I promised an analysis of This Week in Virology x Bob Garry on #OriginsOfCovid but was stunned by recent events, e.g., the lead, most vocal author of Proximal Origin @NatureMedicine correspondence article deleting half of his tweets and then his account.

microbe.tv/twiv/twiv-762/
I'll do it now, after spending a large amount of time reassuring (rebutting) people that I'm not a Canadian-Chinese-US NIH-suck-up scientist-spy with connections to the billionaire class.

S = scientific arguments
NS = non-scientific arguments
Garry says the 1st Proximal Origin draft was completed Feb 1.

SARS2 (Covid-19) genome was released Jan 11.

By Feb 1, they did not yet have access to RaTG13 (the closest genome match still) or the pangolin coronaviruses... unless we get more FOIA'ed emails to show otherwise.
S1: The genome of SARS2 was not found in the literature and its spike receptor binding domain (RBD) looks natural. You could not design this from scratch using other viruses published so far.
Suffice to say, scientists do not publish discoveries on time (RaTG13 was fully seq'ed 2018, only revealed post-COVID because a short fragment w 99% match to SARS2 was already in the literature) + occurrence of lab incident does not require "intelligent design" of a novel virus.
NS1: Scientists are bad at keeping secrets and would've leaked the secret of a lab leak immediately.

Don't really need to say much about this. Different countries, different cultures, sometimes keeping a secret keeps your life and your family and your lab safe.
Thank you @trvrb
My mistake: the genome of RaTG13 was available but not its actual sequencing data... the NGS would be deposited later and the amplicon data only in May 2020 after other scientists had emailed for it. The data doesn't match the genome.
NS2: We don't know the credibility of the intelligence that 3 Wuhan Institute of Virology employees were sick with COVID-19 symptoms. It could've been the flu. "Seems completely not noteworthy to me" - TWiV host

That's right. @StateDept you should declassify this data.
NS3: Garry said China did a good job identifying early cases, >50% had been to markets in Wuhan although we don't know who patient zero is.

No, their criteria was biased for people who had visited the Huanan seafood market, patient and blood samples were not tested for SARS2.
S2: There were 2 lineages, A and B in Wuhan. All the Huanan market patients had B lineage. It was likely animals introducing each lineage in different markets.

But these 2 lineages only differ by 2 mutations. That's negligible and doesn't require multiple spillovers in Wuhan.
Not to mention the "natural insertions" RmYN02 data to naturalize the furin cleavage site (FCS). Was that also available by Feb 1 to the Proximal Origin authors?
NS4: No animal samples from the markets in Wuhan or even upstream suppliers tested positive for the virus, but... wild animals might've been removed from the markets!

*conspiracy theory alert!*
NS5: We need China's help. It's a real mistake not to work with Chinese virologists to stop SARS3 or SARS4.
NS6: The @ScienceMagazine and Dr Fauci are asking for an investigation without any evidence or precedent for lab leaks.

cidrap.umn.edu/news-perspecti…
NS7: The US intelligence community doesn't know science.

Ok, US intelligence if you're seeing these tweets, please consult with scientists. Preferably not the "minority of people who think that it is not a lab leak" according to Bob Garry.
S3: If you look at the SARS2 spike FCS sequence, no one would've inserted that specific sequence. Why that Proline? And I could've made a more powerful FCS, and eventually we would've found an FCS in SARS-like viruses.
MERS has a proline in the same spot in its FCS. You're guessing at what insights a scientist would have for inserting an FCS, in or out-of-frame, codon optimized or not.

And, a lab leak is not dependent on an FCS being artificially inserted.
NS8: The Wuhan lab was built there because of SARS1.

Completely wrong.
NS9: Lab leaks take energy away from collaborations with China to sample virus diversity.

No. China already blocked you from sampling once Covid-19 emerged.
That's seriously it. That's the 2 hour long interview.
After Bob Garry leaves, the TWiV hosts shame conspiracy theorists who expose Asian people to danger.
NS10: A lab leak requires a whole bunch of people lying - as opposed to 10,000 people visiting the Huanan market per day and not saying anything about live mammals sold there in mid-to-late 2019.
I don't really know that many scientists who run around the lab alerting everyone to a mistake they've made.
Better to put this in the main 🧵 so people don't miss it. I made a mistake and forgot that the genome sequence of RaTG13 had been posted by Feb 1.

But how to explain the 24h change?
Jan 31, "inconsistent with.. evolutionary theory"
Feb 1, 100% natural?

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More from @Ayjchan

8 Jun
I'm very happy to share that I will be co-authoring a book on the #OriginsOfCovid with @mattwridley - coming this November!

When Matt asked me to collaborate on Viral: The Search for the Origin of COVID-19, I knew that we had to write this book.
I've done an insane amount of tweeting this past year (more than 10,000 tweets) and co-authored 2 articles with Matt in the @WSJ and @Telegraph

But, a friend told me that these would all be lost & scattered with time.

If you write a book (a very good one), it can become canon.
I know that there will be possibly dozens of books on the #OriginsOfCovid - many on the politics & management of the pandemic in different countries (especially the US and China), and several very focused on persuading us that this virus definitely has natural origins.
Read 6 tweets
7 Jun
The problem with being a moderate is that you get bashed by people on both sides, depending on where the momentum is at that given moment.
More than a year ago, I said we should consider the lab leak hypothesis, regardless of how likely, not just natural origins #OriginsOfCovid

The natural origins crowd called me a conspiracy theorist, misinformation-spreader, attention-seeker, outsider with no proper expertise.
This year, I still have the same position: we should consider the lab leak hypothesis, not just natural origins.

Now the lab origins crowd calls me disingenuous, a coward, an apologist, misinformation-spreader, attention-seeker, an insider with ties to gain of function research.
Read 11 tweets
6 Jun
I’m going to make a long thread later today going through natural origin arguments recently presented on TWiV and the Washington Post. But before that, I think the responsible thing to do is to explain what virology is.

What do virus researchers do? Why is this work important?
With the lab leak hypothesis #OriginsOfCovid now being considered seriously, there’s been some new concerns or fears about what virus researchers / virologists are doing in the lab and why they grow and study viruses in the first place.
I’d say that, in my experience, very few virologists are engaged in dual use research. Most of the virologists working on pathogens are sincerely just trying to understand the biology of the virus, build models of the infection, and find ways to treat patients.
Read 12 tweets
5 Jun
Another balanced analysis of the lab leak theory. In @Slate by @RebeccaSohn2

People are going to find that I prefer to amplify articles that give careful consideration to both natural and lab hypotheses.
slate.com/technology/202…
Some scientists & journalists are rushing to say "but the lab leak is so unlikely!" (not a conspiracy theory any more, just unlikely)

I told @RebeccaSohn2: It would be like trying to guess what’s the likelihood of rolling a 6 without knowing how many sides of the dice there are.
The fact remains that we don't know what strains of viruses were collected and under study in Wuhan. We don't know all the research experiments that were done.

We have the scientific literature which describes some of these, usually studies of samples from several years ago...
Read 12 tweets
30 May
Today, karma finally kicked in. After spending the last year "just asking questions" and trying to fish out information relevant to the #OriginsOfCovid, I finally became a target of a conspiracy theory and an anonymous twitter mob.
I had been warned about this situation by well-intentioned colleagues, journalists, and even other anonymous twitter users. That a day would come when I would get attacked by anonymous users.

There was always a stream of online harassment, but it definitely peaked this week.
It definitely made me feel more empathy for other scientists who are in a similar situation. I had already been expressing empathy for them and actively asked people on twitter please not to attack because it just makes the conversation immediately adversarial and non-productive.
Read 10 tweets
30 May
I see this is raising eyebrows so I better nip it in the bud.

The work I did on human artificial chromosomes (HAC) had been widely presented at local meetings & on the lab website. I talked so openly about it that it could not be patented because it had been publicly disclosed.
The rest of the thread above rightly criticizes the meeting being “secret” - but I always thought that it had been labeled “secret” by the organizers to drum up media coverage (sorry, organizers!).

As far as I could tell, all of the research at that meeting was in public domain.
I’m sorry to reveal this gimmick but actually I think many of the scientists and organizers were eagerly awaiting journalists to call them to talk about the “secret” meeting.

In reality, most scientific meetings happen without any journalists paying attention.
Read 12 tweets

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