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Pangolins, link to SARS and Corona viruses

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Old Thursday 26th March 2020, 16:27   #1
andyadcock
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Pangolins, link to SARS and Corona viruses

Not sure where this thread belongs, mods can move it if they identify a more appropriate arena.

'The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of novel coronaviruses and should be removed from wet markets to prevent zoonotic transmission.'

https://www.nature.com/articles/s41586-020-2169-0
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Old Thursday 26th March 2020, 16:48   #2
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Is this a new story or just recirculation of the story that emerged when the virus was first revealed in China?

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Old Thursday 26th March 2020, 17:09   #3
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Is this a new story or just recirculation of the story that emerged when the virus was first revealed in China?

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It's dated today if that means anything?

'Published: 26 March 2020'
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Old Thursday 26th March 2020, 17:17   #4
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It's dated today if that means anything?

'Published: 26 March 2020'
Data from earlier then: looks like the story leaked well ahead of the paper.

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Old Thursday 26th March 2020, 17:23   #5
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It is a new article but the thoughts and science have been circulating for a while, I think. It’s been thought pangolins could be a vector for SARS-Cov2 since they are known hosts of other similar SARS-like coronaviruses but I’m not sure that’s been verified yet. (I can only see an abstract).

As to whether pangolins should be removed from wet markets, yes absolutely, (along with wild birds who are also hosts and vectors of avian influenza viruses and possibly the source of the next pandemic!) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068632/

https://www.nationalreview.com/2020/...rkets-must-go/

However, whether or not pangolins were vectors for this coronavirus or any other zoonotic-human pathogen - they are CRITICALLY ENDANGERED and should not be traded at all

https://www.iucn.org/news/secretaria...n-conservation

(On a personal note, I find wet markets abhorrent - wild and domestic animals are kept in excruciating inhumane conditions, many of which are injured and in pain from rough handling, until they are slaughtered - often on site)

(perhaps the conservation thread as an alternative? ‘critically endangered pangolins link to SARs-Cov2’ etc
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Old Thursday 26th March 2020, 18:25   #6
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In terms of publication, this is a complicated story. 3 other groups have done phylogenetic analysis of SARS CoV 2 with public domain sequences including a single pangolin virus genome.

Probably the easiest to read is this one

https://www.biorxiv.org/content/10.1....full.pdf+html.

Anyway they all show the same thing; SARS-COV-2 clusters with 2 sequences, the horseshoe bat virus RaTG13, and the pangolin virus. The key thing is that although over most of the genome SARS-COV-2 is very similar to the bat virus, in one short but functionally important stretch, encoding the receptor binding domain (RBD) it is much more similar to the pangolin virus.

One theory is therefore that the history of SARS-COV-2 involves a recombination event between a pangolin virus and a virus from another species. All SARS Coronaviruses originate in horseshoe bats but it’s plausible a 3rd host is involved e.g. virus 1 jumps from bats to pangolins, virus 2 jumps from bats to mammal species x, one individual pangolin or mammal x is simultaneously infected with viruses 1 and 2, which recombine to form a SARS-COV-2 type virus that then jumps to humans.

Anyway, this new paper adds a load of new pangolin sequences into the mix but reaches the same conclusion; they all cluster with SARS-COV-2 but less closely than the bat virus, and a couple have the SARS-COV-2 type RBD.

Cheers

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Old Friday 27th March 2020, 10:19   #7
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Do those Pangolin/Bat/etc slaughterers learn anything from this? They sure do not! Next pandemic, welcome...
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Old Friday 27th March 2020, 10:32   #8
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Do those Pangolin/Bat/etc slaughterers learn anything from this? They sure do not! Next pandemic, welcome...
You forgot to add dogs, primates, snakes and other assorted repiles.
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Old Friday 27th March 2020, 12:20   #9
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In terms of publication, this is a complicated story. 3 other groups have done phylogenetic analysis of SARS CoV 2 with public domain sequences including a single pangolin virus genome.

Probably the easiest to read is this one

https://www.biorxiv.org/content/10.1....full.pdf+html.

Anyway they all show the same thing; SARS-COV-2 clusters with 2 sequences, the horseshoe bat virus RaTG13, and the pangolin virus. The key thing is that although over most of the genome SARS-COV-2 is very similar to the bat virus, in one short but functionally important stretch, encoding the receptor binding domain (RBD) it is much more similar to the pangolin virus.

One theory is therefore that the history of SARS-COV-2 involves a recombination event between a pangolin virus and a virus from another species. All SARS Coronaviruses originate in horseshoe bats but it’s plausible a 3rd host is involved e.g. virus 1 jumps from bats to pangolins, virus 2 jumps from bats to mammal species x, one individual pangolin or mammal x is simultaneously infected with viruses 1 and 2, which recombine to form a SARS-COV-2 type virus that then jumps to humans.

Anyway, this new paper adds a load of new pangolin sequences into the mix but reaches the same conclusion; they all cluster with SARS-COV-2 but less closely than the bat virus, and a couple have the SARS-COV-2 type RBD.

Cheers

James
The number of coincidences required sounds like something much more likely to happen in a lab than the natural world: and for the species jump to be as effective in the new host (hom sap) as it is, looks very much like deliberate weaponisation.

Add that to an amoral totalitarian government that first jails a bloke blowing the whistle (to give the virus time to get out of the country) and then uses its infinite powers to squash it in-country, while getting its citizens abroad to ensure modelling of the pandemic is screwed up, then closes its borders to keep its biological first-strike against the countries clamping on its habitual lawlessness in industry, trade and international law especially in the nearby seas, out of its own territory.... looking forward to the novel of this.

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Old Friday 27th March 2020, 13:28   #10
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No need to switch to conspiracy theories. Normally yes, the viruses jumping hosts would be rare events, but given the number of animals that pass through these markets and degree of crowding and poor sanitation, even a rare event becomes inevitable.
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Old Friday 27th March 2020, 15:28   #11
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The number of coincidences required sounds like something much more likely to happen in a lab than the natural world: and for the species jump to be as effective in the new host (hom sap) as it is, looks very much like deliberate weaponisation.
I guess everyone is entitled to their opinion however.....

I doubt you will find more than 1 in 100,000 molecular virologists (like me) who agree with you. I just basically described the evolution of every zoonotic virus in history. The fact these types of events are rare explains why viral pandemics on this scale are not constantly occurring. Just imagine for a moment how many millions of different strains of viruses are currently circulating amongst the tens of thousands of species of warm blooded animals on the planets. Genetic drift, recombination, zoonosis etc. is a simple fact of viral life.

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Old Friday 27th March 2020, 15:32   #12
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No need to switch to conspiracy theories. Normally yes, the viruses jumping hosts would be rare events, but given the number of animals that pass through these markets and degree of crowding and poor sanitation, even a rare event becomes inevitable.
Maybe, but this is several rare events combined, including some for which explanations haven't even been attempted yet. If I remember my basic probability, when you start going "and - and - and - and" things get astronomically unlikely by random chance really quickly. And there's the behaviour of the Chinese government since the start of the business to explain, as well... I should think a number of people whose job titles end with "Service" or "Agency" are looking at this.

Anyway, who's switching?

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Old Friday 27th March 2020, 15:36   #13
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Such a conspiracy might occur to anyone, but it's really no better than imagining the US military planted the vrus in Wuhan. (I even briefly wondered whether that doctor was killed, but the viral load he got was surely sufficient.) This doesn't really work to China's advantage, and creates a huge challenge for the leadership. Prosperity is highly interdependent, and it's the crucial carrot they've been dangling to the Chinese people for decades now. I hope they will actually crack down on the wildlife market now, particularly bats. (And that African countries with bushmeat issues will also.)
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Old Friday 27th March 2020, 17:15   #14
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I think that the main reason why people are sceptical towards natural explanation is the lack of comprehension of the sheer scale involved in the evolution of the viruses. Just for the scale, the average human body has some 40 trillion cells, that's 4 and 13 zeros. That's why life is capable of creating all these extremely unlikely things: it gets an unfathomable number of tries. Most of mutations, recombinations or species jumps are an utter failure. Once in a while, the random combination of genetic sequences does exactly the right thing and starts spreading.

I mean, how likely it is that something as absurd as a birdwatcher evolves in the Universe and yet here we are!
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Old Friday 27th March 2020, 17:41   #15
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Such a conspiracy might occur to anyone, but it's really no better than imagining the US military planted the vrus in Wuhan. (I even briefly wondered whether that doctor was killed, but the viral load he got was surely sufficient.) This doesn't really work to China's advantage
Yes, but how easy to let him out of jail and follow his natural inclination to try to save people, with inevitable results.... plausible deniability is the hallmark of this right down the line. Meanwhile they've minimised the effect on them while effete Western democracies cripple their economies for years to come (leaving them no spare funds for Defence projects) while China continues taking over the South China Sea etc, etc…. You might not think it works to their advantage, but do they?

Like the Lambeth Poisoners - Yeah, they done it. Yeah.

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Old Friday 27th March 2020, 17:43   #16
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I mean, how likely it is that something as absurd as a birdwatcher evolves in the Universe and yet here we are!
There really does need to be a like button.
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Old Friday 27th March 2020, 17:48   #17
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Maybe, but this is several rare events combined, including some for which explanations haven't even been attempted yet. If I remember my basic probability, when you start going "and - and - and - and" things get astronomically unlikely by random chance really quickly.
You must do your nut when someone wins the lottery *every single week*

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Old Friday 27th March 2020, 18:04   #18
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In terms of publication, this is a complicated story. 3 other groups have done phylogenetic analysis of SARS CoV 2 with public domain sequences including a single pangolin virus genome.

Probably the easiest to read is this one
https://www.biorxiv.org/content/10.1....full.pdf+html.

James
Thanks for this James.

I have a question, is there a possibility that the ‘novel’ coronavirus is actually from a milder mutated form of SARS or even MERS - and so had already made the ‘jump’ to humans without the help of an interim third host - or (ok 2 questions ) could another human coronavirus be the missing link - (ie a ‘piggy-back’ mutation) rather than eg pangolins. If coronaviruses can leapfrog using other viruses, given the number of cold viruses circulating that could be a worrisome thought?

ps some reading for John
https://www.thetrumpet.com/22131-chi...-tube-pandemic
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Old Friday 27th March 2020, 18:04   #19
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You must do your nut when someone wins the lottery *every single week*

James
Well, (a) they don't and (b) I'm blissfully unaware of the odds vs the no. of entries. But feel free to tell me if you know.

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Old Friday 27th March 2020, 19:34   #20
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All conservation organizations worldwide should partner with health organizations worldwide and call for and enforce the ban of killing, butchering, trading and eating wild animals in East Asia and Africa.

Such a ban will not be followed in remote areas. There people will probably eat wildlife and sometimes die from viruses without knowing why. However stopping the trade of bush meat to towns and cities is enforceable and would save many species. China apparently made the ban, but only temporary. Then is Indonesia, Vietnam, and eating monkeys in Africa which gave humanity AIDS.

About the viruses: viruses of wild animals are almost unknown. The virus could potentially come from a related species of bat or another pangolin population. However pangolins and bats have normally little to do in the wild. They don't eat each other. Their viruses could recombine most likely when both were brought to the market by humans. Here the industrial trade of wildlife is a perfect breeding ground for viruses: many wild animal species brought together, butchered together in unsanitary conditions, in crowded places with lots of sick people passing by, in big population centers with lots of human travel. It is like a production line of biological weapons.

There are probably 100s of unknown viruses circulating in wild animals in Asia, many of which can become deadly pandemies if they jumped to humans. Bat viruses seem especially dangerous. It is probably because bats live in crowded colonies so their pathogens tend to be very virulent.Then are intermediate vectors which eat bats or share roosts with bats, like small carnivores and snakes. For me the biggest point is not tracing the particular route of this particular virus, but cutting the mechanism creating further diseases.
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Old Friday 27th March 2020, 19:48   #21
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Thanks for this James.

I have a question, is there a possibility that the ‘novel’ coronavirus is actually from a milder mutated form of SARS or even MERS - and so had already made the ‘jump’ to humans without the help of an interim third host - or (ok 2 questions ) could another human coronavirus be the missing link - (ie a ‘piggy-back’ mutation) rather than eg pangolins. If coronaviruses can leapfrog using other viruses, given the number of cold viruses circulating that could be a worrisome thought?

ps some reading for John
https://www.thetrumpet.com/22131-chi...-tube-pandemic
I’m not quite sure I understand the questions, but I don’t think there is any possibility of the involvement of any non-SARS coronaviruses (eg MERS) let alone non-coronaviruses. And no reason to think SARS-CoV-1 was involved in any way. Basically SARS-CoV-2 is very similar to the horseshoe bat SARS strain RaTG13 and where it isn’t it’s mostly very similar to the pangolin CoV. So it’s probably a cross between two pretty closely related type 2 SARS corona viruses. The only unique element is the furin cleavage site which could have evolved through natural selection. Remember that probably the original leaps from bats to the intermediate hosts probably occurred decades ago.
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Old Saturday 28th March 2020, 01:47   #22
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It is probably because bats live in crowded colonies so their pathogens tend to be very virulent.
What I've read is that it's actually insects that carry a lot of virulent pathogens from a variety of sources, and bats eat a variety of insects. (I just checked, the horseshoe bat in question is indeed insectivorous.) So they've evolved a rather special metabolism that's very tolerant/resistant to that... but we have not. Perhaps the worst possible thing one could eat.
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Old Saturday 28th March 2020, 10:41   #23
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Nice article on bats and viruses here
https://www.sciencedaily.com/release...0210144854.htm

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Old Saturday 28th March 2020, 18:41   #24
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This is a good article on the complexity of the issues:
https://www.theguardian.com/world/20...or-coronavirus
See also this article that it references on wet markets:
https://theconversation.com/why-shut...mistake-130625
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