What will be Scott Alexander's P(zoonosis) at the end of April?

COVID origins•Scott Alexander

282

Ṁ8.9K

Ṁ850

May 1

ALL

>90%

90%

60% <= x < 90%

40% <= x < 60%

0.8%

<40%

Resolves to the youngest statement before the end of April 2024 SF time.

Scott Alexander recently published https://www.astralcodexten.com/p/practically-a-book-review-rootclaim , where he says

> For what it’s worth, I was close to 50-50 before the debate, and now I’m 90-10 in favor of zoonosis.

some sus aspects of the debate have been pointed out, which may change the update. If there is no further statement with a number for P(zoonosis), resolves to 90%.

(it's not clear that this is actually P(zoonosis)=90% or just odds compared to gain of function, ignoring other hypotheses. The market will resolve based on the best number for P(zoonosis) we get, 90% if no other number appears)

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Rootclaim have a post in reply. https://blog.rootclaim.com/covid-origins-debate-response-to-scott-alexander/

@MikePa67d omg thanks/lmpao

@warty that's so convincing

@warty I haven't read the full thing but wasn't convinced the debate really shifted the odds significantly. A number of papers since the debate largely undermine the papers relied on for Huanan Seafood Market origin. The claim that an N501Y mutation would result from passage in hACE2 mice was also incorrect. The papers in particular are as follows:

1. Spatial statistics experts Stoyan and Chiu (2024) find the statistical argument by Worobey et. al. that Huanan Seafood Market was the early epicenter is flawed.

https://academic.oup.com/jrsssa/advance-article-abstract/doi/10.1093/jrsssa/qnad139/7557954

2. Lv et. al. (2024) found new intermediate genomes so the multiple spillover theory is unlikely (it was anyway given lineage A and B are only two mutations apart). Single point of emergence is more likely with lineage A coming first. The market cases were all lineage B so not the primary cases. Their findings are consistent with Caraballo-Ortiz (2022), Bloom (2021).
t.co/50kFV9zSb6

3. Jesse Bloom (2023) published a new analysis showing that genetic material from some animal CoVs is fairly abundant in samples collected during the wildlife-stall sampling of the Huanan Market on Jan-12-2020. However, SARS-CoV-2 is not one of these CoVs.
t.co/rorquFs1wm

4. Michael Weissman (2024) shows a model with ascertainment collider stratification bias fits early Covid case location data much better than the model that all cases ultimately stemmed from the market. George Gao, Chinese CDC head at the time, acknowledged this to the BBC last year - they focused too much on and around the market and may have missed cases on the other side of the city).

https://academic.oup.com/jrsssa/advance-article-abstract/doi/10.1093/jrsssa/qnae021/7632556

5. The anonymous expert who identified coding errors in Pekar et. al. leading to an erratum last year has found another significant error. Single spillover looks more likely. t.co/GAPihZu51P

6. The argument that an engineer wouldn't make the furin cleavage site with the features of SARS-CoV-2 overlooks it resembles that of MERS in several structural and functional ways and the sequence looks quite similar. In 2019 WIV researchers were involved in MERS research. Dr Andreas Martin Lisewski discusses similarities with a MERS infectious clone described in 2017 here. t.co/fAVUlJu0TK

Ultimately, WIV was performing in vivo experiments in transgenic (human ACE2 expressing) mice and civets in 2018 and 2019 in SARS-like CoVs. They had been sampling SARS-related bat coronaviruses in Yunnan and Laos where the nearest known relatives to SARS-CoV-2 are found. They won't share their records. WHO is still calling for data on both the animal trade and Wuhan labs.

@MikePa67d

animal CoVs is fairly abundant in samples

Coronaviruses aren't equivalent. You are talking about a bamboo rat coronavirus largely concentrated in one stall with lots of bamboo rats and a canine coronavirus most closely related to viruses sequenced in sick dogs, raccoon dogs, and red foxes. In every case the CCoV samples come from diarrheic animals indicating enteric growth. The sample with, by far, the highest number of reads is from a machine used to remove animal pelts, where you'd expect to find a lot of this CCoV but not so much virus deposited where if the highest viral load is in the respiratory tract.