Peer review reduces strength of claims of a wildlife market origin of Covid | Hacker News Reader

Peer review reduces strength of claims of a wildlife market origin of Covid

ayjchan.medium.com

24 pointsayjchan18 comments

The origin story is still under debate? It's been known for 2 years that the Pangolin coronavirus was modified. Just under 97% of the the Pangolin Coronavirus matches SARS-CoV-2. What does not match? The Furin Cleavage Site. There are foreign inserts there (that aren't found in any other Coronavirus) which seem to make it more transmissible and deadly.

MSH3 Homology and Potential Recombination Link to SARS-CoV-2 Furin Cleavage Site https://www.frontiersin.org/articles/10.3389/fviro.2022.8348...

The study is a bit technical but a not-as-techincal summary can be found here https://nakedemperor.substack.com/p/lab-leak-theory-new-arti...

To summarize, a gene sequence from the Furin Cleavage Site found in SARS-CoV-2 shows up in a Moderna patent from 2016.

Don't take my word for it though, research it for yourself.

Still under debate. That theory is indeed 2 years old, I remember seeing a video about it in the early days of the pandemic.

It hasn't been confirmed, not at all, proponents of the theory claim a trillion to one chance of a coincidence (19 bases => 4^19, a naive interpretation), but a lot of scientists disagree. I you said, research it for yourself. And by my own research, the hypothesis is unlikely, so I take it as a "no" until the "further investigations" are done.

Here is my evaluation of a recent Science Magazine publication, "The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic".

Thank you, this gave me a lot to think about.

This feels like a strong claim given the source:

> Medical personnel at hospitals and clinics across the city were informed to only report suspect cases if they were linked to the market. These details have been publicly confirmed (see above)

Source: https://archive.ph/iMQVD

Their sources are:

> Liu Yue ( pseudonym at the request of the interviewee ), director of the emergency department of a tertiary hospital in Wuhan, told reporters that after the New Year's Day holiday, the hospital held a meeting, and the director of the department attended the meeting. The hospital leaders verbally conveyed to them a "reporting standard" for "unknown viral pneumonia"."

> Li Xia ( pseudonym ) , director of the emergency department of another tertiary hospital , also confirmed to reporters that on January 3, the hospital held a similar meeting.

> "The leadership of the hospital requires that this reporting standard can only be communicated through face-to-face, telephone, or WeChat voice." Li Xia said.

This is a strong claim. Is it true? Is there any evidence for this other than two pseudonymous reports?

Yes, there is much more evidence. My medium blog also cites the Chinese CDC in early 2020 and the China-WHO joint report, both of which corroborate the fact that case definitions used in Dec 2019 to mid-Jan 2020 required a link to the market or at least that the patient had to be admitted to a hospital near the market or live in the neighborhood of the market.

See: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8393104/ https://www.who.int/docs/default-source/coronaviruse/who-con... (pages 125 and 161)

This is stated most explicitly in the China-WHO joint report (page 42): https://www.who.int/docs/default-source/coronaviruse/who-con...

"In the first days of the epidemic in Wuhan, cases were identified on the basis of clinical features, including fever and acute respiratory symptoms, radiology and epidemiological features. An association with the Huanan market was identified among some of the earliest recognized cases and, for a short period until mid-January 2020, exposure to the Huanan market was included in the case definition. It rapidly became clear, however, that there were cases without a link to the Huanan market, and this element of the definition was dropped a few days after being introduced (Annex E3)."

The title of the study: "The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic"

Yet: "the observation that the preponderance of early cases were linked to the Huanan market does not establish that the pandemic originated there."

What was the purpose of the study?

Just to muddy waters!!

Figure 1A shows 120 cases from 2019 with no known link to the market, yet they cluster about the market. So the allegation of ascertainment bias does not appear to be substantiated.

Further, the criticism of rewording "these analyses provide dispositive evidence" to "these results provide incontrovertible evidence" is bizarre. The term "dispositive" in this context is equivalent to "the last and final word" which in a scientific context was rightfully removed, though it was replaced by a strong assertion.

With these two matters, I did not think the author has sufficient credibility for me to further investigate their claims.

Thanks for the feedback.

On the unlinked cases - if you read my medium post, it explains that even the cases with no connections to the market had been identified with ascertainment bias. Local investigators had searched hospitals and the neighborhood near the market for cases even if they had no link to the market.

On your 2nd point, I've clarified that it was not a rewording but a removal of both claims of dispositive and incontrovertible evidence from the preprint. This means that peer review flagged both of these strong assertions in the manuscript and the authors had to remove both of them.

You state below that the requirement for cases to be linked to the market was removed after only a few days. Is it possible that all 120 "unlinked" cases were in fact identified within those few days?

Removal of a claim of "dispositive" evidence isn't weakening the case; there could be further incontrovertible evidence that would make the present evidence no longer dispositive.

By the time the case definition requirement for a link to the market was removed (Jan 18, 2020), nearly 200 cases had been confirmed. This is not including the number of cases that were suspected/clinically diagnosed.

The 174 cases with onset in Dec 2019 considered by Worobey et al. include both confirmed cases and clinically diagnosed cases. Therefore, most, if not all, of these cases had been identified using the criteria that the patients had to either be linked to the market or, if unlinked to the market, have been identified at hospitals near the market or in the neighborhood of the market.

See: https://archive.ph/LVU6z

Re: weakening of their claim, not only did Worobey et al. have to remove these instances of unscientific language, but they also had to insert a new study limitations section and this clarification in their article:

“However, the observation that the preponderance of early cases were linked to the Huanan market does not establish that the pandemic originated there.”

"Study limitations" is standard language in epidemiological papers, so that's not a surprise, nor a condemnation.

Further, to my knowledge it is known that "case zero" (i.e. the zoonotic event) did not occur at the Wuhan market, specifically because there was already sequence divergence in early cases.

However, that doesn't prevent the market from being the main source of the outbreak. There's no evidence for any other source.

Damned crazy conspiracy theorists! And their nutjob lab leak nonsense!

Oh wait they were right?

The problem for me is the general weakening of all institutional claims to legitimacy. We don't realize just how much of our society is built on implicit trust. Once trust is gone things grind at a snail's pace, or seize up altogether. We have to trust credit card companies, banks, the postal service, the police, military, big faangs, et cetera. The individual hasn't the resources to deal with a zero trust environment.

The problem with the lab leak conspiracy nonsense is that all the nutjobs were saying it's an intentionally engineered bio-weapon unleashed by China to cripple the US and similar crazy stuff. Those voices you're saying "were right" are the entire reason it's so difficult to talk openly about the origins of the virus without sounding like a conspiracy nutjob.

No, they did not say that at all. This is an excuse while pointing at the most ridiculous argument. This sound you like to justify yourself because you were opposed to the theory, which still can be wrong of course.

There was no problem with the conspiracy nonsense, there were people who denied the possibility and maybe ask yourself about your part in that.

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