Yuri Deigin Profile picture
10 Apr, 11 tweets, 3 min read
1/n

Ok, let me try and harp on my evolutionary, well, harp 😂 And maybe my favorite EvoBio couple, @HeatherEHeying and @BretWeinstein can smack me on the head if say something dumb.

So basically infectivity and virulence/pathogenicity are two different properties of a virus,
2/n

which *might* be correlated but do not have to be. First of all, we must understand: these little viruses are not out to kill us. All they “want” is to replicate. And want is in quotes because of course they don’t have any agency:
3/n

they are just a self-replicating collection of molecules, set in motion by some random LUCA prime mover billions of years ago. So the pathogenicity/virulence of a virus is really an unwanted side-effect for both parties:
4/n

neither we nor the virus want us to die and stop propagating it. But sometimes the virus is too effective at hijacking our cells that it messes up our ability to do something critical to our survival, like breathing.
5/n

And at other times it is actually our immune system that is so effective at killing the virus that it kills us in that good fight as well 🥲
6/n

But back to the evolutionary aspects of a new viral strain. I think it is pretty self-evident that with time a novel virus strain would “benefit” from decreasing in pathogenicity. Orthogonally, it *should* benefit from increasing in transmissibility (infectiveness).
7/n

However, there is a complex dynamic at play here: if the virus is actually gaining in pathogenicity, a gain in transmissibility could be bad for its long-term survival, because it would quickly run out of hosts.
8/n

So the best long-term survival adaptation strategy for a novel strain is to gain in transmissibility while decreasing in pathogenicity. That said, there are also no guarantees that (a) this is possible and (b) this strategy would be found.
9/n

Viruses try to “find” these strategies blindly (recall the Blind Watchmaker) — they just incur novel mutations and the ones that provide some sort of an advantage tend to stick around.
10/n

And “advantages” could change in the course of the pandemic. A spike mutation that would not have provided any advantage early on, could suddenly make a virus less sticky to antibodies that were developed to the previous strain, thereby paving the way to reinfection ability
11/n

In any case, let’s just hope we can stamp out SARS2 quickly before it has enough time to find one of many possible novel ways of escaping our immune memory from vaccines or previous infections.

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More from @ydeigin

19 Mar
1/6 All right, today I got conclusive proof that Eddie Holmes sucks at aligning genomes. And if that’s not enough, I found the last nail in his “PAA insertion” coffin.

But first things first: he is a coauthor of a recent preprint with the following gem of an alignment (yellow):
2/6

See him putting the R in Rc-o319 alignment one aa ahead of others? That should immediately trigger a WTF moment in anyone even modestly familiar with genome alignments. Next, that urge should translate into checking the underlying nucleotides, which will quickly
3/6

confirm that the RSAN shouldn’t be shifted in Rc-o319 compared to its relatives but should neatly align with RSVN just above it, because it is the N in Rc-o319 that got duplicated (duplicate codons AAC AAC are a dead giveaway) — see my alignment above.

Embarrassing!!! 😂
Read 6 tweets
5 Mar
1/12

Ok, here goes nothing. Remember this little thing called a furin cleavage site? You know, the one that made SARS2 into a real promiscuous little virus? Well, as some have pointed out before, the strategy of inserting a furin cleavage site was not only
2/12

investigated by coronavirologists previously as a tool to expand virus tropism, but also by other virologists as a tool to actually ATTENUATE a virus. In other words, a vaccine strategy.

Getting goosebumps yet? I am.
3/12

So how could this be a vaccine strategy? Well, the idea, as I understand it, was to take a virus, insert some FCSs into it in key places, but do so in a cell culture that do NOT normally have furin, and thus the virus won’t get cut in such cells. But then if you infect
Read 13 tweets
22 Jan
Ok, the prize for the craziest and most dangerous gain-of-function research goes out to Italian virologists who took SARS2 and passaged it in vitro in the presence of neutralizing antibodies. It quickly obliged and mutated to escape them. Yay for a novel, more dangerous SARS3! 🤦‍♂️
Oh, and it developed a glycan sequon in vitro — take that, @K_G_Andersen! 😁 Image
Here’s the preprint:

biorxiv.org/content/10.110…
Read 4 tweets
22 Nov 20
Ok, does this conclusively disprove the PAA "insertion" in RmYN02? I re-ran the CLUSTAL W alignment with ALL genomes used in Zhou et al. (middle block below) and it shows NO trace of an insertion in RmYN02. I get the same result if I omit SARS2 from query (bottom block). 1/4
Here is the original figure from Zhou et al. claiming a PAA insertion. Btw, I couldn't find their nucleotide alignment in the paper, even in the Supplementary.

@CellCellPress @CurrentBiology could you please ask the authors to provide those data? 2/4
Here is the link to the paper: cell.com/current-biolog… 3/4
Read 6 tweets
28 May 20
1/n Here’s what still irks me in the EcoHealth/WIV narrative about RaTG13/4991. So in 2011 and 2012 Shi Zhengli goes on 2 expeditions to a bat cave near Kunming, the capital of Yunnan. There she finds CoV strains RsSHC014 and Rs3367 which share 85% and 96% with the first SARS-CoV
2/n This discovery is worthy of a Nature paper in 2013 and many subsequent accolades to its authors. Btw the first author of the 2013 Nature paper is Ge Xingyi, whose name features prominently on many other joint CoV papers. The team then proceeds to extract a live sample of
3/n Rs3367 which they then christen “WIV1” and later use as a backbone for several chimeric constructs. But for their 2015 joint chimera with Baric they used RsSHC014 as a backbone (85% similar to SARS).
Read 7 tweets
26 May 20
Hmm. A 2017 paper by Ge et al. (same Ge of the 2016 paper reporting the discovery of 4991/RaTG13) describing a Yunnan rat CoV with a RRAR furin site (same as in SARS-CoV-2).

link.springer.com/article/10.118…
Hat tip: Kevin Bristol.
I am referring to this 2016 paper:

pubmed.ncbi.nlm.nih.gov/26920708/
Read 4 tweets

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