com/Ayjchan/status/1267101961159131137

The reason why people are starting to talk about the FCS again today, even though no actually new information or data has appeared, is because of this article by Nicholas Wade, who obtained a stunning quote from Nobel laureate David Baltimore: nicholaswade.medium.com/origin-of-covi…

Other less well known scientists and non-scientists had made this observation much earlier in 2020 but no one really paid much attention to them. The same idea was cited in Dr Limeng Yan's controversial September report.

https://twitter.com/Ayjchan/status/1390269637359767552?s=20

For example, I believe that this is the first time that the strangeness of the CGG CGG doublet was publicly written into an article by @ydeigin and @Rossana38510044 in April 2020.
researchgate.net/publication/34…

For people who are just hearing about the CGG CGG, please read Nicholas Wade's article. He explains it very clearly: "how did SARS2 acquire a pair of arginine codons that are favored by human cells but not by coronaviruses?" nicholaswade.medium.com/origin-of-covi…

I personally don't think the double CGG is such a big deal, but I'm a human being so hearing that a Nobel laureate thought it was a smoking gun for the origins of COVID-19 had an impact on me. It clearly had an impact on other scientists and virologists.

https://twitter.com/K_G_Andersen/status/1391432321195155458

Some people on twitter even couldn't believe their eyes and ears. They wondered whether Nicholas Wade had made up the quote or misquoted Baltimore.

https://twitter.com/Ayjchan/status/1390789788580593673

The essence of the argument that CGGx2 = lab origins is that the CGG codon is only used at ~3% frequency in SARS2. So 2 CGGs in a row has ~1 in 1000 chance of occurring.

But CGGs are used more frequently in labs, so the chances are higher than 1/1000.

But @K_G_Andersen countered this argument very soundly in my opinion. I also learnt new things from his thread:

https://twitter.com/K_G_Andersen/status/1391507230848032772

Highlights: (1) Viruses sampled to date are the tip of a very massive iceberg. In the case of SARS viruses, we essentially only have 2 data points for those that have made their way into humans: SARS1 and SARS2. And just a handful from intermediate hosts.

https://twitter.com/K_G_Andersen/status/1391507241556013058

(2) If you compare SARS2's codon usage to other related viruses, it isn't out of the ordinary. Even if you expect a double CGG to occur only 1/1000 times, nature does produce these sequences...

https://twitter.com/K_G_Andersen/status/1391507266050748418

And Kristian points out that a similar FCS in a feline coronavirus also using the PRRAR motif has its first two Rs encoded by CGG CGA, just one letter different from CGG CGG.

https://twitter.com/K_G_Andersen/status/1391507268978446337

(3) If these codons were somehow suboptimal, we would've seen the virus evolve single letter mutations that easily change the codon without necessarily changing the amino acid (R can be coded by six different codons: CGU, CGC, CGA, CGG, AGA, AGG).

https://twitter.com/K_G_Andersen/status/1391507275924180993

I'm not saying that one argument or the other is the correct one. I think it makes sense that a double CGG is a bit suspicious, but is it enough to confidently say that SARS2 came from a lab because of the low probability of a double CGG? I don't think so.

Disclaimer: I don't agree completely with each of their interpretations - just that they each make good points worth ruminating.

But imo this here is the closest to a smoking gun on the origins regarding the FCS:

https://twitter.com/Ayjchan/status/1390773399874678784

This seminal @Nature paper by the WIV did a careful comparison of SARS1 and SARS2, focusing on the spike. Authored by several coronavirus specialists including Shi ZL who had worked on S1/S2 FCS before and, I assume, understood its functional implications.
nature.com/articles/s4158…

Yet, completely failed to point out what should have been a surprising and high impact discovery of the first S1/S2 FCS found in a Sarbecovirus. Not even a single mention of cleavage or furin throughout the article published post-peer review on 3 Feb 2020.

Some might say, maybe they were saving the FCS for another paper. But it's May 2021 & such a paper never emerged. I don't think such a high profile lab would've been rejected by a journal for being scooped by much less well known scientists publishing in less well known journals.

The same paper makes a series of other unjustified statements that I thought would've been caught by veteran virologists who had dedicated years to studying SARS viruses. But, you could argue that they were too panicked by the emergence of the virus.

https://twitter.com/Ayjchan/status/1274462386188161030?s=20

Another paper sent out on the same day (20 Jan 2020) by Shi ZL & other scientists also failed to call out the unique insertion. All they said was "we predicted that the cleavage site for generating S1 and S2 subunits is located at R694/S695."
ncbi.nlm.nih.gov/pmc/articles/P…

Despite all 3 authors having published a paper previously modifying the S1/S2 FCS in MERS and introducing an S1/S2 FCS in a related virus where they found "these mutations therefore played critical roles in the bat-to-human transmission of MERS-CoV."
jvi.asm.org/content/early/…

Some scientists might say "what does it matter if top scientists aware of the implications of an S1/S2 FCS insertion did not mention it in both of their seminal papers on the novel coronavirus?"

I think it matters a lot.

As a side saga to discussing the FCS, I think it's very important for scientists to be able to acknowledge good points (and point out wobbly points) in each other's arguments - especially those that challenge your own hypothesis - without going first to ulterior motives.

I know a lot of people want a straightforward answer, e.g., the FCS almost definitely points to a lab leak, or so-and-so's argument is 100% bullet-proof.

This isn't a situation where any one person has come up with a holy, unassailable, immaculate theory about how the FCS arose.

The people on both sides who argue that the FCS must've most likely arisen from recombination or template switching, or from being inserted in a laboratory - how do you know this without having access to Wuhan laboratory records?

I missed another balanced discussion on the FCS by @phylogenomics @P_J_Buckhaults worth reading!

https://twitter.com/phylogenomics/status/1391098263227408384?s=20