Comments on the Early Stages of the Outbreak

A few comments on this article.

My understanding is that environmental swabs at the Huanan seafood market have been shown to contain sequence reads from racoon dogs. This is relevant but the importance of this observation remains somewhat unclear to me
1/ https://t.co/HqAqzIkZK8

— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

Presence of racoon dog reads may provide a piece of evidence in favour of the involvement of racoon dogs in the early stages of the outbreak. Racoon dogs have always been one of the top candidates as an 'intermediate host' for SC2.
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

That said, at this stage, no supporting paper, preprint, data, or even a clear description of what the data might be is currently available. Thus, we can only speculate about the importance of those results at this stage.
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

Presence of racoon dog raw reads in environmental samples from the Huanan market is in itself underwhelming. There is essentially no dispute that racoon dogs were on sale at the market pre-pandemic.
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

The evidence for racoon dogs having played a role in the early spread of SC2, possibly as 'the' intermediate host would be far more compelling if the samples with high SC2 read content were preferentially those also containing racoon dog reads.
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

The article contains a confusing section about data submitted on the GISAID database and then rapidly removed before being spotted by 'scientific sleuths'. This cannot directly be the data that was analysed to show 'racoon dog contamination' in environmental samples.
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

Indeed, the GISAID database does not host raw sequence data, but only 'clean' viral genome assemblies (ie. stripped of all host target reads). It is unclear to me what the relevance of the GISAID submissions may be in this context.
7/ pic.twitter.com/DZLAKkfbC0

— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

I assume the data will be available soon, which will allow for a more informed discussion about the strength of the new evidence. It may well be important in tilting the balance a few % towards a zoonotic spillover, but I seriously doubt it will be dispositive.
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

The uncertainty about the origin of Covid creates a difficult situation with major societal and geopolitical implications, and it will take time for the truth to be uncovered, bit by bit, tiny speck of evidence by tiny speck of evidence.
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

Such articles really don't help as they only polarise the debate further. Those convinced by a zoonotic origin will read it as final proof for their conviction, and those convinced it was a lab leak will interpret the weakness of the evidence as attempts of a cover-up.
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

I would strongly encourage the media to be more responsible in their coverage of the origin of Covid, and try to avoid making strong claims either way at this stage, particularly so when reporting on evidence that is not yet available for public scrutiny.
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

OK, a quick clarification / correction. It looks like the authors of the preprint below (posted on February 25th 2022) submitted assemblies on GISAID with a link to their raw read FASTQ files which some people spotted and downloaded.
12/https://t.co/PYaOUat1fk

— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

A most regrettable outcome of this unnecessary kerfuffle would be for the Chinese scientists to withdraw their submitted manuscript and decide not to share their raw data with the world. All we'd be left with would be yet more fuel for conspiracies ...
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— Prof Francois Balloux (@BallouxFrancois) March 17, 2023

Carefully worded report by the WHO on the current situation. The new 'racoon dog smoking gun' feels underwhelming. The situation looks like a mess. I suspect it will be difficult for the different parties involved to find a satisfactory solution.
14https://t.co/Zgmd2A5b3e

— Prof Francois Balloux (@BallouxFrancois) March 18, 2023

I deleted tweet 6-7 in the thread, which were incorrect. The exact nature of the data that was downloaded before being taken offline is still unclear to me, but the claim it may not have been hosted on GISAID looks incorrect. Apologies for the confusion this generated.
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— Prof Francois Balloux (@BallouxFrancois) March 18, 2023

In my initial thread, I cast doubt on the data having been downloaded from GISAID (deleted tweets 6/7). I recognise this could have been interpreted as @flodebarre being untruthful about the source of the data. I apologise for this incorrect statement.
16/https://t.co/iEY2TQr7PC

— Prof Francois Balloux (@BallouxFrancois) March 19, 2023

The report (below). My expectations weren't sky high but it still manages to underwhelm. Besides confirmation of the presence of farmed mammals at the Hubei seafood market (which was well established before), there is no new information in there.
17/https://t.co/iCZQUoWeMi

— Prof Francois Balloux (@BallouxFrancois) March 21, 2023

GISAID are not happy with the publication of the report and have released a strongly worded statement. The report's authors have apparently had their account revoked (which is a major problem for any scientist working on SARS-CoV-2).
18/https://t.co/dVQlUEHTnA pic.twitter.com/WdgJu8JG1n

— Prof Francois Balloux (@BallouxFrancois) March 21, 2023

I believe that one element in the GISAID letter that has been largely overlooked or misunderstood is that GISAID is primarily an (avian) flu genome platform. GISAID have worked very hard to gain the trust of the CCDC, and flu genomes from China get submitted early on GISAID.
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— Prof Francois Balloux (@BallouxFrancois) March 22, 2023