1 of 9: Thank you SO MUCH @profvrr, Kathy Spindler, and @alandove for your excellent discussion of my recent COVID origins Perspective in @ScienceMagazine
2: You hit on key points I wanted people to take home, especially that there really was a preponderance of early COVID cases linked to Huanan Market and this can't be dismissed as ascertainment bias (undue searching for cases linked to the market, while ignoring unlinked cases).
3: This, along with the fact that if the pandemic started there you should *expect* to see some cases unlinked to the market early on as people were infected then moved the virus into the nearby community, points squarely at the market as the overwhelmingly likely site of origin.
4: Also liked your highlighting how Dr. Zhang Jixian, at Hubei Provincial Hospital of Integrated Chinese and Western Medicine, had worked out on the *same* day she saw her first case (Dec 27) that this was a new virus, was human to human transmissible, and could be asymptomatic.
5:
Nearly a month before China admitted H2H transmission!
And your noting that the system set up in the wake of SARS to identify new viruses broke down completely because clinicians were not reporting unexplained pneumonia through the national reporting system.
6: It is *outrageous* that China CDC has attempted to credit the Pneumonia of Unknown Etiology mechanism with identifying the outbreak in Wuhan. It didn't. Zhang Jixian did.
Falsely crediting the PUE system in this way will prevent the changes needed to make it work next time.
7: Finally, thanks for the shout out about my timeline of key early events in Wuhan, which is buried in the supplementary materials, but which I will paste here in hopes that people might have a look.
8: Along with the figure legend:
9: Finally, @profvrr, sick burn about me declining your earlier invitation to be on TWiV. What a primadonna I was - sorry!
Never again: I'd be delighted to be on TWiV in the future, if you'll have me.
Ai Fen and colleagues at Wuhan Central Hospital also played key role in identifying early cases, plus first identification of the news SARS-related virus on Dec 26, full genome Dec 27.
15 days before Zhang Yong-Zhen, @edwardcholmes and @arambaut broke the gag order and published
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1 of 10: The B.1.1.529 (omicron) Spike looks a whole lot like a 'polymutant' Spike experimentally generated to evade antibody responses from infection or vaccination, as noted by @theodora_nyc.
What does this portend for its immune escape properties?
2: @theodora_nyc and colleagues conducted a *super* cool experiment where they drew on their experiments to evolve Spike proteins that were resistant to polyclonal antibody responses, as well as data on escape mutations in natural variants of concern...
And @Drinkwater5Reed and other DRASTIC members had advanced additional research along the same lines, including of the same news video I analyzed in my paper:
I feel I must reply to a comment from @DavidRelman in a recent @nytimes article on a piece of mine in @ScienceMagazine on why a careful analysis of the earliest known cases in Wuhan indicate that the pandemic started at the Huanan Market.
“It is based on fragmentary information and to a large degree, hearsay,” David A. Relman, a professor of microbiology at Stanford University, said... “In general, there is no way of verifying much of what he describes, and then concludes.”
Here is the article, for those who would like to test David's dismissals against what I actually present in the piece. I do hope you'll do so.
I have spent the last few months trying to poke holes in the hypothesis of a natural origin of SARS-CoV-2 by asking:
Was the apparent preponderance of early cases linked to Huanan Market real or just a mirage because that is where people were looking for cases?
This is a key question, because if the pattern is real, it is *very* hard to explain why we would observe it if the outbreak had not started at the market, in particular the western section where illegal wildlife like raccoon dogs was sold. It's about the size of a Home Depot.
2/ In 1987, FDA approved the first HIV antiviral, AZT. Hope quickly turned to despair though, because in patient after patient the virus quickly evolved to become resistant to AZT.
It wasn't until 1996 that the key breakthrough emerged.
3/ At a conference in Vancouver BC, researchers revealed that if patients were given "triple therapy", cocktails of drugs that attacked HIV in different ways, resistance could be averted.
1/ Medium thread on #SARSCoV2's furin cleavage site and a strikingly similar region in some of the new BANAL genomes from Lao, and in RmYN02 from China.
Seems worth trying to clear up the confusion of @ydeigin on this issue (even it means broadcasting my pic, below).
2/ The furin cleavage site of SC2 is the RRAR in the NSPRRAR stretch of amino acids in the alignment I'm holding up there. It is what makes the virus 'pop' in humans.
The BANAL viruses have NSPAAR. A couple other ones, including RmYN02, have NSPAAR or NSPVAR.
3/ So, having barely scratched the surface of the genetic diversity of these viruses in the wild, we've found several that are literally a *single* amino acid away from having a furin cleavage site.