5 ms·

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

53 points by bgentry 5y ago

lame-robot-hoax 5y ago
Author’s GitHub relating to this paper: https://github.com/jbloom/SARS-CoV-2_PRJNA612766 https://github.com/jbloom/SARS-CoV-2_PRJNA612766
paulpauper 5y ago
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.
- m0llusk 5y ago
  Identifying the source of MERS took 14 years and that had less political interference. We need to be open and thorough but also patient.
  - JPKab 5y ago
    The source of MERS was identified as camels after 9 months.
- SlipperySlope 5y ago
  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.
  - okamiueru 5y ago
    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.
  - powerapple 5y ago
    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.
    - zozbot234 5y ago
      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.
    - lm28469 5y ago
      > 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
      - powerapple 5y ago
        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.
zozbot234 5y ago
> 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.
- rossdavidh 5y ago
  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?
  - zozbot234 5y ago
    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.
    - zx90 5y ago
      Please, rouge is red. You meant rogue.
    - JPKab 5y ago
      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.
    - sschueller 5y ago
rossdavidh 5y ago
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."
Metacelsus 5y ago
The fact that this was deleted is more interesting than the sequences themselves.
- maeil 5y ago
  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.

53 points by bgentry 5y ago

Author’s GitHub relating to this paper: https://github.com/jbloom/SARS-CoV-2_PRJNA612766 https://github.com/jbloom/SARS-CoV-2_PRJNA612766

paulpauper 5y ago

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.

m0llusk 5y ago
Identifying the source of MERS took 14 years and that had less political interference. We need to be open and thorough but also patient.
- JPKab 5y ago
  The source of MERS was identified as camels after 9 months.
SlipperySlope 5y ago
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.
- okamiueru 5y ago
  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.
- powerapple 5y ago
  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.
  - zozbot234 5y ago
    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.
  - lm28469 5y ago
    > 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
    - powerapple 5y ago
      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.

zozbot234 5y ago

> 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.

rossdavidh 5y ago
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?
- zozbot234 5y ago
  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.
  - zx90 5y ago
    Please, rouge is red. You meant rogue.
  - JPKab 5y ago
    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.
  - sschueller 5y ago

rossdavidh 5y ago

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."

Metacelsus 5y ago

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

maeil 5y ago
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.