There has been much recent misinformation about COVID-19 origins that we can now debunk.

A thread on 2 topics:
A. How the ODNI report debunks multiple lab origins rumors.
B. Where these inaccurate media reports originated, and why we knew they were wrong.
dni.gov/files/ODNI/doc… Overview of ODNI report:
1. No evidence for genetic engineering (virologists agree!)
2. Rumors of sick researchers at the WIV are uninformative of COVID-19 origins, and previously reported details are wrong.
3. The virus was not at the WIV before late Dec 2019 outbreak.

Glad to see someone else really have a proper look at the data, and to see our raw analysis be replicated. After looking briefly at Jesse's results, I agree, it largely in agreement!
That said there are some enormous issues in interpretation and presentation here to address (1/7)

https://twitter.com/jbloom_lab/status/1651428639676960769

Most inaccurate to me is table 1. It relies on an arbitrary 20% cutoff of all chordates to dismiss many samples with wildlife DNA/RNA. I've put it below, with a corrected version on the right without this cutoff. Multiple viral positive samples had raccoon dog DNA. (2/7)

(A weekend SARS2 origins thread)
Last week Liu et al. provided an extensive update to their preprint on sampling the Huanan market:
chinaxiv.org/abs/202303.103…

Their supplementary notes locations of all samples in the market, so we can map Jan 2020 positivity rate across the market: The above plots the significance of relative sample positivity (comparing + vs - samples) across the market, and confirms a prediction from Worobey et al. 2022 Science: samples from the southwest corner of the market where wildlife was sold were more likely to test positive.

Hoped to not have to, but briefly before I logout to get work done:
1. Now known that the team did not violate GISAID ToS. Shocked at how people who were supposedly advocates of open data on this issue attacked for that: the hypocrisy of that contingent has never been clearer 2. The main finding was that susceptible animals were in fact exactly where they were predicted to be, in two wildlife stalls on the side of the market where the earliest cases were, and the area where most positive swabs were taken. That conclusion is robust.

[CW: politics]
Another conspiracy bites the dust, and now there are a great number of people who owe Anthony Fauci and others an enormous apology. Here Fauci and Collins asked for honest evaluation of the evidence, alerting authorities, and pushing for a WHO investigation And here Fauci first pushes for what would become the WHO investigations into the origins of COVID-19, at the suggestion of Jeremy Farrar. All of the new emails here *should* be bigger news than the original conspiracies were - especially with any upcoming drama from House Rs

I know he was a climate change denier... but presumably at one point he understood basic principles of evolution, given his biology books... But now he has no clue how recombination works or how to read a phylogeny. How consistently does this conspiracy turn brains to mush?

https://twitter.com/mattwridley/status/1590967171517394947

RaTG13 is not the most similar virus to SARS-CoV-2 at the whole genome level: BANAL-20-52 is. (96.8% for BANAL-52 and 96.1% for RaTG13) At the whole genome level, RaTG13 and SARS-CoV-2 diverged several decades ago.

Alright, I had a look last night and will quickly do a thread on it.
There are many kinds of 'wrong' in science, but this preprint is False. There are many reasons (links at end), but the main one: the “unusual” sites are all *exactly* found in natural bat coronaviruses. 1/n

https://twitter.com/BallouxFrancois/status/1583165259799412737

The authors focus on cut sites of BsaI and BsmIB. Why these two REs? The simple answer is there is no good reason- they were just cherry-picked as the “most unusual”. Here's a plot of just a few RE cut sites possibilities across coronavirus genomes (SARS-CoV-2 at top)

I am personally negative on this. Problem #1: There are two kinds of "gate-keeping" in publication: editors and peer reviewers. This model entirely retains editorial power and removes peer power. I think we actually want the exact opposite: democratizing the desk decision.

https://twitter.com/mbeisen/status/1583067586589208576

Problem #2: the idea here is that readers will read the paper, read the reviews, read the response, and reach a conclusion. I think that rarely works in practice except for field experts- we've been trying this on the rest of the internet for decades without a lot of success

Recommend reading this perspective out today in Science, and this thread by @MichaelWorobey. I'd just like to emphasize the four crucial questions he answers about the origins of SARS-CoV-2, identifying that that the pandemic most likely began at the Huanan Seafood Market.

https://twitter.com/MichaelWorobey/status/1461417259600023556

#1: He identified a mistake in the earliest case reported by WHO w/ symptoms Dec 8. Turns out the patient had a fever due to a tooth infection on Dec 8, while his COVID symptoms started Dec 16. Today in NYT, a WHO team member agrees with that assessment.
nytimes.com/2021/11/18/hea…

This summary of the intelligence community's report is closely in line with our recent review of the evidence for the origins of SARS-CoV-2. If or when a version of the report itself is made public, it sounds like it may be very enlightening. Key quotes below:

https://twitter.com/josh_wingrove/status/1431340451899006980

"We judge the virus was not developed as a biological weapon. Most agencies also assess with low confidence that SARS-CoV-2 probably was not genetically engineered; however, two agencies believe there was not sufficient evidence to make an assessment either way"