COVID-19: Genome Analysis Suggests 2 Viruses May Have Combined

Alexandre Hassanin reports on the case for COVID-19 being a chimera between two pre-existing viruses.

The origin of the Covid-19 virus is still unclear: a cave, the forest…
(Michal Ico/Unsplash, CC BY)

By Alexandre Hassanin
The Conversation

In the space of a few weeks, we have all learned a lot about COVID-19 and the virus that causes it: SARS-CoV-2. But there have also been a lot of rumours. And while the number of scientific articles on this virus is increasing, there are still many grey areas as to its origins.

In which animal species did it occur? A bat, a pangolin or another wild species? Where does it come from? From a cave or a forest in the Chinese province of Hubei, or elsewhere?

In December 2019, 27 of the first 41 people hospitalized (66 percent) passed through a market located in the heart of Wuhan city in Hubei province. But, according to a study conducted at Wuhan Hospital, the very first human case identified did not frequent this market. Instead, a molecular dating estimate based on the SARS-CoV-2 genomic sequences indicates an origin in November. This raises questions about the link between this COVID-19 epidemic and wildlife.

Genomic Data

The SARS-CoV-2 genome was rapidly sequenced by Chinese researchers. It is an RNA molecule of about 30,000 bases containing 15 genes, including the S gene which codes for a protein located on the surface of the viral envelope (for comparison, our genome is in the form of a double helix of DNA about 3 billion bases in size and contains about 30,000 genes).

Comparative genomic analyses have shown that SARS-CoV-2 belongs to the group of Betacoronaviruses and that it is very close to SARS-CoV, responsible for an epidemic of acute pneumonia which appeared in November 2002 in the Chinese province of Guangdong and then spread to 29 countries in 2003. A total of 8,098 cases were recorded, including 774 deaths. It is known that bats of the genus Rhinolophus (potentially several cave species) were the reservoir of this virus and that a small carnivore, the palm civet (Paguma larvata), may have served as an intermediate host between bats and the first human cases.

Since then, many Betacoronaviruses have been discovered, mainly in bats, but also in humans. For example, RaTG13, isolated from a bat of the species Rhinolophus affinis collected in China’s Yunan Province, has recently been described as very similar to SARS-CoV-2, with genome sequences identical to 96 percent. These results indicate that bats, and in particular species of the genus Rhinolophus, constitute the reservoir of the SARS-CoV and SARS-CoV-2 viruses.

Bat, Rhinolophus affinis. (Alexandre Hassanin) 

But how do you define a reservoir? A reservoir is one or several animal species that are not or not very sensitive to the virus, which will naturally host one or several viruses. The absence of symptoms of the disease is explained by the effectiveness of their immune system, which allows them to fight against too much viral proliferation.

Recombination Mechanism

On Feb. 7, 2020, we learned that a virus even closer to SARS-CoV-2 had been discovered in pangolin. With 99 percent of genomic concordance reported, this suggested a more likely reservoir than bats. However, a recent study under review shows that the genome of the coronavirus isolated from the Malaysian pangolin (Manis javanica) is less similar to SARS-Cov-2, with only 90 percent of genomic concordance. This would indicate that the virus isolated in the pangolin is not responsible for the COVID-19 epidemic currently raging.

However, the coronavirus isolated from pangolin is similar at 99 percent in a specific region of the S protein, which corresponds to the 74 amino acids involved in the ACE (Angiotensin Converting Enzyme 2) receptor binding domain, the one that allows the virus to enter human cells to infect them. By contrast, the virus RaTG13 isolated from bat R. affinis is highly divergent in this specific region (only 77 percent of similarity). This means that the coronavirus isolated from pangolin is capable of entering human cells whereas the one isolated from bat R. affinis is not.

In addition, these genomic comparisons suggest that the SARS-Cov-2 virus is the result of a recombination between two different viruses, one close to RaTG13 and the other closer to the pangolin virus. In other words, it is a chimera between two pre-existing viruses.

A coronavirus from the pangolin could be one of the sources for COVID-19.
(Wildlife Alliance/Flickr, CC BY)

This recombination mechanism had already been described in coronaviruses, in particular to explain the origin of SARS-CoV. It is important to know that recombination results in a new virus potentially capable of infecting a new host species. For recombination to occur, the two divergent viruses must have infected the same organism simultaneously.

Two questions remain unanswered: in which organism did this recombination occur? (a bat, a pangolin or another species?) And above all, under what conditions did this recombination take place?The Conversation

Alexandre Hassanin, Maître de Conférences (HDR) à Sorbonne Université, ISYEB – Institut de Systématique, Evolution, Biodiversité (CNRS, MNHN, SU, EPHE, UA), Muséum national d’histoire naturelle (MNHN).

This article is republished from The Conversation under a Creative Commons license. Read the original article.

The views expressed are solely those of the author and may or may not reflect those of Consortium News.

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24 comments for “COVID-19: Genome Analysis Suggests 2 Viruses May Have Combined

  1. Miklós Dávid
    March 24, 2020 at 03:46

    I have a question. There are different species of pangolins involved with this COVID-19 virus. The Asian and African pangolins had never met in history until man started to meddle and possibly store them alive next to each other. Could their different viruses combine, or do they carry exactly the same type of viruses?

  2. Robert Carl Miller
    March 23, 2020 at 11:24

    Back in the seventies Litton Bionetics, a military contractor, had a program running which combined different animal viruses, to include simian viruses, sheep viruses, etc. One scientist working on this project was Robert Gallo. It seems like yesterday, but our military-industrial complex has been working on this stuff for about fifty years now. Think of all the amazing creations our secret government programs could invent!

    When someone says that two naturally occurring viruses combine to create a new one, you have two choices for the creator: Mother Nature or your government.

    And those of you who think that our government would never do such a thing?

  3. Zhu
    March 23, 2020 at 00:38

    Thanks for some hard science!

  4. March 22, 2020 at 21:12

    This is the great benefit of bio-warfare for the control freaks. You can hit the enemy, in this case, the middle class, with a bio-weapon, and buy up all the cheap assets when the economy tanks, bailing yourself out anyway. Too much real estate was in the hands of regular Americans.

    Just because these similar virii exist in multiple species of animal is not evidence in any way that these virii combined. The article cites no references to any analytic data, unlike the numerous papers that illustrate how it was genetically engineered. Namely:

    “The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade.”

    “Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag”

    “A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence.”

    From what I have read, even the most skeptical scientists are now acknowledging that there are unknown strains of DNA in the code of the Coronavirus, which cannot be proven to have originated from either a lab or nature, so there is still a legitimate debate as to the origin of this biological disaster if you are a brainwashed moron who doesn’t know how elite globalists try to dominate the human race and control every element of society desiring to enslave you and your family under a Totalitarian slave factory. It’s called EVIL. Wake up, ladies and gentlemen, wake up!

  5. SteveK9
    March 22, 2020 at 19:55

    A bat, a pangolin or … a laboratory. Not suggesting anything sinister, just a potential accidental release.

  6. Jacques
    March 22, 2020 at 17:32

    And what if those two viruses recombined with a little nudge from your friendly neighborhood bioweapons lab? Just sayin’…

  7. March 22, 2020 at 15:06

    Nice article!

  8. w. chirnside
    March 22, 2020 at 13:54


  9. Rodion Raskolnikov
    March 22, 2020 at 11:38

    This article is a disappointing mix of good science and popular mythology. It seems rather obvious that the virus was brought to Wuhan by some of the several thousand soldiers from 114 nations that gathered for the Military World Games in Oct. 18-27. Some 369 military athletes came from the US, and some were trained at Ft. Detrick, MD, where the United States Army Medical Research Institute of Infectious Diseases is located (USAMIRID).

    Interestingly 5 US soldiers were taken sick and hospitalized during the games. The games were in mid October. The first identified case of Covid -19 was in November.

    This story is gaining credibility in China but is it mostly being scoffed at in the US as a conspiracy theory. Good genomic research could discover if the Covid-19 was created in a lab, say at USAMIRID.

    The bat theory is just non-sense. There have been bats in China for millennia. Bats and many other animals carry corona viruses. There were no sicknesses from Covid-19 before the World Military Games in Oct. 2019. The fairy tale about people a passing through a market is just colonialist reporting.

    Nothing is known for certain at this point. But the most probably explanation is a transmission by US soldiers at the World Military Games. People at USAMIRID know the answers for sure. They will, however, never talk. The science should be able to prove the origin of Covid-19.

  10. Ken Garoo
    March 22, 2020 at 10:19

    The combination took place in a lab in the US in 2015, a reported in the prestigious Nature Medical journal. The work triggered off widespread publication of correspondence about the ethics of this work.

    “A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence”


    The transfer may have happened naturally, so what could go wrong if man helps nature along?

  11. Athula
    March 22, 2020 at 02:21

    Good point Marko. Another point. ACE inhibitors. If the binding site for virus entry may possibly be promoted by the presence of ACE inhibitors (antihypertensive), then thus could explain the vulnerability of those with hypertension.
    This is another (not controlled) naturalistic retrospective study which could be immensely valuable

  12. robert scheetz
    March 21, 2020 at 18:23

    It still didn’t answer how it was transmitted to humans.

    • Anonymous
      March 22, 2020 at 14:36

      Probably people who work with animals. Possibly furries.

  13. elmerfudzie
    March 21, 2020 at 17:04

    In case anyone might be wondering, RNA viruses represent the best example of what can never be deliberately transformed into a weapon or threat against potential adversaries. All corona-viruses are included in the RNA class or group. In the natural environment they frequently evolve with a mutation rate over one million times faster that human DNA. This explains why the Italian COVID-19 is genetically distinct from the Wuhan version? Intermediate vectors (animal) may not be necessary? This is not entirely clear, to me that is, what mutations COVID 19 may undergo when exposed to ordinary UV (sunlight) or sudden temperature changes. The virion(s) that survive and find their way into another host, be it man or animal may not structurally resemble what is currently undergoing research or for that matter, can justify using dangerous experimental procedures such as gain of function (GOF) research. For details and ethical analysis, visit the US National Science Advisory Board’s (NSABB) corresponding authors such as Michael J. Selgelid circa 2016.

    I’m beginning to understand why the military prefer exo or endo toxins used as debilitation agents rather than live organisms…

  14. Mark Stanley
    March 21, 2020 at 12:46

    Thanks for the intelligent, scientific report. Refreshing. The media-waves are dominated by essentially the same repetitive frenzy that leaves me with questions concerning actual data and the progress of practical research.

  15. March 21, 2020 at 08:33

    Read the article in Consortium by Pepe Escobar titled COVID 19 – China locked in a Hybrid War with US…What do you think is more likely – wild animals passing on the virus, or humans screwing around then releasing the virus?

  16. March 21, 2020 at 08:27

    My money is on humans screwing with the virus then releasing it into the atmosphere…

    • robert e williamson jr
      March 23, 2020 at 23:07

      The article is amazing and should give everyone pause. Seems that reverse engineering using info from similar articles could very well lead to humans tampering with things best left alone. The truth is we likely do not want to know what world governments have done in the interest of “Protecting their homelands”. And it’s just as well because the CIA, DOD and NSA ain’t talking!

      Now today the SUPREME LEADER is talking about removing distancing guide lines and calling off quarantine measures.

      The behavior of this idiot, members of his cabinet and congress surly by now have exceeded the threshold considered by the law for engaging in criminally neglect dereliction of duty.

      He wanted the job and the “BUCK STOPS” with him and his “GANG”.

  17. robert e williamson jr
    March 20, 2020 at 22:25

    This is amazing stuff. Mean while the Supreme Leader is still lying and Putin is still winning!

  18. Sam F
    March 20, 2020 at 19:31

    Thank you, Mr. Hassanin for this illumination. It will be interesting to learn more about our viral vulnerabilities and immune strengths as the virus and proposed vaccines are investigated. It would be helpful to know what investigative resources are being retargeted toward vaccines, and what manufacturing resources are being retargeted toward ventilators and ICU equipment.

    It very much appears that grant procedures need to more effectively constrain the wandering curiosities of our biological researchers to useful results, and to prohibit patenting of treatments found in grant-funded research.

  19. Jpc
    March 20, 2020 at 19:09

    The simplest explanation generally turns out to be the best one.
    This article is one of the calmest and best descriptions of the actual virus (viruses) yet.

  20. Marko
    March 20, 2020 at 19:05

    It’s painful to watch these press conferences , with Trump touting hydroxychloroquine ( Plaquenil ) as a miracle cure while Fauci says ” Whoa , big fella ! “, and advises controlled trials to determine efficacy. Does nobody realize that there’s a huge controlled trial currently underway across the US and other countries , one that we seem to be making absolutely no effort to access ?

    Plaquenil is a highly-prescribed drug in the US , with ~ 5 million scrips , according to Wikipedia. There’s your test group , and we know who every one of them is. The rest of the country is the control group. So , ~ 1% of patients , or more , of those infected with coronavirus are taking Plaquenil. How do they fare compared to the rest ? There’s your trial. Now , go out and look at the results.

    This shouldn’t be this hard. We’re being led by mental midgets.

    • Guy Little
      March 21, 2020 at 18:30


      I know, I know…you wrote mental midget.

      I’m probably missing your point and what’s salient in the article that could help one conjecture in the right direction. Feeling inadequate to the task.

      Theory: Some lab was studying “the effectiveness of their immune system[s]” (both species), and that’s where it happened? Bad QC?

      Paranoid theory: They didn’t plan to vanquish the epidemic outright (but mainly warn anybody), because the bigger the drug-trial the better?

      Theory: The test for the exception (who had it in Nov) was flawed?

  21. John P
    March 20, 2020 at 17:39

    Thank you for a very good article. The virus probably got going in the human population at the market where I gather some sect believes in eating these wild animals. They take them home believing the effects they get from eating these animals is more powerful the fresher the meat.

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