Begin at the Beginning: The Malayan Pangolin Hypothesis

[McCamy Taylor]

Last edited Fri Mar 27, 2020, 04:17 AM - Edit history (1)

How do you begin at the beginning if you do not know where the beginning is? You speculate. You check various bits of data, cross reference them with other bits of data and then you come up with a hypothesis. After doing the research for this, I am convinced that COVID 19 is the result of our mismanagement of tropical forests. I also have a hunch that the tropical forests in question might be on Borneo (but a hunch is not a hypothesis)

Here is a quick refresher on the origins of RNA viruses that infect humans:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157708/

An important point: the ability to infect humans and the ability to be transmitted from human to human are two separate things, i.e. going from Level 2 to Level 3. There are whole lot more Level 2 than Level 3. And there is a stage beyond Level 3. It is not enough to simply be transmissible human to human. You have to have a perfect situation to transmit enough of the virus if you want to reach Level 4—and epidemic.

“Level 4 corresponds to the ability to transmit sufficiently well that the virus can invade human populations, causing epidemics and/or establishing itself as an endemic human pathogen. In epidemiological parlance this corresponds to the condition that R0 is greater than one within the human population, where R0 is the basic reproduction number, defined as the number of secondary cases generated by a single primary case introduced into a large population of naïve hosts. In contrast, Level 3 viruses have an R0 of less than one in humans, which implies that although self-limiting outbreaks are possible, the infection cannot “take off” and cause a major epidemic. Although R0 is partly determined by the transmissibility of the virus, it is also a function of the behaviour and demography of the human host population; for example, changes in living conditions, travel patterns, sexual behaviour (for sexually-transmitted viruses) can all greatly influence R0. This argument is reflected in the term “crowd diseases”, which implies that certain human viruses (and other pathogens) could only become established once critical host population densities had been reached [10]. Our best estimate is that there are 47 Level 4 RNA virus species in humans “

Since labs all across the world including China typically retain serum and tissue samples of people who have died of unknown causes, it ought to be possible to trace the current COVID 19 epidemic back to a source. Maybe it killed someone before the first known victim who shopped in the Wuhan Seafood Market where more than just seafood was sold

https://www.bloomberg.com/news/articles/2020-01-14/wuhan-doctors-tried-to-save-pneumonia-patient-with-life-support

Note that since there is a mild form of the infection, the victim did not necessarily catch it from a freshly butchered animal. It could have easily come from a human vendor of that animal.Or this could not have anything to do with the meat being sold in Wuhan Market. But, I have to start somewhere, I will assume that it does.

We have a newly identified disease-causing RNA virus, most likely it was a zoonosis before it got into our populations (since that where most RNA viruses come from). If someone died from it, the evidence is there, waiting to be uncovered in a lab.

If the first case did not die--say that person was basically healthy and brought a few sniffles home them to Wuhan China from who knows where---then things will get more difficult. How do you track down a virus that left no foot prints until it had passed from two to three to more people before leaving evidence of its passage (e.g. a fatality)?

Since this virus has already been well primed to infect humans, then it is likely that it already exists somewhere in the world as a well-controlled human (or, less likely simian) viral pathogen—much like the common cold is for most of us. People in that isolated part of the world get COVID 19 and get over it in childhood. But if you do not get your immunity at the right time, it can become deadly. (Has anyone seen how sick people get when they catch measles as adults, even young adults?) This implies that it exists in the wild—somewhere.

Bats are speculated to be the world’s biggest carrier of coronavirus. However, the disease is not thought to jump straight from bat to humans. Instead there is likely to be an intermediate host. It has been reported that COVID 19 resembles a virus found in the diseased lungs of a pair of Malayan pangolins. It is not a full match suggesting that the disease did not jump straight from the two dead pangolins to humans. Since pangolins are eaten and used for medicine in China, a logical step to look would be those who make a living hunting Malayan pangolin.

https://www.cell.com/pb-assets/journals/research/current-biology/CURBIO_CURRENT-BIOLOGY-D-20-00299-compressed.pdf

Or, if you go back to the first article, look for simians in the region where the region where the Malayan pangolins are naturally found since

“Although humans share their RNA viruses with many different mammalian taxa, those from other primates appear most likely to be capable of spreading through human populations”

We do no know that COVID 19 came from Malayan pangolin. But say it does. South Asian and South East Asian Pangolins are endangered. Their forest habits are being cut down. Humans poach them for food and medicine and their scales. According to this recent article, South Asian and Southeast Asian pangolins are now the most trafficked mammals around the world. Local bow and hunter hunters in some region have been squeezed out by poachers who have come in armed with rifles, driving on new roads through forests that have been newly leveled. A perfect storm if there is a well-controlled animal origin RNA virus to which the locals have adapted. So yeah, the timing is right.

https://www.jstor.org/stable/26393255?seq=1#metadata_info_tab_contents

More on how clearing tropical forest land is associated with increased rates of viral disease. Note the ten times higher viral diversity in coronaviruses in bats in tropical forest which have been highly disturbed.

https://pmac2018.com/uploads/poster/A11-ZAMBRANA-TORRELIO-5600.pdf

Different coronaviruses have been show capable of exchanging their RNA in vivo.

“RNA-RNA recombination between different strains of the murine coronavirus mouse hepatitis virus (MHV) occurs at a very high frequency in tissue culture. To demonstrate that RNA recombination may play a role in the evolution and pathogenesis of coronaviruses, we sought to determine whether MHV recombination could occur during replication in the animal host of the virus. By using two selectable markers, i.e., temperature sensitivity and monoclonal antibody neutralization, we isolated several recombinant viruses from the brains of mice infected with two different strains of MHV. The recombination frequency was very high, and recombination occurred at multiple sites on the viral RNA genome. This finding suggests that RNA-RNA recombination may play a significant role in natural evolution and neuropathogenesis of coronaviruses.”

Meaning cleared tropical forest which is also being targeted by poachers might have two things going for it if your goal is accelerated mutation and spread of a new coronavirus pathogen.
https://jvi.asm.org/content/62/5/1810.short

If the Malayan pangolin is the (original source) of COVID 19, then checking the indigenous populations of the areas where the pangolin live and have been hunted by locals might detect antibodies to the virus. Or turn up local remedies that have been used to limit its virulence. And checking for mysterious illness and death among those who poach pangolin and then carry them back to China might also be fruitful.

Oh, and about the simian intermediary hypothesis. The proboscis monkey is on the top ten list of most desirable poached wild animals in China—along with the pangolin. So be sure to check Borneo where both proboscis monkeys and pangolin live--and are threatened with extinction.

https://www.borneoecotours.com/blog/the-disappearing-wildlife-of-borneo/

But watch out. Heavy deforestation in Borneo is giving rise to a bunch of disease.

Mosquitoes are not the only carriers of pathogens from the wild to humans. Bats, primates, and even snails can carry disease, and transmission dynamics change for all of these species following forest clearing, often creating a much greater threat to people.

https://e360.yale.edu/features/how_forest_loss_is_leading_to_a_rise_in_human_disease_malaria_zika_climate_change

And being an island with some pretty unique animals (like the proboscus monkey) Borneo would have had a very long time of relative isolation in order to cook up an RNA virus that we, the rest of the world, are not prepared for.

Edit. The video tagged on YouTube is not the Wuhan Seafood Market as was posted below. I found several different videos online all claiming to be The Wuhan Market but which were actually filmed elsewhere. Films taken in Wuhan are very brief and show little detail so maybe filming was discouraged. But there are stories confirming that bats, pangolin and other animals were sold there.

[lunasun]

1. The video is of a market in Cameroon. Maybe you posted the wrong video?

Cameroon is in central Africa not near Borneo or Malay - SW Asia

[McCamy Taylor]

3. Hmm . It was tagged as the Wuhan Market.

Will do another search. You are correct. Thanks. Have edited post.

[lunasun]

7. Thank you for editing

[peacebuzzard]

2. this helps ponder the magnitude of this new reality

and as a side thought I heard a commentary on a report from Brazil that the corvid19 infecting that country has mutated from the original structure. The numbers from Brazil are rapidly climbing from double digits on 14 March to 2433 today. That is, reported cases. Which, we all know under-reporting and no testing is a bigger problem there than here.

[intrepidity]

4. Interesting reading, thanks for posting

As for a local indigenous population with immunity, I wonder about an isolated tribe, namely the one on that island that killed the missionary a few years back--that uncontacted tribe that is protected by law (and arrows, turns out) from contact. That sort of scenario makes for a great film plot (or reality, as the case may be).

[Meowmee]

5. The first known case was on Nov 17, 2019 and had no known connection to the market

there were some others as well....



“A 55-year-old individual from Hubei province in China may have been the first person to have contracted COVID-19, the disease caused by the new coronavirus spreading across the globe. That case dates back to Nov. 17, 2019, according to the South Morning China Post.

That's more than a month earlier than doctors noted cases in Wuhan, China, which is in Hubei province, at the end of December 2019. At the time, authorities suspected the virus stemmed from something sold at a wet market in the city. However, it's now clear that early in what is now a pandemic, some infected people had no connection to the market. That included one of the earliest cases from Dec. 1, 2019 in an individual who had no link to that seafood market, researchers reported Jan. 20 in the journal The Lancet.”


https://www.livescience.com/first-case-coronavirus-found.html

[McCamy Taylor]

8. Thanks!

Even with this Nov. 17 case identified, doctors can't be certain the individual is "patient zero," or the very first individual to have been infected with SARS-CoV-2, and there's a chance even earlier cases will be found, the SCMP reported.

[superpatriotman]

6. Kick

Deforestation, poaching, wet markets, magical medicine and many other things are all possible nurseries for new, deadly RNA virus.

The autopsy of Covid-19 will be an interesting look at how the planet is fighting back harder than ever.

[McCamy Taylor]

10. I hope we will learn but I am afraid we won't

And all the tropical forests will be leveled to make more disposable chopsticks, TP and to kill animal to use as "medicine" for all the new viruses we unleash in a spiraling circle of doom.

[intrepidity]

9. Nature Medicine paper: The proximal origin of SARS-CoV-2

https://www.nature.com/articles/s41591-020-0820-9

[McCamy Taylor]

12. Great link! Thanks!

For a precursor virus to acquire both the polybasic cleavage site and mutations in the spike protein suitable for binding to human ACE2, an animal host would probably have to have a high population density (to allow natural selection to proceed efficiently) and an ACE2-encoding gene that is similar to the human ortholog.

Here is a study that reports that the ACE2 receptors of humans and other animals tested (including other primates) are very diverse.

https://figshare.com/articles/The_diverse_of_ACE2_receptor_made_the_inference_of_host_Difficult_copy_pdf/11796642

Our results showed that the viral binding sites in the ACE2 receptors are diverse between human and other animal species. In contrast, the protein sequences of the MERS receptor CD26 have only one amino acid difference between camel and human (camel V, human T). These analysis indicates complexity of the development of the infection mechanism of 2019-nCov and challenges in identifying the intermediate host(s) solely by bioinformatics approaches.

[llmart]

11. I believe PBS is televising a show on pangolins.

It's supposed to be very interesting, though I haven't had time to watch it yet. I will probably watch it tonight.

[McCamy Taylor]

13. Pangolin