There has been much controversy regarding the origin of the Wuhan coronavirus. It appears that both possibilities, naturally occurring or man-made, are legitimate enough to be debated fully. However, although voices on social media are equally strong from both sides, when it comes to written pieces, there is a predominance of scientific literature and other forms of writing that were produced to disapprove the “conspiracy theory”. In contrast, not nearly as much literature or other forms of substantial writing have been put out to describe or argue for the other possibility – this virus is man-made. My goal here is to use scientific evidence and logical thinking to evaluate, and legitimate, the possibility that the Wuhan coronavirus (2019-nCoV, SARS2-CoV, etc.) is of non-natural origin. Importantly, I will base my reasoning on solid, credible evidence; I will exclude any unqualified evidence that may have been thrown in by the Chinese Communist Party (CCP) with an intention to disturb the “investigation” and thereby cover up the truth. My role or perspective here can be considered as a combination of a scientific reviewer, a detective, and a judge on a criminal trial. Why are people suspicious of the origin of the Wuhan coronavirus This has a lot to do with how the sequence of this virus (in other words, its genome) compares with those of related coronaviruses. When comparing sequences, one can compare either gene sequences or protein sequences. For viruses, however, this makes almost no difference as the whole genome of a virus is practically translated into proteins (in fact, a virus typically produces a single polyprotein by translating its entire genome and then cuts this long polyprotein at specific places to produce a set of particular proteins for specific use). Here, we will compare different viruses only on their protein sequences. By doing such a comparison, one can see that the Wuhan coronavirus is about 86% identical to the SARS coronavirus, which caused a pandemic back in 2003. This level of sequence identity basically says that the Wuhan coronavirus could not have come from SARS, something the field agrees unanimously. At the same time, the Wuhan coronavirus is STRANGELY similar to two bat coronaviruses, ZC45 and ZXC21. Overall, the sequence of either of the two bat coronaviruses is 95% identical to the Wuhan coronavirus. In fact, for most part of the genome, such level of identity is maintained or even surpassed. The E protein, in particular, is 100% identical. The nucleocapsid is 94% identical. The membrane protein is 98.6% identical. The S2 portion (2nd half) of the spike protein is 95% identical. However, when it comes to the S1 portion (1st half) of the spike protein, the sequence identity suddenly drops to 69%. This pattern of sequence conservation, between either of the closely related bat coronaviruses and the Wuhan coronavirus, is extremely rare and strange! This is extremely rare because natural evolution typically takes place when changes (mutations) occur randomly across the whole genome. You would then expect the rate of mutation being more or less the same for all parts of the genome. Could other forms of evolution lead to such a strange pattern of sequence identity? Yes, there is one evolutionary event that could lead to drastic changes in only one part of the genome. It is what is called “recombination”. We would defer to the next section to explain why recombination is also practically impossible in this case. For now, let’s fix our eyes on the part that is seeing this sudden drop of sequence identity, the S1 portion of the spike protein. Figure 1. Coronavirus particle with spike proteins (red) decorating its surface. Image from the CDC website (not a photo of a real virus, but a model generated based on scientific knowledge). Spike proteins are the protrusions that you see on the outside of the virus particle (Figure 1). They are literally responsible for the name “corona” as they make the virus look like a “crown”. However, spike proteins are located here for reasons beyond decoration. They are actually the “key” that coronaviruses use to open the “lock” so that viruses can enter our (host) cells. Figure 2 shows the structure of the spike protein of the SARS virus (such structure images are as real as photos of actual people). Given the sequence similarity/conservation here, the spike protein of the Wuhan coronavirus would look pretty much the same, which is indeed confirmed by a recent publication (1). Figure 2. Structure of the SARS spike protein and how it binds to human ACE2 receptor. Pictures generated using the published structure (PDB ID: 6acj) (2). A) Three spike proteins, each consisting of a S1 half and a S2 half, form a trimer. B) The S2 halves (shades of blue) are responsible for trimer formation, while the S1 portion (shades of red) is important for binding human receptor ACE2 (dark gray). C) Details of the binding between S1 and human ACE2. The part of S1 that is important and sufficient for binding are colored in orange, with most crucial amino acid sidechains shown as sticks. This orange piece is presumably what’s “taken out of” SARS spike and “inserted” into a bat coronavirus spike protein, thereby creating a novel human-infecting coronavirus. Three spike proteins have to come together to function properly as the “key”. This three-protein assembly is what they call a “trimer”. To form this trimer, you would need the blue portion of the spike protein, which is referred to as S2 of spike. This S2 part can be regarded as the part of the “key” that you hold with your fingers; it does not actually go into the lock. However, for this “key” to work, S2 has to be there and has to preserve the ability of forming trimers. The other half of spike, the red portion or what is referred to as S1, is responsible for binding the host receptor. S1 can be considered as the portion of the “key” that literally enters the “lock”. It has to fit precisely to the delicate shape of the “lock” (host receptor) so that the “door opening” action can be accomplished. Whether or not a particular “lock” can be opened by a specific “key” is decided exclusively by this S1 part of spike. In other words, S1 of a coronavirus dictates which host(s) or cells the virus can infect. Now you may be able to appreciate what I call extremely strange. While everything else of the Wuhan coronavirus remains almost identical to the two bat coronaviruses, the S1 portion, which dictates which host a coronavirus targets, has changed significantly from the two bat coronaviruses to the Wuhan coronavirus. Let’s zoom in further (Figure 2C) and look at the exact part on S1 that dictates whether or not S1 binds a host receptor (in this case, the human ACE2 protein). This most critical part of S1 is a relatively small stretch of amino acids, labeled in orange in Figure 2C with important residues shown as sticks. This part includes everything needed for interacting with the human ACE2 receptor. You will see below how this segment, known to be unique to the SARS spike and sufficient for its interaction with human ACE2, is practically “copied” over by the Wuhan coronavirus. Figure 3. Sequence alignment of the spike proteins from relevant coronaviruses, including viruses isolated from current pandemic (Wuhan-Hu-1, 2019-nCoV_USA-AZ1), closely related bat coronaviruses (Bat_CoV_ZC45, Bat_CoV_ZXC21), and SARS coronaviruses (SARS_GZ02, SARS). Region marked by orange lines is the segment important for interaction with human receptor ACE2. Crucial residues for interaction are additionally highlighted by a red stick on top. Region marked by green lines is a furin-cleavage site that exists only in the Wuhan coronaviruses but not in any other beta coronaviruses. Alignment was done using the MultAlin webserver (http://multalin.toulouse.inra.fr/multalin/).
Figure 3 is the sequence alignment of the spike proteins from six coronaviruses. Two are viruses isolated from current pandemic (Wuhan-Hu-1, 2019-nCoV_USA-AZ1); two are closely related bat coronaviruses (Bat_CoV_ZC45, Bat_CoV_ZXC21); two are SARS coronaviruses (SARS_GZ02, SARS). By glancing through this figure, you can easily tell that the second half of spike (690 and beyond), namely S2, look pretty much the same for all six viruses. The difference is in the front half (1-~690), or the S1 portion. Now if you look at the top four sequences — the two Wuhan coronaviruses and two bat coronaviruses, you can see that they are largely the same across the S1 half of spike. Only a couple of places are different. However, the details of these differences and the way the human and the bat viruses differ from each other here in S1, in my and many other people’s eyes, practically spell out the origin of the Wuhan coronavirus – it is created by people, not by nature. First important difference is what is highlighted in between two orange lines in Figure 3. Clearly, this part of the Wuhan coronavirus spike differs significantly from those of the bat virus spikes, despite the overall high identity between them. Intriguingly, this same segment of the Wuhan coronavirus resembles, on a great deal, the corresponding piece on the SARS spike protein. Indeed, this is precisely the region highlighted in Figure 2C in orange. As we have pointed out earlier, this segment contains everything needed for human ACE2 interaction. Here, it seems that this critical piece was “copied” from the SARS spike protein and then “pasted” into a bat coronavirus. There are of course differences between these two, which may make it seem unlikely a direct “copy and paste”. However, careful examination shows that all residues essential for binding (orange sticks in Figure 2C and residues highlighted by red short lines in figure 3) are either precisely preserved or substituted with residues of similar properties. At the same time, differences lie mostly at residues non-essential for binding ACE2. Judging from this observation, one can safely envision that not only Wuhan coronavirus spike will bind ACE2 but also it will bind ACE2 exactly the same way that SARS spike does (Figure 2BC). For the two bat coronaviruses here, given how they lack many of the key residues (what is marked by red sticks in Figure 3) for binding human ACE2, it is easy to predict that these two bat viruses would not be able to infect human. The Wuhan coronavirus, while being almost identical to their bat relatives (ZC45 and ZXC21) everywhere else, has somehow “inherited” the critical, short piece from SARS spike to replace the incompetent piece in the bat coronavirus spike. As a result of this miraculous “replacement” in S1 — all key residues preserved and many non-essential residues changed, the Wuhan coronavirus has practically “acquired” the ability to infect humans, something its closest bat relatives do not have. Could natural evolution achieve something this precise and, at the same time, this deceptive??? If you have not been “awed” enough, let’s move on to appreciate magic trick #2. Please look at the region marked by two green lines in Figure 3. Here only the Wuhan coronaviruses contain an additional piece, SPRRA. Importantly, this added piece allows the spike protein to be readily cleaved by a host protease enzyme – furin, a desirable property known to produce more infectious viruses in the case of influenza. Note that no beta coronaviruses in the same lineage (lineage B), except this new Wuhan coronavirus, contain such a furin-cleavage site. Further explanation on why these changes could not have come from nature We have briefly explained why random mutations could not result in the weird pattern of sequence identity between the Wuhan coronavirus and related bat coronaviruses, ZC45 or ZXC21. Let’s dig a little deeper here. Although the spike proteins of different coronaviruses are more likely to differ, greater discrepancy in S1 may only be expected if two viruses have been long separated during evolution and have adapted, through random mutation, to their respective hosts for a long, long time. In that scenario, the overall sequence identity would be low as well. In the present case, however, the sequence identity between either of the bat coronavirus and the Wuhan coronavirus is over 95%, suggesting these two viral lineages must have diverged from each other fairly recently. Therefore, a sequence identity of 69% for the S1 portion of spike protein is simply insane. The S1 of Wuhan coronavirus could not have originated from the S1 of a bat coronavirus, a recent common ancestor that the Wuhan virus shares with ZC45 and ZXC21, through random mutations. Now let me explain why recombination also could not be responsible for the observed pattern. What happens in a recombination event is that one segment of a gene can be “replaced” by a similar segment from another gene. In evolution, recombination events happen much less frequently than random mutations. When recombination happens, however, it often brings abrupt changes to certain areas of the genome. If naturally-occurring recombination event(s) lead to the creation of the Wuhan coronavirus, how would it transpire? First, it would have to take place when an ancestor bat coronavirus, something very similar to ZC45 or ZXC21, co-existed with another coronavirus in the same cell of the same animal. Under extremely rare circumstances, recombination may occur, where a random piece in the ancestor’s genome is replaced by a similar but different piece from the other coronavirus. Importantly, to go from such ancestor to the Wuhan coronavirus, one combination event is not enough. What has to happen is that recombination has to take place twice during the evolution of the Wuhan coronavirus. In one occasion, the ancestor bat coronavirus would have to acquire, through recombination with a SARS-like coronavirus, the precise short segment of S1 that is responsible for human ACE2 interaction (region highlighted in orange in both Figure 2 and Figure 3). In another occasion, the “improved” bat coronavirus would further swap in a furin-cleavage site through recombination with yet another coronavirus that carries a furin-cleavage site between its S1 and S2 of spike. Also, again, given the overall high sequence identity (95%) between the bat coronaviruses and the Wuhan coronavirus, it is reasonable to believe that these two diverged from each other fairly recently. Therefore, both recombination events must have taken place fairly recently as well. Now, we know that SARS crossing over to infect human is a very rare event. To have another SARS-like sequence exist in nature so that the ancestor bat coronavirus can do recombination with is a very unlike event. Not to mention that this SARS-like virus must have a spike that binds ACE2 the same way as SARS and yet the piece of S1 that is most critical for binding ACE2 would differ with that of SARS spike only at non-essential sites. On top of that, furin-cleavge site has not been observed in any beta coronaviruses in the same lineage so far. Although similar furin-cleavage sites have been observed in other coronaviruses, none of them contains the same exact sequence. Therefore, the chance that the furin-cleavage site in the Wuhan coronavirus was obtained through recombination with another furin-cleavage-site-containing coronavirus is very low. Now, what are chances for both of these next-to-impossible recombination events to take place? My answer is NO CHANCE. This Wuhan coronavirus cannot be coming from nature. Why some literature has to be excluded in the analysis Someone who has been following the recent literature on this topic would point out that the above analysis failed to take into account some crucial evidence. Such evidence, coincidentally, supports a natural origin of the Wuhan coronavirus. Then how dare I leave it out in my analysis? The short answer: that “evidence” was very likely fabricated. Please allow me to switch my mode now, from a scientist to a detective or a judge. If we consider this matter as a crime under investigation, then we have so far one big suspect, Dr. Zhengli Shi from the Wuhan Institute of Virology and the biosafety level 4 (P4) lab for virology research. As the top coronavirus expert in China, since the beginning of the outbreak, Zhengli Shi has been singled out as THE suspect who may have created this virus, which somehow leaked out of the P4 lab. Intriguingly, Shi published an interesting paper in Nature a couple of weeks ago (3). There she compared the freshly obtained sequence of the Wuhan coronavirus with those of other beta coronaviruses, which allowed her to delineate an evolutionary path of this new virus. All of a sudden, out of nowhere, she reported a bat coronavirus, RaTG13, which shares high sequence identity with the Wuhan coronavirus. Strikingly, between RaTG13 and the Wuhan virus, the mutational rate is low (or sequence identity is high, 98.5%) for all parts of the genome, including the spike protein. If we have questioned the origin of the Wuhan coronavirus because of the weird pattern of sequence conservation between the Wuhan coronavirus and the two bat coronaviruses, ZC45 and ZXC21, then RaTG13 does not show any concern in that regard. Here, the spike protein is just as conserved as other proteins. From the first look, it seems that RaTG13 belongs to the same small lineage as the Wuhan coronavirus and that the two must share a very recent common ancestor. Such finding strongly suggests a natural origin of the Wuhan coronavirus. This paper reporting the RaTG13 coronavirus (3) is the evidence that I “failed” to take into account in the earlier analysis. According to credible sources, Shi has admitted to several individuals in the field that she does not have a physical copy of this RaTG13 virus. Her lab allegedly collected some bat feces about 7 years ago and analyzed these samples for possible presence of coronaviruses based on genetic evidence. To put it into plainer words, she has no physical proof for the existence of this RaTG13 virus. She only has its sequence information, which is nothing but a string of letters alternating between A, T, G, and C. Can the sequence be fabricated? It cannot be any easier. It takes a person less than a day to TYPE such a sequence (less than 30,000 letters) in a word file. And it would be a thousand times easier if you already have a template that is about 98% identical to the one you are trying to create. Once the typing is finished, one can upload the sequence onto the public database, without being really questioned for its authenticity or correctness. Once uploaded and released, such sequence data becomes public and can be used legitimately in scientific analysis and publications. Then, can this RaTG13 sequence be used as evidence in judging the matter? Well, remember, a central part of the matter is whether or not this Wuhan coronavirus is engineered or created by ZHENGLI SHI. It is Shi, not anybody else, who is the biggest suspect of this possible crime that is grander than any other crime ever committed in human history. Given the circumstances, if the evidence she raised to prove herself innocent is nothing but a bunch of letters recently typed in a word file, should anyone treat it as valid evidence? Unfortunately, in several recent reports, scientists indeed based their analyses on this RaTG13 sequence and thereby reached conclusions such as the Wuhan coronavirus is a result of natural evolution. I hope you now agree that these conclusions could not be trusted because they are based on data that is most likely FABRICATED BY SHI. Now, let us think about this from the other direction. The RaTG13 virus has a highly alarming sequence. Glancing at the sequence of the spike protein of this virus, any expert would immediately realize that this virus resembles SARS in its potential in binding human ACE2 and therefore may very likely be able to infect humans. Shi herself is such an expert. According to Shi, her lab studies bat coronaviruses so that they could someday predict novel coronavirus outbreaks and better prepare the public for such events. If her statement is true, then how could she possibly overlook this extremely interesting finding of RaTG13, something that clearly has the potential to infect humans? If this RaTG13 was discovered SEVEN years ago, why did Shi not publish this astonishing finding earlier? Why did she decide to publish such a sequence only when the current outbreak took place and people started questioning the origin of the Wuhan coronavirus? None of these make sense. All in all, these facts should make people question Zhengli Shi even more in terms of her possible involvement in the matter; she either was directly involved in the creation of this virus/bioweapon, or helped cover it up, or both. Of course, these facts also speak the necessity to exclude this RaTG13 sequence from any scientific analysis. The same goes to the notion that pangolins might be the intermediate host responsible for transmitting the virus from bats to humans. In early Feb, a press conference was held, where three researchers from South China Agriculture University (SCAU) claimed that their recent findings point to Pangolin as a possible intermediate host. First of all, the timing of the press conference is interesting – just when people are saying that bat viruses cannot directly infect humans and an intermediate host must exist (where the viral spike protein would “learn”/adapt to bind an ACE2 similar to human ACE2). When something MUST exist to favor the side of the CCP, this something always miraculously appears, just like Shi’s RaTG13. This time, it is the Pangolin coronavirus. Before even publishing the paper, these researchers showed their evidence – sequence of the receptor binding domain of the pangolin coronavirus that looks almost identical to the Wuhan coronavirus. Again, no live virus exists here, just the sequence (not even released back then). It is the same deal as the RaTG13 case; a person can literally type this sequence out in a few minutes. Therefore, for similar reasons, one has to be extremely cautious and alert that this may again be fabricated by the CCP with an intention to help cover up the truth. Fortunately, the field seems to have excused pangolins. The pangolin coronavirus sequence that was finally released by the SCAU group and another research group in Hong Kong fell short in convincing people about pangolin’s role as an intermediate host (4, 5). This is in part because, according to its sequence, the pangolin coronavirus also does not have the furin-cleavage site. Nonetheless, like RaTG13, these recent papers claiming the role of pangolin as an intermediate host should be discarded (4, 5). In fact, very recently, these SCAU researchers admitted to the press that, upon further analysis of the complete sequence of the Pangolin coronavirus, they also do not believe Pangolin is a possible intermediate host of the Wuhan coronavirus. Some scientific literature that deserves the spotlight We have just laid out the reasons why certain “scientific evidence” should be excluded. Now let us switch over to see why some other scientific evidence deserves our complete attention. First, the two bat coronaviruses, ZC45 and ZXC21, that are STRANGELY CLOSE to the Wuhan coronavirus were collected by a military research lab of the CCP. They published the finding and the sequences of these two viruses back in 2018 (6). I want to emphasize two facts here: 1) if the Wuhan coronavirus was man-made, then it must have been created using ZC45 or ZXC21 as a template; 2) nobody in this world has these bat coronaviruses, except for the CCP as evidenced by this publication. Second, Zhengli Shi co-authored a paper in Nature Medicine back in 2015 (7), where she collaborated with Ralph Baric at the University of North Carolina to show that replacing the spike protein of a non-human-infecting coronavirus with a spike protein capable of binding human ACE2 led to a novel coronavirus that gained the ability to infect humans. Now, what is happening in the Wuhan coronavirus essentially follows the same scheme; the changes, although minimal, are sufficient to turn the bat coronavirus into a virus that can infect humans. The only difference is that, when changes are this subtle, tracing the origin of the virus becomes much difficult. Third, a 2006 publication showed that inserting a furin-cleavage site in the junction region of S1 and S2 of spike of the SARS coronavirus led to much enhanced membrane fusion activity of the virus (8). Although viral infectivity enhancement was not observed in their study using pseudo viruses, presence of such furin-cleavage sites is known to be associated with high pathogenicity in influenza virus infections. Miraculously, this is precisely what is observed in the Wuhan coronavirus (region marked by two green lines in Figure 3). Furthermore, influenza viruses containing such furin-cleavage sites often infect a greater variety of cells and are therefore more likely to target organs in addition to the lung. Now you should recall multiple recent reports describing that the Wuhan coronavirus infects multiple organs, including lung, heart, blood vein, liver, central nerve system, etc. Simple and yet clear logic on how this Wuhan coronavirus may be made by the CCP If you put the pieces together, you should be able to appreciate how easily this virus can be created by the CCP. Obviously, the starting virus template used here, either ZC45 or ZXC21, is owned only by the CCP (6). What they would do then was to modify things such that this bat coronavirus, non-infectious to humans, could be converted to a novel coronavirus that infects humans with high efficiency. They did so by following two published concepts (7, 8): 1) they converted the crucial spike protein to something that follows the scheme of the SARS spike protein so that the virus can target human ACE2; 2) they inserted a furin-cleavage site in between S1 and S2 of spike, which may make the virus more pathogenic. These two concepts are the only ones out there to get such a job done. Yet, miraculously, they are being followed precisely here. If it were mother nature who has created this virus, then mother nature must have studied recent scientific literatures very carefully and followed these key findings faithfully in her work (2, 6-8). Also, let’s go back a little and think why they spend so much time fetching coronaviruses all over the place. Is it really like what they claimed – to understand the potentials of coronaviruses and therefore better predict future emerging coronaviruses? Why didn’t they put as much effort on vaccine research or drug discovery targeting a function/protein conserved in most coronaviruses then? The latter is not only more beneficial to the public but also way easier than predicting emerging viruses. Another possibility, of course, is that they are collecting these things to create coronavirus-based bioweapons. What is the truth? You can make up your own mind. As of me, I am fully convinced that this is a bioweapon made by the CCP. Given all the facts and the logic connecting them as laid out above, it is completely reasonable to argue that, unless the CCP can prove otherwise, the world has all the right to believe that the Wuhan coronavirus was made by the CCP. Reference 1. Daniel Wrapp NW, Kizzmekia S. Corbett, Jory A. Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S. Graham, Jason S. McLellan. Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation. Science. 2020. 2. Song W, Gui M, Wang X, Xiang Y. Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2. PLoS Pathog. 2018;14(8):e1007236. 3. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020. 4. Kangpeng Xiao JZ, Yaoyu Feng, Niu Zhou, Xu Zhang, Jie-Jian Zou, Na Li, Yaqiong Guo, Xiaobing Li, Xuejuan Shen, Zhipeng Zhang, Fanfan Shu, Wanyi Huang, Yu Li, Ziding Zhang, Rui-Ai Chen, Ya-Jiang Wu, Shi-Ming Peng, Mian Huang, Wei-Jun Xie, Qin-Hui Cai, Fang-Hui Hou, Yahong Liu, Wu Chen, Lihua Xiao, Yongyi Shen. Isolation and Characterization of 2019-nCoV-like Coronavirus from Malayan Pangolins. bioRxiv. 2020. 5. Tommy Tsan-Yuk Lam MH-HS, Hua-Chen Zhu, Yi-Gang Tong, Xue-Bing Ni, Yun-Shi Liao, Wei Wei, William Yiu-Man Cheung, Wen-Juan Li, Lian-Feng Li, Gabriel M Leung, Edward C. Holmes, Yan-Ling Hu, Yi Guan. Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China. bioRxiv. 2020. 6. Hu D, Zhu C, Ai L, He T, Wang Y, Ye F, et al. Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats. Emerg Microbes Infect. 2018;7(1):154. 7. Menachery VD, Yount BL, Jr., Debbink K, Agnihothram S, Gralinski LE, Plante JA, et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med. 2015;21(12):1508-13. 8. Follis KE, York J, Nunberg JH. Furin cleavage of the SARS coronavirus spike glycoprotein enhances cell-cell fusion but does not affect virion entry. Virology. 2006;350(2):358-69.
2276 Comments
Polo
3/27/2020 01:50:44 am
If true..then dna sequencing can help gene editing to get cure...let us not worry as detective has found answer..all go back home and use this evidence to get cure..bye all and dont worry..thank you detective/judge/biologitst/darwin
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Nerd has power
3/29/2020 07:42:51 pm
Well, it is true that this has nothing to do with how to cure someone with coronavirus infections. But keeping a blind eye and not taking actions may have consequences. If you know someone in your neighborhood is a serial killer, would you feel comfortable giving him freedom and keeping him active? If CCP got away this time, you bet they will throw another one at you next time around. Things can be much worse than coronaviruses, and CCP definitely has more than one thing in their pocket.
Reply
Alberto Rubio Casillas
5/22/2020 08:08:05 am
Dear NERD HAS POWER. I have important information to share with you.
Henri
5/23/2020 04:57:38 pm
Why don't you submit a letter to Cell detailing your analysis? The Editor should send the letter onto Zhengli Shi, allow a reply and publish both together in a future issue. 5/23/2020 06:03:26 pm
I see that you are concerned that the sequences being discussed are merely sequences obtained by analysing materials(eg bat poo), and no live virions or viral nucleic acid are available. In fact much of virology is being done in this way nowadays - the sequences are called metagenomes, they are assembled in computers from short sequences read from various materials - even water.
Kumar
7/6/2020 03:21:00 pm
WHO Visit to China to inquire into Virus Origin (gleaned from reading detailed Research Papers by an anonymous 'Nerd has Power') 7/7/2020 11:23:53 am
Good comments, but this is the moment in history that such research have been speculating about..in situ! Keeping the world's best minds in synch, and in science in a no blame environment is critical. Apart from that, Congress needs to explore EcoHealth.org's publically available 1090's and their auditor's required supporting docs to help unravel their research. This science would help with vaccines and therapeutics. 7/16/2020 09:49:22 am
There have been a few apologetic comments whose authors note; "but I realize this is beyond the scope of this scientific piece." In these historic times, however, our analysis could benefit now and then from a Voltaire who could see that we are living in an age of survival where his "all things are related" thesis might now have a deeper relevance (with certainly the original authors of this blog). It might be that if we now and then see a purpose to function we can develop new relevant sets of discoveries that can further assist our virology, especially now with an additional overlay personal survival but on a shared massive scale. Its an awareness of purpose that comes from our own personal (and according to Voltaire, relevant) level of consciousness.
coolbean
8/2/2020 06:00:38 pm
Nerd Has Power,
Craig Paardekooper
10/5/2020 07:55:18 am
When you know someone in your neighbourhood is a serial killer....
Vivian Wang
10/21/2020 08:15:21 pm
Hi there, I'm a New York Times reporter hoping to reach you about your assessment here. If you're willing, would love to hear from you. Thanks very much.
新新
6/7/2021 02:18:44 am
Even if it is a human-made virus, it is not necessarily made by the Wuhan Virus Laboratory. Before the epidemic of the new crown virus, Wuhan held a military games. Who can say that it is not a virus released by the relevant personnel? This is not the first time the United States has done such things, and it cannot be the last. At least the Americans have done this, and personally will not be surprised. The fake is planted and the thief shouts about the thief,
Rascal
9/4/2021 02:54:42 pm
I would like to understand why it is reasonable to believe ZC45 & ZXC21 are both natural taking from your article;
Errata
9/6/2021 01:41:46 pm
@Rascal
Adrian Gibbs
5/12/2020 04:05:10 pm
I am a long retired virologist living in Canberra Australia. Is there any chance of getting that alignment from you as I would like to have a look at it, but, as a very elderly person, I baulk at the task of assembling and aligning so many long sequences.
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Adrian Gibbs
5/12/2020 04:10:02 pm
Apologies. I am interested in obtaining the nucleotides not the amino acids. Adrian
charly
5/18/2020 03:31:03 am
you can find all published sequence on websites like genbank, eg: https://www.ncbi.nlm.nih.gov/nuccore/MT439597.1 for your concern
Nerd has power
5/18/2020 07:39:45 am
Thank you, chary, for the help.
Geo
8/6/2020 10:36:59 am
The point is if they can make this virus that is hard to detect in who made it and created a weapon. It shows the CCP is making illegal biological weapons of mass destruction. Can you imagine if they did the same thing with small pocs?
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Dave Romain
6/1/2021 07:11:38 am
PLEASE send me a copy of your 'proof' that RATG13 is fake and permission to use it. I intend to include it in a self-published book's chapter on the |Cov2 virus.
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Chris
3/27/2020 06:55:03 pm
about the publications 3,4,5 even if I understand that the dates of publications arrive at the right time just when it was necessary to justify the theory of natural genetic evolution, do you have more convincing elements which could accredit the thesis cheating?
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Na
3/29/2020 05:54:10 am
These papers were published by the Chinese (government) and used as evidence to discredit this theory. 1. These papers came after the initial accusation 2. They are taken by most scientists as evidence to disprove the man made theory. That's all he is telling you - paper was written claiming this was man made. Fake reports were then published by China to disprove this theory, scientists keep citing these papers as a reason this theory is wrong. He is telling you these papers need to be discounted as a reason, plus he is asking why would they have been necessary, all published by CCP scientists.
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Nerd has power
3/29/2020 08:01:13 pm
Technically, I do not have more elements. A lawyer or a judge don't have to show proof to discredit certain evidence, right? It's common sense that the defendant's own words don't count. I am simply saying, given the circumstances (timing of publication being only one, but not the only one), the RaTG13 sequence cannot serve as credible scientific evidence. The same goes to the other two papers on pangolin coronaviruses (there are odd things in the way they acquired their samples, BTW. I can't spend the time describing this though). The CCP should show proof on RaTG13 and pangolin coronaviruses. Again, when the evidence against them is strong, they cannot prove themselves innocent only with their own "words" (sequences).
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Nerd has power ---- corrections made on 3/29/2020
3/29/2020 08:17:42 pm
I updated some things in the article. Someone kindly pointed out two errors in my earlier version. First, in the 2006 paper (reference 8), they actually did not see enhanced viral infectivity. My memory fooled me during my writing. I have corrected this mistake and clarified that insertion of Furin cleavage site lead to greater infectivity and greater cell tropism in INFLUENZA virus, not the pseudo virus in this 2006 paper.
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Debbie
5/15/2020 05:19:56 pm
Dr. Judy Mikovits confirms much of your evidence, and I hope you have watched her interviews online - thank you for your great courage and integrity.
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Andrew M
5/16/2020 01:42:28 am
https://www.snopes.com/collections/plandemic/
Pete Ross
5/21/2020 10:57:02 am
Dr. Mikovits does not refer to the analysis here.
a
4/1/2020 08:08:29 pm
Interesting article.
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Nerd has power
4/6/2020 09:19:13 pm
These sequences are all on the public database (https://www.ncbi.nlm.nih.gov). I will list the accession numbers and you can use them to retrieve the actual sequences of these viruses.
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Piguin
4/6/2020 08:01:13 pm
Nicely written and very hard to dismiss.
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Nerd has power
4/6/2020 09:10:52 pm
I have some thoughts on what methods Shi or others might have used to create it. I might put it into another writing. I know what paper you are referring to though. It's the nature medicine paper published by Andersen, right? His statement that it is easy to detect if a virus is artificially made is laughable. He is either deliberately helping cover things up (his co-author Lipkin is a longterm partner with the CCP) or is simply ignorant about current tools for cloning. Nowadays you can easily edit genes without leaving a trace. Even if it is tedious to remove the trace, wouldn't you do all you can to achieve so when you are making a bioweapon? That nature medicine paper is a shame.
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J17
5/8/2020 06:28:56 pm
Which nature medicine article "The proximal origin of SARS-CoV-2"??? I have computer modeling background as well as virus/bacteria manipulation. I can't believe that made it into nature.
Nerd has power
5/10/2020 04:25:36 am
Thank you for sharing these info. Yes, we were referring to that Nature Medicine paper.
Hugo S. L.
5/10/2020 07:09:02 am
Could you explain if Kristian Anderson's paper is full of flaws then why no other academic papers challenging him and why Dr. Fauci quoted it? A statement made by Anderson to dismiss the lab-manipulation is that the RBD of SARS-CoV-2 is not optimized for affinity with ACE2. I found that argument is somewhat vulnerable if someone only aimed to using lab-manipulation to create a artificial chimeric virus from pangolin and RaTG13(let's ignore its authenticity in nature for now). I found several other weakness in his argument especially when he was interviewed by NYTimes because he could not articulate a persuasive argument to explain how the evolution process could have produced SARS-CoV-2 from pangolin and RaTG13. So I am wondering why there is no academic paper to challenge Anderson's view? Does that mean the whole academics are corrupted because, for example, they all want to find grants from Dr. Fauci or someone else who has supported gain of function research in China? Why did not Ralph Baric say something about it as he was the one who helped China to gain the genetic technology to manipulate virus genes in the lab?
John F Signus
5/10/2020 08:54:39 pm
In fact, when you look at the RBD domain, the underlying nucleotide sequence diverge significantly from the pangolin sequence. Which rule out recent recombination as a possible source of the RBD assuming that sequence was real. (BTW. the "new" Nature paper was a reprint of the 17/02/2020 paper where MP789 first came out, and none of the pangolin strains were submitted to GenBank before 08 Feb 2020. They likely waited for the E gene of SARS-CoV-2 to come out, before using it to finalize the "reconstruction" of the genomes. which explained the fact that they does not show up in an "identical protein report" from the E protein data of any of the SARS-CoV-2 E proteins.)
John F Signus
5/10/2020 08:57:11 pm
For the reference on the Restriction sites, go here
Nerd has power
5/18/2020 08:26:17 am
Thank you, John! Powerful analysis and reasoning as always. I do see restriction sites flanking the RBD, even before I read Yuri's article. I agree that there is a very good chance that the RBD was cloned in using the traditional method of cloning.
Nerd has power
5/18/2020 08:52:27 am
Forgot that ioderESTEl shared this on May 5th:
David Rivard
7/16/2020 09:54:15 pm
Aside from the etiology, but perhaps supporting your general thesis, is the continued forward thrust of information focused upon mortality. WHO is still echoed by most other national authorities. Perhaps the most important information that the public should be focused upon is morbidity. Other than delayed reporting, WHO continues to: 1) Relate C-19 to the common flu. This influenced much of the global public to take it both lightly and politically. 2) Emphasis on deaths, rather than morbidity presented to policy makers to distill the danger, while emphasizing alleviation of respiratory conditions as defining the cure. Note the tens of thousands, and at least 50% of those testing positive, have actually been on their own "recuperation" phase, some since the disease was revealed. There have been support groups established in almost every country. No centralized, (WHO??), or local national authorities, are cataloging long term outcomes (gathering and sharing local epidemiologic data). This population is complaining about being much less vital. Additionally, the only measurable morbidity would be if they were athletic and had past performance or work levels they could measure against (in te scientific world). In fact, a perfect bio-weapon would make populations less vital, with an albeit inevitable, but much smaller but consequential death rate. In concourse it is truly amazing that every country on earth is following the only effective treatment, the science of avoidance, and there is such a dearth of information shared with the public.
Haha
4/7/2020 01:55:50 pm
But Shi's research on collecting virus all over China is funded by ecohealth alliance, via the PREDICT program funded by USAID.
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Nerd has power
4/9/2020 04:44:16 am
Ecohealth alliance may be one of her funding sources. But researchers receive funding from many sources. Shi is funded much much more by the CCP. She is the top expert in virology and leads the top lab at the top facility in China. You can find a bunch of titles that the CCP has given her. If you think she is not under the control of the CCP, then you probably don't really know how things are in China. USAID might have given her some money, but that doesn't mean that they get to watch what her team is doing every minute. However, the CCP can and will. Has Shi obeyed and served the CCP? These titles of hers may tell you a bit on that.
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Well written. I am not a virologist. But can you take a look to see if ihttps://www.pnas.org/content/early/2020/04/07/2004999117 is valid? 70 cent army paid by CCP posted this link almost everywhere in YouTube. Here is what I replied to them:
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Chris
4/11/2020 11:17:15 am
Do you have the YouTube Links ?
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Nerd has power
4/11/2020 11:22:05 am
I saw this paper. You have made a very good point that the sample size in this PNAS paper is too modest. Furthermore, although I'm not a huge expert in bioinformatics, I can say that the way they analyzed these sequences (tracing individual mutations) is very old fashioned and not powerful in today's standards. The combination of these two already diminished their conclusions. But the biggest problem is that they did their analysis by assuming that the RaTG13 virus is the origin of the Wuhan coronavirus (reference 7 in their paper). Their conclusion is reached based on which sequence resembles the RaTG13 sequence more. As you probably know, I am convinced that any scientific analysis based on this RaTG13 sequence should be discarded.
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List Mist
4/11/2020 12:15:23 pm
Thank you for your explanations! Well said! Here are the videos:
Shaun
4/12/2020 12:25:49 pm
This is the most insane paper. I've read the whole thing from top to bottom and have shared it with the world. I am also convinced that this is a bioweapon. The timing is too perfect, everything from the furin-cleavage site to the S1 protein being a SARS variant, and the fact that these "recombination" techniques were previously used by the "Bat Lady" in research *specifically* for simulating potential human coronaviruses.
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Nerd has power
4/12/2020 02:54:07 pm
Thank you for sharing it with others. The matter itself is insane and everybody deserves to know what's really going on.
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Referring to the confusion that arose towards the very beginning of the epidemic re: Seattle coronavirus vs. Wuhan
*Furthermore* if the "recombination" event (i.e. addition of SARS-like spike protein) happened on two separate bat coronaviruses, that would almost *solidify* the fact that it were not by natural selection if those SARS-like spike proteins were similar.
Nerd has power
4/14/2020 09:33:19 pm
Thank you for the clarification. I see your point now. As far as I know, the evidence predominantly supports a single origin of the virus. There appear to be questions of where it originated (although there is actually no doubt that it came from Wuhan), but I don't think any scientific literature really hinted about different strains initiating independently at different places. Again, I think the evidence strongly support a single origin of the pandemic.
Jim jones
5/8/2020 04:31:17 am
Communism is great and has nothing to do with dictatorships. Capitalism dictates. You gave the game away with your scientific bias there. This appears to be about your personal fears and political predudices.You haven't even given a motive for creating this virus or how it benefuts china. Viruses and RNA sequence evolution are far more complex than you make out. Just like your politics.
Nerd has power
5/10/2020 04:38:44 am
Thanks, Jim Jones, for sharing your thoughts. You and I apparently have different views on communism. I just want to bring up one fact. Many countries have converted from communism to capitalism. Have you seen much complaints or people there wanting to go back? I never said capitalism is perfect, but in my opinion it is far more superior than communism. Also, if Kim Jong Un can be interested in making nuclear bombs, we will have to admit that communism is not against having massively disruptive weapons.
David Rivard
7/18/2020 11:44:19 am
I participate in several scientific blogs regarding C-19. Our office also gets up-to-date information from the executive offices of many different countries (typical of many executive offices) and the Health Minister then produces health policies regarding C-19. I have reached my own conclusions from my experiences so far.
sam
5/8/2020 05:20:13 am
Did Zhengli Shi say, "There's more where that came from"? Can you show me where she says that?
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I'm relieved that so many have been eyeballing this virus' origin question! I am not a scientist or biochemist in background but have spent some years learning bits and pieces. My educational tool through this Pandemic has been MedCram.com. They blessedly covered biochemistry basics along this journey as well as what the virus DOES and HOW it is mutating. My husband has been my captive audience throughout our SIP as we both have underlying conditions of concern. I mentioned to him in February-March about how this virus didn't seem to be "acting" like a normal virus we see. I started watching this one in DECEMBER 2019. Our other viruses I've glanced at and just went over "laundry list" of "do's" and on with life. Not so for this one; how would our household prepare and meet this one. I told husband at different times that "this one acts engineered".
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Seek The Truth
4/13/2020 07:19:26 pm
Fascinating...I notice that the comments are "split" (no pun intended)...between here and the Chinese version...I noticed some interesting comments from Elannor D Allens (and your responses) in the Chinese comments section....could you do an 'edit' to incorporate newly provided info/discovery from Elannor D Allens here as well? (I noticed from your comments here...English section...that you made updates as made aware by the commenters)...I think that inclusion of Elannor D Allens' additional info to your write-up would strengthen your assertion considerably...
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Nerd has power
4/14/2020 09:38:37 pm
Great suggestion! I completely agree that comments made by Elannor D Allens are very powerful and supportive of the conclusion here. I will work on translating these over to this English section soon. Thank you!
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Chris
4/16/2020 03:44:13 pm
Yes please translate this comments by Elannor
Greg Felton
8/26/2020 04:37:30 pm
Who is Elannor (Eleanor?) Allens and where did she publish her findings about those 79 codons?
Greg Felton
8/27/2020 07:53:59 am
Who is “Elannor D Allens” and is that spelling correct? a google search turned up nothing. Is it supposed to be Eleanor D. Allen?
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Greg Felton
8/29/2020 10:16:00 pm
STT:
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CCP is NAZI
8/29/2020 10:24:25 pm
Search "Elannor D Allens" in the next door for Chinese comments
Nerd has power
4/16/2020 03:56:59 pm
As noted by Seek The Truth in the comment above, Elannor D Allens made an excellent point in the Chinese comments section next door, which strongly supports the claim that the Wuhan coronavirus is man-made. I have looked into this aspect myself and found it very convincing. Below is this finding and its implications in English. Please note that it is not an exact translation of the comments made by Elannor, although the contents are largely the same.
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Nerd has power
4/16/2020 03:58:21 pm
a bioweapon made by the CCP.
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Ilius
4/24/2020 07:51:18 am
It appeared that there have already been amino acid mutations, acquired during the spread of this virus in humans, that are located at this particular part of the S protein, found in the later samples of this virus which have mutated in humans since it’s contnued spread about a month ago— further indication that such a part of the S protein can indeed tolerate changes and have started to change once it have been spreading intensively in humans. Further proof of the unnatural origin of the original SARS-COV-2 genomes, of which the protein sequences here are all identical with RaTG13.
Nerd has power
4/25/2020 06:12:21 am
Thank you so much for sharing your finding. It is very powerful and strongly supporting the claim that the virus is man-made.
Annette
5/12/2020 04:49:01 pm
A very interesting article and I will need to read it again. I was most interested in the E proteins as they to my understanding cause the immune reaction and possibly the cytokine storm. Please can you comment on the use of E proteins in SARS Cov 2? https://thenativeantigencompany.com/products/sars-coronavirus-envelope-protein-e-coli-2/
Nerd has power
5/18/2020 08:39:52 am
Hi Annette, my knowledge on the E protein came largely from reading this review: 5/8/2020 02:36:22 pm
Thank you for your work.The youtube channel Peak Prosperity has backed up some of your conclusions. He is a trained virologist.
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Nerd has power
5/10/2020 05:05:15 am
Thank you for the comments, John. I have seen one video from Peak Prosperity. It was fantastic. I think it's a believable source of scientific insights into this issue.
Alesh Aras
5/27/2020 06:42:05 am
Where did you get the info that the Peak Prosperity guy is a “trained virologist?” Below is is the public profile I could get from his website:
Greg Felton
8/19/2020 09:26:28 pm
Hi Nerd:
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Greg Felton
8/30/2020 12:21:11 am
Sorry, CPP is Nazi: Beijing tightens grip over coronavirus research, amid US-China row on virus origin: https://www.cnn.com/2020/04/12/asia/china-coronavirus-research-restrictions-intl-hnk/index.html. Exactly, what are CCP trying to hide? The more CCP are trying to hide, the more they are actually exposing the origin of this lab made CCP virus. We definitely need to investigate this thoroughly and hold CCP accountable for their virus. Otherwise, we don't even know how we die one day in the future with more evil virus CCP are so eager to develop!
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Nerd has power
4/17/2020 05:56:14 am
Completely agree. When we say the CCP is anti-human, we risk of understating its evilness. It used to be that not everybody believes this -- because people are generally nice and probably never even tried to comprehend things of such evil nature. But now is the time that everybody be brought to the same page. The CCP must be held accountable. The world cannot afford having communism around any longer.
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Chris
4/17/2020 03:26:39 am
Can I spread your text in France ?
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Nerd has power
4/17/2020 06:10:11 am
Please do! I was disgusted by how some high-profile scientific publications misled people, intentionally or not. That's why I wrote this. I just want more people to know the truth. The more the better. Thank you for your efforts. We are doing the same things.
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Pete Ross
5/21/2020 11:35:23 am
There are experts, including Luc Montagnier, who assert that the SARS-CoV-2 genome contains HIV-like sequences. Thoughts?
Nerd has power
5/23/2020 09:07:18 am
Hi Pete, I have said a few times in the comments that I'm not convinced that there are insertions of HIV sequences into the SARS-CoV-2 genome. Please scroll down to find such comments if you are still interested.
Patric Hausammann
4/17/2020 10:11:36 am
I have checked your work by comparing it to the published sequences on "ncbi" sources of the viruses and I couldn't find any mistake. I think the virus was pretty sure lab made. The mutations do not look natural at all, and I guess some virologes should study more, or they should not take money from the CCP.
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Nerd has power
4/18/2020 09:39:00 am
Thank you very much for your efforts. There are indeed more mutations than what I have focused on describing. The reason I didn't discuss about all mutations is because I wasn't sure how the rest of them might be involved in the actual function. I'm pretty sure about the mutations I did talk about and highlight in terms of how they are important in function and might have been manipulated. There could be more manipulations than what I was able to detect, which may involve the additional strange mutations that you've marked out. But, again, I wanted to focus on things that are more solid and well supported. I don't want to include any less-than-convincing arguments because they may take advantage of those arguments to trash the whole article.
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Patric Hausammann
4/22/2020 01:57:08 pm
Thank you for your appreciated answer. I absolutely agree to use your suggested sequences in your article to prove the claim of man made manipulations. Maybe, there comes out some evidence about the other "strange" changes later.
Greg Felton
8/26/2020 12:23:00 pm
Nerd: I have read that you oppose the HIV origin of the PRRA insert at aa 681. What is the reason for your doubt, and where do you think the insert came from?
Annette
12/12/2021 01:54:52 am
Looks like the discussions on HIV and sARS Cov-2 lab chimera is not rearing its ugly head blaming SA and some sick man as patient ) for omicron! Has anyone explored the Omi genome yet?
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Patric Hausammann
4/17/2020 04:58:09 pm
Here I have a link to the uploaded first 1501 positions of the sequences of WUHAN HU-1, 2019-nCoV, bat CoV ZC45, bat CoVZXC21, RaTG13("invention"), SARS, SARS_GZ02 and MERS in comparison to eachother.
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Jean Claude perez
4/20/2020 09:02:47 pm
> Jean-Claude PEREZ. (2020). “WUHAN COVID-19 SYNTHETIC ORIGINS
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Visitor
4/21/2020 07:12:02 am
Your article appeared to have been deleted. Could you please upload it again?
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Perez
4/21/2020 07:48:22 am
> Jean-Claude PEREZ. (2020). “WUHAN COVID-19 SYNTHETIC ORIGINS
Patric Hausammann
4/22/2020 01:43:41 pm
I couldn't open the link to the article of Mr. Perez too. But I think I've found a working link to his work.
Nerd has power
4/23/2020 07:01:19 am
Dear Mr. Perez, thank you very much for sending your published work. I have to admit that the mathematics involved in your study is way beyond me. Although I am in agreement with your conclusion that the Wuhan coronavirus is a result of human manipulation, I'm completely disqualified to comment on this part of your study.
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Simen D arreighher
4/21/2020 02:20:53 am
This is something that you may wan’t to see.
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Nerd has power
4/23/2020 07:25:05 am
Thank you for your work. What you have posted are all quality info in my opinion. Among them, the most intriguing is the link to ferrets and tree shrews. These really may have been the lab animals that they used in the course of selecting and improving viral strains, which should have followed their initial manipulation of the genome via molecular cloning.
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John F Signus
4/25/2020 04:45:51 am
The nucleotide sequence coding for the E protein in Bat-Cov-ZC45,ZXC21 and RaTG13 are exactly the same, indicative of an extremely well conserved gene that have not seen a single mutation during the entire 5 years of divergent evolution across the two very distantly related viruses(as indicated by the vast differences in the S protein) —but curiously, the first sample of SARS-CoV-2 show 3 nucleotide substitutions within this gene (without changing the amino acid sequence), and newer examples of SARS-CoV-2 have shown amino acid substitutions within up to 4 different locations within this protein, in merely 3 months of human-to-human transfer. An indication of an extremely high mutation rate within the E gene, and the permissivity of the E protein toward changes in it’s amino acid sequence.
Nerd has power
4/25/2020 06:09:47 am
Wow!!! Powerful evidence! Thank you so much for sharing. I completely agree with your analysis. The E protein being identical among ZC45, ZXC21, RaTG13, and initial samples of SARS-CoV-2 is highly suspicious to begin with. Now amino acid changes in E protein have already been observed in such a short period of human-to-human transmission. It's just such a strong proof.
John F Signus
4/25/2020 10:30:36 am
Closer analysis of RaTG13 and ZC45 have also revealed that the identicality of the E gene on these two viruses being highly suspicious.
Nerd has power
4/28/2020 08:20:31 am
Thank you again for these excellent analyses. I looked at the nucleotide conservation myself for the E proteins. There are actually two single nucleotide substitutions between ZC45/ZXC21 and RaTG13, although they did not lead to amino acid changes. It's a small error, which of course does not alter your whole logic or conclusion.
John F Signus
4/29/2020 01:59:56 am
Did you use ZXC21? I am not aware of that sequence. I did a Multalin on the sequence ZC45 and RaTG13 and the nucleotide sequences were exactly the same. If the 2 substitutions on the ZXC21/ZC45-RaTG13 were on the ZXC21 sequence, then it will be a more solid evidence that the RaTG13 N protein gene was a direct clone from ZC45. Further evidence that RaTG13 was unnatural.
John F Signus
4/29/2020 02:47:45 am
Sorry for the mistake. I think I compared the wrong sequence.
Nerd has power
4/30/2020 07:37:39 am
Thank you for the update. Please don't apologize. Your analysis was brilliant. I'm still working on that updated version of the article. I will show a sequence alignment/comparison by following your suggested strains. That, in combination with what you have described for E proteins, is very convincing.
Silverfox
4/22/2020 01:27:10 am
I I have read your analysis carefully and I do find that it stands completely.
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Nerd has power
4/23/2020 07:37:36 am
Thank you for your comments. I was made aware of Dr. Li's work, although I did not get to read it in full. I think her work is very relevant in developing therapeutic and treatment strategies, which may or may not hint the origin of the virus. My two cents.
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Pete Ross
5/21/2020 01:47:51 pm
Anyone address this type of contention?
Lois Geerhardt
4/8/2021 07:04:46 pm
Hi, Sir, you have only shown that a stretch of amino acids of S1 looks like “copied” from the SARS spike protein and then “pasted” into the Wuhan coronavirus. Don't you think that, to confirm your hypothesis, you should verify that the same does not hold true for the S1 segment from other species?
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Nerd has power
4/23/2020 08:03:53 am
Thank you. It's a very good question. Most coronaviruses don't contain this "copy/pasted" piece in their S1. The exceptions are SARS (of course) and about two SARS-like bat viruses. However, none of these SARS-like viruses "copy/paste" this critical piece as precisely as what's seen in the Wuhan coronavirus (residues important for SARS spike/ACE2 interaction all preserved/conserved and changes only occur at non-essential locations).
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MZ1234
4/24/2020 12:40:39 am
A leading Russian microbiologist has claimed the coronavirus is the result of Wuhan scientists doing 'absolutely crazy things' in their laboratory.
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List Mist
4/24/2020 11:08:13 pm
Well, https://www.newsmax.com/navrozov/china-biological-russia/2009/09/17/id/335042/ written over 10 years ago speaks well regarding whether the Chinese scientists created variants of the virus with or without malicious intent.
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Nerd has power
4/25/2020 05:46:13 am
Thank you! I obviously agree that this virus is a result of human manipulation. However, I don't think this Russian expert should so confidently say that they did it "without malicious intent". In my opinion, the evidence speaks the opposite.
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Nerd has power
4/25/2020 06:33:27 am
Thank you for bringing up this article. It actually proves two of my predictions. First, it proves that the S1 of the Wuhan coronavirus (SARS-CoV-2 as everyone else prefers) binds ACE2 the same way as SARS S1 does. I predicted this by just looking at the sequence comparison. As I mentioned in the article, there appears to be a well-plotted "copying" of a critical piece in S1 of SARS and then "pasting" it into a template virus to create the S1 of SARS-CoV-2.
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NotA~A
4/25/2020 02:51:35 am
From the comment section of this article: https://www.virology.ws/2020/02/20/pangolins-and-the-origin-of-sars-cov-2-coronavirus/
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Nerd has power
4/25/2020 06:46:00 am
Thanks for sharing! Whoever made the comment has captured something very interesting, which successfully eluded the public's attention.There seems to be a reason that Zhengli Shi does not bring this up herself -- she would struggle to explain it one way or the other. Again, great catch!
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Hydride
4/25/2020 12:19:20 pm
bits and pieces. RaTG13 used for gene assembly, the optimize to get SARS-CoV-2. How could an RdRp from an alphacoronavirus (phylogenetic distance so high that even recombination (require homologous sequences flanking the RNA fragment)was considered impossible with betacoronaviruses.) wind up in a “Natural” bat Betacoronavirus?
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Bryan
5/7/2020 01:56:43 pm
Great find. This is real evidence that RaTG13 did exist prior to 2020 and wasn't completely made up.
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Veltra
5/10/2020 10:31:55 pm
Did look at the publication--and they did not actually post any of the sequence data in regard to RaBt4991/RaTG13. Except a single figure of the phylogenetic tree. We can still not prove that RaTG13 is not manipulated.
Bryan
5/11/2020 07:45:16 am
It doesn't prove that the rest of the genome wasn't made up, but they did share at least part of the replicase gene in 2015 https://www.ncbi.nlm.nih.gov/nuccore/KP876546.1/
Biohazard0808
6/9/2020 03:30:05 pm
First of all, when looking at the "viruses" isolated from bats, it should be noted that no replication-capable viruses were actually sampled in most cases. As Shi's Science paper from 2005 describes, not a single active virus was isolated from the first 408 samples including blood, respiratory and faecal swaps. P.D. said in a recent interview that a total of 15,000 samples were taken to date just to find a few replicable viruses. Apparently, everything else was "reproduced" from RNA fragments, reverse transcribed into cDNA and re-assembled. In fact bat SL-CoV-WIV1 was the first viable CoV that was isolated in 2013 (described in nature paper). From only about 1.5% of the (mostly faecal samples) a positive RT-PCR was obtained according to the first paper in Science (although sampling methods have improved since then - in 2013 there were 23% that delivered at least a positive PCR result).
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NotA~A
4/26/2020 07:54:47 am
something is moving:
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Nerd has pwer
4/26/2020 07:47:23 pm
Thanks for sharing. The more we dig, the more people digging it, the sooner we will get to the bottom of this. We are moving along.
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Sir, thank you for your patience and consideration. I have a few questions. First, that the S1 of the SARS-CoV-2 binds ACE2 the same way as SARS S1 (or as the S1 segment from other species, not only bats, does) does not prove that binding is necessarily infectious. For example, does SARS-civet infect humans? Second, isn't the fact that the high level identity for most part of the genome with that of bat coronaviruses is not maintained in the S1 segment of the Wuhan coronavirus only a prove of how nature has learned to preserve the ability to bind ACE2, whatever random mutation or recombination may take place? Others seem convinced that SARS-CoV-2 might be a recombinant virus between viruses closely related to SARSr-Ra-BatCoV RaTG13 and pangolin-SARSr-CoV/MP789/Guangdong/2019. Indeed, coronaviruses have been shown to have a high frequency of recombination (Adv Virus Res, Volume: 48, Pages: 1-100, 1997). Their tendency for recombination and high mutation rates may allow them to adapt to new hosts and ecological niches, including natural recombination in coronavirus associated with human infection. Last, but not least, you suspect that a colleague of yours has only recently published a paper about RaTG13 infectiousness, of which she was aware SEVEN years ago, which has no other explanation than her involvement in spike protein engineering. How could she know that without having checked human infection?
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Nicholas V Thartkins
4/26/2020 09:31:18 am
(Translated from the Chinese section of this blog, originally by Dithionite)
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Nicholas V Thartkins
4/26/2020 10:03:15 am
Especially L449K, of which a major steric clash from the much longer Lysine side chain would shave off at minimum 150KJ/Mol of binding affinity of MP789/SARSCoV2 to the pangolin ACE2 receptor -- bringing the affinity from 699Kj/mol typically seen in Coronaviruses to it's native host ACE2, down to at most 550KJ/Mol.
Nerd has power
4/26/2020 08:31:24 pm
Thank you so much! Great translation and analysis!
Nicholas V Thartkins
4/30/2020 05:22:44 am
The units should be Kcal/mol not Kj/mol.
Nerd has power
4/26/2020 08:27:43 pm
I will try to answer each one of your questions.
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Nerd has power
4/26/2020 10:20:24 pm
Forgot to comment on the high frequency of recombination in coronavirus. Yes, it is a true fact. However, that does not mean that any type of change in coronavirus evolution is reasonable. I did the best I can to explain how I think recombination is unlikely to lead to the weird pattern of sequence similarity between SARS-CoV-2 and ZC45/ZXC21. Anyone can of course make up his/her own mind on this claim. Again, please check the comment made on Apr 16th. That one, in my opinion, is a very strong evidence.
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Metabisulfite
4/26/2020 08:15:33 am
https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf
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Metabisulfite
4/26/2020 08:22:55 am
Also, leronlimab, a CCR5 antagonist, seems to work well for treating COVID-19.
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Nerd has power
4/26/2020 08:42:40 pm
Thank you for your comments. I have answered this in the Chinese section, I believe. I am actually skeptical whether there are any insertions of HIV sequences in the SARS-CoV-2 genome. I have read this preprint article when it first came out and was not convinced by the evidence within. According to my own blasting, those "inserted" pieces do not necessarily come from HIV.
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Kathy
4/26/2020 08:31:31 am
KP876546 is a SARS-related betacoronavirus
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Nerd has power
4/28/2020 08:37:23 am
Thank you for sharing these!
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Silverfox
4/27/2020 11:42:20 pm
Hi again, I read every day comment on your article, and I realy appreciate your analyse. Then I would like to submit you a new article, from Jean-Claude PEREZ and Luc MONTAGNIER published in preprint on april 26.
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Nerd has power
4/28/2020 08:46:53 am
Thank you for sharing these articles. Unfortunately, I have been a little busy the last few days and did not get to read them. Hopefully I will get to later this week. I may not be able to offer much insights though because I don't have the proper knowledge in Mr. Perez's research area and methods.
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Nerd has power
5/3/2020 06:34:02 am
Sorry for the delayed response. I did get to read Mr. Perez's work here. It's different from the one he shared with us earlier. Although I'm in agreement with Mr. Perez on the conclusion that the Wuhan coronavirus is of a synthetic origin, I again would have to admit that I'm not the best person to judge such an article. Based my limited knowledge, I would say that the sequences suspected as insertions are all on the shorter end, which tend to make things inconclusive in terms of where (HIV or other origins) they could be from. I did find the higher mutational rate of the EIEs over the whole genome very interesting. This could be a sign of artificial manipulation. On the other hand, it seems to me that these EIEs are located within Orf1b and the Spike regions (correct me if I'm wrong as I'm not 100% sure I have this right). I believe that these two regions of the coronavirus genome do tend to see higher frequency of mutations. This could just be a natural trait of coronavirus evolution. Of course, this may also mean that this bioweapon did not go through exhaustive optimization/passage before being put on the real mission and therefore is now adapting to the new host.
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Tholix
4/28/2020 04:15:24 am
https://www.researchgate.net/publication/340786428_COVID-19_Pandemic_Its_Origin_Implications_and_Treatments
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Nerd has power
4/28/2020 08:49:06 am
Thank you for sharing the info!
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Ana Salinas
5/1/2020 05:32:23 am
Hi Nerd has Power, I would like to talk to you a little further. Would you give me your mail? thanks in advance!
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Nerd has power
5/3/2020 06:46:53 am
Do you mind sharing your thoughts here in the comments section? I would prefer public discussions. The communications here have been great. Thank you!
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Edix
5/1/2020 07:58:27 am
I did the Homology based modeling analysis on the MP789 RBD and the pangolin ACE2 receptor.
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Exins FG Adam
5/2/2020 07:18:54 am
https://drive.google.com/open?id=1opowSQgcvpSb58piY1mvSf4AIGzpjssS
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Chris
5/2/2020 10:52:18 am
Thank you. Tell us if the paper is accepted or not
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Exins FG Adam
5/2/2020 06:59:29 pm
Sorry but biorxiv.org have rejected my paper--citing that is should be sumbitted on a peer-reviewed journal instead of on BiorXiv.
Nerd has power
5/3/2020 07:51:28 am
Thank you for posting it here too. Great work! Too bad that they turn it down at bioRxiv. I saw some other preprints on this place: zenodo.org. Maybe you can give it a try here?
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Exins FG Adam
5/5/2020 04:30:13 am
https://zenodo.org/record/3786451#.XrFN4YijeUk
Nerd has power
5/7/2020 09:55:17 am
That's great! Congrats on the preprint! Thank you for doing it. 5/2/2020 01:52:45 pm
I’d love to discuss this with you. I would love to make a video summarizing your take. It’s very similar to mine and others. Harvard2Thebighouse has done some of the first coverage in Jan.
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Nerd has power
5/3/2020 07:35:08 am
Great video! I love the concept of journal club on a bike. You properly shattered that Nature Medicine paper.
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ioderESTEl
5/2/2020 10:09:02 pm
You may want to check this as well:
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Nerd has power
5/3/2020 08:05:49 am
Thank you for sharing these info. I love the article written by Yuri Deigin. It's so thorough, rich in information, and in the end convincing (although I'm already convinced). I learned quite a lot of details and side stories reading it. The only thing I would be picky about is that he was too scientific in his discussions and did not properly factor in how evil the CCP can be. It's certainly not Yuri's fault. The CCP certainly want to and can make bioweapons. They are also professional on covering things up, using all sorts of resources. Here they chose to use, among other things, fake science (RaTG13, Pangolin coronaviruses, Nature Medicine paper by Andersen and Lipkin, etc).
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ioderESTEl
5/5/2020 02:00:39 pm
Some other science community commentary on the original Nature Andersen, et al paper.
Nerd has power
5/10/2020 05:43:18 am
Thank you so much for sharing these. So glad to see prominent scientists coming out publicly to challenge that Nature Medicine paper and the claim that the virus is of natural origin. I thoroughly enjoyed reading these two articles as they articulated many of the same things that have been in my mind for a long time. I focused on describing the logic and evidence of human manipulation, but I had similar thoughts on how they might have worked on creating this artificial virus. Directed evolution could easily be involved.
Nerd has power
5/3/2020 12:48:17 pm
As you may have noticed, there are new pages added to this site. I just published an updated version of the earlier article on GNEWS (a great news platform created by the heroic Miles Kwok). However, there were quite a few editing errors of my GNEWS article. So I'm posting this updated article here too (RATG13 IS FAKE). This new version benefited tremendously from the insightful comments made here, especially by Ellannor D. Allens and John. F. Signus. I have acknowledged their contributions at the end. Thank you!
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Viennah K Erchus
5/3/2020 06:59:55 pm
A takedown on the recent study claiming that the furin site may have been from HKU9 through "Co-infection"
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Viennah K Erchus
5/3/2020 07:01:08 pm
Could it be ZC45/ZXC21 and HKU9 in humans?
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Nerd has power
5/4/2020 05:23:27 am
Thank you for the thorough and powerful analysis! I think you successfully dismissed all possible routes of its natural occurrence. However, they can always fall back to say that there might be a perfectly identical furin-cleavage site in a bat virus out there that we just haven't discovered yet (don't be surprised if one of the Chinese research labs will soon publish such a sequence). The burden is definitely heavier on our side, but it's becoming more apparent. The truth will come out.
Eitcherius F Asken
5/5/2020 03:55:23 am
https://www.youtube.com/watch?v=uZUJhKUbd0k
Nerd has power
5/5/2020 05:19:24 am
Thank you for posting this YouTube video. I listened to the whole thing. It's wonderful. I apparently agree with you and Chris in this video that the natural occurrence of the Furin-cleavage site is impossible. What I did not appreciate in full earlier was that all the viruses containing a similar (no one has the exact) sequence are less than 40% identical to SARS-CoV-2. That makes the chance of such a site arising from natural recombination close to zero. It's a great finding. Of course, that family tree, portraying SARS-CoV-2 being the one in that half of the branch that has a furin-cleavage site, is also very powerful. Better than what words can describe. Overall, the claim that this furin-cleavage site is a result of lab manipulation is becoming rock solid.
Ornius
5/3/2020 07:47:38 pm
Someone kindly reminds me that such co-infection experiments have already taken place in IMMUNOCOMPROMISED BAT CELL LINES by Zhengli Shi. So a recombination during cell passage may also be a plausible origin of the Furin site, in addition to deliberate insertion.
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Nerd has power
5/4/2020 05:39:12 am
Completely possible. They could introduce it in several different ways and animal passage might very likely be involved. The method that was actually used may only be revealed by the one(s) who did it.
Viennah K Erchus
5/4/2020 10:57:40 pm
I have seen bad comments on your Gnews article.
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Nerd has power
5/5/2020 05:24:27 am
I certainly can! Thank you for providing these sequences. I don't think I get to update the GNEWS article, but I can update the version here by adding an amendment. I will leave a comment on GNEWS and direct people to check it out on this blog. I hopefully will get it done by the end of tomorrow. Thanks again!
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Nerd has power
5/10/2020 05:52:34 am
Hi Viennah, sorry for the delay, but I had finally updated the article per your suggestion. Thank you so much for retrieving these sequences and put them into the right format. It made creating the figure so much easier. I will leave comments under the GNEWS article and encourage people to migrate over here to see the updated info.
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Kathy
5/6/2020 03:25:27 am
I have a question: the furin cleavage site sequence is inserted in SARS-CoV-2 in a way that produces a split of the codon for Serine in the pangolin sequence MP789 and Ratg13. Please see fig.1 here:
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Firox TD Jackinson
5/6/2020 04:45:26 am
It maybe that the insert was made in that way. Site-directed mutagenesis experiments are very conservative about the number of nucleotides they can insert/delete, and would normally be designed in such way that it minimizes the change to the original genome while achieving the goal of the operation. Making the result look as natural as it can. So if the one who made the insert found out that by splitting the Serine codon one can minimize the overall change toward the entire genome and make it look more natural than just inserting in-frame, then it will be such an insert that ended up being chosen.
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Firox TD jackinson
5/6/2020 05:30:56 am
Looked up the codon table-- and the +1 insert is very easy to design. the codon for A/Alanine can have any nucleotide at the 3rd position, so just keep the 3rd position of the original S679 at the last 1bp of the PRRA. So leave it unchanged & save 1 nucleotide on your primer. The Codon for Serine TCA/TCT can also have any nucleotide at the 3rd location and it's not in-frame with the P-R-R-A. So just change it to anything else.
Firox TD Jackinson
5/6/2020 05:42:26 am
4^8=65536.
Kathy
5/6/2020 07:52:31 am
Thank you very much for checking this and the links!
Nerd had power
5/6/2020 12:39:26 pm
Thank you for the analysis and explanation. I did not get to read the original article, but I don't think there is anything that you did not cover :). The Youtube video was excellent. It made it so crystal clear that the furin-cleavage site was not out of natural evolution.
Firox TD Jackinson
5/7/2020 05:49:54 am
Thank you for your analysis. Technically the insert could be either +1 or +2 out of frame, or is a 12nt in-frame insertion+1 silent mutation. With the +2 insert however, it would make the needed primer 2nt shorter than the in-frame 12, by shifting the reverse primer by -2. reducing the total absolute extra length need for synthesis to 10. Unlikely to have slipped past the eyes of the designer/software when designing the insert/primers.
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Firox TD Jackinson
5/7/2020 06:02:41 am
Protein being of Non-natural origin is more than 3833/3834, or more than 99.9739%
NasCinx
5/6/2020 04:01:58 am
It seems that a lot of debate was going on a short 370bp partial RdRp sequence known as RaBtCoV/4991, claiming that it was the first sample of RaTG13. However, this does not remove any of the questions surrounding RaTG13.
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Nerd has power
5/6/2020 12:40:28 pm
Exactly!
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Kathy
5/9/2020 02:35:51 pm
Now we know it:
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Nerd has power
5/10/2020 06:27:23 am
Thank you for sharing these, Kathy. I invited Peter under that tweet to come over and see how "RATG13 IS FAKE". I would love to see his comments coming up in this section.
RV
5/7/2020 12:10:59 pm
I find your hypothesis very compelling and I also find an article arguing the opposite very compelling. What do you think? You both argue your cases very well and as a layman I don't know who is right. I hope you will look at it and consider a rebuttal.
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Alix
5/7/2020 07:02:07 pm
See Viennah K Erchus’s comment on the takedown of that hypothesis.
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Firox TD Jackinson
5/9/2020 09:07:03 pm
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7075523/
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Nerd has power
5/10/2020 10:24:32 am
Thank you, Alix and Firox. Very nice info and analysis!
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NM
5/7/2020 01:26:08 pm
hopefully you have seen this ....
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Rikaja
5/7/2020 01:58:00 pm
Amazing research. Please, try to publish in a peer-reviewed journal for scientists to see.
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Bryan
5/7/2020 02:10:06 pm
One thing that really throws off estimations of similarity between RaTG13 and SARS CoV2 is the weird mutation pattern. Almost all the SNPs are C<->T or A<->G changes. This is not the mutation profile of replication errors. A recent article makes a pretty good case that this could be the result of deamidation by host cell APOBEC or ADAR proteins.
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Argin
5/7/2020 05:41:34 pm
Technically, this will not affect the mutation rate analysis as the same holds true for ZC45/ZCX21 and the rest of RaTG13/CoV2.
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Bryan
5/9/2020 09:11:04 am
That's not quite right. I'd assume enzymes like APOBEC edit any position in a codon equivalently. But the type of mutations done by APOBEC or ADAR are transitions (APOBEC: T<->C and ADAR: A<->G). Generally in the 3rd, or "wobble" position of a codon, transitions do not change the encoded amino acid, whereas a transversion does. Transitions will still usually change the encoded amino acid if they occur in the 1st or 2nt position of a codon. Interestingly, I just did a quick analysis of the SARS-CoV2 spike protein and there is a somewhat higher percentage of Cs and T/Us in the 3rd codon position (62% C/T content) compared to the first (41%) or second (54%). If APOBEC randomly converts any C/T, it's more likely to occur an the wobble position just because of the abundance of C/Ts. Overall, this means that APOBEC mutations are much more likely to cause silent (synonymous) mutations than more random mechanisms (like coping errors).
Argin
5/10/2020 08:15:41 am
However, when you look at the mutation rates between the rest of RaTG13/CoV2, the Syn/Nonsyn ratio is completely normal near 5:1. If an RNA modification system was involved, why it would selectively modify just the S2 but not the rest, like ORF1ab, M or N?
Argin
5/10/2020 08:26:36 am
62% compared to (54%+41%)/2 was not that high. Assuming only conversions from APOBEA/ADAR possible, it will only cause a minor (6.526-to-1 instead of 5-to-1 "natural") deviation from the established pattern. Not the complely unnatural 44-to-1 ratio as we see here. Even factoring the RNA modification, this ratio still return a chance of 2.76e-6 for the entire S2 protein to be natural. a 1 in 361730 chance.
Argin
5/10/2020 04:54:37 pm
In fact, if APOBEC and ADAR causes more synomynous changes than normal mutation processes in the viral RNA, we should have seen a change in the codon preference between RaTG13 and SARS-CoV-2--the ratios of codon usage should have changed since an elevated level of synomynous changes over non-synomynous changes will bias the codon preference of SARS-CoV-2 significantly from "the extreme CpG deficiency of SARS-CoV-2" when compared to RaTG13.
Nerd has power
5/10/2020 06:25:36 pm
Can't agree more. Wonderful discussion and analysis. Thank you!
Exid
5/10/2020 08:11:15 pm
It also appeared that the CpG deficnency in RaTG13 and SARS-CoV-2 was ancestral-- it likely happened BEFORE the two viruses branched away on the evolutionary tree. So Whatever kind of modification system at work in the ancestor have stopped working when RaTG13 and SARS-CoV-2 came to place.
Nerd has power
5/12/2020 02:18:42 pm
Thank you, Exid. Great finding! Unless they argue that SARS-CoV-2 directly crossed over from bats, they would not be able to answer why the codon bias is the same between SARS-CoV-2 and RaTG13.
Bryan
5/14/2020 10:33:56 am
Argin,
Nerd has power
5/18/2020 09:18:30 am
Hi Bryan, I would like to comment on the last point you raised. I agree that the 5:1 ratio is very raw. It's a general trend due to the purifying pressure that most proteins experience in evolution. You are also correct that different protein/sequences, when facing different selection pressures, would exhibit different dS/dN ratios.
Bryan
5/19/2020 03:51:34 pm
Hey Nerd Has Power,
Argin
5/20/2020 06:21:11 am
See Farvous's comment on the next door. the ORF1ab dS/dN is a normal 6.22:1. not a sign of the extreme kind of purifying selection or an APOBEC/ADAR transition jockey here. also, ORF1ab is more purifying for viruses that have different host than S since the main mutations are on the S to mediate host switching. While in the same host the ORF1ab is less purifying than the S since the S will be more conserved to maintain host adaptation.
Nerd has power
5/23/2020 12:32:14 pm
Thank you, Argin, for bringing up Farvous' analysis.
John F. Signus
6/18/2020 07:29:46 am
https://drive.google.com/file/d/1Xp1zBf2d-hu32XSKkyJ7UBOg9ZHuAURS/view?usp=sharing
Bryan
7/5/2020 08:11:48 pm
Hey Nerd, sorry it's taken me a while to respond.I don’t think it’s a reasonable assumption to have uniform mutation frequencies or syn/nonsyn ratios throughout a viral genome. That might be an alright first null hypothesis, but if one actually want’s to make a case that a genome isn’t natural (either that it’s engineered or that it’s made up) you really need to look to nature, not a naïve assumption of uniform mutation rates. Is the relationship between SARS-CoV2 genome and RaTG13 different than the relationship between other related coronaviruses?
Exidos B freeman
5/7/2020 09:13:23 pm
https://zenodo.org/record/3786451#.XrTZjCV6uEc
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Bryan
5/9/2020 08:20:31 pm
I'll look at that link, is it a similar argument to that posted here?
Exidos B freeman
5/9/2020 08:52:31 pm
Well, My analysis is done on the nucleotide level-- Even assuming a highly conserved protein, the underlying nucleotides should have seen synomynous changes since it shouldn't affect the Amino Acid sequences, therefore it shouldn't affect anything at all. The point is that The newer "Evidence" (e.g. RaTG13, pangolins, etc.) Had too little synomynous substitution rate when compared to the rate that is seen in the rest of the genomic sequence. Which isextremely unusual, and seems to point out a common E sequence that were used for the fabrication of the "evidences", which were all obtained from short sequence metagenome sequencing data.
Nerd has power
5/10/2020 06:42:35 pm
Great finding on the severe discrepancies of the nucleotide sequence identity on E vs. whole genome! It seems that the more different ways we compare RaTG13 to other viruses, the more evidence we could find supporting its fabrication. Thanks, Exidos!
Farvous
5/11/2020 12:01:15 am
Did a BLAST on the ORF1ab polyprotein on RaTG13 to SARS2-- the Syn/nonsyn ratio is about 6.22:1.
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Nerd has power
5/12/2020 02:31:17 pm
Thank you for the work! Again, they must have manipulated the sequence of Spike more than anything else --- they know people would scrutinize the RBD of S1 more than anything. However, they apparently spent too much time "editing" RaTG13's RBD that they had to be stingy about non-synonymous mutations when "editing" the sequence of S2. It is really nice to confirm that the syn/non-syn ratio is largely normal when other parts of the genome are being compared between RaTG13 and SARS-CoV-2. Thanks again!
Jogn F. Signus
6/18/2020 07:31:17 am
Also, may want to try SARS/YNLF31C.
Exid
5/16/2020 06:52:58 pm
However,
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Exid
5/20/2020 06:00:53 am
Therefore, nomatter how your hypothesis claimed, it should *Not* give an overal skewed dS/dN to >9:1 . but this ratio is not observed for the overall genome of RaTG13/SARS-CoV-2. Therefore, the APOBEC/ADAR hypothesis is still invalid on a mutation rate standpoint.
Jon1717
5/7/2020 02:22:27 pm
Ok silly question, can you help me reproduce the sense / nonsene graph? I'm not getting the same results. I don't get the flatline for nonsyn mutations.
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Exip
5/7/2020 06:00:37 pm
Maybe you accidentally made the alignment out-of-frame. Look at the assembly and locate the CDS for the “S” gene. Make sure you start with “AUG”. Your sequence may be misaligned.
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Bryan
5/14/2020 09:20:36 pm
Those are the right sequences. I think you are missing the alignment step. The input to SNAP needs to be aligned on a codon basis. I use a program called seaview that allows me to view the DNA sequences as proteins, align them (Clustal or Muscle), and then switch back to the DNA view. Then put the DNA seqs into SNAP. If you put unaligned sequences into SNAP, It will all be full of random syn and nonsyn mutations as soon as you hit any INDELs. In this case, once you hit amino acid 681 (SARS-CoV2's polybasic cleavage site) it'll all be noise.
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Mitch
5/7/2020 03:29:24 pm
While I appreciate your efforts, I agree with those who have pointed out that blog publishing is probably not the first choice of those who would like to have their information fully vetted by experts in the field.
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Nerd has power
5/10/2020 06:58:27 pm
Thanks for the suggestion. I don't mind having the article judged by anybody, including reviewers/experts. Apparently, the comments/discussions we got here are excellent. I have tried to reply to each one before, but I started to feel a bit overwhelmed and may not be able to keep up -- some comments are made by people who are real experts (I am an half expert) and there are too many of them now. You don't get this in a peer-review process. Reviewers' comments are typically not seen by public -- they can be unreasonable (more frequently so than you might expect) and yet the public wouldn't know. Here, on the open platform, you see everything. I personally believe that this article is being judged harsher than a manuscript undergoing peer review. If I were you, I will feel safer about the contents as they are being constantly validated.
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Alesh
7/5/2020 11:06:28 pm
Good point 5/7/2020 05:03:44 pm
I ran your analysis of SARS Cov 2 with RaTG13 by downloading a FASTA alignment file MN996532.1 x NC_045512.2.aln from NCBI virus and loading it on SNAP. I got a slightly different curve. I was wondering if I could send it to you?
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Fight Against CCP
5/7/2020 05:35:31 pm
CCP dog has finally arrived. Why cannot you just disprove it? Barking around only shows your weakness!
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Kathy
5/7/2020 10:36:23 pm
Articles that clearly state an artificial origin for SARS-CoV-2 do not have a chance to be published. There is a huge censorship on the topic. What else we have that to make preprints and meet on these platforms? I am grateful that they exist.
I am no native English speaker.An alternative view on it.Very impressive article and comments.I tought I was intelligent but you guys put me in my place at least in biology.I was suspicious about the way they said it was from nature in the first place because it break out where the only lab is of mainland china and where they do research with this kind of virus.Also patient zero not found on market which plays role in nature speculation.I think there were lots of infections on market because a lot of people come together there, just that. If objective mind the researchers should lower the odds of naturel accuring already a bit on that.But I often see that people have bias against a possible truth they dont like.Also scientist. When there is social research with differnt gender, race for example and they dont like the result they come with very long explanation of the least controversial possible explanation they can find.When it is 99,999 % chance from lab and you bring evidance which makes it 99,99999% from lab they would hold on to nature version.I saw some bias against bio-weapen in myself some time ago. When I realised humans are capable of nuclear weapons I changed my mind and not longer saw accident as 99% the couse.
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Nonameneeded
5/7/2020 11:51:44 pm
Can someone do an in silico analysis of the role of the proline in the PRRA insert. What happens when this is removed or substituted with alanine? Asking because this may kink the secondary structure and increase solvent and protease exposure.
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Kathy
5/8/2020 11:38:48 am
....If the virus can even sustainably infect bats, or causes a very harsh disease that would obviously be incompatible with this being the natural host. This is worth looking into.
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nonameneeded
5/8/2020 12:33:15 pm
Not sure why they did it in the fruit bats rather than intermediate horseshoe bats (and pangolins), which are the hosts that are bandied about.
Nerd has power
5/10/2020 07:09:22 pm
Agree that some lab really should look at whether RaTG13 can infect its alleged natural bat host. I thought about this too -- what if it can't??? Maybe Zhengli Shi will blame it on the incompetency of the ones who did the test. I'm sure that, if she does the test in her lab, the infection will be "successful" and yet the bat will die very quickly -- leaving just the remains which contains the RaTG13 virus in the proper organs.
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Malcolm
5/8/2020 01:03:01 am
Re: RATG13 IS FAKE
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Malcolm
5/8/2020 05:30:56 am
Calculations if anyone is interested.
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Kathy
5/8/2020 05:48:53 am
Can you exclude that RaTG13 is real but "just" edited? There is a possible record of if named BtCoV4991
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Malcolm
5/8/2020 07:05:33 am
BtCoV-4991 is a very small fragment (370 nucleotides or 123 amino acids) of the ORF1a gene, collected at the same time and place that RaTG13 was claimed to be found. A blast search gives a 100% match with RaTG13 and 98.92% with SARS-CoV-2, which is only a three nucleotide difference.
Mitch
5/8/2020 06:53:58 am
I understand that some of those coming here are used to an environment of strict censorship. But unless you are ready to declare that the journals covering virology have peer-review committees which are all corrupt, it seems contradictory to point to evidence of scientific fraud which is (1) obvious and (2) incapable of being published in a peer-reviewed journal.
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Kathy
5/8/2020 08:37:05 am
I am aware that BtCoV4991 is a short sequence, but as you say, it was collected the same year, by the same group and in the same place as RaTG13 is supposed to. Coincidence? Perhaps. I am a fan of the pangolin theory, with the switch of the RBD of RaTG13 (edited) with the one from the pangolin CoV plus a furin cleavage site from another bat living in the same cave (I am still hunting this). An evolutionary study with the potential to develop a global corona-vaccine gone wrong. Interesting that these two articles were sponsored bathe same grant (Baric+Shi).
John F Signus
5/9/2020 04:13:42 am
The paper is actually a repost of a February 17 preprint under the same title. Parts that concludes that the pangolin coronavirus have no furin cleavage site were redacted. As well as the full S gene that is very distant.
John F Signus
5/11/2020 02:49:01 am
Read the Nature article more thoroughly.
John F Signus
5/11/2020 06:24:50 am
Which was used for "Assembling" the genome. It's very easy for the researchers to mistake a contamination from SARS-CoV-2 itself, or other "more similar sequences" that they pulled off "The raw reads from public databases" as something that is more close to SARS-CoV-2, and mistakenly assemble it into the resulting genome.
Troy T Dow
5/8/2020 11:59:34 am
I wish John F Signus would comment again. I'm worried his real name is Bing Liu, murdered in Pittsburgh on May 2nd.
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J17
5/8/2020 07:23:23 pm
I talked to my lab guy and he agrees with the Yuri article. He wonders how often furin sites are so perfectly added to close relatives without any extra junk. So I'm going to be doing analysis of closely related RNA viruses w/ and w/o furin to see how often that happens.
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Anonymous
5/9/2020 12:01:24 am
If the argument is that the COVID-19 E protein mutated over time and that E proteins mutate at a constant rate within bat populations, why then are ZC45 and ZXC21 identical? Or am I missing part of the logic?
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John F Signus
5/9/2020 03:27:53 am
ZC45 and ZXC21 are very closely related—while RaTG13 or CoV2 are very distantly related to ZC45/ZXC21.
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Anonymous
5/9/2020 04:11:50 am
Sorry, John F. Signus, but I still do not understand the logic of your argument. Although they were collected 1.5 years apart, because ZXC21 and ZC45 are "related," they should have not undergone any mutation and, therefore, are identical. RaTG13 is not related to them, but has an identical E protein. How does the short term mutation of COVID-19 fit into that argument? That is, would not any E protein mutation also apply to ZXC21 and ZC45, which would then show a sequence difference? Thank you in advance for a clarification.
John F Signus
5/9/2020 11:26:51 am
ZC45/ZXC21 was 98% similar. They are more similar to each other than RaTG13 to SARS-CoV-2. Also collected at the same site. The evolutionary distance is very short between ZC45/ZXC21. Much shorter than ZC45/ZXC21->RaTG13/CoV2. See the RaTG13 article to see how short their distance was, Evolutionarily. The reason that E was suspicious, was, due to the fact that there were closer Bat-CoVs and SARS-CoV, with a different E protein and genetic similarity higher than RaTG13->ZC45/ZXC21.
FreeFreedomain
7/2/2020 07:14:03 pm
John, thanks for the detailed explanation. I'm trying to understand it. If ZXC21 and ZC45 are 97% similar and CoV2 is 95% similar to both ZXC21/ZC45. Why having identical E protein when similarity is 97% is ok and natural, but when similarity is 95%, then it's nearly impossible to have identical E? There is only 2% difference between these two cases.
John F Signus
5/10/2020 02:51:09 am
https://zenodo.org/record/3786451#.XrFN4YijeUk
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John F Signus
5/10/2020 03:00:28 am
And whenever a chimeric/synthetic coronavirus was engineered, the particular E protein sequence was used for it's construction. It may then acquire the (unnaturally few) synomynous mutations after brief passage in cell culture.
John F Signua
5/10/2020 03:11:01 am
"By comparing the ORF1ab polyprotein with a very distantly related coronavirus that is not on the same lineage, SARS, "
Nerd has power
5/10/2020 07:36:56 pm
Thank you, John. Fantastic analysis and reasoning as always!
Physics Guy
5/11/2020 02:44:00 pm
Hi John F Signus, Nerd has Power and others. As my name suggests I am not a biologist, but I follow this discussion with interest. As an outsider I can in any case see that a moratorium was tried on research that creates viruses with pandemic potential
John F signus
5/11/2020 05:01:38 pm
The actual problem it that the E protein is a protein coding gene—it is Significant in the sense that it is Both a distinct part of Coronavirus biology and Coronavirus reverse genetic systems. It is not a “random sequence”. Other sequences are non-significant, therefore they Can not be compared to a plausible synthetic origin By engineering.
Physics Guy
5/12/2020 01:02:48 am
Great. I don't follow your last bit 1/(29855*6)=1/179130. My estimate for the "look elsewhere effect" was just a maximum. How many of these locations like the E-protein one are there, for which you could a priori expect something "fishy" if the virus is not natural? Roughly the "look elsewhere effect" says that if there are for example 4 of such a priori locations and you find something fishy for 1 of those 4, then you divide your final probability by 4.
John F Signus
5/13/2020 12:01:56 am
Well, there is only ONE E gene in SARS-CoV-2. the only other suspicious protein is the first part of S2. using the "look elsewhere" effect, for the specific sequence (btw it was an 225bp sequence out of 29855, not a 75bp sequence), the maximum should be 1 in 6*(225/29855)=796.16, or based on the only 2 identical proteins of significance, 1 in (1655/2)=827.5.
K. Evangeline Luk
5/9/2020 02:37:34 am
I'm not sure if @Raoul89573207 that tweeted me this blog was you, but you need to come onto our Riot server.
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Eva Celia
5/9/2020 11:23:36 pm
Have you read about the odd pneumonia outbreak in Virginia back in summer 2019 https://www.nbcwashington.com/news/local/health-officials-to-give-update-after-respiratory-illness-sickens-dozens-at-virginia-retirement-community/135890/ and also this from France in Nov 2019 https://www.scmp.com/news/china/society/article/3083599/france-had-covid-19-november-hospital-says-after-analysis-chest
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Kathy
5/9/2020 11:28:55 pm
COVID RIDDLE Fears coronavirus arrived in Europe in OCTOBER ‘when French athletes at World Military Games in Wuhan brought it home
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Fight Against CCP
5/9/2020 11:41:06 pm
Well done, Kathy! :) Such a large scale virus couldn't have originated from anywhere else and hidden for so many months until the first largest outbreak in Wuhan. That's why COVID-19 = CCP Originated Virus Infectious Disease-19. As you can see, CCP propaganda and dogs are everywhere. They would not know how evil CCP are until they themselves become CCP's victims.
Fight Against CCP
5/9/2020 11:48:54 pm
Here are more to add to your list:
Nerd has power
5/10/2020 07:46:59 pm
Agree. Given how easily this virus spreads and how little people know back then about having to use masks to stop it, there is no chance that France (or any other place that the CCP wants to mis-label as the "true origin") could have avoided community spread back then.
to go deeper
5/10/2020 12:21:12 am
But summer comes before fall
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CCP is NAZI
5/10/2020 09:58:57 am
Have you actually compared its sequence with CCP Virus' sequence side by side? If so, why don't you bring its sequence here to let virus specialists verify? Even look at it from a non scientific perspective view, with such a high infectious rate that CCP virus has, why nothing happened in U.S. afterwards until after Wuhan lock down? Interestingly, CCP tried their very best to help this deadly CCP virus spread as fast and wide as possible all over the world by silencing 8 doctors like Li Wenliang , by destroying all virus samples, by stressing it's preventable and controllable, by denying the fact about human to human transmission, by letting people out from Wuhan to everywhere in the world but not within China? Were CCP able to prevent and control it? Exactly, what's CCP's hidden agenda? Well, aren't these https://www.newsmax.com/navrozov/china-biological-russia/2009/09/17/id/335042/ and https://www.theepochtimes.com/did-chinas-plan-to-destroy-the-united-states-backfire_3223117.html enough to tell CCP's world domination goal?
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Jane
5/18/2020 05:37:49 am
Did you read this?
CCP is NAZI
5/10/2020 11:16:38 am
Where is the bat woman and the virus queen - Shi Zhengli? Why don't you invite her here to see what she has to say? Where is the Patient Zero, Huang Yanlin? Is she already dead or hidden? Why did Wuhan P4 lab take her picture down while still leaving her name there? Look at her with her lab mates on 2018 New Year Day: https://www.youtube.com/watch?v=NVzne_ZQ0Vo I'm sure that CCP really has hard time to find someone who not only looks like her, but also has a virologist's knowledge. Further, U.S. has the best CCP virus tester to test her to see if she was infected with or is currently infected with CCP Virus.
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detailfreak
5/10/2020 02:07:13 am
Two tracks to follow now that we know that RaTG13 is BtCoV4991:
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Lincolin
5/10/2020 06:31:43 am
Did a BLAST on all of them.
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Lincolin
5/10/2020 07:00:55 am
There were a total of 8 Spike proteins Listed there.
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Lincolin
5/10/2020 07:46:28 am
Therfore, there were still no Spike gene dequence data, or any pieces of data other than the tiny 370bp BtCoV/4991 Partial RdRp, of RaTG13 that were published, or confermed, before the pandemic.
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Dartagnan
5/12/2020 03:00:04 pm
Wow... so the gene fragment that codes for the RdRp of the virus is conveniently put out there 3-4 years ago. Just enough time for someone to develop an effective RdRp Inhibitor drug (like remdesivir or likely something even more effective given in pill form which is not public yet) that can be given prophylactically to high level officials or others you want to favor. These people will be protected from infection or treated quickly once the pandemic hits, while the rest of the world is physically and economically paralyzed. Gilead's tenofovir, which is the adenine analog chain terminator cousin of remdesivir, is already used this way as a reversetranscriptase inhibitor prophylactic for HIV. Then folks like Peter Daszak can go on 60 Minutes and say that their dangerous GOF research helped lead to life saving breakthroughs like remdesivir...
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CCP is NAZI
5/12/2020 03:35:08 pm
No surprise. CCP's evilness is way more than what you can imagine. CCP's Nazi conduct are doomed to be severely punished. I wish more people can wake up to knock down CCP with whom the world would not have any peace.
Javier
5/10/2020 07:46:23 am
Hello. Excellent work here in this blog. Thanks.
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John F Signus
5/10/2020 07:51:03 am
The article claimed that the Furin site arose in humans-- However, if that was the case, why the very first sample of SARS-CoV-2 already had the exact perfect PRRA furin cleavage site? Why there were never a detection of a "Progenitor virus" in humans that lacked this site? If it arose in humans, it should have already been detected. no intermediate CoV2 W/O PRRA is a clear indication that id did not arise that way.
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John F Signus
5/10/2020 08:03:41 am
From phylogenetic data and the comment made by Firox TD Jackinson, We already knew that a furin site will not survive nor persist in wild animals for Spike gene that is more than 40% homologous to SARS-CoV-2. So it can't arise in an animal. And there were no detection of a "intermediate virus" in humans that is near-identical to SARS-CoV-2 while laching the PRRA. Therefore, it can't arise in animals and did not arise in humans, leaving the only possible source of the furin site as either deliberate insertion or lab-based passage. Cell passage may cause it to arise in the lab in that mechanism, however. (the AIV example cited by the paper is actually in-vitro passage data) Since cell culture lacked an immune system, they will not eliminate the furin-cleavable spike immediately like wild animals, but since they are not humans, the intermediate will be shielded inside a lab and therefore will not be discovered in actual, live humans. explaining the lac of an intermediate in humans.
Javier
5/10/2020 09:12:50 am
Very interesting reply John.
John F signus
5/11/2020 05:20:05 pm
The problem is that both the FCS containing precursor and the RBD containing precursor are potent enough to cause an epidemic in humans. More so than SARS. We already knew that the FCS is not tolerated in wild animals for betacoronavirus spike protein genes that is more than 40% homologous to SARS-CoV-2. So it can’t arise in that way.
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IdoNotLikeCherries
5/10/2020 09:36:32 am
Anther cherry on the cake:
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Nerd has power
5/10/2020 08:21:50 pm
Fantastic efforts, everybody! This place is becoming alive, with all your insights and excellent analyses. I must admit that they are much better than what I was able to offer in the original article. Please keep adding it.
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In 2013-15, Zhengli Shi and colleagues thought the Rhinolophus sinicus bats they had found in Yunnan caves had a Coronavirus capable of infecting human lungs.
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Marco Belladama
5/11/2020 05:37:25 am
I'm a system integrator.... need to download the genome and a little guide to remake the picture like in this post
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Sam
5/11/2020 09:52:18 am
Does the existence of BtCoV/4991 RdRp - a fragment of a viral genome that got published in 2016, 4 years before RaTG13, and seems the same as the RatG13 sequence published in Jan 2020 affect your argument (that RatG13 is a fake) at all? https://www.ncbi.nlm.nih.gov/nuccore/KP876546
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Simen
5/11/2020 08:03:47 pm
The existence of RaBtCoV/4991 actually does not prove anything. The sequence is only 370bp in length and everything elve were still not published until 27-JAN-2020 . The only other reference of RaBtCoV/4991 was a single figure in that 2019 paper, which published no sequences. Notably, if what they claim was true on the S protein, we should already seen the RBD of RaTG13 being published before. We didn't.
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Nerd has power
5/12/2020 03:22:37 pm
Thank you, Simen! Agree with your analysis.
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Sam
5/13/2020 03:35:14 am
Thank you so much for your interesting reply and for taking the time to respond. Much appreciated.
Robespierre
5/11/2020 10:34:31 am
China knew at least on March 7, 2020, probably earlier, that RaTG13 and BtCoV/4991 were the same. Why the charade?
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Batwoman
5/11/2020 11:36:33 am
Maybe few in China knew it, but most of the others not. Are you aware that in science you can’t change the name of a sample that it has been published to avoid to lose the track of previous works? Only who has something to hide would do it. Are you a friend of Peter Daszak?
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Sam
5/11/2020 12:45:40 pm
Not at all. I think he has very little credibility and has clearly lied about a number of things, not least his claim to “have no conflicts of interest”! But I am interested in what Nerd makes of 4991.
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Nerd has power
5/12/2020 03:20:10 pm
Hi Sam, here is my take on this 4991.
Dusha
5/11/2020 11:51:09 am
Many thanks for your interesting article! I have one question. You say, "As stated in the [Shi's] paper, RaTG13 was discovered from Yunnan province, China, in 2013." What is the reference for the 2013 date please, as I can't find it anywhere in Shi's 2020 paper here:
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Batwoman
5/11/2020 11:59:32 am
The article where BtCoV4991 is cited is here:
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Nerd has power
5/12/2020 03:32:39 pm
Yes, the publication listed by batwoman is the original one that reported about how this 4991 was discovered back in 2013. Please see my answer right above for my take on this 4991.
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guesswho
5/13/2020 02:34:18 pm
Something more on BtCoV4991. Here https://www.ncbi.nlm.nih.gov/pubmed/26920708
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Aydin
5/11/2020 03:27:28 pm
Interesting to read Peter Daszak@PeterDaszak's tweet:
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Dalstra
5/11/2020 05:25:59 pm
Also add in the fact they have never produced a physical copy of RaTG13 nor let anyone else resequence it’s genome. And the fact that it was not submitted nor published anywhere (Except for the 370bp RaBtCoV/4991) until January 27, well after the outbreak.
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Tongguanzhen
5/12/2020 08:56:58 pm
https://twitter.com/paleovanguard/status/1257416405835792388
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cippi
5/13/2020 02:17:17 pm
TG sounds to me more Total Genome
Aydin
5/11/2020 03:44:01 pm
Per "The Bats Behind the Pandemic" Wall Street Journal by Matt Ridley (4/9/2020)
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John kelleher
5/11/2020 03:46:53 pm
https://connect.biorxiv.org/relate/content/181
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Nerd has power
5/12/2020 03:35:30 pm
I have commented on this article a few times, I believe. Sorry that I won't repeat myself here again, except to say that I'm not completely bought by their evidence and conclusions (although I agree that the virus is of non-natural origin).
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Jane
5/18/2020 06:00:28 am
Can we exclude that Daszak & co. figured out that the spike of BtCoV4991 modified with the RBD of the pangolin CoV and furin site had HIV properties and for this reason they inserted in the BtCoV4991 backbone to develop a super vaccine/drug?
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Nerd has power
5/18/2020 09:39:07 am
Sorry that I don't think I fully understand your question. But I would simply say that 1) I personally have not been convinced that there are HIV sequences inserted into the genome of SARS-CoV-2; 2) no one would try to create a vaccine this way --> making it resemble SARS and then, on top of that, adding a Furin-cleavage site to make it more infectious. The manipulations are intended for the opposite.
Hans Fields
5/11/2020 07:49:46 pm
I ran a sequence alignment on RaTG13 vs Sars-CoV-2 and it only turns up 4 nonsyn mutations on the N protein (419 len). It seems a bit low given that there are 18 nonsyn mutations comparing ZC45 to Sars-Cov-2.
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BreakingBad
5/12/2020 05:06:10 am
China’s own scientists have provided evidence that COVID-19 is man-made
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yano
5/12/2020 06:39:07 am
What is the probability that the SARS-CoV-2 E protein become 100% similar to ZC45 and ZXC21 naturally?
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Nerd has power
5/12/2020 03:43:18 pm
Please scroll back to see the conversation between Anonymous and John F. Signus on this topic. John explained it very well.
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yano
5/12/2020 06:51:11 am
The Feb 11 2020 E protein for SARS-CoV-2 is 100% similar to ZC45 and ZXC21. It is thought that the virus went into humans in Sept-Oct 2019.
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Nerd has power
5/12/2020 03:46:57 pm
You need the size of infected populations to be big enough to see these mutations showing up in sequencing. Please note that not all samples are sequenced. There might be mutations in E from earlier patients, but those may not be selected for sequencing.
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Claire Robinson
5/12/2020 06:53:46 am
An article has been published about Nerd Has Power's research here:
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Nerd has power
5/12/2020 04:05:04 pm
Thank you, Claire and your team, for publishing the article. You have successfully identified me being a male. One error in your article is that you mentioned (twice, I believe) that ZC45 and ZXC21 were discovered by Zhengli Shi. It's not correct. The discovery was made by another lab in China that has a military background. Here is the publication:
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Claire Robinson
5/13/2020 02:14:06 am
Corrected the article--many thanks!
Claire Robinson
5/12/2020 06:55:31 am
An article has been published about Nerd Has Power's research here:
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ioderESTEl
5/12/2020 05:41:15 pm
As if on queue, now that questions about the cleavage site have been raised more widely, Shi has produced another 'natural' bat coronavirus with the requisite cleavage site.
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nonameneeded
5/12/2020 08:14:25 pm
Chinese propaganda in overdrive. I hope no one buys into this nonsense about a new lineage B betacoronavirus with a furin cleavage site that was reportedly collected in May-October 2019 that they sat on until April 2020.
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Lima
5/13/2020 12:19:46 am
It was actually the very old paper on RmYN02. you will need to look at the sequence/alignment more closely.
yano
5/13/2020 10:10:30 pm
What kind of crazy system allows un-verified and possibly fake virus data to be manufactured and uploaded without verification.
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Henri
5/18/2020 03:31:46 pm
Has it not occurred to you that sending live, potentially pathogenic viruses through the post to another lab would be a serious safety risk?
Henri
5/18/2020 01:08:19 am
Are you suggesting that RmYN02 is also a 'fake' sequence?
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Lima
6/18/2020 07:53:32 am
https://drive.google.com/file/d/1gGX4EobrnP3EKYLQDsl9Xa6tKoiwmI8O/view?usp=sharing
yano
5/12/2020 07:42:07 pm
Is this new work with the likely copy and paste 100% E protein and the mysteriously appearing furin cleavage site causing virologists to accept the lab creation theory?
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nonameneeded
5/12/2020 08:16:13 pm
It is not ignorance. It is a conspiracy of silence by virologists who know much, much better.
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nonameneeded
5/12/2020 08:45:25 pm
Edward Holmes is also on the Malayan pangolin coronavirus paper that appeared in Nature.
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John F Signus
5/13/2020 12:22:09 am
See my takedown on it at 5/9/2020 04:13:42 am.
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Dex
5/19/2020 09:54:46 pm
Edward Holmes lab work was outsourced to the PLA.
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Even Yahalom
5/13/2020 11:26:20 am
Who are you?
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Lilian
5/13/2020 02:44:51 pm
I have a question abt the RaTg13 spike protein:
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Lilian
5/13/2020 02:55:26 pm
I just noted that it has 100 % match with SARS Urbani, just after Ratg13
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Lilian
5/13/2020 03:04:09 pm
but missing there the starting ATG...mmh...
Nerd has power
5/23/2020 01:08:10 pm
It may be a conserved sequence at the end of Orf1b. Orf1b and Spike are located right next to each other in the genome, so the end of Orf1b should be right in front of the beginning of the spike.
John F. signus
5/30/2020 08:49:03 am
However, this leader sequence were not found in other SL-CoVs as this in-frame insert. All the other SL-CoVs appeared to have 1 less Nucleotide on the junction meaning that they won’t translate to such.
Physics Guy
5/14/2020 02:23:24 am
Has someone checked the non-synonymous to synonymous ratio of the S2 part of the spike for the mutations that are now naturally occurring in COVID-19? Is there evidence/non-evidence for natural selection in favour of synonymous changes there?
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Libres
5/14/2020 03:20:23 am
Well, the dS/dN on the ORF1ab between RaTG13 and SARS-COV-2 was 6.22:1. Ruling out the possibility that selection in this lineage favoring Syn over Nonsyn.
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Physics Guy
5/14/2020 03:36:38 am
I know, but further evidence as I suggest could further prove/disprove the hypothesis.
nonameneeded
5/14/2020 09:09:16 am
Can you check the dS/dN between specifically GD pangolin vs SARS-CoV-2?for
John F Signus
5/14/2020 03:20:50 am
https://www.sciencedirect.com/science/article/pii/S0092867420302622
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yano
5/14/2020 07:30:52 am
Great! I am so happy people are digging out this information. The world is waiting for justice. Keep up the good work!
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Javier
5/16/2020 09:07:07 am
Congratulations, good work. I'm trying to understand your reasonings, but I have one doubt.
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John F Signus
5/20/2020 05:55:31 am
Well, the hACE2 transfected BHK cells had less affinity to FCS removed S than the FCS on S. BHK itself does not express any ACE2 and is used to model human cells by transfecting it with hACE2 and overexpressing it on the cell surface. the real point is that SARS-CoV-2 fur/mut had the highest affinity to VERO E6 (13500 RLU) than any other assays done. including the SARS-CoV-2 S on hACE2/BHK (13000 RLU).
Nerd has power
5/23/2020 01:33:01 pm
Thank you so much, John. Great finding and analysis!
Bugsy
5/14/2020 06:45:46 am
A two-step approach, first receptor binding, then the addition of a furin site was implied in a study by Ralph Baric's group "SARS-like WIV1-CoV poised for human emergence," replacing the spikes of SARS Urbani and WIV1.
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nonameneeded
5/14/2020 08:39:45 am
For those who are interested, this is the 2014 patent for the chimeric virus construction and serial passaging by Ralph Baric at UNC. The patent was assigned to NIH in 2017.
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Andrew M
5/14/2020 01:01:17 pm
Isn't the differential ratio of synonoymous to non-synonymous mutations simply down to the effect of purifying selection in the region concerened - exactly what you might expect?
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John F Signus
5/14/2020 05:03:38 pm
Well, ZC45 and ZXC21 uses the same host, yet their ds/dn on the S2 was 5:1 with 5 nonsyn mutations. CoV2/RaTG13 have different hosts— we should see both a bigger difference on the S2 and at least a similar dS/dN. However, In RaTG13/CoV2 it was 44:1 with just 2 nonsyn substitutions. Somehow it ended with more nucleotide substitutions than ZC45/ZXC21, yet had less Nonsyn substitutions on the S2 with ZC45/ZXC21. This is completely unnatural.
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Tony
5/15/2020 07:19:04 am
https://www.biorxiv.org/content/10.1101/2020.02.27.969006v1.full.pdf
Physics Guy
5/15/2020 08:20:23 am
As I have suggested above I think it would be good to also look at syn/non-sym ratio of the spike regions in the current mutations of COVID-19. As an outsider to this field to me it seems that this could either further prove the the hypothesis or disprove it.
Andrew M
5/16/2020 01:37:29 am
Sorry, I can't follow this. You just seem to be asserting that different ratios in different places are "unnatural", when in fact it could just reflect stronger selection in certain region(s). The article linked by Tony below seems to this.
Tony
5/16/2020 07:53:45 am
Why there can not be higher “purifying selection” in RaTG13/CoV2 than ZC45/ZXC21?
John F Signus
5/20/2020 05:38:17 am
ZC45/ZXC21 never left the same cave and had the exact same host. There can't be a more stable, purifying selection than this.
John F. Signus
6/18/2020 07:57:05 am
And--unfortunately, CoV2 S2 is not the type of S2 that is under purifying selection. https://drive.google.com/file/d/1Xp1zBf2d-hu32XSKkyJ7UBOg9ZHuAURS/view?usp=sharing
John F Signus
5/14/2020 05:07:08 pm
Sorry, but it keep saying that you does not have the permission to view this page. Could you update it?
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Andrew M
5/14/2020 03:47:27 pm
Another question having read your paper more carefully. You say recombination is rare and thus can't explain differences between the S1 portions of the various coronaviruses. But I have read elsewhere that recombinations are quite common in coronaviruses. The % difference between the genomes and typical mutation rates of such viruses suggest their evolutionary paths 2 diverged decades ago - plenty of time for such recombinations to have taken place. Any thoughts on this?
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Nerd has power
5/19/2020 09:07:40 pm
Sorry for having missed this. I posted something on 5/18 in a reply to charly. You will find my answer to your question there. Please scroll down to read it. Thank you!
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John Kelleher
5/14/2020 07:45:19 pm
I think our governments have no brakes on their train. If the release was planned ,Shi could have published the RaTG13 paper before the release. Maybe ?
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Tony
5/16/2020 08:19:08 am
"nonameneeded the patent you posted seems to be worded to be a vaccine . ,https://patents.google.com/patent/US20170096455"
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Jane
5/18/2020 06:12:46 am
5/15/2020 02:10:17 am
A Nerd has Power.
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John Kelleher
5/15/2020 12:48:49 pm
https://www.youtube.com/watch?v=GUW51MYQ_XQ
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Andrew M
5/16/2020 02:11:47 am
https://www.metabunk.org/threads/debunked-funvax-pentagon-briefing-on-removing-the-god-gene-hoax.317/
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Adam
5/15/2020 08:12:31 pm
I am not a virologist so can't comment on the analysis and its accuracy however why don't you reveal your identity? Are you are based in China and forsee a threat? As you judge others of being biased, would be great if you let the readers judge your biases as well. Not accusing you of anything just making sure we know the person behind the article. I dont understand Chinese hence can't really read the Chinese version.
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Fight Against CCP
5/16/2020 12:26:54 am
I'm not a virologist either. Neither am I the author of this article. However, why do everyone have to disclose their identity especially on internet? Have you ever tried to figure out why and how the world known virologist died suddenly and mysteriously back in this January? Have you ever tried to figure out Czech Senate leader Jaroslav Kubera's sudden death right before his trip to Taiwan? What about the vaccine developer, Liu Bin's being assassinated? I'm sure that you have this common sense as well, as otherwise, you would have disclosed your real full name.
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Nerd has power
5/18/2020 04:38:02 pm
Thank you, my brother. We are in this fight together.
True Crime
5/16/2020 06:56:39 am
Is Shi trying to say now (new paper) that it was not Rhinolophus affinis from Yunnan, but may be Rhinolophus sinicus from... Hubei?
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True Crime
5/16/2020 07:17:54 am
All out:
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5/16/2020 12:40:37 pm
EXCLUSIVE: Virus researchers uncover new evidence implying COVID-19 was created in a lab:
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Lori
5/16/2020 04:11:07 pm
I've been following your work along with reading the comments and just wanted you to know you are not the only one who thinks this virus was manipulated to make it transmissible to humans.
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nonameneeded
5/16/2020 06:51:02 pm
Sad that it's the dailymail that reports on this and not the more "prestigious" mainstream media a la NYT, BBC, Guardian, WaPo. I doubt this will go into a high profile journal, although quite excellent.
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Nerd has power
5/18/2020 01:42:49 pm
Thank you for sharing it. Great article! Reading in between the lines, I can tell that the authors are as convinced as many of us here, and yet they just can't say it in a submitted manuscript. They are so brave to bring their work to the public in this manner. Doesn't matter whether it makes to a top journal, we should spread it.
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Lori
5/16/2020 11:31:11 pm
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Henri
5/18/2020 01:34:14 am
No, it was not 'ordered destroyed' according to the news article. 'The article says 'made substantial changes' which, upon further reading, turns out to be 'remove the terms 'wild life' and 'wild animal'.
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Lilian
5/18/2020 01:41:44 am
You need to practise reading Henri:
Henri
5/18/2020 02:46:58 am
Read the article more carefully, Lilian. Read ALL OF IT. That 'censoring' was not destroying the data base at all. It was changing some words or deleting some words viz: wild animals. Your other points, even if true (which I doubt) does not involve the database.
Lilian
5/18/2020 04:38:49 am
Who is using the word destroying in relation to the database? The article says that the samples were destroyed, not the database.
Ridan
6/18/2020 07:58:36 am
Unfortunately, that 64.3MB database is now gone. completely.
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When asked by Zhong Nanshan if her lab is responsible for creating and losing the virus, Shi says, "She said that's totally ridiculous, she had never been doing anything like that," said Zhong, who called Shi a "good friend."
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CCP is NAZI
5/17/2020 10:05:03 am
How would you expect a CCP criminal to admit their crime? They know exactly what kind of consequence admitting their crime would lead to. None of those CCP's mouths has any credibility including CNN which is short for ChiNiese News who serves as CCP's propaganda. Sadly, none of the sources you use have any professional ethics.
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Henri
5/18/2020 01:10:53 am
What are these 'reliable sources' that the Wuhan lab does not have a hard copy of RaTG13?
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Lilian
5/18/2020 01:18:18 am
Is it not enough that the name of the sample was changed from BtCoV4991 to RaTG13? What do you need more than this demonstration of scientific fraud?
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Henri
5/18/2020 01:41:18 am
This does not answer my question
charly
5/18/2020 03:34:28 am
You can see there https://www.ncbi.nlm.nih.gov/nuccore/MN996532 that they published in 2020 a sequence from a sample collected in 2013. While this does not constitute any fraud, and their claims support it, it is unusual.
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Lilian
5/18/2020 04:31:16 am
It is a fraud to change the name of a sample. In 2016 BtCoV4991, in 2020 RaTG13.
Nerd has power
5/18/2020 02:02:20 pm
This is what I was told by people I trust (hence my reliable sources):
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Henri
5/18/2020 02:49:30 pm
Do, your 'reliable source' is hearsay snd nothing else. You email Zhengli Shi and get a response before you make unfounded allegations
Henro
5/18/2020 03:34:55 pm
So, your 'reliable sources' turns out to be hearsay.
Nerd has power
5/18/2020 04:16:00 pm
You are right. I am the one making the allegation that RaTG13 is fabricated. I wrote a whole article about it. However, this "reliable sources" thing is just a small part of my reasoning. Don't forget there are other more substantial evidence in there. Calling the allegation unfounded is, in my opinion, unfounded.
Henri
5/18/2020 06:06:58 pm
In other words you want someone else to do your dirty work because you din't have the courtesy or courage to do it yourself
Nhele
5/18/2020 09:02:11 pm
How curious Henri that you make such a statement about 'dirty work' and a lack of courtesy and courage. It appears the author of this article has, in a very reasonable way, indicated that he has invited these experts to share their point of view here. Your response sounds childish and repudiates your attempts to present a serious alternative to some very in depth analysis appearing here in the commentary.
Henri
5/18/2020 10:09:00 pm
Nhele,
Leo
5/18/2020 11:38:55 pm
I bet that RaTG13 is not functional. Otherwise someone would have already synthetized it to make a proof of existence using this method:
Justice Defender
5/19/2020 12:03:51 am
The author wrote down his or her analysis, hence s/he is already done with his/her job. Now that you are the one making "unfounded allegations" statement, why cannot you first prove how it is unfounded? If you can show your so called "unfounded"
ll11ll11
5/19/2020 10:19:53 am
I wouldn't argue with this "henri", he apparently just a stupid troll, just ignore him.
Lilian
5/18/2020 01:21:29 am
Synergistic China–US Ecological Research is Essential for Global Emerging Infectious Disease Preparedness
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Lilian
5/18/2020 01:24:32 am
Here you are:
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charly
5/18/2020 03:44:53 am
Some red flags triggered during my reading:
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Nerd has power
5/18/2020 03:27:46 pm
Thank you for the comments. I was just about to call the day for blogging and move on to other things. Your red flags gave me a reason to linger here a bit longer. I will address each of the points you raised.
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John
5/19/2020 07:04:06 pm
People win the lottery sometime too, Covid likely a gain of function experiment but not impossible that is came from wet market. On the other hand, how many doctors get reprimanded for using WeChat for simply noticing a SARs like infection in the hospital and sharing it with other Docs in Wuhan. No real reason to "kill the messenger" over a natural spillover event unless they are covering something up.
Nerd has power
5/23/2020 02:08:11 pm
Yes, you are right in that they can always argue that, even if the chance is one out of one million years, it is still a possibility. That's the beauty of recombination.
Shannon Entropy
5/20/2020 07:44:36 pm
I tried to do my own mathematical analysis of the Wuhan virus genome compared to the other known beta corona viruses. I was able to download all the genome data from www.viprbrc.org.
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Verner Von Rovan
5/21/2020 06:42:22 am
RmYN02 actually had two deletions. one at T678 and the other at S686. the nt sequence appears to possess multiple short indels scattered across the S1-S2 junction when compared against ZC45. a hallmark of an low-quality sequence being used for assembly and resuled in a misplaced contig at S1-S2.
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Henri
5/21/2020 09:41:29 pm
If what you say is correct, then why not send a letter to the Editor of Cell and see if you get a response? They should pass you letter on to the authors and allow them to reply followed by publication of both letters at the same time.
yano
5/22/2020 07:54:46 am
https://www.biorxiv.org/content/10.1101/2020.05.01.073262v1.full.pdf
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Andrew M
5/22/2020 11:26:06 am
You appear to be reading something in this article which isn't in it. Search this discussion thread for "Bill Gallagher". Read that. Go to his site and read the rest of his comments. There is nothing about the S protein which implies a man-made creation.
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yano
5/22/2020 12:14:41 pm
I understand I am reading something into this article. This is why I am asking for input.
Tony
5/23/2020 10:25:28 am
You mean Bill Gallaher(?):
Nerd has power
5/23/2020 02:35:49 pm
Thank you, Yano, for bringing up this preprint article again (someone did it in an earlier comment too). It is THE best work so far, in my opinion. Very powerful analysis. The pattern is not just seen in the S protein. It's the overall feature of adaptation: SARS-CoV-2 is well adapted to humans from the very beginning, while SARS clearly worked diligently in the earlier stages to gradually settle down in the human population. In other words, SARS did look like a virus jumping from an intermediate host to humans. SARS-CoV-2 did not.
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Med
5/22/2020 11:29:53 am
Hi,
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Andrew M
5/22/2020 12:33:34 pm
The Epoch Times is Falun Gong propaganda. They have less interest in science and more in discrediting the CCP. Their motives may well be good ones - I make no comment on that. But the HIV insertion story is nonsense - it has been thoroughly debunked and is not worth pursuing. It detracts from Nerd's theory, which is at least worth parsing,
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Shakti
5/22/2020 12:52:21 pm
You have presented a lot of very interesting information here but I don't understand one thing - why is everyone referring to Dr. Shi Zhengli as Dr. Zhengli Shi? I'm pretty sure that Shi is her first name.
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mz1-2-3-4
5/22/2020 03:38:50 pm
You are simply clueless in this very topic (the name). Her name: Last = Shi; First = Zhengli. In Chinese: 石正丽
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Shakti
5/22/2020 03:51:46 pm
My sincere apologies for the mistake. I only read articles in my native language, English, where she is always referred to as Dr. Shi Zhengli - and in English, the name that comes first is the first name.
Andrew2
5/22/2020 02:44:37 pm
I think This is HIV insertion paper...Please discuss it after reading not before reading!
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Andrew M
5/22/2020 03:41:31 pm
I can't say I understand this paper - particularly when I got to the part about the golden ratio numbers in DNA. The 2 authors really do not check out very well. Montagnier, true is a Nobel prize winner who made excellent discoveries in the past but is now an 87 year old embracing some quack homeopathy "science" theory and the other guy - well - read his Twitter.
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Annette
5/23/2020 01:13:51 am
I found Montagnier paper very informative and robust. My understanding is he was able to detect electromagnetic signals at high dilutions and is quoted as saying "High dilutions of something are not nothing. They are water structures which mimic the original molecules.” A Homeopathy uses high dilutions the proof that remedies have an effect when prescribed professionally should not be debunked but further understood. It is a poor scientists who closes his mind to research as it will limit his/her ability to see things outside of the expected.
Andrew2
5/22/2020 04:15:54 pm
I am sure there is something there as original sars was also had similarity with HIV...also some of the signs of this disease are similar to aids but no one compare those! I am especially worried for long term chronic form of disease with some kind of immunodeficiency for life ..also a paper shows the same genetic risk factor for HIV, could influence your resistance to covid, please see PMID= 23361009 ...I really hope I am wrong!
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Andrew M
5/22/2020 04:39:30 pm
There isn't "similarity" - they are completely different viruses. They have different proteins doing different things (with some overlap, admittedly). This paper seems to find repeated short sequences, after searching through all HIV genomes available (there are quite a few!). Before we even get to considering why viruses and their proteins might have common short sequences for natural reasons, where is the statistical analysis to demonstrate this is anything other than random?
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Andrew2
5/22/2020 04:52:51 pm
I know but those sequences are unique to this virus...don't forget francis Boyle that for many years claim all SARS are man made!
Andrew2
5/22/2020 04:48:48 pm
oops...that was older paper...The pmid=32348495. In that paper please check ref10.
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Andrew2
5/22/2020 07:36:32 pm
Ref8
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Greg
5/22/2020 11:58:41 pm
Hello, I found your blog post very interesting but I have one question regarding the dn/ds ratio that you use as evidence to show that either ratg13 or sars-cov-2 is not natural. First, isn't it a more parsimonious explanation that the skewed dn/ds ratio in certain portions of the S protein gene is due to the fact that cov-2 contains sequences from the pangolin derived coronavirus, specifically in the RBD region of the S protein gene and therefore in those regions, the dn/ds ratio would be different compared to the rest of the genome? Shouldn't one compare the dn/ds ratio in the RBD region of cov-2 to the RBD region of the pangolin derived virus? Also, even if they are different, a skeptic could say so what. Although this may not occur often, it could occur just due to random chance. Is there any way to test whether the differences are statistically significant using a Chi square test or something like that?
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Nerd has power
5/23/2020 02:19:28 pm
Thanks for the comment. The RBD is in S1, not S2. So the comparison of dn/ds for S2 is not affected by a possible RBD-specific recombination.
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Greg
5/24/2020 06:51:50 pm
Thanks for your response. But what about the fact that positive or negative selection can also skew the dn/ds ratio? Couldn't a skeptic just say that the S2 region underwent strong positive selection, accounting for a high dn/ds ratio, while the rest of the genome is under negative or purifying selection which produces a low dn/ds ratio? This alternative explanation could account for the genetic peculiarities of Cov-2, but it seems like it would raise more questions, specifically it seems like cov-2 is well adapted to humans, its genetic polymorphism resembling the original SARS virus late into the epidemic after human adaptation. The question then becomes in what host this adaptation (positive and negative selection) occurred. It wasn't pangolins and it wasn't bats since the binding affinity of the S protein to human ACE-2 receptors is greater than to the bat/pangolin ACE-2 receptor. There's also no evidence of early adaptation of Cov-2 to a human population. Isn't the most likely explanation that Cov-2 adapted to human cell culture lines?
John F Signus
5/25/2020 10:40:53 am
Even the pangolin strain had 8 sense mutations on the S2. The virus itself is about 10% different and the mutations on the S2 appears to have been saturated. However, with the ZC45/ZXC21 bearing 5 dN at a level of similarity being ~97% and pangolin/CoV2 bearing 8dN at a level of similarity being ~90%, the ~96% similar RaTG13/CoV2 can never have just 2dN. The expected dN should be between 5 and 8– and the pangolin strain tells that the dN on RaTG13/CoV2 is far from saturated. The 44-to-1 ratio should never happen at all.
John F Signus
5/25/2020 10:42:33 am
John F Signus
5/25/2020 04:13:59 pm
The tens of million refers to all sequencing reads.
Greg
5/25/2020 10:22:38 pm
John F Signus, that’s quite an explosive claim. You are saying that the pangolin lung tissue has up to 40 percent human DNA? It would be easy to test whether this came from a cell culture or whether it was a contaminant, if it was a contaminant it should’ve been from human rna from skin epithelial cells, ie basal cells in the skin or something like that. If it’s a cell culture, there should be a particular rna that’s more likely to be expressed in human cell lines
John F. Sugnus
5/26/2020 08:52:08 am
Exact RNA type may not be known or important--there are hundreds of different cell culture lines, many of hich were used to culture viruses within. also, we do not know how the samples were contaminated, other than the fact that it can only happen after the sample have been taken and that it formed significant mass fractions in all samples with reads positive for the "pangolin coronavirus". with samples that tested negative showing no such contamination.
John F. Signus
5/26/2020 08:57:11 am
Lung09 is nearly 65% hominid DNA in total-- and judging by mass of the sample (Human DNA/pangolin DNA), the actual mass fraction directly attributed to humans is more than 69% the total weight of the sample--and they do say that some of the S reads were mapped there......Very likely thatthe RBD was one of the previous GOF experimental cultures being mixed up with the actual sample.
Nerd has power
5/26/2020 09:14:13 pm
That is fantastic, John. Thank you for sharing it with us. Have you seen this preprint article?
John F. Signus
5/27/2020 05:46:54 am
On the Dataset SRR10168374, or Lung12. This dataset was claimed by the third article to contain Coronavirus-related reads. however Genomic analysis on the NCBI database failed to identify any.
Nerd has power
5/27/2020 06:17:52 am
Thank you so much, John. I have to read it a few more times to better understand it as I'm no expert in such research. But from what I can understand so far, it's already rock solid. Amazing work!
Nerd has power
5/27/2020 06:22:17 am
Judging from the quality of the figure, I can see a publication coming out of this, which would be amazing. Thanks again for revealing this truth! I look forward to the published article!
John F. Signus
5/27/2020 06:34:18 am
17% human by sequence and 26.1% human by total sample mass--Indicating a heavy contamination by SARS-CoV-2 containing COVID-19 test material. The strange dataset was heavily redacted and contained no other non-coronavirus-related reads making analysis of contamination difficult. However, the sequencing date was after the Outbreak and are very close to the Nature article sequencing date, meaning that it was likely a workbench version of the "pooled reads" from the method section of the early Nature article, which have sequenced a contaminated sample that returned the same two signals with a total mass fraction being 26.1% human, so far remaining the only unabridged dataset that had these two hits.
Rubber Ducky
5/23/2020 04:14:21 am
Synonymous mutations and the molecular evolution of SARS-Cov-2 origins https://doi.org/10.1101/2020.04.20.052019
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Johnny M
5/23/2020 05:33:02 pm
1. CoVID-19 symptoms relates to Nipah Virus - it has massive cell-to-cell fusion and primarily relates to endothelial cells.
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yano
5/25/2020 02:27:48 pm
https://arxiv.org/abs/2005.06199
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CCP is NAZI
5/25/2020 04:52:02 pm
Australian scholars reveal that CCP virus is carefully lab engineered and optimized to infect human:
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Alesh Aras
5/25/2020 05:22:34 pm
How will the below change your conclusions?
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Mr. Tuesday
5/25/2020 10:23:37 pm
https://www.biorxiv.org/content/10.1101/2020.02.15.950568v1.full
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John F Signus
5/26/2020 08:38:29 am
Did you just say "unique synomynous codon usage" on the S protein? it would be exactly what is expected for a synthetically constructed protein being back-translated to a nucleotide sequence, with a bunch of synomynous mutations thrown in to make it more "distinct" from known nucleotide libraries. they failed to account for the codon usage, though.
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Nerd has power
5/26/2020 09:27:43 pm
I know it's hard for any author in a submitted manuscript to call it out, but really our claim here works perfectly in interpreting their finding that "SARS-CoV-2 and RaTG13 might have undergone different evolution pathways". It is this way because at least one of them is not natural. I will have to study their paper more, but can't help comment on it first.
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Mother Jones
5/26/2020 10:40:00 am
https://link.springer.com/article/10.1186/s12985-017-0766-9
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Nerd has power
5/26/2020 09:47:03 pm
Thanks for sharing. Yuri first found out about this and posted it on Twitter. It's an alpha coronavirus that is far away from SARS-CoV-2 or beta coronavirus in general in terms of sequence identity. Therefore, RRAR in SARS-CoV-2 could not be acquired through recombination.between a precursor beta coronavirus and this alpha Coronavirus.
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Henri
5/27/2020 02:58:26 am
I have asked you this before and got no reply. I'll ask again. Why don't you write up your hypothesis that RaTG13 is fake, based on your analyses presented in this blog, and submit a letter to the Editor of Nature Medicine? The Editor should pass the letter to Zhengli Shi and allow a reply. Then, the two letters might be published together in a future issue of nature Medicine.
Nerd has power
5/27/2020 05:38:19 am
Thanks, Henri. I appreciate your suggestion. Challenging Shi and RaTG13 in a reputable journal would be a powerful approach. However, these journals may not be as accommodating for "conspiracy theorists" as people wish. If you looked back on some earlier comments, you will see how Nature has refused to publish an article written by a reputable scientist, arguing for a lab origin of SARS-CoV-2. My attempt would not turn out any better. On top of that, I prefer to not reveal my identity as many do here. Things might change, who knows. If you can't wait, please check out the link below. Some people have already published preprint manuscripts challenging the authenticity of RaTG13:
Henri
5/27/2020 07:42:31 pm
Nerd has power
5/29/2020 04:14:09 am
Thank you very much, Henri. That's a wonderful proposal. It would be great if you could send a letter to Nature Medicine, drawing their attention to my blog. I would be more than happy to edit your letter. When you post the letter, please use a fresh comment as it gets hard to roll back and check old comments.
Uncle Weatherby
5/26/2020 10:01:07 pm
China Rules Out Animal Market and Lab as Coronavirus Origin
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CCP is Nazi
5/26/2020 10:11:07 pm
Who gives it a damn shit on what China has to say? What did they say that is not a lie? Isn't WSJ bought by CCP as CCP's mouthpiece? Which NAZI criminal would admit their NAZI conduct?
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Alesh Aras
5/26/2020 11:01:13 pm
I would rule out wet market as well: China in a hurry to reopen wet markets is prima facie evidence that the CCP doesn’t think that the virus came from there.
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CCP is NAZI
5/26/2020 11:12:54 pm
But CCP rules out their P4 lab as the CCP virus origin as well. It's like saying this shit is not from their ass but from someone else'. Once I see the subject in the URL, I would not even waste a single second to read on.
Alesh Aras
5/26/2020 10:59:20 pm
Bat woman Shi Zhengli has resurfaced.
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Nerd has power
5/27/2020 05:55:49 am
The head of the Wuhan Institute of Virology also gave an interview:
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Tony Soprano
5/27/2020 09:12:04 pm
The Wuhan Seafood Market theory of the origin of SARS-CoV-2 is out and the "multiple origins" theory is in.
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CCP is NAZI
5/27/2020 10:15:30 pm
Who gives it a damn shit on what China has to say? Ya, Nature with a bunch of Chinese "scientists" who only speak what their NAZI CCP want them to say. Otherwise, the lab in Shanghai would not have been ordered to shut down shortly after the lab shared the virus sequence. But are you sure Nature is still science centric and not bought by CCP if CCP have already bought bigger organization like WHO, WTO and many other world organizations? I am so glad that President Trump stopped funding WHO. Let's see how many lies WHO continue to tell the world without the world's biggest donar.
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Leo
5/27/2020 11:11:26 pm
The journal Nature is corrupted, they have so many connections with EcoHealth Alliance.
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CCP is NAZI
5/27/2020 11:26:17 pm
Have you actually compared its sequence with CCP Virus' sequence side by side? If so, why don't you bring its sequence here to let virus specialists verify? Even look at it from a non scientific perspective view, with such a high infectious rate that CCP virus has, why nothing happened in U.S. afterwards until after Wuhan lock down? Interestingly, CCP tried their very best to help this deadly CCP virus spread as fast and wide as possible all over the world by silencing 8 doctors like Li Wenliang , by destroying all virus samples, by stressing it's preventable and controllable, by denying the fact about human to human transmission, by letting people out from Wuhan to everywhere in the world but not within China? Were CCP able to prevent and control it? Exactly, what's CCP's hidden agenda? Well, aren't these https://www.newsmax.com/navrozov/china-biological-russia/2009/09/17/id/335042/ and https://www.theepochtimes.com/did-chinas-plan-to-destroy-the-united-states-backfire_3223117.html enough to tell CCP's world domination goal?
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Leo
5/28/2020 12:35:24 am
We need a forensic analysis on these early cases in USA.
CCP is NAZI
5/28/2020 06:38:24 am
I know everything including how NAZI CCP have been faking their total sum of infected cases, how Obama administration used their tax payers' money to fund HIN who then outsourced to Wuhan P4 lab, how CCP have been threatening each country and scientist who is revealing the truth and facts, how CCP have been developing biowar non stop with still tons of under developed virus in their P4 lab which are far more lethal than what was already released, the so called CCP virus, how CCP have been destroying the virus samples, how CCP have been shirking their crime, how https://nextstrain.org/ncov/global shows all CCP virus mutation could be traced back to China. Oh, too much to list.
Bubba Gump
5/28/2020 12:31:29 am
This article "Viral and host factors related to the clinical outcome of COVID-19" https://www.nature.com/articles/s41586-020-2355-0, published on May 20th, which is now being used by China and the media as the basis for the "multiple origins" theory for SARS-CoV-2, appears to suffer from many of the same problems as "On the origin and continuing evolution of SARS-CoV-2" https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwaa036/5775463, published in March 2020, as explained in a criticism of it http://virological.org/t/response-to-on-the-origin-and-continuing-evolution-of-sars-cov-2/418
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CCP is NAZI
5/28/2020 06:45:19 am
At this moment, the most important is not who has published what considering how many world organizations and journals CCP have been buying, threatening and silencing(Isn't WHO the best example to prove my point?) but when CCP can open their Wuhan P4 lab.
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Leo
5/28/2020 07:02:16 am
I am not sure if USA has the most accurate testing for covid19 cases:
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Leo
5/28/2020 07:04:52 am
This article is quite good for an overview of the facts
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Leo
5/28/2020 07:20:32 am
This is also interesting:
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CCP is NAZI
5/28/2020 07:32:53 am
I'm sorry, but I don't waste even a single second on CCP propaganda such as global times, cnn, nytimes. Trump should craft executive order on fake news just like how he crafts one for social media. I cannot wait to see how 50 cent army will suffer from this: https://www.foxnews.com/politics/trump-crafts-executive-order-on-social-media-weighs-commission-to-probe-bias-amid-twitter-fight I will be eager to test out if anti CCP words still keep disappearing on YouTube and will definitely sue them once the order comes to legal effect.
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Leo
5/28/2020 07:47:12 am
It is probably hard for CCP to open their lab as it is for Fort Dietrich.
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Bubba Gump
5/28/2020 07:53:02 am
Can we stick to scientific analysis here? Political diatribes contribute nothing to what we are trying to achieve.
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Leo
5/28/2020 08:02:52 am
You are right, but it is difficult to avoid to make the discussion political. If this virus is lab made, it is normal to try to find out from which lab it might come. We probably need to wait for more analysis like the one done by Forster with more data.
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charles
5/28/2020 10:31:50 am
Stop sidetrack the discussion. You are just trying to throw in multi-origin conspiracy theories to deflect the spot light on CCP - a typical CCP propaganda and a trick by the Global Times shills. The quickest and easiest way is always transparency from CCP. They are stonewalling from day 1 and their further actions to destroy evidences speak loudly of their complicity in their role in the pandemic to say the least.
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Nancy
5/28/2020 11:02:40 am
You're absolutely right, charles! 50 cent army is everywhere. Luckily, this site isn't paid or operated by CCP. Otherwise, the truth and facts discussed here would be censored or deleted just like YouTube /Twitter/Facebook. There isn't anything easier than being transparent or opening CCP's P4 lab to prove if CCP are NAZI criminals or not. Unfortunately, Xi Jinping suggested to open their lab to the world in a year, after all evidence are destroyed or everyone forgets about it. Come on, no one would ever forget this NAZI crime! If we let it go this time, we don't even know how we die tomorrow!
Bubba Gump
5/28/2020 11:26:00 am
I recommend that the administrator delete the childish political comments before they ruin the site. The children can go waste people's time ranting on Twitter or elsewhere and let the adults have a serious discussion about the science here.
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Nancy
5/28/2020 01:21:27 pm
Which adults fist started the political games here? Which adults only talked about who says what, but nothing substantial or scientific from
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CCP is NAZI
5/28/2020 12:20:17 pm
I also request the administrator to remove CCP's "multiple origins" conspiracy theories along with CCP propaganda to clean up the trash and lies. Just bring your own analysis, virus sequence and facts here.
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Bubba Gump
5/28/2020 08:08:35 pm
Here's the problem in a nutshell - when you have people like "CCP is Nazi," who pollute a scientific discussion with useless political comments, it ruins the site. "CCP is Nazi" either did not read or did not understand the articles about "multiple origins" upon which my post was based. The last citation is a scientific criticism of the articles supporting "multiple origins." So, my post about "multiple origins" debunks rather than supports the theory of "multiple origins." Not surprisingly, "CCP is Nazi" got it all wrong, is the one who is the distraction, adding nothing to the scientific discussion and will end up ruining it for everyone. Sadly, that type of behavior is all too common on social media sites, people with big mouths and little brains.
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CCP is NAZI
5/28/2020 09:56:47 pm
This is not the first time I name like this. I don't know why you are the only one fussing about this. Anyone can decide what name to use just like how you name yourself as Bubba Gump instead of your
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Bubba Gump
5/28/2020 10:23:05 pm
The irony is people like "CCP is Nazi" and "Nancy" practice exactly what thw communists and Nazis did, that is, the political interpretation/use of science e.g. Soviet Lysenkoism and Nazi racial science. Offer scientific analysis here and reserve your political views to a more appropriate forum.
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CCP is NAZI
5/28/2020 10:42:01 pm
While Bubba Gump is asking others not to talk about politics, he himself is just doing the same. How funny! Those who do not agree with CCP is NAZI are undoubtedly NAZI themselves.
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Rose
5/28/2020 11:21:45 pm
I suggest to use rather our energy to definitely demonstrate that SARS-CoV-2 is lab made, in a way that it is finally accepted from the rest of the people who still think is natural, because I fear they are still the majority.
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Bubba Gump
5/29/2020 03:07:47 am
"Rose," Peter Daszak started his career in parasitology and migrated into virology. Here is a review article he published in January 2000 with some of his citations. He was into Nipah virus before coronavirus, I believe.
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Rose
5/29/2020 03:46:44 am
Ah yes thanks, it is the same article I posted. I am just wondering if he could have seen before emerging of SARS, that bats carried CoVs, since he was already studying their viruses before 2000.
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Nerd has power
5/29/2020 04:50:06 am
I appreciate everyone's contributions to this comments section. It has certainly surpassed my exceptions. Many analysis and findings that people shared here are just brilliant. We are piercing deep into the thickness. It's great.
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Henri
5/30/2020 04:42:22 am
I have composed a 'diplomatic' letter for Nature Medicine. The technical bit, which I need you to check over and correct if necessary is below.
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Henri
5/30/2020 07:26:24 pm
The letter to nature is ready to be submitted. Please check the technical bit given above and make any changes you feel necessary. If I don't hear from you soon, I shall submit on the assumption I have described your main objections correctly.
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Lilian
5/29/2020 06:09:28 am
I have found some interesting information on the ORF10 in SARS-CoV-2
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Jule
5/29/2020 09:47:41 am
What I do not understand is why Shi did not simply synthesize RaTG13 to avoid any suspicion.
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Rose
5/29/2020 10:31:21 pm
I bet that RaTG13 is not functional as designed. Let’s see if someone try to synthetize it.
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Tim Pearson
5/29/2020 12:51:36 pm
When the SIV of sooty mangabees crossed over into humans and became HIV, there weren't any alternative theories that some local laboratory within West Africa had been responsible for that occurring.
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Rose
5/29/2020 10:34:47 pm
You can ask Fauci, he is the HIV expert and best friend of Daszak
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ioderESTEl
5/29/2020 03:00:16 pm
So SARS-CoV-2 has another dangerous characteristic tied to ORF8. I wonder if another animal virus sample showing this particular characteristic will suddenly be published.
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Rose
5/29/2020 10:18:32 pm
You can have a look here:
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Reminder
6/8/2020 07:16:05 am
If the link is down, here is a mirror to that file.
Pete Ross
5/30/2020 05:56:29 am
To add or subtract from the mystery of SARS-2 (CoV2) origins are this series of tweets from Dr. Peter Daszak of EcoHealth Alliance, recently deprived of NIH funding just last month.
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Alexandrian LC rocks
5/30/2020 09:11:06 am
This is an important lead. Remember Shi’s previous statement? They were gathering bits and pieces from naturally occurring viruses throughout the world, mix and match them in the lab not necessarily with seamless ligation, put them throughout cell and animal passage Until they generated the perfect disease X to be unleashed into humans. All in the name of “saving wildlife”.
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pangolin
5/30/2020 10:44:17 am
I perfectly agree with disease X possibly being SARS-CoV-2 but the market has nothing to do with the initial spread. The real boosters were the military games in Wuhan in October 2019. There are posts here on it.
Alexanderian TD Rocks
5/30/2020 09:13:24 am
From an early source. Explain the EcoHealth agenda very clearly.
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Babstar
5/30/2020 01:04:39 pm
Alina Chan just tweeted ?
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Henri
6/1/2020 07:47:19 pm
Why does the noose tighten? No one denies such reearch has been performed.
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George Formby
5/30/2020 10:48:01 pm
This first appeared as a pre-print at the end of March, published on May 29th.
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Nerd has power
6/2/2020 06:15:44 am
Thank you for bringing up this paper. I think their evidence proves the opposite. They mainly argued that because all the suspicious elements of SARS-CoV-2 (RBM, furin-cleavage site) are hinted to exist in nature, then recombination must be responsible for the appearance of SARS-CoV-2. Of course, in my eyes, they used all the wrong sequences, RaTG13, pangolin coronaviruses, YN302, to do their analysis and thus support their "conclusion". But I think their data revealed the opposite. When they analyzed the syn/non-syn mutations, they showed extreme high purifying pressure for SARS-CoV-2, RaTG13, pangolin viruses in S gene and in other genes (figure 4 and 5). Unfortunately, they did not always include a similar analysis of another group. I think they probably did those analysis in figure 5 and I suspect that the results are too daunting and not aligned with their "conclusion" of natural recombination being the source. I will try to find the time to do that comparison for them.
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John F. Signus.
6/8/2020 07:06:18 am
Also, Here is a complete, detailed analysis on why RmYN02 itself--Not only it have no furin site, but it was also Not viable!
Javier
6/2/2020 12:59:54 pm
ZXC21 and ZC45 : strong purifying selection and same habitat (in caves collected by a military research lab of the CCP)
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Henri
5/31/2020 06:09:21 pm
Open request to NerdHasPower:
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yano
5/31/2020 09:16:52 pm
E) At the beginning of the 2019 pandemic SARS-CoV-2 was better adapted to infect humans than any other animal. No selective mutations or adaption to humans was needed (or observed). This suggests the virus was already well adapted to human cells and did not come from animals
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Henri
6/1/2020 03:41:43 am
Letter submitted. Let's see what happens.
Nerd has power
6/2/2020 05:08:10 am
Sorry for not responding earlier. Did not find the time to pay a visit here for two days. You were saying that you needed 1 or 2 weeks to draft the letter. So I didn't think you have it ready already. Anyways, the letter looks very good to me. Point C did not explicitly state that comparison was done for the Spike, but that does not hurt the argument or make anything incorrect. Thanks again for doing it. Please keep us posted with the results.
John F. Signus
6/8/2020 06:59:41 am
Also YNLF31C/SARS.
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MagmaHombre999
6/2/2020 12:40:07 am
Have you considered the possibility that rather than the changes in the ratios of synchronous to non-synchronous mutations were in the published "RaTG13" genome were an intentional signal from Dr. Shi as she was probably ordered to conduct the cover-up??? Could there be a coded message in the changes???
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Nerd has power
6/2/2020 06:59:36 am
I don't know, but I do hope that's the case. If one day she would be able to come out and tell the truth to the public, it would be good for the world and for herself. Maybe she desires for such an opportunity too.
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Henri
6/2/2020 07:20:09 pm
The Letter to Nature was rejected outright. I appealed. The appeal failed. I now intend to take the matter up with the Editor-in-Chief. If that fails to get the letter published, we must discuss our next move.
Henri
6/4/2020 03:32:54 am
Radio silence form the Editor in chief and Nature. So, NerdHasPower, where we do we go from here? I have a couple of ideas. Your thoughts please.
Lilian
6/2/2020 10:41:35 am
The Case Is Building That COVID-19 Had a Lab Origin
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Javier
6/2/2020 12:42:37 pm
Three well done summaries, reported by Claire Robinson
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6/3/2020 08:33:59 am
Hello Nerd,
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Henri
6/3/2020 07:20:51 pm
You seem to have misunderstood my position. I am on the side of 'it was NOT made in a lab'. NerdHasPower has put forward SOME arguments that RaTG13 is fake. As a scientist, I believe his arguments summarised in my letter require addressing by the Wuhan group. I believe there are satisfactory answers in scientific terms.
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Robert Cartwright
6/4/2020 02:17:44 am
Here the new paper of Perez and Montagnier 6/4/2020 02:42:14 am
Sorry, I meant to address the blog owner and the author of the original post.
Robert Cartwright
6/4/2020 02:42:39 am
I think Henri's comment about Montagnier and Perez is exactly the same as that of the mainstream scientific community: many, many organisms came up with the same short HIV sequences. This, in my opinion, completely misses the point. The problem is not that the sequences are short and common but where they are located, and what mutations it induces subsequently (i.e. the S1 protein). This, I seem to understand, has been deduced by artificial intelligence simulations and, contrary to what Henri thinks, is the most sensible research direction to explore. This hypothesis, in the absence of information from Wuhan) is a hypothesis that can be verified ex-post only by analyzing whether the evolution of the virus deletes the exogenous RNA Sequences. The new Perez and Montagnier show that this is happening
Nerd has power
6/4/2020 09:52:09 pm
Thank you, Lila, for the comment and thoughts. I have answered the question of whether or not HIV sequences have being inserted into the SARS-CoV-2 genome. But I understand that it is very hard to screen all the comments now. My short answer is that I'm not convinced that such insertions are true. Or I should say that my own analysis failed to convince me in believing so. My conclusion that the virus is man-made is apparently based on other evidence and reasoning.
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Greg Felton
8/21/2020 02:02:45 pm
Hi Nerd:
Lilian
6/3/2020 03:12:53 pm
Another article worth to read
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Wilson Volleyball
6/4/2020 01:06:12 am
Exclusive: Coronavirus began 'as an accident' in Chinese lab, says former MI6 boss
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Andrew M
6/4/2020 03:41:02 am
Some of the commenters don't leave facility for a direct reply - I don't know why that is. So, a general post about HIV, Montagnier and Perez. And Dearlove. |