@stgoldst Following on @CNN's poor coverage of the debate around COVID-19's origins, @npwcnn also fails to do justice to the amount of "coincidences" that definitely point to a lab scenario.
1) A bat coronavirus (CoV) started an outbreak on the doorstep of a lab (in the Wuhan Institute of Virology or WIV) that specializes on bat CoV research, the lab where SARS-CoV-2's closest known relative was sequenced.
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@stgoldst@CNN@npwcnn 2) Three of the lab's staff fell ill and were hospitalized with respiratory symptoms just before the outbreak
3) The Wuhan CDC lab moved in early December 2019 to a location near the Huanan Market, a market where some early COVID-19 cases were later traced to.
To find them we need to look a little bit deeper into the context.
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@stgoldst@CNN@npwcnn The research carried out by the WIV bat virus group involved sampling bats and collecting bat viruses across China (and elsewhere), then bringing them to the lab in Wuhan where their potential to cause human disease was experimentally assessed.
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@stgoldst@CNN@npwcnn This was done for natural viruses, but also for artificially built ones (made by combining parts of natural viruses), via innoculation in different types of cell culture and also on live animals (e.g. mice genetically modified to mimick human tissues).
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@stgoldst@CNN@npwcnn Most of this work was conducted in low safety BSL-2 conditions (equivalent to a standard dentist office) and the risks associated with it were highlighted in the widely reported 2018 diplomatic cables (another coincidence).
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@stgoldst@CNN@npwcnn SARS-CoV-2's closest known relative was collected in 2013 by WIV scientists in a mine near a town called Tongguanzhen in Mojiang County (Yunnan province, China), about 1,800 kms away from Wuhan.
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@stgoldst@CNN@npwcnn The Mojiang mine wasn't just sampled by chance: WIV scientists conducted at least 7 sampling expeditions there between 2012 and 2015 in the course of an investigation into a cluster of severe pneumonia cases that in 2012 had caused the death of 3 out of 6 infected miners.
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@stgoldst@CNN@npwcnn They all worked in that mine & their symptoms were similar to COVID-19's. Although the cause of those pneumonias was never conclusively stated, contemporary assessments pointed to a viral etiology & specifically to the bats that infested the mine. Ain't that a coincidence!
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@stgoldst@CNN@npwcnn Not surprisingly, samples taken from these miners were found to be positive for bat CoV-related antibodies, tests that were done at the WIV (minor coincidence :).
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@stgoldst@CNN@npwcnn Accordingly teams that sampled the mine were led by virologists who published papers in virology journals. Another coincidence: in 2016 WIV authors published a paper reporting results from their mine expeditions in 2012/2013. Results from 2014/2015 sampling were withheld.
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@stgoldst@CNN@npwcnn Coincidentally, the closest known relative that WIV scientists admittingly knew before the outbreak was reported in a way that obfuscated its connection to the Mojiang mine: up to 2019, that virus was mentioned in several WIV publications as BtCoV/4991 or Ra4991.
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@stgoldst@CNN@npwcnn But in the crucial Feb. 2020 Nature paper where WIV scientists reported the 96% similarity between a bat virus and the one causing COVID-19, they gave the bat virus a new name (RaTG13) and omitted both its previous ID, and the miners backstory.
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@stgoldst@CNN@npwcnn Of course, someone still reading might ask: if they wanted to cover this up why didn't they simply remain silent about this close relative?
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@stgoldst@CNN@npwcnn Here's why: they'd published a short but highly conserved section of 4991's genome in 2016 & this sequence is 98.7% identical to SARS-CoV-2's homologous section (meaning they're really close relatives). Since that sequence was publicly available, it had to be acknowledged.
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@stgoldst@CNN@npwcnn Besides 4991 (aka RaTG13), it was recently confirmed that WIV scientists knew beforehand at least 8 other bat CoVs closely related to SARS-CoV-2, all collected from bats in the said Mojiang mine.
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@stgoldst@CNN@npwcnn Until recently these 8 CoVs had not been reported in any WIV paper (they were notably omitted in Zhou et al. Feb. 2020). But they show up along Ra4991 under the heading "Lineage 4" in a recently found WIV master's thesis, supervised by Zhengli Shi & submitted in June 2019.
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@stgoldst@CNN@npwcnn Adding to the coincidences, several WIV researchers published a paper summarizing the findings of Ping Yu's master's thesis. This paper (Yu et al. 2019) includes a very similar figure that surprisingly doesn't mention this new lineage of close relatives of SARS-CoV-2.
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@stgoldst@CNN@npwcnn Another coincidence was noted by some in early 2020: how did a novel SARS-related CoV start a pandemic in a metropolis, hundreds of miles from any bat caves, right in the middle of a country that excels in SARS-related virology, SARS epidemiology & general social control?
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@stgoldst@CNN@npwcnn How did this bat coronavirus come out of the blue, without an identifiable intermediate host, devoid of previously known relatives, despite 15 years of extensive bat sampling?
Turns out this was an illusory coincidence stemming from, let's call it, asymmetric information.
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@stgoldst@CNN@npwcnn Now we know that SARS-CoV-2, the "novel coronavirus", was a complete novelty only to outsiders.
For WIV insiders, SARS-CoV-2 was just another member of Lineage 4, of which at least 9 close relatives had been known for years, linked to a prior outbreak not unlike COVID-19.
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Another try by @tgof137 at explaining that since the Wuhan outbreak began in a market it must have involved a double spillover where an evolutionarily derived virus emerged first & its ancestral sibling jumped later.
Is there a better, non-circular, alternative explanation?
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Peter's favorite visualization of early genomes (green=lineage A, blue=lin.B) immediately reminded me of an old thread in which I dissected a similar figure from Tang et al. 2020, a pioneering analysis of the 2 early lineages (red=lin.A, blue=lin.B).
As I said then, it's instructive to zoom in these figures & pick out the Wuhan sequences. My observations at the time:
- By 25 Feb 2020 Tang et al reported 103 publicly available SC2 genomes
- 27 of them were from Wuhan
- 26 of those were lineage B
Stoyan/Chiu's takedown of Worobey et al, followed by the publication of an early draft of DEFUSE (disclosing even more clearly the 2018 project to screen & tweak SARS2-like viruses in Wuhan) have outranked news that SC2's genome was known in Beijing way earlier than thought. 1/🧵
The news that SC2's genome was known 2 weeks before China acknowledged the "novel coronavirus" was broken by the @WSJ () building on a @HouseCommerce investigation (see ), and analysis by
@jbloom_lab ()
@WSJ @HouseCommerce @jbloom_lab The context of SC2's earliest patients, samples and sequences remains unknown, but the fact that scientists affiliated with the Chinese Academy of Medical Sciences and National Health Commission possessed this genome no later than 28 Dec. 2019 has far-reaching implications.
Building on an earlier thread (quoted below by @niemasd) let me elaborate on some of the explicit & implicit assumptions that in my view permeate the recent Pekar et al. preprint, how they influence their conclusions, and why I think those assumptions might be unwarranted.
Strictly speaking, even the assumption that mitigation started only in January 2020 can be ill-founded.
If a more bat-like A variant emerged earlier, in a different context, discrete mitigation measures might have been implemented, slowing the spread of that lineage.
A lot has been written already about four recent preprints that look into the origins of the Wuhan outbreak from various perspectives.
A thread with some additional thoughts.
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Gao et al reported additional data from the environmental & animal sampling led by China's CDC at Huanan market in Jan/Feb 2020. Part of these data were presented in the China/WHO report over a year ago, so one might expect final results by now? Nope
Unfortunately that's not the case. It's a long overdue but still very insufficient report, lacking in detail about the sampling methodology and providing no raw data for detected sequences or isolated viruses.
Whereas the phylogenetic analysis in Pekar et al. 2021 pushed human-to-human transmission back to mid-October to mid-Nov. 2019, Worobey's epidemiological analysis now seems to suggest the outbreak started in December. So what changed between these two different assessments?
Because of his late arrival to the origins debate & near exclusive reliance on quotes from hard core zoonati, @hiltzikm's writings on Covid origins are arguably irrelevant.
Here, however, he proclaims "more debunking of the lab-leak theory for COVID" so I gave it a read...