Genomic Study Points to Natural Origin of COVID-19
Posted on by Dr. Francis Collins
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.
 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]
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
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Posted In: News
Tags: ACE2, bats, bioengineering, camels, civets, coronavirus, Coronavirus Rumor Control, COVID-19, evolutionary biology, FEMA, genomics, man-made, MERS, natural, natural origin, new coronavirus, pandemic, pangolin, SARS, SARS-CoV-2, social distancing, spike protein, viral pandemics, virology
Excellent debate …
Highly flawed “models” again. Have we not learned that “models” have been a disaster in the Covid-19 pandemic?
If your study points to natural occurrence of Civid19 and excludes bioengineering, how can you explain the sparing of epidemic in some part of China, Russia, North Korea . It seems to me that it could be China’s bio warfare to affect US’s And the rest of the world for it’s own benefit in many ways. Also China seemed to be well prepared for self rescue properly and fast and now playing roll of knight of shining armor ! After all China is communist!
Those nation states mentioned above also lack a free press. China had been grotesquely lying about their death number. In order to maintain crucial supply chains American policy makers and their cohorts choose to say nothing.
Are you sure Covid 19 is not man made ?
Pointless question if you provide no evidence you found any part of the footnoted article unpersuasive and provide no reason to believe this novel coronavirus is unnatural. (“Covid-19” is not a virus of any kind.)
so the argument for not man-made in the article has a scientific “point”? “provide no reason” to do so? Many criminal actions are “no reason”, meaning “hard to believe”.
If we consider the possibilities of the research been helpful in guiding our beliefs of Covid19, one may not be wrong to strictly reconsider their arguments as highly possible as related “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”. We may further our understanding by constructive criticism, if any, as an objection to their claims. I suggest that if one has to disprove, then at least provide a little scientific argument to support your claims.
This article uses the words “outrageous” and. “Debunks” – two words that we never see in real science. It tells us that this is an opinion written by a non-scientist who has an agenda.
Francis Collins a non-scientist? OK…
You’re right. But what agenda. Defending communist China?
Did you read the study this blog article referenced?
He has a medical degree and a doctorate in physical chemistry, and he’s a non-scientist? …
Dr. Collins, Do you think Covid-19 is a recombinant virus with a bat-pangolin genome hybrid?
This does nothing to refute the fact that very close to the Wuhan market, there is a bio research lab that studied coronavirus in bat species that are not native to the area. Maybe virus was not engineered but could be accidentally released from a bio research lab. There is no way at this time to know if it was malicious or not and there is no way to scientifically prove it either way. I do find the proximity of that lab to be highly coincidental. Especially since they were studying coronavirus. Does not constitute proof of any kind? There are also as yet unconfirmed reports of a researcher selling lab animals illicitly. Again, not proof but intriguing to me.
I also question the non-scientific nature of this paper. Why the need to disprove this theory with such nonscientific language? Is it not possible that this was research gone awry?
I would venture that, using AI, this novel design of the “corona” could in fact be “researched” into existence.
“I also question the non-scientific nature of this paper. Why the need to disprove this theory with such nonscientific language? Is it not possible that this was research gone awry?”
I suspect the answer to your question is that the piece was written to speak to a non-scientific audience.
Thanks for this amazing information
Social distancing is a good way to avoid this
I fail to see how this is “proof” that the virus did not originate in a lab. The authors also fail to address the 2015 paper in which authors associated with the Wuhan CDC and Virology Institute posit that the ACE2 receptor WOULD be a good target for bat coronavirus with SARS like symptoms. Their entire argument seems to rest on the fact that their computer models wouldn’t predict such effective ACE2 binding, and therefore no one would pursue this as a line of research or genetic engineering. This is directly countered by this paper, as it clearly was being considered back in 2015 and there are even earlier work going back to at least 2008 in this same area.
Menachery, V., Yount, B., Debbink, K. et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med 21, 1508–1513 (2015). https://doi.org/10.1038/nm.3985
Also the idea that because a virus or protein spike cannot be found in nature, therefore it MUST be a natural mutation seems like some serious cognitive dissonance to me. Wouldn’t it be more reasonable to conclude that if we cannot find something in nature, mankind must have had a hand in it’s creation?
See my post above.
I agree with Ms Williams and also wonder why researchers are not looking at more genetic questions since we know Type A blood does not have the same ACE2 protiens on the outer covering of their blood cells. Viruses can attack them easily and that would be approximately one third of world populations. It would be a way to attack the world and sucessfully damage the economies giving China advantage.
Thanks for this amazing information
“Also the idea that because a virus or protein spike cannot be found in nature, therefore it MUST be a natural mutation seems like some serious cognitive dissonance to me.”
At no point in the article has the author said: “a virus or protein spike cannot be found in nature.” It states right there: “the region that binds ACE2 resembles a novel virus found in pangolins”
is it possible that the bats and the pangolin at one of the wet markets in china are cross contaminated causing the covid-19 meaning that the bats having one strain 99.9% match and then the pangolin being infected with a different strain of corona virus causing it to mutate to what we know as covid-19 virus sweeping the nation? they live slaughter the animals there on the spot meaning the killed and infected bat then killed a pangolin that had a diff strain and mutated to a much stronger strain being born cross contamination from the surfaces not being cleaned after each slatter. then the handler doing the slattering not having a clue of infection and spread it…
Thanks for this important piece of information. The line on natural selection on ACE2 is particularly interesting. I am just wondering, given the wide spread of COVID-19, how likely is it that natural selection acted on ACE2 in a similar fashion across continental populations at the same time? A population genetic diversity study of the ACE2 enzyme might be profitable.
There is a big gap between ACE2 in 2003 and 2020. Natural selection cannot explain how and for what that gap happened.
I have heard 2x now that the virus is dead?
High frequency EM waves?
I would like to hear more on the EM waves if you recurved any information.
im waiting to see when one of these scientist inject the covid-19 into a cockroach and see if the roach genomes and antibodies react an kill the virus because we all know that roaches will be here long after humans and their bodies dna and structure are a work of art created by god they have grown to survive every insecticide we throw at them an any elements their is. not to mention they can grow legs back at early ages of life if we pull them off and they can sense a damn crumb of food you dropped on the other side of the house deep in that carpet that we never knew was there but their sensory and genes and body resistance is out of our world.
Just a curiosity, accepting the conclusion that it is not “engineered”, could it be manually selected and manually recombined? A bio-engineer doesn’t have to “engineer” everything thing. He/She can accelerate certain natural process to achieve the particular strain he/she needs.
why did China reopen the meat markets in Wuhan if they would not be certain, Covid-19 did not originate there?
how does it have a 100% match to a bat protein? if there was an intermediate host this could not be 100%. the only way to achieve this is reverse engineering….?
If you cant tell me EXACTLY WHERE Sars-cov-2 came from and evolved with 99.9% certainty ,,
Then If it looks like a duck, walks like a duck, and quacks like a duck , It must be a Chinese Duck the escaped from the Wuhan Institute of Virology!
I Find the comments more interesting and informative than the actual information in the article.
Has anyone seen any scientific discussion regarding the genetic changes which allow the corona virus to remain viable (infectious) on surfaces (e.g. stainless steel, plastic) for 72+ hours – which is beyond the duration of similar viruses?
Paragraph 6 wraps it up in a petri dish.
The paper published in nature (e.g. https://www.nature.com/articles/s41591-020-0820-9) lists two discovered mutations:
1. Mutations in the receptor-binding domain of SARS-CoV-2
2. Polybasic furin cleavage site and O-linked glycans
However, I haven’t seen anything regarding the ‘mutations’ which allow the virus to remain infectious for 72+ hours (which is substantially longer then other corona viruses.
All of the comments are interesting, and for the most part. Pointing in one direction.
I found paragraph 6 pretty much the process in a petri dish.