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1/n It is vital we get objective analyses of the SARS-CoV2 origin to prevent future outbreaks and recurrence. This long thread details what I’ve learned, hoping to encourage those with background in molecular evolution or protein function to devote more time to the origin of CoV2
2/n There is a Clique of virologists who control the narrative regarding the source of the CoV2 virus and while it is important to hear from these individuals, they have a conflict of interest and it is equally important that independent voices from outside virology contribute
3/n You will find @PeterDaszak @Baric_Lab @arambaut @edwardcholmes @sciencecohen @AliceCHughes @K_G_Andersen @angie_rasmussen @MackayIM @EpsteinJon etc. repeat ad nauseam on Twitter and in media that a lab origin of CoV2 is for the “tin foil hat crowd” or a “conspiracy theory”
4/n These are not independent voices but highly connected collaborators and colleagues, along with virologists in Wuhan. They have expertise. There are two reasons they would dismiss a lab origin of CoV2 – 1) if true, this would be highly detrimental to their research and…
5/n what I’m inclined to believe, 2) there would be a massive psychological barrier to admit a colleague’s lab may have contributed in any way to a pandemic that resulted in thousands of dead. I can’t see getting past this, and this highlights the necessity for outside voices
6/n So where did the virus come from? Initial reports (and basis of the zoonotic theory) is that CoV2 came from a crossover event connected to the Huanan Seafood Market. This is no longer an accepted narrative as 1) many early CoV2 cases had no connection with the market, and
7/n 2) the virus is most similar to bat coronaviruses but there is no record of bats at the market nor of an appetite for bats in Wuhan. Chinese authorities have now discounted the market. Environmental and animal samples were taken but no results or sequences have been disclosed
8/n So again, where did the virus come from? Local bats were hibernating at the time. Possibilities are then 1) a jump to a secondary species which was brought to Wuhan, then a jump to humans, or 2) infection of a laboratory worker that transmitted the disease to the community
9/n There is scarce evidence to support either of these hypotheses to date, but one is now considered ‘scientific consensus’ and the other a ‘crazy conspiracy theory,’ so let’s debunk that notion
10/n There is one obvious retort to the dismissal of a lab origin as ‘conspiracy theory’ – escape of deadly pathogens from research laboratories is not rare! Nicely detailed here. The original SARS virus leaked from labs on SIX SEPARATE OCCASIONS, including four times in Beijing
11/n Wuhan is home to the only BSL4 (highest biosafety containment) virology lab in China. There are also numerous satellite institutes, including the Wuhan CDC (BSL2). A major theme of research in these institutes is the surveillance and study of BAT CORONAVIRUSES
12/n These institutes are located remarkably close to the Huanan market, particularly the WCDC. The location of this research center seems to have been removed from Google Maps, but I indicate here where the buildings were previously designated:
13/n Numerous Wuhan researchers are connected to the Clique, most prominently Shi Zheng-Li or ‘bat-woman’, a foremost expert on bat coronaviruses responsible for collecting thousands of bat samples and ID of key viruses including the likely SARS-1 ancestors (RsSHC014 or Rs3367)
14/n Many other Chinese virologists have strong ties (including funding) to the Clique, including Yong-Zhen Zhang, Weifeng Shi, Lin-Fa Wang, Xing-Yi Ge, Jinping Chen, Wei Zhang, and George Gao. Many were trained in the US. Together, these are the experts on bat coronaviruses
15/n Surveillance of bat viruses is centered in Wuhan but they rarely collect samples there. Why? Bats are less prevalent in Hubei province and coronaviruses less frequent in this population. Instead they collect in the Southern provinces of Yunnan, Guizhou, Guangxi and Guangdong
16/n So bat SARSr coronavirus researchers doing field work 1k-2k km away, bringing samples back to WIV or WCDC. The first piece of evidence suggesting that CoV2 comes from Yunnan concerns the sequence of its RNA-dependent RNA polymerase gene (nsp12 or RdRp)
17/n RdRp is fundamental to viral replication and is consequently highly conserved (low mutation rate) allowing lineage tracing of bat CoVs as the RdRp sequence is highly correlated with geographic location, independent of the host bat species (Lin et al Virology 2017)
18/n When the CoV2 RdRp is aligned with other bat beta lineage CoVs, where does it align? With two recently identified CoVs (I’ll return to this…) from Yunnan province. The little sequence divergence suggests that CoV2 comes from Yunnan, not Hubei (Wuhan).
19/n These RdRp sequences are extremely unique, with 17 major aa substitutions in surface residues to charged or polar amino acids. These are not found in any other bat CoV RdRp that I can find
20/n They have been identified in one other case: beta coronavirus RdRp recently sequenced from samples of diseased Malayan pangolins (no current explanation…??) that were rescued from smugglers and taken to the Guangdong Wildlife Rescue Center
21/n From the above alignment you see the Yunnan viruses clustering with CoV2 are designated RaTG13 and RmYN02. Both RdRp PCR and metagenomic approaches should have ID’d these in thousands of previously processed samples, but they were not discovered until after the outbreak
22/n RaTG13 is CoV2’s closest ancestor across most of the genome. It was originally designated RaBtCoV/4991 by Shi Zheng-Li (Vir Sinica, 2016) and was collected in 2013. @PeterDaszak indicated it was not interesting enough for further study (11% different from SARS-1 in RdRp)
23/n There is evidence that RaTG13/4991 was isolated from a mine shaft implicated in a SARS-like pneumonia in miners. Internet ‘sleuths’ retrieved these data from Chinese language thesis reports. Shi Zheng-li has not addressed it, or why the name was changed to RaTG13
24/n So how does a Yunnan virus get to Wuhan? From the laboratory perspective, this could occur in two ways: 1) accidental infection during field work, or 2) accidental infection during laboratory work. It is clear that PPE is not always worn when collecting the bat samples:
25/n Regarding infection during laboratory work, there is widely circulated intel that officials were concerned about the level of training at the WIV. But the real question is: what work were they doing with CoVs and could they have a virus responsible for the pandemic?
26/n Here I invite you to look into: 1) synthetic assembly of viral genomes and 2) gain-of-function (GOF) research in which viruses of no concern to humans are manipulated into deadly pathogens. Both of these approaches are real, well documented, are were happening.
27/n So it is possible that CoV2 could have been a lab accident and this is certainly not a ‘wild conspiracy theory’, so why has it been dismissed as such and what is the source of the zoonotic narrative that has apparently become the ‘scientific consensus’? This:
28/n The Clique published this speculative piece shortly after the outbreak and it remains the primary source of the zoonotic hypothesis. Nonetheless, the major points here remain conjecture or have already been debunked…
29/n 1) Mutations in the receptor-binding domain. CoV2 binds human ACE2 with extraordinarily high affinity and they suggest it could not be designed. But no protein engineer would ever attempt this – it would be evolved through selection (like monobodies or nanobodies)
30/n 2) Polybasic furin cleavage site and O-linked glycans. The new O-linked glycans predicted here are not present in experimentally derived data. The furin site is not observed in any beta coronavirus with any significant homology to CoV2. Inserted are PRRA (before RSV)
31/n This furin site, key for S1-S2 cleavage of the viral spike protein and its entry into human cells, is completely unexplained. One of the recently identified CoV2 ancestors, RmYN02, was suggested to also have amino acids inserted in this region, but this is false:
32/n RmYN02 has low homology through the S gene and its PAA residues are consistent with nucleotide substitutions rather than “insertion and deletions”: This very site has previously been used for GOF studies of the SARS-1 CoV, whereby researchers introduced polybasic residues
33/n Unfortunately, the idea that RmYN02 has a polybasic insertion has taken off resulting in publications like this: Neither @CurrentBiology nor the researchers involved will comment on the nucleotide alignment, and instead chose to further disseminate the ‘insertion’ view
34/n To the credit of the Clique, in “Proximal origins” they include the below paragraph. Indeed, natural passage of an RaTG13-like virus in cell culture or animals (e.g. ferrets) could generate something like CoV2 and these experiments are routinely performed in labs
35/n I will end by saying there are other circumstantial suggestions of a lab origin. The virus is inexplicably well-adapted to humans and highly stable ( @Ayjchan preprint). Some have flagged issues with waste removal at WCDC. There are key missing databases of viral sequences
36/n As this will affect us all for years to come, more people with appropriate expertise need to put pressure on the authorities to allow independent analysis of the experiments in these labs, and to re-sequence some key samples (RaTG13/RmYN02/pangolin).
37/n The NGS data from some of these have been questioned, when available at all (RmYN02!), as detailed here. Independent sequencing and analysis would dispel the speculation around these samples and allow further comparison of these viruses to CoV2
38/n I have no idea where the virus came from and there are no evidence to date suggesting either the zoonotic or lab theory are correct, or crazy. I hope the zoonotic origin is right. Nevertheless, there should be an end to viral surveillance work and GOF research.
39/n Consider that the virus most similar to CoV2 was sampled in 2012. It was considered uninteresting because it ‘only’ had 89% identity to SARS-1. How to identify the next pandemic pathogen? You can’t, it is not possible and brings viruses back to densely populated cities.
40/ More people please look into this! Here are some on Twitter doing an admirable job and need support from scientists and international media @BillyBostickson @TheSeeker268 @jjcouey @franciscodeasis @flavinkins @Rossana38510044 @luigi_warren and @ydeigin (Medium article here)
Laughter, ridicule, contempt, jokes about conspiracy theories. I'm not a "real scientist" who could even "find a genome sequence" despite the thread I just wrote. You all see what's happening here?
