When you hear all the media news, you might think that the world's opinion on the origin of SARS-CoV-2 has suddenly changed. You might even think that maybe the science has changed. It has not. An intense debate has been going on for months, which remains largely hidden from the general public.
Much of this happened in low profile newspapers, leaving major publications such asNaturein the dust. Nature is trying to catch up by releasing aSummaryto the general public on their website entitled "The COVID Lab Leak Hypothesis: What Scientists Do and Don't Know".[1]You write:
Scientists don't have enough evidence about the origins of SARS-CoV-2 to rule out a laboratory leak or to prove the alternative - that the virus is natural in origin. . . . . . . Many other coronaviruses have furin cleavage sites, such as the coronaviruses that cause the common cold.[2].
You cite a non-peer-reviewed article by Lytrasand otherstating that a virus called RmYN02 is more closely related to SARS-CoV-2 than RaTG13.[3]Those of us who are better at remembering virus names than personal names will recall that RmYN02 was quoted by renegade Chinese dissident Yan Limeng[4]as a possible precursor of a manipulated SARS-CoV-2. The Lytrasand otherThe article basically says, "Nothing to see here, just horseshoe bats or something. . . possibly . . .”, and suggests that wildlife samples are needed to find it. In other words, “More research is needed”.
Just a detail: RmYN02 isNOcloser than RaTG13 to SARS-CoV-2. This is an undeniable point and easy to find. Why thenNatureGet it wrong?
The furin cleavage site
The answer is that the real debate is not taking placeNature,Science, or the big virology journals, but in smaller places likeBioensaiosestem cell research. When the sequence of SARS-CoV-2 was published in early 2020, it was immediately clear that the furin cleavage site could not have evolved by itself. It can only have come about by recombination or by engineering.
The furin cleavage site is important because (1) furin is ubiquitous in mammalian tissues, (2) cleavage at this site is required for SARS-CoV-2 activation and entry into mammalian cells, and (3) the likelihood of a 12- Nucleotide insertion consists CTCCTCGGCGGG (encoding a PRRA amino acid sequence), which occurs by random mutation containing only two arginines (abbreviated as RR), is very low. Adding a furin site increases the tropism of the virus, meaning the virus is now able to infect more tissue types. By examining the Indian strain B.1617, which has an even larger furin site, the scientists also know that the furin site increases the pathogenicity and/or transmissibility of the virus.[13](Update: Transmissibility is increased, pathogenicity does not appear to be.)
The origin of the false claim about RmYN02 was an article by a group of researchers in Shandong, China reporting the discovery of RmYN02 in batsRhinolophus malayanusand claimed that it was "characterized by the insertion of several amino acids at the junction of the S1 and S2 subunits of the spike (S) protein," meaning that it contains a potential furin cleavage site.[5]They also claimed that RmYN02 is "the closest relative of SARS-CoV-2 reported to date across most of the genome." His own table, some of which is reproduced here, shows that this is not the case.
Percent identity with SARS-CoV-2 (from [5])
| diversity | whole genome | S | RBD | 1ab | E |
|---|---|---|---|---|---|
| RmYN02 | 93,3 | 71,9 | 61.3 | 97.2 | 98,7 |
| RaTG13 | 96.1 | 92,9 | 85,3 | 96,5 | 99,6 |
RmYN02 has only 93.3% overall identity with SARS-CoV-2 and only 61.3% identity with the receptor-binding domain (RBD) of the spike (S) protein in SARS-CoV-2, meaning it is unlikely that it binds to your human angiotensin converting enzyme receptor 2 (hACE2). The overall spike sequence is also much less similar (71.9% vs. 92.9%) and even the highly conserved E protein is less similar. Only the 1ab region, which is a DNA replicase, is slightly closer than RaTG13 of SARS-CoV-2.
The paper makes other speculations that have since been abandoned, such as the alleged pangolin connection, but its important claim concerned the possible origin of the furin site. If true, it would be evidence that it may have evolved naturally, thereby disproving claims that it was engineered by the Wuhan Institute of Virology (WIV). No doubt because of thatNaturegives you credit.
By the way, a relief for Dr. Fauci that his acknowledgments make no mention of funding from the US National Institutes of Health.
Virologists dispute Zhou's claims
The findings of this paper were disputed almost immediately by virologists Rossana Segreto and Yuri Deigin[6]on oneBioensaiosArticle published March 2021. They pointed out where in the literature WIV researchers published gain-of-function experiments on the spike protein and identified a short region in the spike protein (aa 310 to 518) as “necessary and sufficient for Conversion of Rp3-S into a huACE2-binding molecule”[7]. Shi Zhengli of the WIV and the Baric group at the University of North Carolina have published several articles describing their gain-of-function research.[8–10]If one agrees with the wisdom of such experiments, there can be no denying that the WIV conducted them.
However, the main point made by Segreto and Deigin was that the putative furin binding site in RmYN02 is not real. Your article is not easy to follow as your reasoning depends on understanding the complexities of virus sequencing (which is not as easy as sequencing a pure clone like we have in the lab) and some of your numbers are mislabeled. But their argument is that a comparison with the closest ancestors of RmYN02, including bat-SL-CoVZC45, bat-SL-CoVZXC21, and RacCS203, convincingly shows that Zhouand otherused a methodologically incorrect way of aligning their sequences by actually shifting their bases to the right to create a 4-AA deletion that is not genuine and incorrectly making it appear that RmYN02 has a primordial furin site (SPAAR), which corresponds to the SPRRAR site of furin on SARS-CoV-2.
Below is a small portion of Zhou's alignment of RmYN02 (MW201982.1) with SARS-CoV-2 (NC_045512.2) and ZC45 (mg772933.1).and otherand the new one from S&D using the well-known CLUSTALW algorithm in Figure 2 of the Bioassay article.
What they say is that ZC45 and RacCS203, which are known to have no furin cleavage sites, combine with RmYN02 before and after without insertions. There are only mutations. This implies that the NSPAA region in RmYN02 thatZhouand otherClaiming to be a furin linking nascent domain is not real. There are no deposits. There is another two amino acid deletion in RmYN02 compared to ZC45 about 30 bases down (not shown), after which the two sequences begin to show high identity.
Updated 06/17/2021We can see this most clearly by manually aligning the DNA sequences. If RmYN02 contained a 12 base insert, it would be easy to spot. Here is the result:
This diagram may look very small when you read it on a small screen, but it makes it clearer what's going on: the two sequences match fairly well before insertion and very well after insertion. The good alignment will continue for some time on the right side. Surrounding the 12-nucleotide insertion in SARS-CoV-2, starting at CAACTCACCT, are many mutations that make it difficult for the computer to match the two sequences.
The scatter plots below demonstrate this. The two sequences have homologous regions before and after the insertion as shown by the green line on the right. A variable area starting around the AGT TAT in the diagram above is shown in red. Then the alignment jumps about 18 bases to the right. This is the notebook. Regardless of where this pesky CCT finds its place, it is clear that there is a major gap in RmYN02 that is absent in SARS-CoV-2. This suggests recombination (although engineering cannot be ruled out), and that confused Zhou.and other
Scatter plots of SARS-CoV-2 and RmYN02 spike. Only a small portion of the entire sequence is shown. The variable region is shown in red. This is followed by a clear gap where the alignment shifts to the right. This is the insertion into SARS-CoV-2. There are no other recognizable inserts in the sequence of S that is in the database.
The original sequence of RmYN02 is still in the gene bank, but the new alignment from the S&D analysis is clearly better: it is a better match for its relatives. The alternative hypothesis is not parsimonious - it has too many gaps, which is considered bad because it looks like a product of wishful thinking.
This means that if the evolutionary path is from ZC45→RmYN02→SARS-CoV-2, the furin site in SARS-CoV-2 might not have evolved. It had to be some kind of recombination event. A laboratory origin cannot yet be ruled out, and assuming it as a possibility is not an unfounded conspiracy theory. That's a perfectly plausible conclusion - just as it was back in March when the S&D paper was published.
Confusion in the tabloids
Meanwhile, reporters in the general press are completely confused. The UKdaily mailclaims that there are two BSL-4 facilities in China instead of one, and that Shi Zhengli denied that anyone in the WIV had fallen ill and asked for names. StillReview of the pharmaceutical industry quotesBeijing News Today [11]As I said, Patient Zero was Huang Yanling, a WIV researcher who started in 2012.
It's easy for people to forget that the Wuhan CDC, where samples of the virus were no doubt couriered and stored for safekeeping or study, is just meters from the wet market.
However, during the pandemic, the American press had only one criterion for factuality: whether the fact could be used to harm President Trump. OWashington Postcalled the idea of the leak a conspiracy theory in an article titled "Tom Cotton Keeps Iterating on a Debunked Coronavirus Conspiracy Theory." We have to deal with that. Who knows what the story will be like in six months? As the Russians in the USSR used to say: the future is certain, the past is ever changing.
There are also claims cited in ared stateArticlethat sequenceCGG CGG, which encodes two arginines, is almost never found in viruses. This is not true: it is rare for these viruses, but not absent. Only 5% of the arginines in SARS-CoV-2 or RaTG13 are encoded by CGG, while 16.7% of those should only happen to be CGG. Sure, gain-of-function research could have gotten them there just as easily as Ma and Pa Nature, but it's pretty weak evidence.
Most scientists view gain-of-function as a threat, as evidenced by the 2011 conviction of two scientists who considered an alteration that would have made highly pathogenic H5N1 influenza viruses transmissible from ferret to ferret through respiratory droplets.[12]This little coup led to a US ban, which Obama lifted shortly before Trump took office. All of this leads to comparisons between Fauci, who advocated this type of research, and Frankenstein in the political media (cfHere).
(As an aside, there are pictures of Anthony Fauci in a clean, starched lab coat, proving that he is not a true scientist. Lab coats are only worn when the risk of soiling one's clothes is greater than the risk of falling on a beaker to let those big sleeves. The lab coats also have slits through which you can access their pockets. These slits routinely get caught in lever-shaped door handles. If you're lucky, the lab coat will tear. If you don't, whatever our sling flies down the hall and, along with the security guy who checked it, triggers the emergency eyewash, so we only use it when security is around - or when we're talking to the press.)
What if biologists created Covid?
The editors ofNatureare obviously concerned about what might happen to international scientific cooperation, not to mention their dream of securing and influencing internationally if the PRC turns out to have created Covid. Of course, we don't vibrate much in the lab these days. After what online lynch mobs did to Tim Hunt, we're also trying to stop holding hands in the lab.
Congratulations go toBioensaiosestem cell researchfor having the courage to publish these important articles. But whyNaturenot even quote?
At least now they realize there is a controversy. Maybe they've realized that if you tell everyone you're super awake and political, you won't be surprised if people don't believe what you're saying. Or maybe they've finally figured out that the only thing worse than doing dangerous research that's killing thousands of people is covering it up.
1. The COVID Lab Leak Hypothesis: What Scientists Do and Do Not Know https://www.nature.com/articles/d41586-021-01529-3shortcut
2. Wu Y, Zhao S. Furin cleavage sites occur naturally in coronaviruses. stem cell res. 9 December 2020;50:102115. doi: 10.1016/j.scr.2020.102115. PMID: 33340798; PMC ID: PMC7836551.
3. Lytras S., Hughes J., Martin D., de Klerk A., Lourens R., Kosakovsky Pond S., Xia W., Jiang X., Robertson D. (2021). Exploring the Natural Origins of SARS-CoV-2 in Light of Rekombination Preprint auf bioRxiv https://doi.org/10.1101/2021.01.22.427830.shortcut
4. Yan LM, Kang S, Guan J, Hu S (2020). Unusual features of the SARS-CoV-2 genome, suggesting elaborate laboratory modification rather than natural evolution, and description of its likely synthetic pathway.https://zenodo.org/record/4028830
5. Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, Wang P, Liu D, Yang J, Holmes EC, Hughes AC, Bi Y, Shi W. A novel bat coronavirus closely related to SARS is related - CoV-2 contains natural insertions in the S1/S2 cleavage site of the spike protein. Curr Biol. 2020 Jun 8;30(11):2196-2203.doi:10.1016/j.cub.2020.05.023. Epub 2020 May 11th. Errata in: Curr Biol. 5 Oct 2020;30(19):3896. PMID: 32416074; PMCID: PMC7211627.
6. Segreto R, Deigin Y. The genetic structure of SARS-CoV-2 does not preclude a laboratory origin: The chimeric structure of SARS-CoV-2 and the furin cleavage site could be the result of genetic manipulation. bioassays. March 2021;43(3):e2000240. doi: 10.1002/bies.202000240. PMID: 33200842; PMC ID: PMC7744920.
7. Maier HJ, Bickerton E, Britton P (2015). Coronavirus methods and protocols. London: Humana Press.
8. Wang N, Luo C, Liu H, Yang X, Hu B, Zhang W, Li B, Zhu Y, Zhu G, Shen X, Peng C, Shi Z. Characterization of a new member of the alphacoronavirus with unique genomic features in Rhinolophus bats. Virus. 24 Apr 2019;11(4):379. doi:10.3390/v11040379. PMID: 31022925; PMC ID: PMC6521148.
9. Li X, Zai J, Zhao Q, Nie Q, Li Y, Foley BT, Chaillon A. Evolutionary history, potential intermediate animal host, and cross-species analyzes of SARS-CoV-2. J Med Virol. 2020 Jun;92(6):602-611. doi:10.1002/jmv.25731. PMID: 32104911; PMC ID: PMC7228310.
10. Hu B, Zeng LP, Yang XL, Ge XY, Zhang W, Li B, Xie JZ, Shen XR, Zhang YZ, Wang N, Luo DS, Zheng XS, Wang MN, Daszak P, Wang LF, Cui J, ShiZL. Morcego's discovery of a rich genetic pool of SARS-related coronaviruses provides new insights into the origin of the SARS coronavirus. Duck PLoS. 30 Nov 2017;13(11):e1006698. doi: 10.1371/journal.ppat.1006698. PMID: 29190287; PMCID: PMC5708621.
11. https://www.rfi.fr/cn/China/20200216 - Wuhan Institute of Virology back in spotlight - PhD students are infected with the disease, Shi Zhengli again ensures there will be no infectionshortcut
12. S. Herfst, E. J. Schrauwen, M. Linster, S. Chutinimitkul, E. de Wit, V. J. Munster, EM Sorrell, TM Bestebroer, DF Burke, DJ Smith, GF Rimmelzwaan, AD Osterhaus, RA Fouchier. Airborne transmission of the influenza A/H5N1 virus between ferrets. Science. 2012 Jun 22;336(6088):1534–1541. doi: 10.1126/science.1213362. PMID: 22723413; PMC ID: PMC4810786.
13. The SARS-CoV-2 variant associated with infections in India, B.1617, shows furin-enhanced apical cleavage. Peacock TP, Sheppard CM, Brown JC, Goonawardane N, Zhou J, Whiteley M, PHE Virology Consortium, de Silva TI, Barclay WS. bioRxiv 2021.05.28.446163; doi: https://doi.org/10.1101/2021.05.28.446163
Jun 16, 2021 5:42 am. Updated June 17, 2021 6:36 am. Scatter chart added on June 18, 2021