Recovered deleted sequencing data sheds more light on early SARS-CoV-2 epidemic | Hacker News Reader

Recovered deleted sequencing data sheds more light on early SARS-CoV-2 epidemic

biorxiv.org

53 pointsbgentry25 comments

From the paper:

"The fact that such an informative data set was deleted has implications beyond those gleaned directly from the recovered sequences.

Samples from early outpatients in Wuhan are a gold mine for anyone seeking to understand spread of the virus.

Even my analysis of the partial sequences is revealing, and it clearly would have been more scientifically informative to fully sequence the samples rather than surreptitiously delete the partial sequences.

There is no plausible scientific reason for the deletion: the sequences are perfectly concordant with the samples described in \citet{wang2020medRxiv,wang2020small}, there are no corrections to the paper, the paper states human subjects approval was obtained, and the sequencing shows no evidence of plasmid or sample-to-sample contamination.

It therefore seems likely the sequences were deleted to obscure their existence.

Particularly in light of the directive that labs destroy early samples~\citep{pinghui2020SCMP} and multiple orders requiring approval of publications on COVID-19~\citep{chinacdc2020, Kang2020}, this suggests a less than wholehearted effort to trace early spread of the epidemic.

Another important implication is that genomic epidemiology studies of early SARS-CoV-2 need to pay as much attention to the provenance and annotation of the underlying sequences as technical considerations.

There has been substantial scientific effort expended on topics such as phylogenetic rooting~\citep{pipes2021assessing, morel2021phylogenetic}, novel algorithms~\citep{kumar2021evolutionary}, and correction of sequencing errors~\citep{turakhia2020stability}.

Future studies should devote equal effort to going beyond the annotations in GISAID to carefully trace the location of patient infection and sample sequencing.

The potential importance of such work is revealed by the observation that many of the sequences closest to SARS-CoV-2's bat coronavirus relatives are from early patients who were infected in Wuhan, but then sequenced in and attributed to Guangdong."

Author’s GitHub relating to this paper:

https://github.com/jbloom/SARS-CoV-2_PRJNA612766

so where did it come from and how did it spread? It's frustrating how after 1.5 years of intense interest and research, our best hunches are either it came from the lab or market (or from the lab to the market), which is the same as it was in January 2020, so after nearly a year and a half, no further progress has been made.

Identifying the source of MERS took 14 years and that had less political interference. We need to be open and thorough but also patient.

The source of MERS was identified as camels after 9 months.

There is sufficient evidence in the coronavirus genome to assess the origin without any further cooperation from China.

The crime against humanity is not the lab leak, instead the crime against humanity is the CCP cover up actions that allowed the spread of the outbreak beyond Wuhan to the rest of the unprepared world.

Porque no los dos?

They aren't mutually exclusive.

I'd also throw in the funding for gain-of-function research that lead to this. In which the US is not devoid of blame.

I don't know how to make the western world prepared: the sequence of virus is out; CCP has locked down a whole city of 20+ million people; following lockdown in most Chinese cities. They managed to get rid of the virus in less than two months. I remember one of the European health minister said on TV that they will not have problem because their hygiene is better than Chinese.

Europe and US are the leaders in biotech and pharmaceutical industry, and yet they failed. Countries had politicians trained in UK also failed, because they just want to follow what UK did, those politicians don't know what to do. I have to say that if UK or US decides to lock down multiple cities gradually, the world will follow because their influences, things will be a lot different. Your politicians betrayed you, they put their ego before people's interests.

The issue is not what the CCP did, but the Wuhan local authorities while the outbreak was still manageable. They did not advise the local population to wear masks or avoid social contact and travel, even though they knew quite well that a SARS-like outbreak was occurring. WHO was actually advised of the situation well before any such clear advice was given to the people in Wuhan. So you had people traveling everywhere with no masks, no distancing etc. only to suddenly be forced into a "hard" lockdown as you mention. But this was too little, too late.

> If < the lab leak is confirmed then China knew much earlier than the rest of the world just how bad what they were dealing with was and apparently didn't communicate it that way.

If you set your building on fire by mistake you ring the neighbours to tell them to get out before the whole building burns, if you don't do it you can't blame the people living on the top floor for not being prepared

What I am trying to say is that, after Wuhan lockdown, we have European health minister saying it is a hygiene problem and American politicians say it is a flu, and media painted the lockdown to be unnecessary and human rights crisis, is something I didn't understand. Wuhan lockdown is not a secret operation.

Anyway, I think the world should take a different view on lock down now. I would imagine technology in next 10 years would enable average person to launch bio attack in any city, and we need to have a way to deal with it better than 2020.

Are you sure the US failed here? From what I can tell we had a combination of technology to make a medical solution and the capital and drive to order enormous numbers of vaccine doses, to the point where we've been able to reopen (with thousands of people in close proximity without masks).

China is not in that situation. What they got right was initial containment (the US got that wrong, but that's because we had an ineffective leader and have a populace which is highly resistant to social control). The initial containment didn't completely help, because the chinese vaccine appears (I say appears because I'm not 100% sure yet) to be much less effective than Pfizer or Moderna, and China still has outbreaks that lead them to quarantine large sections of cities.

I don't think anybody really failed here. This was an event that the world partly prepared for for decades (vaccine tech, study related viruses) and partly ignored (our public health apparatus feels very slow and old now), and realistically, if we hadn't done what we did it woudl have been far worse.

I think US is great, and it didn't fail itself. I don't worry about developed world to be honest, they have the technology and resources to deal with this problem. US and Europe is so far ahead than anyone else in this field.

I believe many developing countries are lack of good decision makers, they blindly follow US and UK, without realizing that the reason behind US and UK's decision. Developing countries couldn't develop vaccines, not well equipped for medical support, and didn't have resources, they are not the same as US or UK.

The fact that this was deleted is more interesting than the sequences themselves.

How so? It provides us with no new information whatsoever. "The CCP does everything in its power to block any kind of substantive outside research on the origins of Covid-19" has been known for over a year now.

> Instead, the progenitor of known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2's bat coronavirus relatives.

So, it came from a bat not a rouge lab experiment, and the early sequences sampled at the seafood market only looked "unusual" because they were not a fully representative sample of the Wuhan epidemic as it later spread out from there. Good to know.

Hmmmm...does that follow? I mean the alleged lab source would have been from bat coronaviruses anyway. Is there something about these mutations that would be key to the lab leak theory?

The rouge experiment theory is that the virus is the product of intentional mutations to make it more dangerous to humans. What this paper is saying is that this looks increasingly like a perfectly ordinary bat coronavirus, and what initially looked like unusual mutations actually happened well outside of any lab environment.

Please, rouge is red. You meant rogue.

It's a perfectly normal bat virus that has difficulty infecting any mammals other than humans and mice genetically engineered to have human ACE2 receptors lining their respiratory system.

Jon Stewart made a great point:

This is the equivalent of rabidly, aggressively denying the possibility of the Hershey's factory having anything to do with the outbreak of "chocolatey goodness" in Hershey, PA.

The interpretation you stated is very one sided, and doesn't mesh with the author's own writing.

I don't think a lab leak needs to be connected in anyway with humans modifying the virus. It could easily been the case that these bats were studied in this lab without modification and a leak occurred.

There are two controversies here:

(1) Were the first human infections of C19 the result of a random zoonotic outbreak (perhaps from a seafood market), or (alarmingly) from samples mishandled in a laboratory?

(2) Was the origin of C19 "naturally" zoonotic, or (alarmingly) was it in some way the product of laboratory manipulation of an existing bat coronavirus?

I don't know that there's much serious evidence for the alarming case on (2). But there's increasing evidence for the alarming case on (1).

I guess I disagree that (1) would be especially alarming. Mishandling of lab samples occurs all the time (even with good precautions), everyone knows this, and this is actually an excellent reason to be all the more cautious about whether GoF research should be allowed. Zoonotics are also a fact of life. Ultimately, it comes down to what one's priors are re: what actually happened in this case; it doesn't really matter much either way.

You seem be shifting the goal posts.

Do you find it fishy that these early samples were not fully sequenced, and that the parts that were sequenced were later deleted?

Mishandling of novel or virulent pathogens that cause widespread outbreaks do not in fact occur all the time. It's not hard to see why it matters how C19 happened: if it was in fact a lab leak, that would suggest strongly that it's problematic to site this kind of research in densely populated areas (contra the stereotypes, Wuhan, "the Chicago of China", is a densely populated metropolis). Had novel coronavirus research been centered in Casper, Wyoming, and an outbreak occurred there, we wouldn't much have to wonder where the virus came from.

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