James Lyons-Weiler, PhD – 1/30/2020

UPDATE – 2/9/2020 – IPAK HAS CONDUCTED FURTHER, IN-DEPTH STUDIES OF THE GENOMIC AN PROTEIN SEQUENCES OF THE 2019-nCoV CORONAVIRUSES AND THEIR RELATIVES AND HAVE COMPELLING RESULTS OF A KEY SIGNATURE USEFUL FOR IDENTIFYING A PARTICULARLY PATHOGENIC CORONAVIRUSES LINEAGE. GIVEN THAT WE HAVE FOUND THIS SIGNATURE, A FUNCTIONAL MOTIF FINGERPRINT, PRESENT IN THE HK-3 CoV FROM 2005, WE BELIEVE THIS EXONERATES RECOMBINATION IN THE LAB AS A SOURCE OF THE VIRUS. THIS DOES NOT EXONERATE ACCIDENTAL RELEASE, HOWEVER. WE ARE WORKING TO PUBLISH OUR FINDINGS.

IN THE INTEREST OF TRANSPARITY, WE ARE KEEPING THE ARTICLE BELOW AS ORIGINALLY PUBLISHED FOR POSTERITY AND PROVENANCE. – JLW

RECOMBINATION technology has been in use in molecular virology since the 1980’s. The structure of the 2019-NCoV virus genome provides a very strong clue on the likely origin of the virus.

Unlike other related coronaviruses, the 2019-nCoV virus has a unique sequence about 1,378 bp (nucleotide base pairs) long that is not found in related coronaviruses.

Looking at the phylogenetic tree recently published derived using all the full genome sequence, we see the 2019-nCoV virus does not have clear monophyletic support given the bootstrap value of 75 (Fig 1).

Close-up on Bootstrap value of 75 for available 2019-nCoV from Lu et al., 2020 The Lancet article [Full Text]

There is no doubt that there is a novel sequence in 2019-nCoV; we confirmed this via sequence alignment. Here’s the DOT plot:

The gap in the line shows a lack of sequence homology beween the most similar bat coronavirus and 2019-nCoV. The inserted sequence, which should not be there is here:

A database search by the first team to study and publish the whole genome sequence for the origins of the inserted sequence turned up no hits (Ji et al., 2020). They conducted a codon-bias analysis which led them to speculate that perhaps there had been a recombination event between a coronavirus in snakes with a coronavirus from bats (Ji et al., 2020). [Full Text]

This led to criticism on Wired(3) with quote dismissing the snake origin hypothesis as lacking evidence. There is, however, clear evidence that the novel sequence, which I will refer to henceforth as INS1378, is from a laboratory-induced recombination event. Specifically,

(1) The sequence similarity to other coronavirus sequences is lower to its most similar sequences in any coronavirus than the rest of the genome (IPAK finding)

(2) The high sequence similarity of INS1378 to a SARS spike protein (2; IPAK Confirmed).

(3) We also found significant sequence similarity of INS1378 to a pShuttle-SN vector that was in use in the 1980’s in China to create a more immunogenic coronavirus (IPAK finding, details below, Option 4).

Here, I review four Option on the origins of the 2019-nCoV Coronavirus isolated from human patients from Wuhan, China.

Option 1. Natural coronavirus related to bat coronaviruses, Not a Recombined Virus.

Evidence for: Phylogenetic clustering with Bat coronaviruses.

Evidence against: Low bootstrap support (N=75) and presence of a INS1378.

Status: Falsified hypothesis.

Test: Survey coronviruses in animals in the wild.

Option 2. A recombined virus that naturally picked up a SARS-like spike protein in it N-terminus (3′ end) of the viral genome.

Evidence for: The INS1378 codon bias similar to snakes ($)

Evidence against: Insufficient match in database search to other known CoV spike proteins (Ji et al., 2020)

Status: Speculative hypothesis. Unlikely.

Test: Find an isolate that matches 2019-nCoV in the wild and reproducibly independently isolate the virus from a wild animal (a match will confirm).

Option 3. A recombined virus made in a laboratory for the purpose of creating a bioweapon.

Both China and the US hinted at the other side’s potential liability in playing a role in bringing about a novel coronavirus in the lab specifically for the purpose of being used as a bioweapon. To add to the intrigue, a Chinese Scientist was released from BSL-4 laboratory in Manitoba, Canada for violating protocols, allegedly sending samples of deadly viruses to mainland China.

On January 26, The Washington Times published this article citing an Israeli defense expert claiming that China has likely proceeded with a bioweapons program, but ending the article with a quote to London’s Daily Mail from a US scientist Rutgers University microbiologist Richard Ebright that “at this point there’s no reason to harbor suspicions” that the lab may be linked to the virus outbreak.

The same person was quoted in a Feb 2017 Nature article stating that SARS had escaped the Wuhan a facility in Beijing (corrected 2/2/2020) “multiple times”.

Evidence for: Presence of BSL-4 laboratory 20 miles from the Wuhan seafood market

Evidence against: Published opinion.

Status: Rumor. But see below.

Option 4. A recombined virus made in a laboratory for the purpose of creating a vaccine.

IPAK researchers found a sequence similarity between a pShuttle-SN recombination vector sequence and INS1378. Here’s a shot of the alignment and the DOT Plot.

Here’s the nucleotide sequence at NCBI’s Nucleotide database. Here’s a patent for its use in recombination virology.

The pShuttle-SN vector was among many described in a 1998 paper by Bert Vogelstein et al; here is a company where one can purchase the pShuttle-SN vector: {CORRECTION: THE P-SHUTTLE VECTOR PLASMID WAS DESCRIBED BY VOGELSTEIN ET AL; THE PSHUTTLE-SN VERSION IS WAS PUBLISHED IN 2005 AS CITED AT THE ADDGENE PAGE; THE RECOMBINED ADENOVIRUS PATENT LINK CITES P-SHUTTLE-SN AS WEL IN USE FOR INSERTING SARS SPIKE PROTEINS INTO OTHER ORGS }

It turns out that the sequence from pShuttle is most closely related to the Spike protein from SARS coronavirus.

This particular technology was used in 2008 to attempt to develop a more immunogenic vaccine against coronavirus. Here’s a Chinese patent for that technique and product intended for use in a vaccine.

The patent summary reads:

SARS vaccine of adenovirus vector and preparation method, application of coronavirus S gene
Abstract
(translated from Chinese)
The present invention belongs to the field of genetic engineering, particularly relates to adenoviral vector SARS vaccines, their preparation and coronavirus S genes in SARS (SARS) on vaccines for the prophylaxis. By means of biological engineering, the coronavirus S gene in combination with deficient recombinant adenovirus, the protective immunogen protein or polypeptide expressed therein, through expansion culture, purification, and formulation to prepare a mucosal immunogenicity can cause the gene vaccine, respiratory mucosal immune response induced by the body to produce antibodies against the virus infection. Specific conditions of the present invention, compared with conventional inactivated virus particle vaccine, safe, easy to use, without limitation intramuscular, have broad clinical applications.

In 2015, The US called for an end to research creating new viruses in the lab that have increased threat (higher transmissibility, higher pathogenicity, higher lethalithy) (3)

The very researchers conducting studies on SARS vaccines have cautioned repeatedly against human trials;

“An early concern for application of a SARS-CoV vaccine was the experience with other coronavirus infections which induced enhanced disease and immunopathology in animals when challenged with infectious virus [31], a concern reinforced by the report that animals given an alum adjuvanted SARS vaccine and subsequently challenged with SARS-CoV exhibited an immunopathologic lung reaction reminiscent of that described for respiratory syncytial virus (RSV) in infants and in animal models given RSV vaccine and challenged naturally (infants) or artificially (animals) with RSV [32], [33]. We and others described a similar immunopathologic reaction in mice vaccinated with a SARS-CoV vaccine and subsequently challenged with SARS-CoV [18], [20], [21], [28]. It has been proposed that the nucleocapsid protein of SARS-CoV is the antigen to which the immunopathologic reaction is directed [18], [21]. Thus, concern for proceeding to humans with candidate SARS-CoV vaccines emerged from these various observations.” – Tseng et al.,

The disease progression in of 2019-nCoV is consistent with those seen in animals and humans vaccinated against SARS and then challenged with re-infection. Thus, the hypothesis that 2019-nCoV is an experimental vaccine type must be seriously considered.

Evidence for: Sequence homology between INS1378 to pShuttle Coronavirus vaccine; presence of a SARS-like Spike protein in bat coronavirus, otherwise most similar to bat coronaviruses; low bootstrap value.

Evidence against: Low sequence homology (but highly signifiant). NB these viruses are RNA viruses and they can evolve quickly, even under laboratory conditions.

Status: Most likely.

Test: Determine the nucleotide sequence all laboratory types of coronavirus being studied in China (a match will confirm). Find an isolate that matches 2019-nCoV in the wild and reproducibly independently isolate the virus from a wild animal (a match will falsify).

The available evidence most strongly supports that the 2019-NCoV virus is a vaccine strain of coronavirus either accidentally released from a laboratory accident, perhaps a laboratory researcher becoming infected with the virus while conducting animal experiments, or the Chinese were performing clinical studies of a Coronavirus vaccine in humans.

Dr. Dale Brown brought to my attention the studies that have reported serious immunopathology in animals – rats, ferrets, and monkeys – in which animals vaccinated against coronoviruses tended to have extremely high rates of respiratory failure upon subsequent exposure in the study when challenged with the wild-type coronavirus.

“Caution in proceeding to application of a SARS-CoV vaccine in humans is indicated”- Te et al., 2012 [Full Text]

Yasui et al., (2012) reported severe pneumonia in mice who were vaccinated against SARS who were subsequently infected with SARS.

Another study of a double-inactived SARS vaccine found increased eosinophilic proinflammatory responses in vaccinated mice, especially older mice, writing:

“Importantly, aged animals displayed increased eosinophilic immune pathology in the lungs and were not protected against significant virus replication.”

If the Chinese government has been conducting human trials against SARS. MERS, or other coronviruses using recombined viruses, they may have made their citizens far more susceptible to acute respiratory distress syndrome upon infection with 2019-nCoV coronavirus.

The implications are clear: if China sensitized their population via a SARS vaccine, and this escaped from a lab, the rest of world has a serious humanitarian urgency to help China, but may not expect as serious an epidemic as might otherwise be expected.

In the worst-case scenario, if the vaccination strain is more highly contagious and lethal, 2019-nCoV could become the worst example of vaccine-derived contagious disease in human history. With an uncharacteristic aysmptomatic prodromal period of 5-7 days, individuals returning from China to other countries must be forthright and cooperative in their now-prescribed 2-week quarantine.

RELATED: Moderately Strong Confirmation of a Laboratory Origin of 2019-nCoV

Citations

Lu, R et al., 2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding The Lancet. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2820%2930251-8/fulltext

Tseng et al., 2012. Double-Inactivated Severe Acute Respiratory Syndrome Coronavirus Vaccine Provides Incomplete Protection in Mice and Induces Increased Eosinophilic Proinflammatory Pulmonary Response Upon Challenge https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3209347/

Te et al., 2012. Immunization with SARS coronavirus vaccines leads to pulmonary immunopathology on challenge with the SARS virus. PLoS One 7(4) https://www.ncbi.nlm.nih.gov/pubmed/22536382

Yasui et al., Prior immunization with severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) nucleocapsid protein causes severe pneumonia in mice infected with SARS-CoV. J Immunol. 181:6337-48 https://www.ncbi.nlm.nih.gov/pubmed/18941225 https://www.jimmunol.org/content/181/9/6337.long

RECOMMDED RELATED:

CLEAR EVIDENCE it is NOT a Bioweapon. So What’s All This About ACE2 and nCoV-2019 (COVID-2019)?

2019-nCov Vaccine Recommended Readings

Why over the next two weeks the world will learn how bad the 2019 nCoV Coronavirus Pandemic will be

Advertisements

136 thoughts on “On the Origins of the 2019-nCoV Virus, Wuhan, China

  1. The question is not “are you paranoid” but “are you paranoid *enough*.”

    Still, there just isn’t any logic where the Chinese would inflict this virus on their own people, or even any evidence they were working on a vaccine.

    1. I don’t know anyone who proposed that… we’ve considered natural origin, with or without recombination origin, accidental release from laboratory of
      wild type or recombined type, recombination in the lab, recombination in humans, intentional laboratory origin via recombination technology, vaccine sensitization and secondary exposure.

      1. I am wondering why in your update, the possibility of SARS 2 as a lab event was exonerated? The ACE2 finding is not conflicting with the “lab event” hypothesis, right? or is it because the SARS 2 Insert you mentioned is not 100% aligned with the pShuttle-SN? Could you please explain? Thank you!

    2. The genocidal Communist Party that murdered at least 70,000,000 Chinese wouldn’t kill a few thousands in vaccine trial ?
      There is a patent of the virus granted back in 2013.

      1. While that might be true (under Mao), but it could also be exaggerated by simply adding all the victims of the Chinese Civil War to the Communists account.
        Anyway, you should also consider, that British imperial rule has killed 100 Mio. in India alone, and started more wars, than any other empire in human history. And always ask: Cui bono.

    3. Chinese communist Party has several groups inside and fighting to death for the ultimate power. The most dangerous group is called “Shanghai cult”, composed by the ex CCP leader Jiang Zeming and his deputies and lieutenants. Jiang and his assistants have the motivation to start this bioweapon civil war to force the current leader Xin Jinping to step down. Then Jiang will set up a puppet for his group’s own interest.

    4. Please check out Dr Paul Cottrell’s YouTube channel. On one he discusses how the virus is designed to target Asian males and could be a means of population control and unlikely that the Chinese are responsible for its creation.

      1. This is utter nonsense. The state of the art is not up to specifically targeting Asian males, and it unlikely to *ever* get there. Plus population growth does not depend on the number of males. See the population rebound from the Paraguayan War (1864–1870(.

  2. Pingback: - UncoverDC
  3. In media reports death rate = death count / infected count = 2 to 3%. Should it not be: death count/(death count+recovered count)? The former underestimates the latter by a factor of 10.

      1. Say I’m diagnosed with ncov. I look at the table that shows: Dead, Recovered, and Undetermined, such that Infected=D+R+U.

        To agree with the death rate reported by the Sanjay Guptas, MD, of the world, that is D/I,
        the thought process has to be: “if I haven’t been diagnosed as dead or recovered, I’ll count myself as recovered regardless”. It’s a biased low, in other words optimistic, estimate.

        Assuming time to death = time to recovery the other estimate, that is D/(D+R), is unbiased. Already that makes it a better candidate.

        Any second thought?

  4. Great work here- much appreciated! Quick question…

    ” GIVEN THAT WE HAVE FOUND THIS SIGNATURE, A FUNCTIONAL MOTIF FINGERPRINT, PRESENT IN THE HK-3 CoV FROM 2005, WE BELIEVE THIS EXONERATES RECOMBINATION IN THE LAB AS A SOURCE OF THE VIRUS.”

    Does that mean that the lab has been ruled out as a source? If so, what might be the source? (My apologies – I read the entire article, but as a lay-man, I missed it?

    Thank you?

    1. Not entirely. There are no lines in which his Laboratories propagate. Viruses from bad and other organisms it is certainly possible. For a laboratory technician to have become infected. With a virus captured from nature

    1. We would need to try to infect Han cell lines in comparison to others to truly
      answer the question. Other studies with pseudovirions to study functionality
      may be of interest. To my knowledge, no one has tackled the question directly
      with rigorous studies.

  5. Hi Dr, I found this post via the interview you did on HighWire which wad uploaded to YouTube. I would like to request that you create a YouTube channel of your own to share your findings and hypotheses because the way you teach and communicate is absolutely exceptional and so very needed.

    People are hungry for the TRUTH and I’m not sure if you’ve gone back to the HighWire video but everyone is annoyed about how the host kept interrupting you. PlEASE consider creating your own videos!! If you check out Dr “Paul Cottrell” on YouTube you could make videos as simple and informative as that.

    Thank you so much for all your time and efforts and for sharing it all. God bless you!

    1. Thank you – I will be addressing these issues via peer-reviewed publications, on my channel “Unbreaking Science” – find @WWDNYK studies on YouTube and Facebook. We have learned a lot with new data, and assessments change as new data becomes available. More soon.

  6. Hi James,

    check this link out: https://www.the-scientist.com/news-opinion/scientists-compare-novel-coronavirus-to-sars-and-mers-viruses-67088

    It refers to this paper: https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(20)30072-X

    I don’t know if this is related to your latest update, but I think this explains the phylogeny and indicates this 2019-nCoV is a natural recombinant of bat viruses.

    I don’t know if you are familiar with the details of the way the coronaviruses replicate their genome but there is a step where it is possible for the replicase to jump templates because of identical TRS sequences interspersed between the protein coding sequences in the second half of the genome, after the replicase polyprotein coding sequence. So when two closely related coronaviruses infect the same cell, closely related as in having identical TRS, this jumping by the replicase can take place and you get a natural recombinant coronavirus.

    One could say that the cell where this recombination event took place could be a cell in a lab as opposed to a bat pneumocyte in a living animal, but there is really no reason to mix two closely related viruses in the lab unless you are studying this very recombination mechanism. But if that is what you are interested in, why do it with a BSL3 virus that is dangerous to you when you can do the same mechanistic studies with murine hepatitis virus, a coronavirus that you can work with at the BSL2 level? And if the goal is to engineer a bioweapon, there is no in vitro system that is going to substitute for the full animal (us).

    Cheers

    1. Marc – Timely reference to share – yes I think about 60% of the transcripts don’t make it to the Spike protein as I recall – The study I submitted today
      nails a likely pathogenic signature in protein motifs – VERY easy to do on a predicted transcript of S1, S2 through to N-terminus, look for a short S1, a missing She3 and KxDL and a Gp4 at the end… you won’t believe it but i found the signature from a sequence in 2005 – the UNC team didn’t know that had it!!!!!!!! – Sherlock Holmes

  7. Hi Dr James,

    As there are different voices on the Internet from other scientists which assert the 2019-nCoV virus is definitely natural. I suggest when you have a next interview, like on Youtube, respond to these controversies to support your ideas. And It might be helpful as to review your study from a different perspective.

    Thank you for your efforts to reveal the secret all the world are concerned with.

    Ricky.

  8. This is from the article:

    Bats, Gene Editing and Bioweapons: Recent Darpa Experiments Raise Concerns Amid Coronavirus Outbreak

    https://www.unz.com/wwebb/bats-gene-editing-and-bioweapons-recent-darpa-experiments-raise-concerns-amid-coronavirus-outbreak/

    The Pentagon’s Defense Advanced Research Project Agency (DARPA), recently spent millions on research involving bats and coronaviruses, as well as gene editing “bioweapons” prior to the recent coronavirus outbreak. Now, “strategic allies” of the agency have been chosen to develop a genetic material-based vaccine to halt the potential epidemic.

    DARPA began spending millions on such research in 2018 and some of those Pentagon-funded studies were conducted at known U.S. military bioweapons labs bordering China and resulted in the discovery of dozens of new coronavirus strains as recently as last April. Furthermore, the ties of the Pentagon’s main biodefense lab to a virology institute in Wuhan, China — where the current outbreak is believed to have begun — have been unreported in English language media thus far.

    The U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), has recently been involved in research borne out of the Pentagon’s recent concern about the use of bats as bioweapons.

    USAMRIID has a decades-old and close partnership with the University of Wuhan’s Institute of Medical Virology, which is located in the epicenter of the current outbreak.

  9. The analyses are poorly-incorrectly done.

    Here is what should have been done:

    If anyone looks at the pShuttle-SN vector, it carries the spike protein in the NCBI database:
    https://www.ncbi.nlm.nih.gov/nuccore/57791694

    Under CDS, it clearly indicates, “990..2507
    /codon_start=1
    /transl_table=11
    /product=”truncated SARS coronavirus spike glycoprotein S1
    subunit”

    In short, pShuttle-SN was deposited in 2005 as a vector carrying the spike glycoprotein S1. Does one really need to test or guess what happens if you blast SARS or nCoV against it?

    If you blast:
    SARS (NC_004718)
    w/
    pShuttle-SN (AY862402)

    Results:
    1518/1526(99%)
    You can obtain these results using the RID: 50UEHSVS016
    Search expires on 02-23 06:37 am

    Anyone can see that pShuttle-SN clearly contains the SARS spike glycoprotein S1. As indicated in the notes for the original deposit.

    If you blast:
    nCoV (e.g. 1798174254)
    w/
    pShuttle-SN (AY862402)

    Results:
    987/1484(67%)
    You can obtain these results using the RID: 50UJZ7DP016
    Search expires on 02-23 06:40 am

    They match (67%) because the spike proteins are similar between SARS and nCoV.

    Lastly, if you use the “empty” pShuttle vector (AF334399) from Addgene against SARS or nCoV, there is no significant homology.

    Sincerely,

    Dr Bob

  10. I had a friend who shared an article in a comment. He said the article “debunked” the original article. I don’t like that word as I think it stifles needed debates. I fail to see how an article just discussing possibilities can be debunked. His article went through evidence showing why the virus couldn’t have been created in a lab. Your original article presents a cool headed, dispassionate discussion of four origin possibilities. I think we should have some peer reviewed articles published in leading journals before we say one way or another. Unless one solution is just obvious to trained eyes and peer reviewing isn’t necessary. Could you comment on whether peer reviewing is needed at this stage of this virus?

    1. Thank you for your comment. Peer review is certainly appropriate for knowledge claims made on new data. I concur with you that posed hypotheses are not knowledge claims and therefore cannot be “debunked”. They can be tested, however, with critical tests capable of potentially refuting them. I have a study under peer review noe that tests and refutes the laboratory origin of SARS-CoV-2.

  11. The populations estimated to be most at risk based on the genetic variants associated with higher ratios of ACE2 cells: East Asians, Japanese, and Han Chinese are the most likely people to become severely sick by the coronavirus with a chance of more than 90% when exposed. Europeans only rank in the 50%, Africans in the 60% range, and considered low to medium. https://img.auctiva.com/imgdata/1/9/6/8/1/0/0/webimg/1051684762_o.jpg

    A comparison between eight individual samples had originally demonstrated that the Asian male has an extremely large number of ACE2-expressing cells in the lung and has a much higher ACE2-expressing cell ratio than white and African American donors (2.50% vs. 0.47% of all cells). It should be noted however the asian male in this study was a former smoker- image (FIgure 1). https://www.biorxiv.org/content/10.1101/2020.01.26.919985v1.full

    A significantly higher ACE2 gene expression was found in smoker samples compared to non-smoker samples https://www.preprints.org/manuscript/202002.0051/v1/download
    Up to 68% of Chinese men Smoke (B.C.T) https://qz.com/521662/68-of-chinese-men-are-smokers-and-millions-will-die-because-of-it/

    My current theory on another main factor is this (In china) “We found substantial gender differences in dietary zinc intake and zinc deficiency, with nearly half of the men at risk of zinc deficiency. Males of younger age, with higher education and incomes, and who consumed higher levels of meat, had higher zinc intakes, higher zinc intake densities, and higher rates of meeting the EAR. Among all participants, 31.0% were at risk of zinc deficiency, with dietary zinc intakes of less than the Estimated Average Requirement (EAR) (males 49.2%, females 14.8%, p < 0.050) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986452/ Combining zinc deficiency with smoking and genetic higher ratios of ACE2 cells could certainly explain why its hitting much harder there. Zinc deficiency during sepsis appears to cause a catastrophic malfunctioning of the system, resulting in a amplified and prolonged inflammatory response. Zinc helps control infections by gently tapping the brakes on the immune response in a way that prevents out-of-control inflammation that can be damaging and even deadly. Zinc-deficient mice developed overwhelming inflammation in response to sepsis and were three times more likely to die than mice on a normal diet https://sha.rest/B1MK2A and https://www.sciencedaily.com/releases/2013/02/130207131344.htm

  12. Thank you for presenting the original article, with the UPDATE above. Reading the article provides a great journey through the fog of uncertainty, and the update dispels the innuendo and shows how one additional data point can dissipate the fog.
    The comment string reinforces that many of us prefer the fog.

Leave a Reply to Lara Cancel reply