SARS-CoV-2 is a hybrid from a Bat and a Pangolin

[Tom.G]

from: https://arstechnica.com/science/202...hybrid-of-viruses-from-two-different-species/

Analysis of the virus's genome was ambiguous. Some analyses placed its origin within the local bat population. Others highlighted similarities to pangolins, which might have been brought to the area by the wildlife trade. Less evidence-based ideas included an escape from a research lab or a misplaced bioweapon. Now, a US-based research team has done a detailed analysis of a large collection of viral genomes, and it finds that evolution pieced together the virus from multiple parts—most from bats, but with a key contribution from pangolins.

The original article (which I have not read) is at:
http://dx.doi.org/10.1126/sciadv.abb9153

Cheers,
Tom

 

[Astronuc]

Four weeks ago, May 12, ACS hosted a webinar on coronaviridae and SARS-CoV-2. At the time, the involvement of pangolins was suspected, yet to be proven.

How this Coronavirus is (and isn’t) Different from Other Viruses
https://www.acs.org/content/acs/en/acs-webinars/popular-chemistry/coronaviruses.html

 

[Pythagorean]

I heard a hypothesis from an epidemiologist on the radio - that bats and pengalins were kept together at a wet market where transmission occurred between them, then the pengalin likely transmitted to a human.

 

[Laroxe]

I heard a hypothesis from an epidemiologist on the radio - that bats and pengalins were kept together at a wet market where transmission occurred between them, then the pengalin likely transmitted to a human.

Its a difficult one this as these animals sold as food are usually dead and I think the pangolins are imported (illegally). this raises the question of how long the virus could survive and be capable of reproduction in dead animals. Of course there may be bats that live in a large covered area and their droppings could contaminate the ground. It seems to be the case that a virus can jump species several times or jump to another species, picking up a few genes, then jump back again. Its interesting, though common, that they haven't identified the source, the new virus might have quickly lost its ability to spread in its original species and its now most effectively spread in humans.

 

[Phil Core]

You may find this link of some interest - https://www.physicsforums.com/threads/coronaviruses-in-malayan-pangolins.987501/

FYI - To date no natural source has been found for the Wuhan Virus.

There are problems with both bat and pangolins (anteaters). The RNA match is not close enough. There is no known missing link - source - for a "natural" host.

As an aside you should consider the concept of gain of function. Usually when dealing with viruses they do not naturally become more lethal but less. Human influence can enhance gain of function.

FYI - No notes from the Wuhan Experimental Lab were available for evaluation. Most if not all are though to have been destroyed . ( I actually do not have source for the destruction of records but none, absolutely none, have been made available.)

 

[Ygggdrasil]

You may find this link of some interest - https://www.physicsforums.com/threads/coronaviruses-in-malayan-pangolins.987501/

FYI - To date no natural source has been found for the Wuhan Virus.

There are problems with both bat and pangolins (anteaters). The RNA match is not close enough. There is no known missing link - source - for a "natural" host.

As an aside you should consider the concept of gain of function. Usually when dealing with viruses they do not naturally become more lethal but less. Human influence can enhance gain of function.

FYI - No notes from the Wuhan Experimental Lab were available for evaluation. Most if not all are though to have been destroyed . ( I actually do not have source for the destruction of records but none, absolutely none, have been made available.)

It is not surprising that no natural source for the SARS-CoV-2 virus has been found yet. The virus is very new, and we have only sequenced a small fraction of the huge number of coronaviruses that exist out in the wild. In the case of both the two other recent coronaviruses that emerged zoonotically (SARS and MERS), the animal origin of the virus was not known at the time out the initial outbreaks, and it took a year or so for the wild reservoirs of the virus to be identified (civet cats in the case of SARS and camels in the case of MERS). Absence of an identified natural source is not evidence that the virus is man-made.

Currently, we have no evidence that gain of function experiments were involved in the origins of the COVID-19 outbreak. It is very clear from genetic analysis of the virus that it was not genetically engineered by humans. Features of the virus are also not consistent with evolution during passage in a laboratory. Public release of laboratory notes and records is very rare. In the case of an investigation, these would usually be turned over to an oversight body for examination, but they would not be released to the public. Absence of the public release of these records is not evidence for foul play.

As mentioned above, we've seen two other coronaviruses emerge naturally in the past two decades (the original SARS and MERS) in addition to many other zoonotic viruses in recent history (HIV, ebola, avian flu, swine flu, Zika virus, etc). Researchers have found that people in South China and other areas who live near wild bat populations often show antibodies against SARS-like coronaviruses, indicating that transmission of wild coronaviruses to human populations is by no means a rare event (though evolution of a virus like SARS-CoV-2 that is so easily transmissible between humans is likely a much more rare event). Recombination among viruses is well known, and occurs frequently in nature. Indeed, the article linked to above notes that recombination occurs very frequently in coronaviruses. Nothing about the SARS-CoV-2 points to anything unusual or unnatural about its origins.

 

[phyzguy]

There are problems with both bat and pangolins (anteaters). The RNA match is not close enough. There is no known missing link - source - for a "natural" host.

You have repeated this several times, but it is not true. As has been pointed out to you several times by several people, you should not expect a complete match with the virus taken from anyone animal. The virus can move back and forth between hosts, picking up small pieces of genetic code. The hypothesis that the virus originated in bats, but picked up a small piece of RNA that codes for the spike protein from the pangolin, is quite viable.

FYI - No notes from the Wuhan Experimental Lab were available for evaluation. Most if not all are though to have been destroyed . ( I actually do not have source for the destruction of records but none, absolutely none, have been made available.)

If you have no evidence that notes have been destroyed, you should stop making unsubstantiated accusations.

 

[Phil Core]

I have never stated that the genetic match had to be 100% identical. In fact it would not. However, there has to be a very close match.

Bat - 95 % match but no spike protein. Must have spike protein.
Pangolin - spike protein but only an 80 % match. A 20% difference is too much

Here is an interesting observation that should be considered. I am not sure how long it would take for a transition from original source to human.

"Though no scientists have come forth with even a speck of evidence that humans knowingly manipulated a virus using some sort of genetic engineering, a researcher at Flinders University in South Australia lays out another scenario that involves human intervention. Bat coronaviruses can be cultured in lab dishes with cells that have the human ACE2 receptor; over time, the virus will gain adaptations that let it efficiently bind to those receptors. Along the way, that virus would pick up random genetic mutations that pop up but don't do anything noticeable, said Nikolai Petrovsky, in the College of Medicine and Public Health at Flinders. "The result of these experiments is a virus that is highly virulent in humans but is sufficiently different that it no longer resembles the original bat virus," Petrovsky said in a statement from the Australian Media Center. "Because the mutations are acquired randomly by selection, there is no signature of a human gene jockey, but this is clearly a virus still created by human intervention."

* The hypothesis that the virus originated in bats, but picked up a small piece of RNA that codes for the spike protein from the pangolin, is quite viable. *

I find the mechanics to bring about the etiology you mention extremely cumbersome. "Viable " is a strong word. I am more inclined to state possible but with a very low probability.

 

[BillTre]

"Though no scientists have come forth with even a speck of evidence that humans knowingly manipulated a virus using some sort of genetic engineering, a researcher at Flinders University in South Australia lays out another scenario that involves human intervention. Bat coronaviruses can be cultured in lab dishes with cells that have the human ACE2 receptor; over time, the virus will gain adaptations that let it efficiently bind to those receptors. Along the way, that virus would pick up random genetic mutations that pop up but don't do anything noticeable, said Nikolai Petrovsky, in the College of Medicine and Public Health at Flinders.

You provided no reference for this.
The source of your favorite sequence remains undetermined. It does not, apparently, come from the cultured cells in this scenario.

It seems to describe an unintended (accidental) selection for a more virulent virus among cultured cells.
Culturing viruses over many generations would be required for this scheme to happen.
I expect that most viruses in labs are more conveniently maintained by batch cultures (followed by collecting and storing viruses), rather than continuously propagating a culture over several generations.

 

[Ygggdrasil]

I have never stated that the genetic match had to be 100% identical. In fact it would not. However, there has to be a very close match.

Bat - 95 % match but no spike protein. Must have spike protein.
Pangolin - spike protein but only an 80 % match. A 20% difference is too much

This problem has been solved. The virus is the result of recombination between bat and pangolin coronaviruses. Recombination occurs very frequently in coronaviruses, and the recombination hypothesis fully explains the observations about the genetic sequence you note.

Here is an interesting observation that should be considered. I am not sure how long it would take for a transition from original source to human.

"Though no scientists have come forth with even a speck of evidence that humans knowingly manipulated a virus using some sort of genetic engineering, a researcher at Flinders University in South Australia lays out another scenario that involves human intervention. Bat coronaviruses can be cultured in lab dishes with cells that have the human ACE2 receptor; over time, the virus will gain adaptations that let it efficiently bind to those receptors. Along the way, that virus would pick up random genetic mutations that pop up but don't do anything noticeable, said Nikolai Petrovsky, in the College of Medicine and Public Health at Flinders.

"The result of these experiments is a virus that is highly virulent in humans but is sufficiently different that it no longer resembles the original bat virus," Petrovsky said in a statement from the Australian Media Center. "Because the mutations are acquired randomly by selection, there is no signature of a human gene jockey, but this is clearly a virus still created by human intervention."

* The hypothesis that the virus originated in bats, but picked up a small piece of RNA that codes for the spike protein from the pangolin, is quite viable. *

I find the mechanics to bring about the etiology you mention extremely cumbersome. "Viable " is a strong word. I am more inclined to state possible but with a very low probability.

The genetic features that allow the spike protein to bind the ACE2 receptor with higher affinity are all present in the pangolin Coronavirus sequence. Thus the increased binding affinity comes from a natural source (recombination of the bat Coronavirus with the spike protein from a pangolin coronavirus).

 

[atyy]

With more opinion swaying toward lab, the real area of interest is not whether the Covid virus was influenced in a lab but how it was done.

Despite popular and political opinion, and even some support attributed to very distinguished scientists such as David Baltimore, the lab origin theory remains unlikely. The main obvious routes from lab release as well as many exotic ones are improbable due to a combination of theoretical and experimental arguments found in Andersen et al https://www.nature.com/articles/s41591-020-0820-9 and the comments by Shi Zhengli of the Wuhan Institute on checks done by the institute itself on the possibility of lab release https://science.sciencemag.org/content/369/6503/487.summary. It is noteworthy that Shi Zhengli had commented that a visit probing the lab leak theory would be welcome https://www.bbc.com/news/world-asia-china-55364445.

At the same time, the hypothesis in the title of this thread remains speculation. The closest viral sequences to SARS-Cov-2 seem to be from bats and pangolins. However, it does not mean that their potential common amcestor necessarily had bats or pangolins as hosts. You can see one informed, but still hypothetical, reconstruction of the evlutionary relationships among various coronaviruses (including SARS-CoV-2, and various sequences from bats and pangolins) at https://nextstrain.org/groups/blab/sars-like-cov.

There are also interesting comments by Krystian Andersen on Twitter about furin cleavage sites in SARS-CoV-2 and other coronaviruses.

 

[Laroxe]

I think the real problem is in the fact that we have a very limited knowledge of all the viruses out there, the coronaviruses, one family that can be subdivided into 4 genera can cause infection in most mammals and birds. In addition to the ones so far classified, its estimated that there may be hundreds to thousands of additional coronaviruses residing in bats alone. Since they became a focus of attention, we also know that in many areas of rural China, we can detect antibodies to infections going back decades. Without some sort of database to compare Sars Cov-2 it's all speculation really, and it's likely to remain so, this is often the case in spillover infections. You also have to consider that the way in which the virus uses the ACE2 receptor in itself doesn't mean a great deal, this receptor with minor variations is common in mammals and the process of transmission and infection is far more complex than simply considering the binding site.
There are labs all over the world working with viruses and in fact now, many more working with unclassified viruses and this may often involve culturing them, but there is a great deal to find out and this work is focussed on specific outcomes. Generally if a virus did escape it would be the same virus that had been collected in the wild, there are probably far more virus escaping from us just walking around.
Personally I actually doubt that we will ever get a clear answer as to this viruses origins, these little bundles of joy are masters of change, they do it all the time, we have a lot of catching up to do.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7489918/

 

[russ_watters]

Anyone have a revised opinion of zoonotic vs lab.

To be more complete about the inference of lab it is that there was an organism found in nature with virus characteristics that was then induced in some artificial fashion in a lab to emerge as the Covid virus. Would think this would take years to do.

With more opinion swaying toward lab, the real area of interest is not whether the Covid virus was influenced in a lab but how it was done.

They blinded me with science.

This isn't acceptable - it sounds more like conspiracy theory than science. You must provide reputable sources for these claims. Looking back over the thread, there was too much lenience regarding similar past claims.

 

[jim mcnamara]

Thread locked.