We don’t yet know the origin story for SARS-CoV-2

By Katherine E Arden, PhD & Ian M Mackay, PhD

The existence of a coronavirus related to severe acute respiratory syndrome coronavirus (SARS-CoV) was first hinted at by a researcher from the Wuhan University School of Medicine. A coronavirus pathogen was confirmed a week later, and its genetic sequence made public days after that. It was later called SARS-CoV-2.

An alignment of SARS-CoV-2s

Fast forward four months.

President Trump continues to present a narrative of lab release; however, the scientific consensus is that SARS-CoV-2 is the result of a natural event during which a bat virus jumped to a human, possibly via an intermediate animal.

The reality is that we still don’t have enough evidence to write an origin story for the cause of coronavirus disease 2019 (COVID-19).

Manufactured or manipulated: a great old movie script

The idea that SARS-CoV-2 is a manufactured virus is titillating but less likely than other origin stories.

Experts in viral genetics and emerging viruses have already described the likely path for SARS-CoV-2; one of stepwise evolution consistent with patterns frequently seen among other coronaviruses in recent history. The manipulation of a bat coronavirus or its synthetic creation would need a very high level of coronavirus and molecular virology expertise, not just to construct it, but to cover the tracks of that construction.

Experts in the field have described an evolutionary pattern to the genetic differences and motifs which distinguish SARS-CoV-2 from any other known coronavirus.

Nefarious agents would also need access to specialised reagents and equipment. This is not impossible but is unlikely. The US intelligence community concurs with the scientific consensus; that SARS-CoV-2 is unlikely to have been genetically modified or created in a lab.

Laboratory study of a wild virus gone wrong?

There is no evidence that scientists anywhere were previously working with SARS-CoV-2, merely allegation. But if SARS-CoV-2 did escape a lab, the story goes, it may have hitched a ride in an infected lab animal or researcher. Biosecurity procedures must have failed for this to occur; something not unheard of. Once in the wild, the concern is that virus spread among animals or humans and travelled worldwide from there. Another obvious problem with this version is that the virus could also have happened naturally, without this convoluted lab intermediary process.

The lab from which SARS-CoV-2 very likley did not originate
Photo by Polina Tankilevitch from Pexels.[3]

Nature as the source, humans as facilitators of the meeting

Over 60% of new or emerging infectious disease in humans originate from animals; they are zoonoses. Humans have a long and varied history of acquiring zoonoses. We know that influenza A viruses – the “usual” cause of human pandemics – are bird viruses that spread to many other mammals, often when those animals are kept close together. The 1918 human influenza pandemic virus shares features with avian viruses while the 2009 pandemic had evolutionary help from pigs. The Ebola epidemic in west Africa in 2014-16 that caused unprecedented levels of infection and death was suspected of starting when a human was infected by a bat.

A defensive pangolin. [2]

SARS-CoV-2 is the seventh coronavirus known to cause human disease and the third linked to bats within 20 years. There is precedent supporting the natural origin of SARS-CoV-2 as a zoonosis. Scientists have traced the origins of different endemic human coronaviruses (229E, OC43, NL63, HKU1) from bats through rodents, cows or camels, now perhaps pangolins, to humans. In the 2002-04 SARS epidemic, the causative SARS-CoV originated from a bat coronavirus that likely passed through either palm civets or racoon dogs. For MERS-CoV, the journey was probably from bat to camel to human. Both viruses relied on humans bringing farmed or exotic animals, each with their own large but poorly studied viral populations, into close proximity to other animals and to us.

Rhinolophus affinis.[1]

Vector-borne zoonoses due to Ross River virus and Zika virus occurred after interactions between an animal reservoir, a mosquito vector and us. We make these interactions more likely by encroaching on habitats, recreating suitable habitats near us, or through climate change.

We don’t have evidence, but we do have precedent

Scientists have allowed for the possibility that new evidence may uncover facts supporting a different origin story. There is no direct evidence to support the lab escape or modification narrative any more, or less, than the evolutionary hopscotch story. But we do have circumstantial evidence for natural evolution: a very closely related horseshoe bat coronavirus – still likely separated by hundreds of genetic differences equating with decades of evolutionary difference; pangolin coronaviruses that are generally more distinct but have contributed some key genetic sequence; millions of potential exposures annually to bat coronaviruses; a broad, varied and unexplored constellation of bat coronaviruses; a well-known pattern of intermingling and mutation among coronaviruses and a lot of precedents. The circumstantial evidence suggests SARS-CoV-2 has originated from humans and animals once again being brought into close contact. Experts aren’t surprised SARS-CoV-2 has emerged as yet another zoonosis.

We also shouldn’t overlook the politicisation of this topic, the desire to apportion blame and the lack of expertise among sources preferring a more exciting, but poorly supported narrative. Underpinning a tale of natural evolution is the knowledge that human habits, once again, created conditions for and perpetuated the spread of a new infectious pathogen.

This won’t be our last dealing with a newly emerged coronavirus. Hopefully, in the future, better-funded research science will have prepared answers for the public and our leaders to address the complex scientific concepts we’re struggling to come to terms with during COVID-19.


  1. https://www.inaturalist.org/photos/56090441
  2. A pangolin in defensive posture, Horniman Museum, London.
    Author: Stephen Dickson
  3. https://www.pexels.com/photo/chemicals-in-beakers-3735712/


  • First posted 04MAY2020, 5:30pm

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25 thoughts on “We don’t yet know the origin story for SARS-CoV-2”

  1. Lab or no lab, the virus came from China. It would be reckless for the Chinese government NOT to study a virus from an animal that’s being illegally consumed in their country. Particularly if that virus were a coronavirus with species jumping potential, in this case mammal to mammal to mammal.

  2. As Yuri Deigin points out [https://medium.com/@yurideigin/lab-made-cov2-genealogy-through-the-lens-of-gain-of-function-research-f96dd7413748], the technology to make a chimera like SARS-CoV-2, and even add a cleavage site, is widely available and no longer requires exotic training or materials. Hundreds of labs worldwide could do it. He also points out there’s no need to invoke “nefarious agents”, as such a chimera would fit right in to existing research programs. To call this something other than “man-made” or “genetically engineered” is at best misleading.

    This *of course* doesn’t prove a lab origin; a purely natural origin remains possible even if all but the last step did take decades. It does however decredibilize those ridiculing hypotheses of lab origin. Real proof of natural origin is needed, not appeals to authority or opinions masquerading as statements of scientific fact.

    1. I would turn that around on you: real proof of LAB origin is required. The default option is “natural” because the very close relatives are out there to see. Is there ANY proof that one of these was being looked at – in ANY lab?

      1. Yes, there is plenty. Papers, grants, articles, etc. On specifically the kind of chimeric virus that would look like sars-cov-2, specifically gain-of-function research on coronavirus on the Wuhan lab on 2019.

        If one is to be scientific, it is a good idea to read before reacting, Yuri Deigin goes to great lengths in the medium article.

    2. Check his Linekidn. Yuri Deigin doesn’t have any academic science background. He has a BSc in IT and an MBA. Of course he worked in the BioTech industry, not as a Scientist, but in Finance and Marketing managerial levels. Besides Medium is just an open source platform to run personal blogs, not a Science journal. The source and the author is not reputable.

    3. Then, you might ask why was Yuri Deigin’s article never got debunked by Scientists? Why would they? It was not Scientific paper, not on a peer reviewed Science journal or Scientific research database. They usually don’t bother about what lay people (he doesn’t have an academic Science background) post on blogs.

  3. We may never know the truth. If it was a bioweapons research gone awry, no state is going to give up that info.

  4. Best (but by no means certain) way to track would be to see if we can find “Patient 0”, the first known human with the virus, and look at there contacts. The first currently known patient has zero links to the “Wet Market”; however they are unlikely to be the actual first patient. There would need to be 2 human to human transmissions though to get to this person from someone who does have a link. It could also be that the virus was present in the lab and it’s escape via an infected an animal or person went to the market to spread further…

    I suspect we will never be able to be certain unless an exhaustive search of the Lab’s files and (including those allegedly removed/deleted) to show that this specific variant of the virus was never present. If there were files deleted though, then we probably can never be sure.

    And isn’t there a suggestion that Turtles could be another possible intermediary host for this CV ?

    1. So you – as others have – prefer to lean on the route of emergence that is unlikely to have any supportive evidence rather than the route that has definitely spawned SARS-CoV, MERS-CoV, 4 other HCoVs and >60% of other viruses in humans. Why? Is it because it can never be disproven so its cooler? Why is this one different for those others I listed? Because the US wants it to be? Because that takes heat off the need to look inward and do better? Because you’ve just learned about labs in countries like the US and China doing work on viruses that could be dangerous? Why?

  5. There are a couple of amateur virologists out there that claim there is homology with HIV that would be very unlikely to have evolved naturally, can you comment on this?

    1. There are some *structural* (not sequence-specific) protein similarities to some motifs, protein functions etc that are shared among mammalian viruses (because there are only so many ways to attach and enter mammalian cells and viruses have done a great job of evolving to use a lot of them). But the sequences are different.

  6. One puzzle … it is over 1500km from Yunnan (where the horseshoe bats are found) to Wuhan (where the virus first spread). Yunnan is remote, transport links are not good, and it is most unlikely that bats are transported that distance to a major urban market. And if the vector was a pangolin nobody has explained where in that journey they get introduced?

    1. I don’t think of this as a puzzle but as a lack of understanding. Bats range a huge distance. Bat populations are unlikely to have been fully catalogued in every location in China or the planet. They most assuredly have not been well samples to see whether different species have this virus and we have a very incomplete catalogue of all CoVs because sampling and testing and characterisation are woefully limited.

      My opinion is that a related virus is out there somewhere – in a bat and perhaps a more closely related adapted one somewhere in another animal – and we just haven’t found them yet. Of course, that could be wrong and if so, I will immediately post a blog about that and admit my hypothesis was crap.
      Hopefully, we’ll find out one day.

    2. During the SARS outbreak in 2002 Russian Scientists said it was a bio-weapon released by Americans.
      In 2004 WHO officials found traces of SARS in a Civet cage in a restaurant in Guangdong (the epicenter). The civets were bought to the restaurant from the nearby wet market. So it’s obvious when a similar outbreak occurs a wet market becomes a prime suspect.
      In 2017 it was found that bats in Yunan caves which is 1600 miles away from Guangdong is the source of SARS. The civet was an intermediate host. So it actually took 15 years to come to a conclusion about SARS.
      It was not much of a controversy back then.
      Historical data is very important to figure things out. Cheers!

  7. Ask a virologist “How did the POLYBASIC FURIN CLEAVAGE SITE PRRA get into Covid 19

  8. At least you admit we don’t have a clue about the origin…bravo.

    The problem is we have a plethora of Professors and PhDs that pretend they know what they are talking about.

    I suppose we can’t have the public panic… that really we have no fuc**n idea.

    Imagine a politician that came out and said ” we exist… so we know viruses are not our enemy and indeed most likely created us.”

    Instead they turn up as if going to war… flanked by “experts” to outline a 3 step approach … a la 1918.

    Wash your hands, hide away and wear a mask!.

    100 years of progress..dysbiotic drift is a bitch… That second wave could be a doosey.

    Viruses to my North, my South, my East and West,
    They are working all week and my Sunday rest,
    They control my noon, my midnight, my talk, my song;
    I thought that love for me would last forever: I was wrong.

    The stars are not wanted now; put out every one,
    Pack up the moon and dismantle the sun,
    Pour away the ocean and sweep up the woods;
    For they are all full of viruses…and nothing now can ever come to any good.

    1. Nobody knows everything. But the biggest problem here is some random internet troll thinks he knows more than the people who study a subject. Anyway, one day there’ll be called the experts. We live in a time when doing a tiktok video is considered as talent.

  9. In the last 20 years there have 3 virus outbreaks originating from chinese “wet markets”: H5N1, SARS, Sars-cov-2. That makes about one outbreak in 7 years. Now how many “wet markets” are there in China? Frankly I do not know but there are 108 towns with 1m population or more. Assuming they all have one “wet market”, that means the probability of having an outbreak in one particular town, such as Wuhan, is 1 in 756 years. It happens the outbreak occurred in the one town in China that had a BSL4 lab. And it was known for having produced chimeric corona-viruses in the past.

    Are you willing to bet that the likelihood of a virus “escaping” a BSL4 lab, whose security has been questioned on several occasions, and doing experiments that would be illegal in a number of countries, is less than 1 in 756 years?

    To the least that makes the following assertion a bit bold:
    “The idea that SARS-CoV-2 is a manufactured virus is titillating but less likely than other origin stories.”

    I know a post-doc in biology, working in virology. He and all his colleagues are intimately convinced the virus was released (not necessarily intentionally) from Wuhan BSL4. The fact that people are reluctant to tell this aloud, let alone publishing it, does not mean there is a consensus.

    Finally, citing a secret service is not scientific: their methods and sources are not open, their goal is not to produce knowledge.

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