SARS-CoV-2 Origins: IPAK Research Exonerates Dr. Shi

It has been alleged that the genetic modifications of a specific SARS-like virus by Dr. Shi makes her complicit for the SARS-CoV-2 pandemic.

I have mentioned at least two dozen times that my in-depth analysis of SARS-CoV-2 sequences and all available Beta-Coronavirus sequences shows no evidence of genetic manipulation of SARS-CoV-2.

Here I share a side-by-side comparison of the Spike protein motif signature of the spike protein from the very viral sequence Dr. Shi was involved in developing so the public can see the evidence I see.

The analysis involves a comparison of protein motifs found in the SARS-CoV-2 sequence to the sequence Dr. Shi had worked on. Importantly, this is not a full showing of all analyses of this kind to date: that analysis is under peer review and I will report that while some sequences published by WIV and by the Military lab in Nanjiang DO have the characteristic motif pattern, those sequences are natural sequences from bats. The spike protein from the Pangolin also has the characteristic signature motif pattern. NO CHIMERIC VIRUS OR LABORATORY-MODIFIED VIRUS THAT I HAVE ANALYZED TO DATE HAS THE SAR-COV-2 CHARACTERISTIC PROTEIN MOTIF SIGNATURE.

So let’s begin.

A. The SARS-CoV-2 spike protein motif signature

Data: NCBI”s Protein Database Entry [surface glycoprotein [Severe acute respiratory syndrome coronavirus 2] https://www.ncbi.nlm.nih.gov/protein/YP_009724390.1?report=fasta

This pattern is unusual – it has a short N-terminal domain spike protein, and is missing a She3 and KxDL motif. It also has a GP41-like motif. The matches are not strong, but evolution – and protein function – works on and because of protein shape, not merely sequence.

B. Dr. Shi’s recombinant SARS-like coronavirus spike protein motif signature

Data: NCBI’s Protein Database Entry spike protein [Bat SARS-like coronavirus RsSHC014] https://www.ncbi.nlm.nih.gov/protein/AGZ48806.1?report=fasta

This protein motif pattern is identical to nearly all other SARS coronaviruses including other chimeria viruses derived from SARS. They do not have a truncated N-Terminal Domain motif, and they have the She3 and KxDLmotifs, and has no Gp40 motif.

These results are reproducible using the Motif Search function here.

I realize that to the public, nearly 100% of this is gibberish. However, these differences (and other, more in-depth phylogenetic analyses under review) exonerates RsSHC014 as being involved in the origins of SARS-CoV-2.

In my analysis I also discovered that one sequence published by a Chinese laboratory in 2005 DID have the characteristic motif – and it was from a bat sequence from Hong Kong.

I strongly recommend that all B-CoV spike protein motif patterns should be studied so we know if any studies of treatments exist that might be relevant for clinical investigations.

Note, hoever, that this result does not rule out accidental laboratory release of a natural virus under study.

I sincerely hope this helps people move on to more pressing matters, such as the lack of animal safety studies in the ongoing COVID-19 clinical trials. You can read more about that here (How the COVID-19 Pandemic Will End), and watch a full interview on why that’s a very serious problem indeed.

To support IPAK and Dr. Lyons-Weiler’s cutting edge research, visit

http://ipaknowledge.org

Advertisements

23 thoughts on “SARS-CoV-2 Origins: IPAK Research Exonerates Dr. Shi

  1. Dr. Lyons-Weiler: Is RT-PCR capable of clearly and accurately identifying in human tissue an infection with a specific virus? I’m having a difficult time believing that the cases of infection reported in the media have any level of reliability. I find this an incredibly important question. In my medium-size city on the Left coast, with one purported infective case (from a cruise ship), panic buying is out of control. In my family we are always prepared, with at least a two-week supply of water and food, and usually much more than that. I was a Boy Scout sixty years ago, and that is the motto: “Be prepared.”

  2. What is your take on this new paper published today in Nature Medicine:
    “The proximal origin of SARS-CoV-2”? ->

    https://www.nature.com/articles/s41591-020-0820-9?utm_source=fbk_nnc&utm_medium=social&utm_campaign=naturenews&utm_medium=social&utm_content=organic&utm_source=facebook&utm_campaign=NatureNews_&sf231597135=1&fbclid=IwAR0SfG5Ls2OjaEnBlVOfW5Qz5VDtaTVSsKytFjNE7j4d-eyfwAmiSiL39WA

    “It is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus. As noted above, the RBD of SARS-CoV-2 is optimized for binding to human ACE2 with an efficient solution different from those previously predicted7,11. Furthermore, if genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used19. However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone”

    1. I understand sci mumbo-jumbo; however, we need to look beyond that. We need to consider motives of Wuhan Institute in light of extensive military involvement. Dr. Shi is one of the cogs in the wheel. She may or may not be the only one involved. Viruses do not originate in vacuum; there is a chain of events; not just speculations. That chain leads to Chinese eating bats, rats and rare species; a country that has advanced so much that it can not even feed its people without resorting to eating vermins!

      If a few computer scientists in India, can analyze gene sequence published by China, and, identify unusual HIV sequences (four?) in the data, and exclaimed that such a mutation highly unlikely (uncanny?), the scientific and political communities silenced them instead of asking how did this happen? What are the chain of events where such a thing can happen? What is the probability of such events happening in nature? And, what is the probability for some entity like Wuhan Institute with exceptionally qualified staff like Dr. Shi and others, be able to fabricate such a virus?

      Here is my take: there was a mishap at the Wuhan Institute lab during scaling up the production of this deadly virus. There was overconfidence that most of the indigenous population is likely immune from it as primary backbone is Corona virus, and, there had been active vaccination of the population. So they sat on the problem until aa lonely doctor blew a whistle and in the process went to heaven while taking care of the first victims.

      There is simple math for viral vector propagation and if one were to calculate the early infection rate in Wuhan, one would know how much of the virus was released accidentally and once such a quantity is known, one would be able to decide the why one would build such a high quantity of deadly virus?

      1. I suspect someone got a phone call or was paid a visit by some individuals that were quite intimidating and decided to shift the narrative a bit (a lot) to calm said individuals down because there is a strict need for the narrative to continue to prevent hysteria and chaos within America and abroad. This is the reason the news makes zero mention of this virus having anything to do with SARS. They talk about COVID19 and they call it the COVID19 virus but truly its a SARS-COV virus and the disease it causes is the COVID19 like HIV is the virus and the disease it causes is AIDS. If people heard SARS in America there would be mayhem. The powers at be are trying to control the masses and its why the Surgeon General just a few weeks ago told the American people that wearing a mask was not patriotic and induced fear in their fellow citizens, but he was really trying to prevent the consumption of masks so that the healthcare workers could have enough etc. Then he comes out now and says we should make our own make shift mask as if that is really going to do anything at all. You make a lot of valid points, I suspect the no response is more of an affirmation of what you said than the opposite. When Dr. Weiler was making his claims in Feb the SARS-COV had not hit America hard, but now it has, and someone out there suggesting that this was man-made, and saying something radically different than what the mainstream media is telling us, is not what the people in charge want to see, especially from someone with the level of respect that Dr. Weiler has. Although, I do believe his reversal, whether he is being honest or not, has probably upset quite a few people, because just like the Surgeon General, you can’t have it both ways, and when people are dying you gotta be willing to take a stand for truth. And in this case, if that is truly what he is doing, then I commend him for admitting the error he made, but if he’s doing it because of being persuaded, then he should have thought about what he was getting into before saying anything because the world doesn’t need people who know the truth to flip flop. There is too much of that going on already. Either way, China is a serious threat, whether its their carelessness, lack of concern for Americans well being since they said were so secretive, or if this was intentional.

        My major concern which I think is extremely valid is that this may have been a practice run. If China was able to quarantine this well, and their numbers are in fact correct, then I can only suspect that this was done on purpose. How would they be able to quarantine so well when this virus can incubate up to 14 days. IT spread all throughout the world, but it only remained in Wuhan? Awfully suspicions if their numbers are true. If this was intentional then they would need it to look that way, so collateral damage is necessary evil, so they can say they are victims too. Next time, they could release something far worse, and the world won;t be able to coordinate, and we will be at our knees to China. There was a Chinese national that was caught at an US airport with MERS in 2018 according to the FBI. He was BRINGING IT INTO THE USA! When they start bringing stuff into our country then you know they are planning something. My gut tells me this was a practice run for a much more nefarious and severe death toll next time which is what China is preparing for and why they are so hell bent on working with these viruses and finding vaccinations. If they can make a disease to wipe out manking and keep their own safe, do you think they wouldn;t considering their moral compass thus far?

      2. Thank you Realness.

        I have not been threatened. I have not been intimidated. I have not be bribed, coerced. etc. I’m not a communist. I’m for a free and open
        society. I am anti-Fascist, and anti-American-Style Fascism in which the gov’t is run my corporate interests.

        The reality is that the USA, my beloved home country, is idiotic. We had a test in Jan – theGerman’s test – and we ignored it. Why? To maintain
        the house of cards illusion that CDC is a centralized authority. They had to have THEIR OWN test, and they fucked up. Badly. They shipped
        a flawed test, allowing SARS-CoV-2 to spread – actually helping it spread – much faster. The CDC prevented any real contact tracing effort to be
        of any significance. When they found the flaw, they didn’t bring on the German’s test. They turned to American corporations. That’s a trade of revenue
        for lives.

        They are still being idiotic, focusing our attention on a vaccine when based on all past experience we have every right to expect that vaccines against
        SARS-CoV-2 will induce Pathogenic Priming (aka “Immmune Enhancement”). The need to make vaccines the be-all and end-all solution has now cost
        us our ECONOMY – just as it is has to hundreds of thousands of American ex-vaxxers, who can only have one income due to a vaccine injured child.

        I’m taking the bully pulpit here and calling CDC to STAND DOWN and for Fauci and Gates to STAND DOWN on the vaccine bullshit and use their high profiles
        to push for (a) a switch to the Sweden model (isolate the at-risk), (b) in-home private antibody testing, therapeutics (yes change your fucking regulatory paradigm,
        FDA), (d) de-regulation of natural and allopathic treatment combinations that appear to be working, (d) major changes in lifestyle across the USA – end diabetes, end smoking, end high blood pressure.

        This virus is a from a bat. It came into labs to find solutions to disease. It likely escaped. Should China capitalize on our idiocracy, it’s through
        no benefit of their own.

        A second virus coming our way from nature related to SARS-CoV-2 after mass vaccination will end America.

        And we will have done it to ourselves.

      3. The question you posed presumes that your presumption is a given, which it is not. It does not help that there were reports of the military destroying material in the WIV labs.

        However, there is no – zero – signal of a bioweapon in the SARS-CoV-2 genome. The so-called HIV sequences were small stretches that happened to match HIV. They also match many many other organisms including plants. The preliminary report published by the Indian team was retracted by that team in part because those sequences had no significant E-values.

        There are features in this virus new to science, including the furin cleavage capacity, and the characteristic motif structure (see http://ipaknowledge.org/covid-19-and-sars-cov-2-research.php) that may provide clues to prophylactics and therapies.

  3. Shi Zhengli- Well I would hope she is smart enough not to publish results on the exact virus that would be used as a bioweapon. The absence of evidence is not evidence of absence. She is certainly a person of interest though.

    2002 -Godfather of corona virus (Ralph Baric of UNC ) patents process for a coronavirus vaccine. He will work with Shi Zhengli in coming years

    2003 After the SARS outbreak Shi Zhengli led a team to collect bat samples across the country for virus detect the Corona viruses

    2010 -Shi Zhengli’s team published a paper to examine the sensitivity of different types of bat ACE2 to human SARS-CoV spike protein (S protein) using live SARS virus and HIV (AIDS) pseudovirus.

    October 30, 2013, Nature magazine published a paper entitled “Isolation and characterization of a bat SARS-like Coronavirus that uses the ACE2 receptor“, from the research team including Ge Xingyi, Shi Zhengli, Dasak and other experts from Yunnan. Shi Zhengli provided the SHC014 Coronavirus S protein sequence and plasmid, which is her field of expertise.

    2014 Shi Zhengli received a $665,000 grant from NIH for a study titled The Ecology of Bat Coronaviruses and the Risk of Future Coronavirus Emergence as well as $559,500 more from USAID for a study titled Emerging Pandemic Threats PREDICT_2China

    November 9, 2015 Ralph Baric of UNC and Shi Zhengli jointly published a study on their efforts to engineer a virus with the surface protein of the SHC014 coronavirus, found in horseshoe bats in China, and the backbone of one that causes human-like severe acute respiratory syndrome (SARS) in mice. Funding for this project was from the DoD

    2015 The Wuhan Institute of Virology opens the first biosafety level 4 (BSL–4) laboratory to be built in mainland China. Shih Zhengli having helped build a hyper-virulent coronavirus from scratch at UNC – just so happens to be working at this lab that also just so happens to be at the epicenter of an outbreak involving a coronavirus

    2018 Shi Zhengli publishes a study reporting the discovery of 89 new “novel bat coronavirus” strains that use the same receptor as the coronavirus known as Middle East Respiratory Syndrome (MERS). That study was jointly funded by the Chinese government’s Ministry of Science and Technology, USAID and the U.S. National Institute of Health

    On January 23, 2020 the Shi Zhengli team published an article on bioRxiv preprinted version of the platform titled, “A pneumonia outbreak associated with a new coronavirus of probable bat origin.” The report proposed that the new Wuhan Coronavirus was derived from bats.

    On Jan 27th, Shi Zhengli submitted the registration information of RaTG13 bat virus referred to in her Jan 23 preprint article, showing that the virus was isolated from the feces of Yunnan horseshoe bats (chrysanthemum bat) as early as July 24, 2013. It was never mentioned in any of her previous papers.

    1. The SHC014 virus from 2015 does not have the signature protein motif pattern.

      None of the published sequences except the 2005 sequence from a bat has the signature pattern.

      I will continue to analyze spike protein sequences as they are published and will of course provide any updates.

  4. In my analysis I also discovered that one sequence published by a Chinese laboratory in 2005 DID have the characteristic motif – and it was from a bat sequence from Hong Kong. Note, however, that this result does not rule out accidental laboratory release of a natural virus under study. Now my issue is not that you might be wrong as with any study there are sometimes variables that cannot be 100% accounted for, plus as someone else said she might not have published ALL the work she did and is it not possible for someone to be able to replicate a virus and modify it just slightly and someone NOT BE ABLE TO TELL? Or as I copied your quote it could have been accidentally released … Its also possible it might have been modified just enough that someone could not tell and been released on purpose. Or the virus harvested and released on purpose knowing that as most viruses do, that it would mutate.

    1. Mike – My position is also that we have no evidnce to rule out accidental laboratory release of a natural virus, or a virus
      that has been in the lab a while acclimating to human tissue lines or primates.

      Thank you for quoting. Feel free to post a link to anything of interest here.

      Stay well.

    1. Each protein sequence for the spike protein for every “SARS” and “SARS-like” protein should be checked using this tool
      https://www.genome.jp/tools/motif/

      To see if it has the SARS-COV-2 motif pathogenicity signature as described in this report

      “Motif Pathogenicity Typing: SARS-CoV-2 Coronavirus May Contain a Unique “Likely Pathogenic” Protein Motif Signature Also Found in a Natural Isolate from 2005” Download_PDF
      http://ipaknowledge.org/covid-19-and-sars-cov-2-research.php

      The pattern is VERY distinctive and was found in a sequence from a bat guano sample (anal swab) in Hong Kong in 2005.

      I wish the rest of the scientific community would routinely check all B-CoV related to SARS and SARS-CoV-2 for this motif pattern, it’s distinctive.

  5. Thank you for posting about this so candidly, and for replying to comments so succinctly. Your website is pure education. It gives me hope that a scientist would take the time to communicate and present information in a way that actually connects to non-experts. It is better to know than not to know. It is better to learn and face something compared to wallowing in fear and ignorance. So thanks again for helping combat fear with knowledge. Good luck to you.

  6. “Construction of recombinant viruses

    Recombinant viruses with the S gene of the novel bat SARSr-CoVs and the backbone of the infectious clone of SARSr-CoV WIV1 were constructed using the reverse genetic system described previously”

    Does this study provide any relevant insights, are procedures like the ones described here possibly causal for what SARS-CoV2 looks like?

    https://journals.plos.org/plospathogens/article?id=10.1371%2Fjournal.ppat.1006698

    1. We should no longer entertain “lab origin” theories because the sequence from 2005 has the SARS-CoV-2 structural motif pattern. No need to find a lab technique to explain a spike protein that nature had already put into a sequence from a isolated in a guano swab from the anus of a wild-caught bat in Hong Kong in 2005. Please read the report here at the IPAK website – #2 We have found a protein motif “signature” of pathogenicity that seems characteristic of 2019-nCoV. Specifically, the oldest sequence we have to date (from 2005) that shares the motif fingerprint is HK-3. HK-1 and HK-2 share part of the pathogenicity signature, but only HK-3 has the complete match. Research Report here.

      IPAK RESEARCH REPORT COVID-19-2020_1

      “Motif Pathogenicity Typing: SARS-CoV-2 Coronavirus May Contain a Unique “Likely Pathogenic” Protein Motif Signature Also Found in a Natural Isolate from 2005” Download_PDF

      Abstract

      Careful analysis of protein motif signatures and iterative phylogenetic analysis of amino acid sequences of coronaviruses reveal a characteristic functional motif signature of the coronavirus first detected in afflicted humans in China in December, 2019, currently responsible for the deaths of over 700 people so far and massive isolation efforts in China. New results show that original conjectures the modified protein signatures as indicative of supporting a likely laboratory origin via recombination technology do not, at this time, appear to be not supported. New data indicate that invoking a recent laboratory intentional modification is not necessary to understand the origins of the pathogenicity. This, however, does not rule out a laboratory escape of pathogenic virus for pathogenicity or vaccine development research. Continuous ongoing detailed sequence analysis is necessary. An evolutionary awareness of the inheritance and acquisition of characteristic functional motif signatures will aid in understanding limits of applicability such studies; studies of “SARS” and “SARS-Like” coronaviruses cannot be expected to be useful to generalize about the pathogenicity from sequence or structural insights alone. Determining, recording and publishing functional motif signatures could prove essential for communicating pathogenic-like coronavirus types with respect to expected pathogenicity. Laboratories with natural isolates, isolates from humans, and recombined coronaviruses that include spike protein sequences should analyze the spike protein for the putatively characteristic pathogenic functional motif signature: which appears at this time to include a shortened N-terminal spike domain, missing She-3 and KxDL motifs in the Spike 2 segment, and a C-terminal Gp41 (retroviral envelope) motif. Research into C-terminal motifs and elements may prove to potentially useful for tracking laboratory modified coronavirus types. The presence of the proposed pathogenicity signature and an understanding of the provenance of the sequence information involves laboratory origin of related sequences, but seems at this time to rule out recent laboratory origin of the SARS-CoV-2 lineage. A recently reported furin-like cleavage site that has a similar phylogenetic distribution in B-coronaviruses also seems like a promising lead for therapeutics.

      http://ipaknowledge.org/covid-19-and-sars-cov-2-research.php

      1. Thank you, my question was not necessarily aimed at intentional modification, but trying to understand whether such procedures might have for example facilitated another scenario you laid out in a podcast, namely a lab worker’s contracting one or multiple such viruses (wild type or other) and their subsequent further unintentional recombination with other SARS-like CoV in vivo.

        Obviously the details are hard to grasp for laymen.

        Is my understanding that Gp41 should not be found in any naturally occurring specimen and was therefore suggested as a ‘control’ of sorts correct?

  7. I would also be interested in your take on the question about PCR testing up-thread.

    As well, I have a question which hopefully I didn’t miss an answer to within the discussion threads: Is it realistically possible to determine with certainty that a virus was *not* artificially recombined? I would think that we could, in some cases, determine pretty confidently that something *was* artificially altered (an extreme example being plants genetically modified with fish DNA — something that couldn’t happen in nature), but that the best we could determine the other direction is that “we don’t have reason to think it *couldn’t* have been naturally created.” But I’m not an expert in this stuff. Is that incorrect and, if so, are you able to explain why?

Leave a Reply to Dr FS Cancel reply