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Genomic Study Points to Natural Origin of COVID-19

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COVID-19 Update

No matter where you go online these days, there’s bound to be discussion of coronavirus disease 2019 (COVID-19). Some folks are even making outrageous claims that the new coronavirus causing the pandemic was engineered in a lab and deliberately released to make people sick. A new study debunks such claims by providing scientific evidence that this novel coronavirus arose naturally.

The reassuring findings are the result of genomic analyses conducted by an international research team, partly supported by NIH. In their study in the journal Nature Medicine, Kristian Andersen, Scripps Research Institute, La Jolla, CA; Robert Garry, Tulane University School of Medicine, New Orleans; and their colleagues used sophisticated bioinformatic tools to compare publicly available genomic data from several coronaviruses, including the new one that causes COVID-19.

The researchers began by homing in on the parts of the coronavirus genomes that encode the spike proteins that give this family of viruses their distinctive crown-like appearance. (By the way, “corona” is Latin for “crown.”) All coronaviruses rely on spike proteins to infect other cells. But, over time, each coronavirus has fashioned these proteins a little differently, and the evolutionary clues about these modifications are spelled out in their genomes.

The genomic data of the new coronavirus responsible for COVID-19 show that its spike protein contains some unique adaptations. One of these adaptations provides special ability of this coronavirus to bind to a specific protein on human cells called angiotensin converting enzyme (ACE2). A related coronavirus that causes severe acute respiratory syndrome (SARS) in humans also seeks out ACE2.

Existing computer models predicted that the new coronavirus would not bind to ACE2 as well as the SARS virus. However, to their surprise, the researchers found that the spike protein of the new coronavirus actually bound far better than computer predictions, likely because of natural selection on ACE2 that enabled the virus to take advantage of a previously unidentified alternate binding site. Researchers said this provides strong evidence that that new virus was not the product of purposeful manipulation in a lab. In fact, any bioengineer trying to design a coronavirus that threatened human health probably would never have chosen this particular conformation for a spike protein.

The researchers went on to analyze genomic data related to the overall molecular structure, or backbone, of the new coronavirus. Their analysis showed that the backbone of the new coronavirus’s genome most closely resembles that of a bat coronavirus discovered after the COVID-19 pandemic began. However, the region that binds ACE2 resembles a novel virus found in pangolins, a strange-looking animal sometimes called a scaly anteater. This provides additional evidence that the coronavirus that causes COVID-19 almost certainly originated in nature. If the new coronavirus had been manufactured in a lab, scientists most likely would have used the backbones of coronaviruses already known to cause serious diseases in humans.

So, what is the natural origin of the novel coronavirus responsible for the COVID-19 pandemic? The researchers don’t yet have a precise answer. But they do offer two possible scenarios.

In the first scenario, as the new coronavirus evolved in its natural hosts, possibly bats or pangolins, its spike proteins mutated to bind to molecules similar in structure to the human ACE2 protein, thereby enabling it to infect human cells. This scenario seems to fit other recent outbreaks of coronavirus-caused disease in humans, such as SARS, which arose from cat-like civets; and Middle East respiratory syndrome (MERS), which arose from camels.

The second scenario is that the new coronavirus crossed from animals into humans before it became capable of causing human disease. Then, as a result of gradual evolutionary changes over years or perhaps decades, the virus eventually gained the ability to spread from human-to-human and cause serious, often life-threatening disease.

Either way, this study leaves little room to refute a natural origin for COVID-19. And that’s a good thing because it helps us keep focused on what really matters: observing good hygiene, practicing social distancing, and supporting the efforts of all the dedicated health-care professionals and researchers who are working so hard to address this major public health challenge.

Finally, next time you come across something about COVID-19 online that disturbs or puzzles you, I suggest going to FEMA’s new Coronavirus Rumor Control web site. It may not have all the answers to your questions, but it’s definitely a step in the right direction in helping to distinguish rumors from facts.

Reference:
[1] The proximal origin of SARS-CoV-2. Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. Nat Med, 17 March 2020. [Epub ahead of publication]

Links:

Coronavirus (COVID-19) (NIH)

COVID-19, MERS & SARS (National Institute of Allergy and Infectious Diseases/NIH)

Andersen Lab (Scripps Research Institute, La Jolla, CA)

Robert Garry (Tulane University School of Medicine, New Orleans)

Coronavirus Rumor Control (FEMA)

NIH Support: National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute

132 Comments

  • Edward Hughes says:

    I am taken aback that Dr. Collins does not even consider non genetic engineering techniques to manufacture such a virus in the Wuhan laboratories. For example, “old fashion” virology techniques with cell lines and laboratory animals conducted over years may yield such a virus as Covid-19. And that’s the way it was done in the 1970’s before genetic techniques. The CCP has isolated over 2,000 corona viruses, nearly doubling the world’s known virus species of any type. To what end? Of course, I am assuming that the CCP is conducting biologic warfare type experiments in Wuhan to make corona viruses an offensive weapon…

    • Harish M.Dalal says:

      We have had pandemics before. Never have the poor and businesses suffered as much as in this pandemic.
      Why the difference?

  • zyl says:

    Simple: by using the same method of the blog-said-paper, the link btw SARS-2 and Bat-virus does not stand at all, i.e., the covid-19 does not come from nature.

    • Federico says:

      If you read carefully the paper from Andersen and the commentary above in the sentence:”Existing computer models predicted that the new coronavirus would not bind to ACE2″.” it is exactly what someone will do if he wants to modify the old SARS virus to get a vaccine. Computer modelling of the old virus (2002 SARS), replacement of AA essential for ACE2 binding, with other amino acids which, by computer modelling, are predicted to establish a weaker interaction with ACE2; get this mutated form, that still maintains a conformation of the spike region, and is able to elicit neutralizing antibodies, used this mutated virus for vaccine. Indeed, the virus we have now (SARS-Cov2 ) is predicted by computer modelling to bind weakly the human receptor as stated by Anderson and in the above commentary. Unfortunately, we all know this is not the case in the real life. Finally, if you think that in lab it is possible to introduce any kind of mutation, even those simulating natural ones, all attempt of convincing about natural mutation hypothesis will fail. In conclusion, I feel we cannot say with certainty if the virus has been artificially mutated or else is the product of natural mutation.

      • zyl says:

        The Chinese authors clearly stated that the new corona-virus caused this pandemic contains synthetic-construction factors, thus, it can directly transmit to human. As we know, synthetic-construction means man/lab work, not a natural process.

  • Liz says:

    If Covid 19 is of natural origin, wildlife bats etc… why isnt the NIH and the WHO and the international community of health scientists generating a global outcry to shut down wild life wet markets in any and all countries these markets are operated?

  • dBruce says:

    I suggest everyone to read the Research directly from here: https://www.nature.com/articles/s41591-020-0820-9.pdf. And you will find these two statements:
    “[Although the evidence shows that SARSCoV-2 is not a purposefully manipulated
    virus,] it is currently impossible to prove or disprove the other theories of its origin described here.”
    “[However, since we observed all notable SARS-CoV-2 features, including
    the optimized RBD and polybasic cleavage site, in related coronaviruses in nature, we
    do not believe that any type of laboratory based scenario is plausible.] More scientific data could swing the balance of evidence to favor one hypothesis over another. ”
    Not quite as this Doctor has claimed: “A new study debunks such claims by providing scientific evidence that this novel coronavirus arose naturally.”

    • Nurbanu says:

      Such a precious contribution! I was looking for such articles. Thank you a lot for sharing the link! 🙂

  • Rakesh Yashroy says:

    The article does not explain, why Covid-19 appeared in Wuhan, and not simultaneously elsewhere on earth.

    • Michael Martino says:

      And why it occurred 3 miles from China’s only P4 Virology lab… where a researcher had multiple publications about making hybrid coronaviruses capable of infecting human cells…which lab was shut down and placed under military control during the outbreak for what reason???

    • Kavod says:

      Why did the Zika virus arise in the Zika forest and not everywhere simultaneously? Why did Ebola arise near the Ebola River and not everywhere simultaneously? Why did humans evolve in Africa and not actress the whole earth simultaneously? If your criteria for natural evolution is that something must arise everywhere on earth at once then one can only conclude by that logic that every living thing on Earth was created in a lab.

      • Jon Blackburn says:

        Well, given that mankind was designed in a lab called “Eden” meaning that the premise of “natural evolution” thereof is implausible, it’s quite possible that these new viruses appear to have evolved, but are in fact created.

  • BERREBI Georges says:

    Dr Montagné – Nobel Price – claims that Covid 19 genone contains some fragments of VIH genone.
    According to your knowledge, is it truth ?

  • Yahuan Lou says:

    Your argument for not being man-made is not based on “science”, but rather on your own thought. To manipulate a viral genome might not initially aim to make the spike protein bind better to ACE2. It could be “accidently” produced, or as a controls, for example. Your argument in fact made me think this virus is indeed man-made.

  • David says:

    The multi-basic cleavage sites: low to highly pathogenic forms. Mutation in animal hosts? Mutation in undetected human-human trasmission? At the moment no info.
    Some human viruses, including HIV and Ebola, have the same cleavage site.
    From Nature article: “… in avian influenza viruses, rapid replication and transmission in highly dense chicken populations selects for the acquisition of polybasic cleavage sites”

    Does highly dense populations and bad hygienic conditions select naturally for multi-basic clevage sites?
    Intensive breedings, pollution (Wuhan), bad life conditions (Central Africa): a weak immunitary system that selects for this mutation.

    My question: could be the scenario, around a low pathogenic virus, to promote this horrible mutation?

    Numerous case of pneumonia had been reported in several countries last year: re-exaniming the records of these patients could reveal more info about the history of this pandemic?

    p.s. I’m only a teacher, passionate about science

  • zen says:

    There is no scientific basis for anyone claiming it is not a natural virus. why? lol

  • phibed says:

    Virtually all of our viral epi- and pandemics were shown to be present in the population for years before they emerged. HIV in 1910 etc. We were unable to find the host reservoirs for decades. My fear is that while everyone is blaming the Wuhan lab, the real culprit is still out there. Yet it took me 5 pages of google to find my first article on natural mutation. Like the homicide investigation that focuses on a single suspect while the killer goes undetected to kill again!

  • Esmeralda says:

    Interesting article.
    I think it raises good discussion abou it.
    Today, over a month later after this article, there are some papers coming out putting this conclusion as a doubt.

    • Leo says:

      You are right.
      Even, Prof Luc Montagner, who first described the HIV virus together with Prof Robert Gallo (both won the Nober prize in Medicine in 2008), has mentioned that there is a strong possibility of fabrication of the virus in laboratory. Several magazines has published his thoughts, but some of them … has rebuked his thoughts.
      It is still a matter of debate and I think it will continue to have lots of comments here.

      • M. Bencheikh says:

        Robert Gallo DID NOT win the Nobel Prize in 2008.
        FACT check: Nobel Prize 2008 was shared among: Pr. Luc Montagnier, Dr. Francoise Barre-Sinoussi and Pr Harald Zhur Hausen.
        The virus was first described at the Retroviruses Conference in September at Cold Spring Harbor, NY, in 1983, by Pr. Luc Montagnier and Dr. Francoise Barre-Sinoussi.

        • BERREBI Georges says:

          I fully agree with you concerning the 2008 Nobel prize winners. Unfortunately I am not a biochemist but just a chemist ! According to my background I think that we will be abble to fight this virus as soon as we will understand where it comes from.

        • Leo says:

          your are right about the nobel prize winners in 2008.
          It was my mistake on this.
          Thanks for correcting this for me.
          But I really don’t know if the vaccine against this virus may still take a while (over 10 months, my guess) even if people manage to discover and describe where it comes from.

  • Helen Markwell says:

    We should get ready for the significant lot of living with phenomenal social isolating. Covid-19 will even now be there… and we won’t be ensured to let our watchman down. I likewise am self-disengaging as I am immuno-exchanged off from treatment for Hodgkins Disease. It is a substitute world for us until a vaccination comes out.

  • ChandraWest says:

    Virtually all of our viral epi- and pandemics were shown to be present in the population for years before they emerged. HIV in 1900s etc. We were unable to find the host reservoirs for decades. My fear is that while everyone is blaming the Wuhan lab, the real culprit is still out there. Yet it took me 5 pages of google to find my first article on natural mutation. Like the homicide investigation that focuses on a single suspect while the killer goes undetected to kill again!

    • David says:

      Virus is a killer, but all killers born in wrong family… All pandemics show the same background: high density population and immune system depression.

      Wuhan: pollution, animals
      Central Africa: war, rapes, malnutrition, prostitution, animals
      Spanish flu: war, chemical weapons, malnutrition, flu A, animals

      Viruses are sentinels of nature.

  • Brian Charles says:

    Well of course the medical world is going to close ranks and deflect attention from the fact a biological lab experimenting with viruses is in Wuhan, the political/medical/economic fallout from any country admitting ownership would be catastrophic worldwide – so we will never be told the truth simply because the truth will cause a LOT of problems.
    Genocide levels of death is more acceptable to these people than taking blame.

  • Barbara Brown says:

    I would like to know more about the spikes.

  • James says:

    Ok, then how did the “PRRA” furin sequence get in there?

  • joseph p yoe says:

    the question should be has wuhan virology lab studied this particular virus before or not. if they believe this is not from their lab show the world on wuhan virology virus study log. if they have what have they studied? what kind of gain function she studied? why is not asking this important questions? we have to demand the record of wuhan virology lab. may be NIH should also let us know what kind of information received from wuhan by providing the grant. Is NIH part of it? we must stop and condemn any biological warfare activity.

    • mdgalperin says:

      “we must stop and condemn any biological warfare activity.”– surely we must. But how we can effect this?

  • Mmmmkay says:

    Well since these fine folks are all done having settling the important and deeply perplexing issue of whether or not wearing masks can in any way stop the spread of this respiratory illnesses. I totally trust they will research this throughly and tell us the truth of the matter.

    Also I’m 1000% percent certain that if the US was funding deadly virus research conducted in a Chinese lab with “unsafe protocols” that “was highly dangerous” “that could cause more harm than good” both governments would be very forthcoming with the public about the entire thing. I am certain both the US and China would be very contrite for having participated creating a chimera virus from a bat and a pangolin that is on a genocidal rampage and taking down the entire world’s economy.

    It’s also a coincidence and unlikely related that virus researchers, both here in the US and in China keep disappearing themselves and getting in the way of bullets.

    • mdgalperin says:

      100%

    • Magog says:

      Yeah lets not trust scientists but Fox News and Facebook, that’s much better…
      You know that influenza viruses emerge from pigs and chicken always undergo natural recombination, so it’s not unlikely that the same went on in bats and pangolins. Also why should one create a virus, it’s totally nonsense especially because everybody knows the consequence like in SARS. Try Ockhams razor blade,really…
      Which virus researcher has disappeared?

  • Lindsey says:

    I am definitely not a scientist, but is it possible that the second scenario has occurred due to phocine distemper virus and/or canine distemper virus? Articles I have read have suggested human infection is more and more possible, such as this article: https://www.ncbi.nlm.nih.gov/pubmed/31615092

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