This Nature "explainer" is unfortunately not a very good one. It's better than the previous Nature article, but some poorly conceived arguments are pushed while some data in print are swept under the rug.

My quick thoughts.…
The good things first: there's no begging the question, i.e. no conclusion is presumed that all other theories must definitively rule out before being considered. There's no overeliance on conflicted people with poor track records.
The three problems I see on quick read: 1. It repeats Shi's blanket statement of sarbecoviris seronegativity in the miners without specifying the speaker, while not mentioning the more granular description of positivity by PhD student Huang.
Thus the writer has researched poorly, or has chosen a side but hides the conflict. If the latter, they've sided with the senior figure whose statement was made during the epidemic and is motivated to avoid blame, over the PhD student who wrote his thesis before the epidemic.
2. Wuhan is not in the midst of a region of bats and caves. It's a bigger city than NYC, the surrounding is primarily flat, and it's 1000mi from Yunnan. It's like saying we'd set up an institute in St Louis to study bats from Carlsbad Caverns because it's the same general are.
The author this seems a bit motivated to get rid of this coincidence by declaring there isn't one, but the quick statistical claim made is just wrong. Which is odd since they do bring up he question.
3. Still no allowance made for the possibility that SARSCoV2 was unknowingly transported by lab workers from southern China to Wuhan, which avoids the need for coverup/secrecy regarding a known SARSCoV2 sample. A lab leak does not mandate that there must have been a conspiracy.
Typos: general are = general area, this = thus, he = the
I don't like to do Nature's job, because they aren't paying me, but this was a better explainer:
BTW on close inspection one sees the article basically constructed a straw man argument by redefining "near". Q: "Is it a coincidence that the epidemic started near where WIV is?" Answer (paraphrased): New viruses often arise "near" institutes that study that type of virus...
Direct quote: "Virology labs tend to specialize in the viruses around them...influenza labs in Asia, haemorrhagic fever labs in Africa and dengue-fever labs in Latin America"
So WIV and coronaviruses both being in China are not a coincidence!!! 🙄🙄🙄
I don't think people meant the coincidence was that WIV was located in the same country as the caves or mines in Yunnan. Hence the reply was not addressing the question but a perverted silly form of the question, i.e. a straw man argument.

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More from @michaelzlin

9 Jun
Two pieces of good news for inactivated vaccines today:

1. Results from Uruguay indicate Sinovac protects 95%/92% against death/ICU cases

2. Neutralization assays indicate antibodies elicited by Covaxin only drop 2.7x in potency vs B.1.617.2 (Delta)

Details below
Uruguay results:

Sinovac: deaths/ICU/symptoms⬇️95/92/61% (HCWs and 18-69yo)

Pfizer/BioNTech: deaths/ICU/symptoms⬇️94/94/78% (HCWs and >80yo)

Confirms Sinovac works well vs. severe disease even with some breakthrough cases. Overall similar to Chile…
These data confirm 2-dose Sinovac, an inactivated virus vax, is similar to 1-dose J&J or 2-dose AZ. All these (and Sinopharm+Covaxin) have breakthrough risk of 20-50% (depending on dose spacing), but still protect >90% against death.

Overall, inactivated vaccines are useful
Read 6 tweets
7 Jun
There have been a lot of stories recently on the search into COVID19/SARSCoV2 origins, but they have been written to tell stories of intrigue or mystery, not to summarize known facts.

Thus I thought it might be useful to succinctly summarize what we actually know...

I'll say from the outset we know zero about where sarscov2 itself came from, so the only facts we can list are those that could be proximally relevant. That is, each of these facts is either about SARSCoV2 discovery or just one potential step removed from SARSCoV2 origins.
First, the briefest bit of background: SARSCoV2 is in the clade or coronaviruses called the sarbecoviruses, named after its first known member, SARSCoV1, the cause of SARS discovered in 2002. SARSCoV1 and SARSCoV2 are 80% identical.

Read 41 tweets
5 Jun
Thank you @nbcnews for clearly stating that you can have a lab leak of a non-engineered virus.

Now if we can get certain scientists to also say this, it would improve our ability to figure things out, instead of just yelling at each other.

Excerpts below…
"Andersen, a professor at the Scripps Research Institute, tweeted this week that "we seriously considered a lab leak a possibility," but reconsidered upon further review of the evidence..."
"Andersen’s use of the term “lab leak” could be confusing, however, because he was talking in the emails about the question of whether the virus had been modified or engineered."
Read 7 tweets
4 Jun
Antibodies elicited by the Pfizer/BioNTech RNA vax are 6x less potent in neutralizing B.1.617 (delta variant that devastated India).

This lowers predicted efficacy for symptomatic COVID19 to ~70%.

This compares to 2x drop in neutralizing activity for Covaxin.

I discuss in 🧵
The advantage of the RNA vax is their simplicity. They encode only the spike protein because it's the viral protein targeted by most of the antibodies that prevent viral entry. Another way to put it is Abs to the right place on spike are sufficient to block entry. (image Siemens) Image
The adenovirus vax also encode only spike but express it from Ad. Both types elicit high levels of neutralizing antibodies (nAbs) after just one dose. RNA is better here; in fact 1 dose of RNA gives you similar nAb levels to natural infection.

Read 21 tweets
3 Jun
Pretty cool story. In a perfect world the DRASTIC group should get their own NIH grant. Except in a perfect world we wouldn't have SARSCoV2.

How amateur sleuths broke the Wuhan Lab story and embarrassed the media…
Interesting excerpt:
'Had the WIV been actively working on RaTG13 during the seven years since they discovered it? Peter Daszak said no: they had never used the virus because it wasn't similar enough to the original SARS...
'..."We thought it's interesting, but not high-risk," he told Wired. "So we didn't do anything about it and put it in the freezer."

Ribera disproved that account...'
Read 5 tweets
2 Jun
A lesson on proper trial design: Was thinking, if nAb levels at 3% of convalescent plasma (CP) prevent severe COVID (…) then infusing 1U of CP (5% body volume) should prevent death.

And it does!…

But weren't we told CP was worthless?
Of course it was the @nytimes who wrote the obituary for convalescent plasma. Maybe nothing factually wrong in their stories, but their writers generally lack the training to dig deeper and find the signal in the noise.…
"When a treatment fails, which is often, it can be difficult for its strongest proponents to let it go. Eventually, studies did emerge to suggest that under the right conditions, plasma might help."

Sloppy @nytimes. 1st sentence implies CP failed. 2nd says success. Which is it?
Read 10 tweets

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