On the Origins of the 2019-nCoV Virus, Wuhan, China

James Lyons-Weiler, PhD – 1/30/2020



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.


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
(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


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


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


  1. We have to consider the horrific air quality in Wuhan due to incinerators spewing out toxins and pollutants with improper filtering in place, as Jon Rappoport has highlighted this week. Also we have to look at the 5G radiation in this city. It is the first Chinese city to implement 5G smart production lines and in employing the 5G EMR frequencies in their city’s street lighting— the plan is to have Wuhan China’s first “smart city.” Scientists and doctors worldwide have shown the deleterious effects of the present levels of EMR in our environment (2G-4G frequencies, all the smart phones and devices, the smart meters, WiFi). The layering in of all the 5G microwaves is simply an experiment on humanity and it’s implementations are egregious acts that we are witnessing worldwide.
    One of those frequencies, the 60 GHz, actually adulterates the O2 molecule in the air (per Lena Pu, 5G researcher) and creates a hypoxic state in those organisms requiring O2 for their very existence.
    This Wuhan pneumonia and what the pathogen might turn out to be, should highlight the danger of scientists tinkering around with the very building blocks of life and patenting their creations. The wrath of the True Creator just might be beyond anything we can imagine. Time will tell.

  2. Wow…. What does this say of scientists who are now rushing to make a vaccine for this new virus? Herds of sheeple who would queue up for the vaccines would become even more susceptible, and now people all over the globe, not just China, can be killed with much greater ease… leaving the antivaxers, hahaha! This is seriously disturbing…. Some nefarious billionaire is surely rushing to produce the first vaccine now.

  3. From James excellent article:
    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.

    A little bit off topic here but as I was reading this it reminded me of Dr. Danuta Skowronski, Canadian Flu study: Association between the 2008–09 seasonal influenza vaccine and pandemic H1N1 illness during spring–summer 2009: four observational studies from Canada. PLoS Med 2010 Apr 6;7(4) sowed signs that taking the Flu shot actually increased you chances of getting the Flu in subsequent years. Does the Flu shot desensitize people and make them more susceptible to Influenza viruses thus contracting acute respiratory distress syndrome or pneumonia? It’s known that the Flu shot can and does cause what the CDC has labeled Influenza Like Illness aka ILI after the Flu shot-rather than saying the shot caused the person to develop the Flu. This seems to be a common reaction and you know all the CDC has to do is change the name of an illness to gaslight the public so they will get the shot the next year and so on. Mass vaccination with the Flu shot is a human trial just like the trials of SARS so could the increase in people who have caught the Flu be caused by the very thing that’s suppose to prevent it? There are several article on other blogs reporting on people who took the Flu shot and died shortly after. Can desensitization be a factor?

    Even though many of us that are not scientist and try very had to understand articles such as this one, we know by the many strains of viruses that are occurring (ie: Measles genotype-there are 19 which are mutations of the original Genotype A strain-wild type, CDC yearly says the Flu vaccines are ineffective because the virus in the vaccine had mutated) vaccines are turning against humanity. It seem like the more scientist mess with nature-the more danger they are putting us in. Antibiotic resistant bacteria & viruses Superbugs come to mind because of overuse.

    “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,”

    If this is the case and something escaped from a lab it is not the first time:
    -Anthrax escape raises worries about lab-grown super-flu

    Makes you wonder, exactly how often does this happen? Makes me wonder how many sick people are out in society because of human error that the government never reports on.

    1. Looks like some tasks are too delicate for a government that is racing in fury to save us from a dubious theory by taxing the air we breath.

    2. The vaccine now is the bioweapon.
      If the virus don’t get ‘ya, the shot will.

  4. Thank you for an excellent article and furthering my education. I have a question. Could there be a fifth scenario where those with the worst lung pathology had previously been infected with SARS 22 years previous? That might explain some of the population dynamics.

    1. Yes that is a possible and even likely mitigating factor. However, it does not explain the existence of a SARS spike protein gene in bat Coronavirus.

  5. Hello Dr Lyons-Weiler,
    Sorry, I’m not a scientist, but would like to know, can it be known or is it possible to assess whether the Chinese are more genetically susceptible to this lab altered virus than other races? Thank you.

    1. Unlikely but possible. It seems as if the use of a modified coronavirus, which is an RNA virus, in a live (“attenuated”) vaccine
      may be a more likely scenario. See here and the lit cited – the Chinese were certainly putting SARS spike proteins into other viruses
      and testing them in animals it seems for years. Adenoviral expression of a truncated S1 subunit of SARS-CoV spike protein results in specific humoral immune responses against SARS-CoV in ratshttps://www.sciencedirect.com/science/article/pii/S0168170205000821?via%3Dihub

      1. If it’s true that an individual who has no contact with China and contracted infection and then transmitted the infection, how does that impact the proposal that the current break-out is due to an experimental vaccine trial that went sideways, as is known to be a problematic feature of using live-attenuated virus as the inoculum?

  6. This article explaiba that cases being treated & tested & studied out side if China have discovered by genetic study of the virus that it has 5 insertions of HIV-1. That infected people test positive for AIDS HIV. They have done tests & found use of AIDS drugs on the virus does causeca reaction. This does affirm this was a lab created bioweapon virus. The Virus mutates & the strains outside of china are more aggressive. And not just a SARS variant of Nov but also HIV-1 that soteads very easily & THAT is the GLOBAL pandenic reality we face. The mutations & factors of its creation have traits desired in a weapon to prevent cure.Man-made modified BIOWEAPON VIRUS 2019 nCoV has 4 inserts of HIV-1 gp 120 & Gag. All people with virus test positive for AIDS HIV-1 via RNA testing. The Corona part is an aggressive SARS. Drs in Germany & India & other workd class labs have identified the genome of virus. The version outside of China is more aggressive as it had already mutated. When they give patients AIDS drugs the virus in patients reacts. The medical Journal Lancet January had limited data at time of publication, but had confused at tgat time tgat yes this is manmade bioweapon virus that mutates (claims out of China days agobeas generation 6 sibce epidemic started killing people in November) to prevent cure & is Corona & HIV-1. https://www.zerohedge.com/geopolitical/coronavirus-contains-hiv-insertions-stoking-fears-over-artificially-created-bioweapon

    Also Chinese officials stated that due to aggressive & multiple rapid mutations that a case of a 6 person household that was infected there were reinfections & 4 different mutations present in just that household alone.

    In other cases similar most persons who seemed to recover symptoms & not die were still contagious & virus MUTATES in them. Then many then cobtract other mutations& become sick again. China stated they can not manage, nor stop or control this. They have basically abandoned Hubei Provence & even taking supplies OUT. They have issued orders that prevent ability to recieve supplies, food, any care for anything & ensured faster & ensured death of the population. They have filled in tunnels, torn up roads, built walls, & obstructed & stolen & intercepted any form of supplies. Reports that even in Novenbercearly December they were creating body’s but not registering & mass graves. Now they have gone through sickness & deaths of workers, & medical staff so bodies stack up & no disposal & people dead in homes left to rot. The officials in CCP system hide & not working & steal supplies. Mass scandals & footage & evidence of Red Cross stealing supplies from hospitals & in transit & depots; as well as intercepted 100s of tons of vegetables/food for Hubei province. The highervCCP officials& elite earlier were altering shipments & hoarding for upper party class enclaves (bugged out) the proper supplies & altering shipments to regions infected with inferior non compliatecitens to make it look like they sent things. Eveb then the Red Cross in region were seizing those. The upper party have cowardly run away too remote Qing Hai island ; & in reality no one is really running anything with what could be called a legitimate functioning government. Meanwhile medical staff have no medicine, no tests, no protective gear, no disinfectant, & have been on frontlines over worked for over 2 months & past breaking points for many & others have become ill. Tgey cant eat for 24 hours as fear taking off suits even to use bathroom as there are no more disposable suits. 1 report & pictures shows staff in a critical Wuhan hospital using operating room wing to use fabric & tey to sew/staple/tape to create their own primitive face masks. This is profound that these 100s of millions in infected zones have been shut off & abandoned, & any efforts are for those area of the elite & their families. A torturous dystopian hell & torment this people decry they are utterly helpless.

      1. I think that if that were actually the case – “crazy virus on the loose” – then that would be the tone of the DHS press conference today.

        What was said is that:

        1. A National Health Emergency has been declared.
        2. The number of ports receiving people from China is more limited.
        3. Returning USA Citizens from China will be subject on a voluntary basis to a 14-day quarantine period.
        4. The type of voluntary quarantine depends on whether the individual had visited Wuhan Province during the 14 days prior to departure or was arriving from China, but had no contact with infected individuals or Wuhan in general.
        5. All of the quarantine periods are for 14-days; those with a Wuhan travel history will receive institutional-quarantine and those with no Wuhan contact will receive self-quarantine with monitoring. In other words, remain in their home and a health professional will monitor their situation by telephone.
        6. DHS.gov provides daily updates.
        7. Some airlines have ceased to fly to China.

    1. I suspect the CCP is gone.

      All the fake plagues are a cover. Keep China in lockdown until stuff is organized properly

  7. Maybe this explains how 2019-nCoV was identified “in record time”?

    You ever listen to that guy Gates and his 100’s of TED Talks all on the same idea: wants to take advantage of epidemic situation to exsanguinate the victims, “process the plasma”, and provide whatever blood product is the result to healthy humans to see how it works – which means keeping them healthy I presume.
    Not making this up. Billionaire zillionaire with the medical knowledge of a 5-year old and the disposition of Mengel.

    US 2017/0216467 A1
    Coronavirus Isolated From Humans

    “Disclosed herein is the isolation of a new form of human Coronavirus (SARS-CoV)…”

  8. Structural analyses confidently predict that the Wuhan coronavirus uses ACE2 as its host receptor. According to their modeling, although the binding strength between 2019-nCov and ACE2 is weaker than that between SARS-Cov and ACE2, it is still much higher than the threshold required for virus infection. Of note, the 2 male donors have a higher ACE2-expressing cell ratio than all other 6 female donors (1.66% vs. 0.41% of all cells, P value=0.07). In addition, the distribution of ACE2 is also more widespread in male donors than females: at least 5 different types of cells in male lung express this receptor, while only 2~4 types of cells in female lung express the receptor. This result is highly consistent with the epidemic investigation showing that most of the confirmed 2019-nCov infected patients were men (30 vs. 11, by Jan 2, 2020). We also noticed that the only Asian donor (male) has a much higher ACE2-expressing cell ratio than white and African American donors (2.50% vs. 0.47% of all cells). This might explain the observation that the new Coronavirus pandemic and previous SARS-Cov pandemic are concentrated in the Asian area. ACE2 is previously known as the receptor for SARS-Cov and NL634–6.

    Alarmingly, our data predict that a single mutation [at a specific spot in the genome] could significantly enhance [the Wuhan coronavirus’s] ability to bind with human ACE2,” the investigators write. For this reason, Wuhan coronavirus evolution in patients should be closely monitored for the emergence of novel mutations at the 501 position in its genome, and to a lesser extent, the 494 position, in order to predict the possibility of a more serious outbreak than has been seen so far.
    Severe infection by 2019-nCov could result in acute respiratory distress syndrome (ARDS) and sepsis, causing death in approximately 15% of infected individuals. 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species – pigs, ferrets, cats, orangutans, monkeys and humans (except mice and rats) with similar efficiency, implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections.

    The 2019-nCoV spike phylogeny is firmly rooted among other b-genus lineage b bat SARS-like coronaviruses, but is ancestral to both human SARS-CoV (epidemic strain isolated in year 2002) and bat SARS -CoV strains that use ACE2 receptor to enter and infect primary host lung cells

    https://jvi.asm.org/content/jvi/early/2020/01/23/JVI.00127-20.full.pdf (Full PDF)

    1. Thank you David, I will be assessing these very data today and tomorrow a the nucleotide level. My dissertation was 100% about the accuracy of phylogenies and in a maleable virus such as this one, and short sequences only considering the Spike protein, “firmly rooted” and the structure of the tree itself have to be taken as hypotheses. Phylogenies are estimates, not data. More soon, I hope.

  9. If this is a bioengineered attempted vaccine or bioweapon (as you appear to imply, at least in the former case), why would the Chinese government have been so rapidly forthcoming in its sharing of genome data with international virologists? Why should the forced proximity of live wild animals in small cages, in severely unhygienic conditions whereby they quite literally consume each other’s feces be considered an “unlikely” place for such novel interspecies recombination? Surely one would EXPECT that to occur?

    1. Steven, your point is one of the reasons I prefer the hypothesis that a recombinant virus had been made and was being tested – at some level, either in animals, or in humans, based on a bat coronavirus that had a SARSs spike protein added in. Any experimenter knows that cross-contamination of recombinant cells lines, bacteriophage lines, mice or rats could compromise the integrity of their study. Precisely HOW a laboratory escape would occur is not the question, as there were reports in 2015 of it happening multiple times in the Wuhan BSL-4 lab anyway. I don’t prefer the bioweapons hypothesis because the virus would not target the elderly and immunocompromised; it would target 18-25 year olds. Given the surprising similarity to pShuttle-SN vector, which we know was used at least in the late 2000’s in China (and elsewhere) to put the SARS spike protein in adenoviruses, the simplest explanation is still laboratory escape of a modified bat coronavirus. The Dot plot between the full genome of the nearest bat coronavirus and 2019-nCoV, as seen in the article you are commening on, is striking in that regard.

      1. Thanks for your research! “Targeting 18-25 year olds” would be too apparent and conclusive, while targeting the elderly and immunocompromised is inconspicuous – but has the same devastating effect on targeted economy. In a trade war scenario, that is. Just thinking outside the box. No matter how old the victims are, the effect on the GDP would be the same, due to the enforced measures and the international hype achieved with the propaganda as we see it going on right now. Perfect a wapon of economic mass destruction it would be. But it is not up to us to claim this. That is for sure.

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

      The screenshot directly after this states that SARS had escaped multiple times from the high level containment facilities in Beijing, not Wuhan.

    3. The Chinese government was being helpful in sharing the sequence. There is no way that they could keep it secret anyway, since international virologists could obtain the whole genome sequence from infected travelers within a matter of days. James, I appreciate your great work on this, and your hypothesis is most reasonable.

    1. The E-values are not significant and the sequences match many other species.
      Hard to say what significance to attribute to four sequences. The hope of course
      would be that HIV drugs might be of some use, but that’s speculative.

  10. Sir you are seriously wrong…

    First of all, let’s get this clear: the “pShuttle-SN” is a recombinant adenovirus carrying SARS S1 encoding sequence, constructed by Liu et al in 2005.

    What you find as “insertion”, so called INS1378, is a highly diverse region in S1 but not an actual “insertion”. It is “unmatched”, because of the background genome match score is so high (~90%).

    But when you compare INS1378, which is actually part of S1 subunit sequence of 2019-nCov, with a SARS subunit encoding vector, pShuttle-SN, it’s guaranteed that you will find the match in the S1 encoding sequence, though the match score is much lower (68%, 807/1182).

  11. Appreciate your providing a coherent and referenced discussion on the 2019-ncov.
    Please continue updating.

  12. Pingback: Parasites Among Us
  13. pshutter-SN vector was inserted SARS-cov spike gene. which is published in 2005 not 1980s(doi:10.1016/j.virusres.2005.02.009).2019-cov has 80%similarity with SARS-cov. therefore, it is no surprise that spike gene of 2019-cov has 67% similarty with pshutter-SN insert sequence

    1. I have pulled my previous comment.
      Thank you for your correction, as is clear from the genbank entry the pShuttle-SN specifically was published in 2005.

      The reason why it is very surprising to see a SARS spike protein in 2019-nCoV is that otherwise it is most closely related to bat coronaviruses.

      And we now have confirmation of >99% similarity of the segment to SARS spike protein, compared to the poor alignment to other Spike proteins,
      including those from bats coronaviruses studied thus far.

      More details soon, a full analysis takes time.

      Thank you for your comment.

  14. thanks james, great analysis, but even if we would get mild infection now, would we not going to be in much more danger if 2019-ncov or some other coronavirus variant makes a second round months or years later (being effectively ‘vaccinated’ or sensitised by the first round)? have they realised this now that they are closing the borders in the us?

  15. You mistook pShuttle-SN as pShuttle. pShuttle-SN is not an empty vector. It contains a DNA segment that encodes part of the SARS S1 glycoprotein. No surprising you find your insertion INS1378 matches this segment, which was originally from a SARS virus. If you align your INS1378 to the pShuttle vector sequence from Addgene, you will find no homology.

    1. Yes, but only to the point of attribution That does not explain why a SARS spike protein is found in what otherwise is a bat coronavirus. More analyses ongoing that will hopefully clarify.

  16. Hypothetical: CCP desires a bioweapon they can immunize their population against,
    then use against a target. They produce weaponized virus, produce what they believe to be is vaccine, use their own population to confirm efficacy of vaccine, but internal population becomes sensitized to virus. Sensitized internal population spreading infection with no immunity apparent. Population dying at logarithmic rate.

    1. Problem w that scenario is that “sensitize” actually means “making more susceptible to serious illness or death” in the case of coronavirus vaccines so far.

  17. 2019-nCov has been reported to share 96.2% overall genome sequence identity to the BatCoV RaTG13 genome which we previously detected in Rhinolophus affinis from Yunnan Province. The receptor binding protein spike (S) gene was highly divergent to other CoVs with less than 75% nt sequence identity to all previously described SARSr CoVs except a 93.1% nt identity to RaTG13. The S genes of nCoV-2019 and RaTG13 S gene are longer than other SARSr-CoVs. To determine whether nCoV-2019 also use ACE2 as a cellular entry receptor, we conducted virus infectivity studies using HeLa cells expressing or not expressing ACE2 proteins from humans, Chinese horseshoe bats, civet, pig, and mouse. We show that nCoV-2019 is able to use all but mouse ACE2 as an entry receptor in the ACE2-expressing cells, but not cells without ACE2, indicating which is likely the cell receptor of nCoV-2019. We also proved that nCoV-2019 does not use other coronavirus receptors, aminopeptidase N and dipeptidyl peptidase. https://www.nature.com/articles/s41586-020-2012-7

    2019 has been reported to share 96% sequence identity to the RaTG13 genome (EPI_ISL_402131). However, the S1 Receptor Binding Domain (RBD) of the nCoV-2019 genome was noticeably divergent between the two at amino acid residues 350 to 550. They found a stark correlation to some Malayan pangolins coronaviruses, which indicates that the proteins associated with some of the novel ways 2019-nCov can infect humans are likely to be expressed by RNA sequences that are recombinant and descend from Malayan pangolin coronavirus strains. http://virological.org/t/ncov-2019-spike-protein-receptor-binding-domain-shares-high-amino-acid-identity-with-a-coronavirus-recovered-from-a-pangolin-viral-metagenomic-dataset/362 (https://sha.rest/TgCu1S)

    pangolins were sold in the wuhan market at the center of all of this https://www.reuters.com/article/us-china-health-wildlife/chinas-latest-virus-outbreak-exposes-perils-of-exotic-wildlife-trade-idUSKBN1ZM0PE The spike protein from the Wuhan strain is closer to RaTG13 overall, probably due to the S1-NTD subdomain being so different in the pangolin coronavirus. From the S1-CTD section on, the Wuhan strain and the pangolin strain are pretty similar (~97%), except for the furin cleavage site insertion. It seems unlikely that the receptor binding domain–and especially the receptor binding motif–would be nearly identical to one found in pangolin through random chance. (comment fron virological site).

    Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat-SARS-like coronavirus sequences. Specifically, in the 5’-part spanning the first 11,498 nucleotides and the last 3’-part spanning 24,341-30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat-SARS-like coronavirus sequences, whereas in the middle region spanning the 3’-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch. The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely.
    We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus https://www.biorxiv.org/content/10.1101/2020.01.26.920249v1

  18. On the basis of your knowledge, is there a change that contracting 2019-ncov for a second time or some similar virus after an initial, mild infection (that sensitizes oneslf) might be much more secer or even lethal? They are now saying that the ’cured’ can contract the virus again in few months. Do they know that they might be fatally sensitised and that the same virus can infect them again instead of giving immunity (by mechanisms similar to the adverse vaccine effects)?

  19. I read Dr. James Lynos-Weiler’s analysis and theory regarding 2019 nCoV ((https://jameslyonsweiler.com/2020/02/02/moderately-strong-confirmation-of-a-laboratory-origin-of-2019-ncov/). I applaud his effort in probing the possible origin of the novel 2019 coronavirus and appreciate his sharing the finding with the world. While I agree with the sequence alignment analysis findings of Dr. Lyons-Weiler, I strongly disagree with his conclusion. In my opinion, the data analysis he presented does not lead to his conclusion.

    Dr. James Lynos-Weiler’s found that the Wuhan virus has a stretch of sequence that shares similarity with the plasmid pShuttle –SN, Genbank accession # AY862402.1. He noted that “the sequence from pShuttle is most closely related to the Spike protein from SARS coronavirus”, and presented the sequence alignment and plot.

    However, it is extremely important to note that the pShuttle-SN is not the same as pShuttle, which is a plasmid vector developed by Vogelstein et al. pShuttle SN, on the other hand, was constructed by the Chinese research team Liu RY et al in 2005 (Virus Res. 2005 Sep;112(1-2):24-31.) As showed in this study, the pShuttle-SN plasmid contains an N terminal portion of SARS coronavirus spike glycoprotein. pShuttle-SN was constructed to help generate an adenovirus containing a truncated N-terminal fragment of the SARS-CoV for experimental immunization of rats, a legitimate and well-designed scientific research.

    As Dr. James Lynos-Weiler’s showed in the plot above, the stretch of sequence that matched between pShuttle-SN and the Wuhan virus is from bp 945 to ~2500. In Genbank entry AY862402.1, the authors who deposited the sequence clearly indicated a CDS from 990-2507 coding for a “truncated SARS coronavirus spike glycoprotein S1 subunit”.

    It is evident that the similarity between the Wuhan virus and pShuttle-SN stems from the shared sequence homology to SARS S protein.

    Observed on the above observation, I came to a conclusion that the analysis Dr. James Lynos-Weiler’s presented does not show that the Wuhan virus is a man-made virus. On the contrary, it shows that pShuttle-SN, a man-made plasmid vector, contains a portion of sequence that exists in coronavirus, which is a stated truth in a valid scientific study.

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