6 ms·

Genetic tracing of market wildlife and viruses at the epicenter of C19 pandemic

19 points by dopylitty 2y ago

jacknews 2y ago
[flagged]
DoreenMichele 2y ago
Retrospective review of early COVID-19 cases identified 174 patients with onset in December 2019, 32% of whom had an ascertained link to this location, within a city of over 12 million...a geospatial analysis of residences of the early cases with no identified link to the Huanan market showed that they lived unexpectedly close to and centered around the market,3,5 even though geographic proximity was not used as a case criterion. The genomic epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shows that there were very few human infections before the earliest ascertained market case with onset on December 10th, 2019. In February 2020, China’s government enacted a far-reaching ban on the sale of wildlife for human consumption. Zoonotic spillovers in wildlife markets have long been known to present risks for viral emergence. This has significant implications for urban planning and community development as a means to protect human health, a function the field once served which was a primary purpose at one time but which gets relatively short shrift these days. Haussman's redesign of Paris was prompted by high death rates due to disease for poor Parisians living in overcrowded slums. His redesign is still world influencing and Paris remains famous as a very livable city. Urban planners used to routinely consider things like walkability of the city not as a matter of convenience for residents but as a means to ensure people got adequate exercise in day-to-day life without really trying or having to join a gym and make time in their day for it. This kind of thinking has largely been abandoned in urban planning circles. Time to bring it back with an eye towards "How do we stop disease transmission across large expanses of space?" Disease wiped out a lot of Natives when Europeans began coming to The New World (aka The Americas). In some cases, entire tribes went extinct. Disease likely killed far more Natives than conflict with European settlers. Hundreds of years later and planet Earth still can't get the memo about travel and disease transmission as evidenced by the pandemic.
derbOac 2y ago
Given all the suppression and secrecy that was going on at the time of the outbreak, I'm never sure what to make of studies like this. It's impressive in how detailed it is but it's also been years and there's so many variables that could come into play. The article even states that it "has been proposed that humans could have introduced the virus into the Huanan market. It is most likely that there were human infections of SARS-CoV-2 earlier than the first documented and hospitalized market cases, including unascertained market cases or contacts thereof." Also, "The detection of SARS-CoV-2 RNA in the Huanan market in January 2020 could plausibly reflect deposition several weeks before sampling, compatible with estimated dates of the first human infections." The authors have counterpoints but I sort of feel like anything is on the table at this point, and I'm not sure I find their counterpoints convincing. In general, these epidemiological/public health-type studies of COVID19 origins have this tendency to assume a zoonotic origin, or a typical "natural origin" and then proceed accordingly, rather than to acknowledge it's one of many possible scenarios, and then proceed from that. For just one example, they add in their counterpoints "any hypothesis of COVID-19’s emergence has to explain how the virus arrived at one of only four documented live wildlife markets in a city of Wuhan’s size at a time when so few humans were infected." But this really should say "when so few humans were publicly known to be infected." It also assumes the data itself is sound, even though it is based on data first publicly published on in April 2023. I suspect they take this approach because to consider the full range of options leads to too much uncertainty they can't address. I hate being so skeptical but there's so much to be suspicious about, including the cover-ups by Daszak and colleagues, the Chinese government, American governmental institutions, and just the sheer amount of time that went by with nothing happening despite the historical import of this virus. It doesn't appear that people who were in a position to do anything about figuring out where the virus came from really wanted to know.
blackeyeblitzar 2y ago
Given that the site visit to Wuhan was delayed by over a year and given that the people involved in the visit were the same people who were suspected of causing a lab leak, like Peter Daszak, I just can never bring myself to trust any other cause as being the answer. There is just no way to go back and decisively investigate the origin now, thanks to a coordinated campaign to suppress speech about the lab leak theory - including the infamous lancet letter, social media censorship, the CCP’s refusal to cooperate, Fauci’s word games about gain of function, and the WHO’s willingness to parrot CCP propaganda.
tripletao 2y ago
The same set of authors has brought us at least two prior attempts ("proximal origin", "multiple zoonotic origins") to reject the possibility that the SARS-CoV-2 pandemic arose due to a research accident. All have been covered credulously in the popular media, contributing to the false consensus that e.g. caused Facebook to delete opposing arguments. This false consensus has now broken to some extent, but apparently not yet among high-impact journals. As for prior attempts, their result is grossly overstated. Biosafety Now has published a detailed call for its retraction: https://biosafetynow.substack.com/p/crits-christoph-et-al-2024-retraction https://biosafetynow.substack.com/p/crits-christoph-et-al-20... I don't think the details are really necessary, though. Approximately zero cases outside China were traced to their introductions, despite the forewarning, and despite the restricted set of options (an airport or seaport). This isn't for lack of trying--it's just really hard to do that from epidemiological data that's necessarily scarce and biased, especially for a virus whose frequently mild symptoms mean most cases never get ascertained. So why would anyone believe they'd succeeded at the much more difficult task of tracing that very first introduction? The usual answer seems to be "because the paper was full of math that I didn't understand, and I trusted the authors"--but that's a pretty bad reason, especially when the authors are funded by and coordinated closely with the agency that advocated for (and funded!) the high-risk research in question.
- DoreenMichele 2y ago
  Thank you for the context. My reasons for thinking it was credible have nothing to do with "math I didn't understand." I actually think the larger problem is how it spread via travelers and that some of the actions taken nominally for purposes of controlling the spread actually made things worse. People were herded together in airports to be checked or some nonsense. We may never know the origin story and I still don't know what to suggest in practical terms for preventing something similar from happening again, but I do think it needs to be addressed someplace other than "wear face masks and use hand sanitizer" while otherwise doing the same stuff that helped spread the virus around the globe.
  - tripletao 2y ago
    I hadn't read your top-level comment here before I wrote mine, but I think you're responding to a different question from the one the authors intended to answer. The paper's language is rather muddy (even vs. the preprint), I assume because Cell required the authors to weaken their claims. The authors' comments to the popular media express their intent more clearly: > "This paper slots into many other studies over the last few years that have been building the case for this very clearly being a natural virus that spilled over, very likely at the Wuhan seafood market," Kristian Andersen, co-corresponding author and professor at Scripps Research, told Newsweek. https://www.newsweek.com/scientists-shed-light-wildlife-species-covid-wuhan-market-1955782 https://www.newsweek.com/scientists-shed-light-wildlife-spec... This paper is about that initial introduction of the virus into humans, not about subsequent human-to-human spread. The authors are arguing that SARS-CoV-2 was "very clearly" natural, and thus not a research accident. This forms the basis for arguments that additional regulation of high-risk biological research is unnecessary, since it's much harder to say that with the possibility that such research just killed ~30M people.

19 points by dopylitty 2y ago

[flagged]

Retrospective review of early COVID-19 cases identified 174 patients with onset in December 2019, 32% of whom had an ascertained link to this location, within a city of over 12 million...a geospatial analysis of residences of the early cases with no identified link to the Huanan market showed that they lived unexpectedly close to and centered around the market,3,5 even though geographic proximity was not used as a case criterion. The genomic epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shows that there were very few human infections before the earliest ascertained market case with onset on December 10th, 2019. In February 2020, China’s government enacted a far-reaching ban on the sale of wildlife for human consumption. Zoonotic spillovers in wildlife markets have long been known to present risks for viral emergence. This has significant implications for urban planning and community development as a means to protect human health, a function the field once served which was a primary purpose at one time but which gets relatively short shrift these days. Haussman's redesign of Paris was prompted by high death rates due to disease for poor Parisians living in overcrowded slums. His redesign is still world influencing and Paris remains famous as a very livable city. Urban planners used to routinely consider things like walkability of the city not as a matter of convenience for residents but as a means to ensure people got adequate exercise in day-to-day life without really trying or having to join a gym and make time in their day for it. This kind of thinking has largely been abandoned in urban planning circles. Time to bring it back with an eye towards "How do we stop disease transmission across large expanses of space?" Disease wiped out a lot of Natives when Europeans began coming to The New World (aka The Americas). In some cases, entire tribes went extinct. Disease likely killed far more Natives than conflict with European settlers. Hundreds of years later and planet Earth still can't get the memo about travel and disease transmission as evidenced by the pandemic.

derbOac 2y ago

Given all the suppression and secrecy that was going on at the time of the outbreak, I'm never sure what to make of studies like this. It's impressive in how detailed it is but it's also been years and there's so many variables that could come into play. The article even states that it "has been proposed that humans could have introduced the virus into the Huanan market. It is most likely that there were human infections of SARS-CoV-2 earlier than the first documented and hospitalized market cases, including unascertained market cases or contacts thereof." Also, "The detection of SARS-CoV-2 RNA in the Huanan market in January 2020 could plausibly reflect deposition several weeks before sampling, compatible with estimated dates of the first human infections." The authors have counterpoints but I sort of feel like anything is on the table at this point, and I'm not sure I find their counterpoints convincing. In general, these epidemiological/public health-type studies of COVID19 origins have this tendency to assume a zoonotic origin, or a typical "natural origin" and then proceed accordingly, rather than to acknowledge it's one of many possible scenarios, and then proceed from that. For just one example, they add in their counterpoints "any hypothesis of COVID-19’s emergence has to explain how the virus arrived at one of only four documented live wildlife markets in a city of Wuhan’s size at a time when so few humans were infected." But this really should say "when so few humans were publicly known to be infected." It also assumes the data itself is sound, even though it is based on data first publicly published on in April 2023. I suspect they take this approach because to consider the full range of options leads to too much uncertainty they can't address. I hate being so skeptical but there's so much to be suspicious about, including the cover-ups by Daszak and colleagues, the Chinese government, American governmental institutions, and just the sheer amount of time that went by with nothing happening despite the historical import of this virus. It doesn't appear that people who were in a position to do anything about figuring out where the virus came from really wanted to know.

blackeyeblitzar 2y ago

Given that the site visit to Wuhan was delayed by over a year and given that the people involved in the visit were the same people who were suspected of causing a lab leak, like Peter Daszak, I just can never bring myself to trust any other cause as being the answer. There is just no way to go back and decisively investigate the origin now, thanks to a coordinated campaign to suppress speech about the lab leak theory - including the infamous lancet letter, social media censorship, the CCP’s refusal to cooperate, Fauci’s word games about gain of function, and the WHO’s willingness to parrot CCP propaganda.

tripletao 2y ago

The same set of authors has brought us at least two prior attempts ("proximal origin", "multiple zoonotic origins") to reject the possibility that the SARS-CoV-2 pandemic arose due to a research accident. All have been covered credulously in the popular media, contributing to the false consensus that e.g. caused Facebook to delete opposing arguments. This false consensus has now broken to some extent, but apparently not yet among high-impact journals. As for prior attempts, their result is grossly overstated. Biosafety Now has published a detailed call for its retraction: https://biosafetynow.substack.com/p/crits-christoph-et-al-2024-retraction https://biosafetynow.substack.com/p/crits-christoph-et-al-20... I don't think the details are really necessary, though. Approximately zero cases outside China were traced to their introductions, despite the forewarning, and despite the restricted set of options (an airport or seaport). This isn't for lack of trying--it's just really hard to do that from epidemiological data that's necessarily scarce and biased, especially for a virus whose frequently mild symptoms mean most cases never get ascertained. So why would anyone believe they'd succeeded at the much more difficult task of tracing that very first introduction? The usual answer seems to be "because the paper was full of math that I didn't understand, and I trusted the authors"--but that's a pretty bad reason, especially when the authors are funded by and coordinated closely with the agency that advocated for (and funded!) the high-risk research in question.

DoreenMichele 2y ago
Thank you for the context. My reasons for thinking it was credible have nothing to do with "math I didn't understand." I actually think the larger problem is how it spread via travelers and that some of the actions taken nominally for purposes of controlling the spread actually made things worse. People were herded together in airports to be checked or some nonsense. We may never know the origin story and I still don't know what to suggest in practical terms for preventing something similar from happening again, but I do think it needs to be addressed someplace other than "wear face masks and use hand sanitizer" while otherwise doing the same stuff that helped spread the virus around the globe.
- tripletao 2y ago
  I hadn't read your top-level comment here before I wrote mine, but I think you're responding to a different question from the one the authors intended to answer. The paper's language is rather muddy (even vs. the preprint), I assume because Cell required the authors to weaken their claims. The authors' comments to the popular media express their intent more clearly: > "This paper slots into many other studies over the last few years that have been building the case for this very clearly being a natural virus that spilled over, very likely at the Wuhan seafood market," Kristian Andersen, co-corresponding author and professor at Scripps Research, told Newsweek. https://www.newsweek.com/scientists-shed-light-wildlife-species-covid-wuhan-market-1955782 https://www.newsweek.com/scientists-shed-light-wildlife-spec... This paper is about that initial introduction of the virus into humans, not about subsequent human-to-human spread. The authors are arguing that SARS-CoV-2 was "very clearly" natural, and thus not a research accident. This forms the basis for arguments that additional regulation of high-risk biological research is unnecessary, since it's much harder to say that with the possibility that such research just killed ~30M people.