Coronaviruses in Malayan pangolins

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Summary:

Why were Malayan pangolins tested for China Virus

Main Question or Discussion Point

" Here, we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. "

How is it that Malayan pangolins would be tested at all for the China Virus?

Is it common practice to examine any smuggled animal for coronaviruses?

My guess would be that if there was a large number of animals dying in the wild that samples would be examined. But this does not seem to be the case here.

***The most important find here is that while the anteater coronavirus codes for protein/s that produce the binding spike that makes the China Virus more contagious, the match in the coronavirus found in pangolins to the China Virus found in humans is only 90%.

There is a missing link. It is not bats. It is not pangolins. It is ????

It is as if an anteater bite a bat and then a human ate or was bit by said bat. This is the most congruent explanation being given outside of the China Virus was manufactured in an indirect way in a Chinese virus lab.
 

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  • #2
Klystron
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{...snip}
There is a missing link. It is not bats. It is not pangolins. It is ????

It is as if an anteater bite a bat and then a human ate or was bit by said bat. This is the most congruent explanation being given outside of the China Virus was manufactured in an indirect way in a Chinese virus lab.
No biting required. Bats commonly relieve themselves before taking flight. Pangolins root beneath bat roosts for edibles, offering transmission either directly or through species such as ants drawn to the feast left by bats.
 
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In this article:

https://www.sciencealert.com/more-e...y-have-passed-coronavirus-from-bats-to-humans

they suggest pangolins for a number of reason. One was that pangolins were sold in the wet market and are valued for chinese traditional medicine. They know bats are the breeding ground for these corona viruses And now suspect that the pangolin is the intermediate host having been infected by bats at one point and then evolving the virus to its near present form that jumped to humans.

How it got from bats to pangolins is likely due to bat guano being ingested in their search for food as I don’t think pangolins actually eat bats.

https://www.dw.com/en/coronavirus-from-bats-to-pangolins-how-do-viruses-reach-us/a-52291570
 
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Your comments still do not suggest why the pangolins would be tested in the first place?

Here is the info we have

1. Bat virus is 99% close to human China virus.
2. Problem - Bat virus does not have spiked protein found in human China virus.
3. Where did the spike protein in the China virus come from??

The offered answered is pangoloin.

This would mean that the pangoloin (90%) would somehow have to infect the bat (99%) and then infect humans.

How probable is this?

They can find all of the above, bat anteater, but not the final link between the China virus and humans?

To me, it suggests that some help intervened.
 
  • #5
jim mcnamara
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You help everyone by actually citing where you read this.

First off there are many different coronaviruses in bats - 300+ species is a gross estimate for example.

This explains what a zoonotic is the context of what you asked.
Hint: finding wild [species name] and testing for coronavirus or whatever is a way to find out the ultimate origin of a pathogen of interest.
This is a reasonable citation for what I am saying:
https://www.ijbs.com/v16p1686.pdf

Plus your bite scenario is not the way it works, please stop making stuff up -last notice. Just to give some thoughts, this is one known way new human influenza virus varieties get into humans.

Fecal transfer:
Wild mallards and other duck species harbor many different influenza viruses. Traditional chinese farms have a pond for food fish and for their domestic ducks and geese. Wild infected ducks visit the pond. They poop in the pond. The domestic duck dabble (duck their heads underwater looking for food to eat). They get the virus. Via the poop. The domestic ducks spend the night bedding down next to the pig pen. Pigs snuffle around and because rain washes the duck droppings into the pig pen -- pigs get the new improved influenza virus. People clean the pig pens, getting the "pig-ified" version of the virus on their hands and clothing. They eat a snack. Voila the pig virus version is a human. If it is sufficiently contagious and does well in the new host other people get it. And off we go.

There are other known vectors like insects, arthropods, mammals. Smallpox came from cows for example, Vibro cholerae is endemic on Asiatic wild shellfish and may become endemic in domestic pigs as well. It causes cholera.

Domestication of animals is a really big source of human pathogens.

Eating foods raw is also a great way to get pathogens into humans as well. i.e, rare beef steak, steak tartare, eggnog, pastoral mushroom collecting & eating... the list goes on.
https://en.wikipedia.org/wiki/Steak_tartare

Are we good on this...?
 
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  • #6
Ygggdrasil
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How is it that Malayan pangolins would be tested at all for the China Virus?
Here's what one group that reported the pangolin link wrote in their paper:
As coronaviruses are common in mammals and birds9, we used the whole genome sequence of 2019-nCoV (WHCV; GenBank accession No. MN908947) in a Blast search of SARS-like CoV sequences in all available mammalian and avian viromic, metagenomic, and transcriptomic data. This led to the identification of 34 highly related contigs in a set of pangolin viral metagenomes (Table S1). Therefore, we have focused our subsequent search of SARSr-CoV in this wild animal.

We obtained the lung tissues from four Chinese pangolins (Manis pentadactyla) and 25 Malayan pangolins (Manis javanica) that were collected from a wildlife rescue center during March-December 2019, and analyzed for SARSr-CoV using RT-PCR with primers targeting a conservative region of β CoV.
https://www.biorxiv.org/content/10.1101/2020.02.17.951335v1.full

In other words, they downloaded the RNA sequence of the SARS-CoV-2 (the "China virus") from a database, and perfomed a BLAST search (the equivalent of a Google search for people working in bioinformatics) against a database of published sequences. They saw that the SARS-CoV-2 virus had similarity to SARS-like coronaviruses that had previously been identified in pangolin species, so they sought out some pangolin samples to do further testing.

Why were there pangolin coronavirus samples in the database? In recent years, a new field called "metagenomics" has become popular. In the past 5-10 years, DNA sequencing has become cheap enough that it is not too expensive to take all sorts of samples, sequence the RNA and/or DNA in the sample, and see what new things come out. Researchers have sequenced human feces to figure out the microbes that reside in the human gut, sailed the oceans to sequence the diversity of oceanic microorganisms, dug around hydrothermal vents to seek out the evolutionary ancestors of complex life, and most relevant to this thread, sought out the viruses living in wild animals through efforts like the Global Virome Project. Somewhere along the line, scientists performed metagenomic sequencing of pangolins to find what viruses they have, published their results, and deposited their data in the databases (likely to little fanfare at the time). By design, these metagenomic studies have enabled researchers to quickly compare the SARS-CoV-2 RNA sequence to the large number of wild coronaviruses in these databases to quickly narrow down the likely species of origin to study further.

In other words, scientists know that new, potentially dangerous diseases can often spring from animal-to-human transmission. Working through efforts like the Global Virome Project, they have been building the infrastructure to allow society to help quickly identify the origin of any new pandemic virus. These efforts show why funding basic science projects (like studying the diversity of viruses out in the wild) is important.
 
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  • #7
phyzguy
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***The most important find here is that while the anteater coronavirus codes for protein/s that produce the binding spike that makes the China Virus more contagious, the match in the coronavirus found in pangolins to the China Virus found in humans is only 90%.
How good the match is to the whole genome of the pangolin coronavirus is not relevant. A small piece of the genome of the pangolin coronavirus recombined with the genome of the bat coronavirus to produce the SARS-COV-2 virus. The sequence match to this small piece is very high. This link explains it in detail and shows the relevant sequences, and also says that according to virologists, who are experts in this area, the genetic sequence is consistent with natural selection, and is not consistent with having been produced in a lab.
 
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  • #8
atyy
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is not consistent with having been produced in a lab.
This is not known for sure (as discussed in the paper below, see the section "Selection during passage"). While a laboratory origin is unlikely, excluding it at this stage is premature.

https://www.nature.com/articles/s41591-020-0820-9
"The genomic features described here may explain in part the infectiousness and transmissibility of SARS-CoV-2 in humans. Although the evidence shows that SARS-CoV-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. "
 
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  • #9
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The story being offered about the China Virus is that there may be a chain of transmission that goes from bat to pangolin to human. The suspect part of this etiology is the pangolin to human. The pangolin sequence is only a 90% match to the China Virus found in humans. The pangolin's only redeeming characteristic is that it codes for a protein/s that produces a spike that makes its virus more prolific. However, again, the pangolin virus is only a 90 % match to the human China Virus - everyone agrees that something is missing - actually a lot is missing.

As an aside the pangolin is an endangered species alluding to a relatively small population that one would suspect would not mutate much.

The pattern being offered in the literature is bat//pangolin//

A better pattern seems to be pangolin//altered bat - bat virus with pangolin spike//human. The reasoning being that the bat virus is 96% match to the human China Virus. Only a small change, the spike, would have to be added.

Mentioned by phyzguy

The bat to pangolin to human

" is consistent with natural selection, and is not consistent with having been produced in a lab."

I did not watch the +1 hr video, however

1. The required changes may be possible via natural selection but the 1. pangolin - 2.bat - sequence is highly improbable.
2. No bat has been found with this combination?
3. I have read some of the literature on not consistent with being produced in a lab and it is not definitive. The current China Virus might not exhibit characteristics that would usually be produced in a lab but that does not mean it was not produced in a lab.

Recap

1. Bat then pangolin then China virus almost impossible
2. Pangolin then bat then China virus highly improbable

3. The China Virus does not have the characteristics that one would suspect in a lab produced virus but that in no way establishes that the virus was not produced in a lab.

4. What is needed to resolve the question of nature vs lab is an animal found in the Wuhan area that (perhaps needs to be something that is eaten. also suspect it would be a mammal.) has a virus that codes for the spike and is a 99% match to the human China Virus. It seems very suspect that this elusive creature has yet to be found. It would literally be worth millions if not billions of dollars.
 
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  • #10
jim mcnamara
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As an aside the pangolin is an endangered species alluding to a relatively small population that one would suspect would not mutate much.
No. Exactly the opposite:
Small isolated populations are more likely to mutate and possibly evolve into new species. Due to lack of gene flow from nearby populations, swamping local changes.

Theodosius Dobzhansky first posited that (geographic) isolation of populations led to speciation.

Theoretical, applied and observed examples:
E. O. Wilson & Robert H MacArthur (1967) 'Theory of Island Biogeography'
Richard Forman & Michael Godron (1986) 'Landscape Ecology' -- Concept of forest islands surrounded by completely altered landscape.
https://en.wikipedia.org/wiki/Tepui example:

525px-Kukenan_Tepuy_at_Sunset.jpg
 
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  • #11
atyy
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The story being offered about the China Virus is that there may be a chain of transmission that goes from bat to pangolin to human. The suspect part of this etiology is the pangolin to human. The pangolin sequence is only a 90% match to the China Virus found in humans. The pangolin's only redeeming characteristic is that it codes for a protein/s that produces a spike that makes its virus more prolific. However, again, the pangolin virus is only a 90 % match to the human China Virus - everyone agrees that something is missing - actually a lot is missing.

As an aside the pangolin is an endangered species alluding to a relatively small population that one would suspect would not mutate much.
No, one of the possibilities being offered is that viruses closely related to the the bat and pangolin were simultaneously present in an intermediate host. In this intermediate host, since both viruses were simultaneously present, a transfer of genetic material between them would lead to a virus even more closely related to SARS-CoV-2 than either precursor.

Can several viruses be simultaneous present in a host? Yes. See "Coexistence of Different Coronaviruses or Other Viruses in Bats" in https://www.mdpi.com/1999-4915/11/3/210/htm.

4. What is needed to resolve the question of nature vs lab is an animal found in the Wuhan area that (perhaps needs to be something that is eaten. also suspect it would be a mammal.) has a virus that codes for the spike and is a 99% match to the human China Virus. It seems very suspect that this elusive creature has yet to be found. It would literally be worth millions if not billions of dollars.
No, it is not suspect, as the diversity of viruses in animals is vastly undersampled. For example, more than 10 years after SARS, there are discoveries of new virus types related to how SARS might have originated.
https://www.nature.com/articles/d41586-017-07766-9
https://doi.org/10.1371/journal.ppat.1006698
 
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  • #12
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Mea culpa

I did not state it very well but I was actually thinking about the conronavirus carried by the pangolin. Does that make any difference?
 
  • #13
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OK - we have an intermediate host. Do you think it would be a mammal and something that people in China eat and be around the Wuhan China area?
 
  • #14
atyy
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OK - we have an intermediate host. Do you think it would be a mammal and something that people in China eat and be around the Wuhan China area?
Yes, I think it would probably be a mammal that was present at or near Wuhan. I'm not sure about whether it has to be eaten by people in China, but that remains a possibility since the Huanan wet market as a source remains a (the?) major hypothesis. Best to keep an open mind at the moment and wait as more data emerges.
 
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  • #15
chemisttree
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In this article:
How it got from bats to pangolins is likely due to bat guano being ingested in their search for food as I don’t think pangolins actually eat bats.
For that to be true, the range for the horseshoe bat and the malayan pangolin would have to overlap. They don’t.
Greater Horseshoe Bat range
Malayan Pangolin range

This means that any bat+pangolin theory would require the interspecies coronavirus swapping happen while in human captivity.
 
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  • #16
Ygggdrasil
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For that to be true, the range for the horseshoe bat and the malayan pangolin would have to overlap. They don’t.
Greater Horseshoe Bat range
Malayan Pangolin range

This means that any bat+pangolin theory would require the interspecies coronavirus swapping happen while in human captivity.
Is the genetic analysis of the virus sufficient to narrow down its origins to the exact species?

My assumption is that we have only sampled a sparse subset of bat and pangolin coronaviruses, so while we may be able to say that parts of the virus originated from recombination between a coronavirus from some bat species and another coronavirus from some pangolin species, we don't have good enough data to narrow down the origins to the exact species.
 
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  • #17
chemisttree
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Is the genetic analysis of the virus sufficient to narrow down its origins to the exact species?

My assumption is that we have only sampled a sparse subset of bat and pangolin coronaviruses, so while we may be able to say that parts of the virus originated from recombination between a coronavirus from some bat species and another coronavirus from some pangolin species, we don't have good enough data to narrow down the origins to the exact species.
Good point. At least for now the only data we have for the pangolin facet to this story is exclusive to the malayan pangolin. The chinese pangolin was not found to have the appropriate genetic match. So if the pangolin should be included in any way, its the malayan pangolin.

If we are going to entertain the possibility of any given species based on the fact that the testing is sparse then why not include the Mexican Freetail Bat. And the Texas Armadillo!
 
  • #18
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I am sorry I am not well read or especially intelligent. I have offered many off the wall comments and some kind soul has always had a little time to humor me.

I especially want to give thanks to the tireless effort of @Ygggdrasil. He is an outstanding individual and if he would make it known what he would like to do, I suspect many of us could make that happen.

I have already been dinged for asking the wrong kind of questions or not supporting what I have to say with peer reviewed journal articles (not a big reader).

Although I do not always understand everything that others offer, I am getting better.

I APPRECIATE EVERYONE'S TIME AND EFFORT.

I am still having trouble understanding this diagram - https://www.nature.com/articles/s41591-020-0820-9/figures/1

I could guess at the G's,A's,C's, and T's - the other symbols are unknown to me.

What keeps blowing my mind is that we seem to have such detailed information but are unable to do much with it.

Any help with the diagram, and I do not care what it is I want to know everything, I would appreciate it.

Me more than All, but hopefully this discussion is beneficial to many.
 
  • #19
phyzguy
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What keeps blowing my mind is that we seem to have such detailed information but are unable to do much with it.
I don't know why you say this. The fact is that people are hard at work making vaccines based on this type of information. In fact, many types of vaccines have already been created. The problem is that it takes a long time to test the vaccines, make sure they are safe, make sure they are effective, and then ramp them up in volume. You can't just make a few billion doses, inject everyone in the world, and hope for the best.
 
  • #20
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Did you see the detail in the prior post. It had everything - everything. Knowing all of this how can you not make an effective vaccine?

Your answer is hiding a lot of the details that are needed to be accounted for.

Again we state that at best a vaccine would be 60% efficient.
 
  • #21
atyy
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I am still having trouble understanding this diagram - https://www.nature.com/articles/s41591-020-0820-9/figures/1

I could guess at the G's,A's,C's, and T's - the other symbols are unknown to me.

What keeps blowing my mind is that we seem to have such detailed information but are unable to do much with it.
The genetic sequence of the virus is used by many vaccine-making efforts. However, it is not sufficient to guarantee an effective vaccine, since the immune system recognizes the 3D configuration of various parts of the virus. When parts of the virus are generated using the genetic sequence for a vaccine, the 3D configuration of those parts in the vaccine may not sufficiently mimic their 3D configuration in the virus.

Also, it is not known exactly which parts of the virus (or which parts of the genetic sequence) are best for incorporating into a vaccine.

Those are some of the reasons we don't know how effective a vaccine is until it is tested in people.
 
  • #22
BillTre
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I could guess at the G's,A's,C's, and T's - the other symbols are unknown to me.
You should probably read an good introductory text on molecular biology.
Diagrams like this involve the use of symbols in diagrams like this represent many different molecular biology concepts: (nucleotide sequence, amino acid sequence, how different a.a. sequences form different 3D structures with different chemical properties in different areas, how splicing can modify the sequences made into proteins, how proteins end up in membranes). They are not trivial and explaining them in detail is beyond the rather short explanations that you could expect here.
You would get a better understanding if you start out learning the basic concepts before instead of blindly hypothesizing and repeatedly asking a bunch of poor questions here.
You can't successfully jump into the middle of a very complex subject without understanding the basics of it.
I don't know what are currently considered good books on this subject because I have been past that phase of my learning for many years. However, there are probably people on this forum who could help you in this matter.
It would be helpful to know how much biology, chemistry, and molecular biology you have had so you could build your knowledge from there.
 
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  • #23
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No progress since April has been made with respect to the origin of the Wuhan Virus. Mea culpa - I do not have the expertise but at least I am bringing up questions that if others reflect upon perhaps they can advance the discussion.

Still to date we have no confirmed source for the virus. Origin of virus has now faded as a question of interest.

Either

1. Occurred naturally
2. Influenced in some way

Naturally
Bat - because the prior coronavirus - (effects respiratory system) - was though to be bat - civet - human. i have not studied this linkage.
The problem with the bat as the origin of the Wuhan Virus is that while it is a 96% match with the current Wuhan Virus, it lacks the protein spike nucleotide that makes the Wuhan Virus more viral then its prior configurations. It does not produce the protein that gives the virus the shape to compromise the ACE2 cell surface. (RNA - protein - shape - infect ACE2)

Amazing, the malayan pangolin contains the the sequence for the spike protein but is only a 90 % match.

Something is missing.

No intermediate host with a > 96% match has been found in China.

This host should be a mammal, in China, that is in contact with humans.

A defense to this statement is that the sample set we have is very small with respect to what is manifest in nature. Meaning many mammals contain all kinds of viruses we know nothing about.

It is still unclear if the more logical candidate would be bat or pangolin. I would suspect if the host occurs in nature it would be bat. The only support I have for this is that less would need to be changed to make a bat a host for the virus.

I have found this article to provide interesting/accessible information -
https://cen.acs.org/biological-chem...novel-coronaviruss-29-proteins/98/web/2020/04

I still say that someone more astute then me can glean additional information on the source of the Wuhan virus from - https://www.nature.com/articles/s41591-020-0820-9/figures/1 My confusion here is that I thought that the Bat "virus" did not code for the spike protein. In this diagram is seems to imply that it does in some fashion.

It is unclear to me what information from the above is missing. You have the protein sequence for the Wuhan Virus in humans, bats??, and the pangolin. What is missing??

Origin

1. Occurred natural - bat - pangolin. What is the probability of this happening?
2. Influenced - How would one combine the bat - pangolin combination in a lab setting?

I do not find strong support that the current Yahun Virus originating in nature.
 
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  • #25
Laroxe
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I think one problem in understanding cross species transmission is that people seem to assume that the virus follows a linear path from one animal to an intermediate to a human (or other host). It is in fact far messier than that, its not unusual for a virus to infect an animal different from its original host and its entirely possible that a single strain of a virus might have been through several different hosts, maybe returning to the original one several times, picking up bits of genetic material as it goes. While this virus seems fairly stable these sort of events increase the opportunity to pick up variations in animals carrying several different strains. This can continue until the right mix arises more or less by chance, because this virus seems optimised for human transmission, the same strain might rapidly disappear from the original animals. This is what appears to have happened with SARS which couldn't maintain its transmission in humans, in the case of MERS each new outbreak is a new episode of the virus jumping species from camels.
 
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