“Darren, You Are the Father!” | China and the Study of Viral Origins

Bat SARSr-CoV Rp3 was obtained from R. sinicus, which is found in Guangxi province. From: A pneumonia outbreak associated with a new coronavirus of probable bat origin

When it comes to empirical claims, I have one main rule for me to consider giving them an ear: less rhetoric, more data. What this rule does is eliminate the wasting of what little precious time we have in this life speculating about something that may or may not be true.

However, one thing this pandemic has done for many is it created an illusion that we have more time given the drastic changes in our daily obligations. With that comes the “research” into why we have this pandemic in the first place, which in our desperate desires to return to our previous normal has many of us latching onto elaborate narratives they construct based on “investigative reports” that “expose” this thing or the other and blow our minds 0_o

The latest “revelation” making the rounds by some on social media is that the coronavirus causing COVID-19 was bioengineered in a lab in Wuhan, China. As in the usual lock-step-and-barrel, the case proving this claim being wildly shared doesn’t include references to genome sequences, research about coronaviruses in general, and this one in specific, or any empirical demonstration providing evidence supporting it.

What it does include are tracings of alleged connections and money exchanges between various notorious figures, coupled with some scientific-sounding jargon and vague references to “a paper in Nature” to make it sound credible, and a story captivating enough to draw the reader into a world of Treadstone but lacking the sufficient detail that would trigger the necessary rational skepticism to ask relevant questions.

For the sake of brevity, there are a couple of questions I’ll quickly deal with here:

Why China?

This is the exact question addressed under the heading “Why Study Bat Coronaviruses in China?” In a review paper published in the journal Viruses in March 201⁹¹. Their answer:

“Two bat CoVs caused outbreaks in China; it is thus urgent to study the reasons to avoid future outbreaks.

China is the third largest territory and is also the most populous nation in the world.

A vast homeland plus diverse climates bring about great biodiversity including that of bats and bat-borne viruses — most of the ICTV coronavirus species were named by Chinese scientists studying local bats or other mammals.

The majority of the CoVs can be found in China. Moreover, most of the bat hosts of these CoVs live near humans, potentially transmitting viruses to humans and livestock.

Chinese food culture maintains that live slaughtered animals are more nutritious, and this belief may enhance viral transmission.

It is generally believed that bat-borne CoVs will re-emerge to cause the next disease outbreak. In this regard, China is a likely hotspot.

The challenge is to predict when and where, so that we can try our best to prevent such outbreaks.”

I think this is straightforward enough it doesn’t warrant further explanatory commentary on my part.

Is this a hybrid virus?

This one is the juiciest source of musings generating traffic for “investigative” and “hard-hitting” articles, and let us not forget the couple of contrarian “experts” who are exposing the truth to all of us sheeple.

Cool Sheeple

A review paper published in Nature Reviews Microbiology in December 2018² summarized the current state of knowledge we had as of that time (close to 1.5 years ago) about the origin and evolution of the SARS and MERS coronaviruses. There’s a lot to go through in this paper but I’ll turn your attention to a passage under the heading “Animal origin and evolution of SARS-CoV” where the authors wrote:

“A 5-year longitudinal study revealed the coexistence of highly diverse SARSr-CoVs in bat populations in one cave of Yunnan province, China. This location is a diversity hot spot, and the SARSr-CoVs in this location contain all the genetic diversity found in other locations of China. Furthermore, the viral strains that exist in this one location contain all genetic elements that are needed to form SARS-CoV.

As no direct progenitor of SARS-CoV was found in bat populations despite 15 years of searching and as RNA recombination is frequent within coronaviruses, it is highly likely that SARS-CoV newly emerged through recombination of bat SARSr-CoVs in this or other yet-to-be-identified bat caves. This hypothesis is consistent with previous data showing that a direct progenitor of SARS-CoV emerged before 2002.

Recombination analysis also strongly supported the hypothesis that the civet SARS-CoV strain SZ3 arose through recombination of two existing bat strains, WIV16 and Rf4092. Furthermore, WIV16, the closest relative to SARS-CoV found in bats, likely arose through recombination of two other prevalent bat SARSr-CoV strains.

The most frequent recombination breakpoints are within the S gene, which encodes the spike (S) protein that contains the receptor-binding domain (RBD), and upstream of orf8, which encodes an accessory protein.

Given the prevalence and great genetic diversity of bat SARSr-CoVs, their close coexistence and the frequent recombination of the coronaviruses, it is expected that novel variants will emerge in the future. Because there were no SARS cases in Yunnan province during the SARS outbreak, we hypothesize that the direct progenitor of SARS-CoV was produced by recombination within bats and then transmitted to farmed civets or another mammal, which then transmitted the virus to civets by faecal–oral transmission. When the virus-infected civets were transported to Guangdong market, the virus spread in market civets and acquired further mutations before spillover to humans.”

Allow me to translate:

1. After collecting data for 5 years from bats in one cave of the Yunnan province in China, a number of studies analyzing one type of coronaviruses showed it had different versions that were quite varied in their specific features
2. This cave is not unique in this because other locations in China showed similar diversity
3. Coronaviruses were shown in other studies to frequently combine with each other in nature and make new versions of themselves
4. After 15 years of searching for it, no progenitor of the SARS coronavirus was found, i.e. it didn’t have a single virus it could be linked to as its “parent”
5. Because coronaviruses have a high recombination rate, they hypothesized that the SARS coronavirus was born out of a recombination event between other coronaviruses
6. A study showed there was a version that had a similarity to the SARS coronavirus which had emerged before 2002
7. When the genome of the SARS coronavirus in the civet cat was analyzed against other coronavirus genomes, they could see that two other coronaviruses from bats had recombined together to make this one, which now had acquired the ability after this recombination to infect civet cats. To understand recombination and the ability to infect a different species, imagine two French novels written by the same author are combined and translated into English at the same time. Some events were omitted in each novel and characters from retained events in both novels are now present in this new novel. The key event to pay attention to here is the contemporaneous translation to English while this combination process is taking place, which now makes the new novel accessible to an English speaking audience that still can’t read the original French novels
8. One of those bat coronavirus strains that was part of this combination process was itself a product of an earlier recombination event. For that one, imagine two earlier French novels by the same author were combined to make a new novel, but without the contemporaneous translation process
9. One gene in the genomic sequence of these coronaviruses was discovered to be the most frequent one where these recombination events are taking place, and it’s a gene for a receptor. In our imagined French novels, this is a common event we find in both novels where the antagonist sneaks into the library of the protagonist
10. Based on how widespread and diverse coronaviruses are in bats, how close they are to each other, how frequent these recombination events are, and the available information about the genomic sequences of coronaviruses that have origins in bats, infected another animal, and finally made their way to humans in the form of SARS, the authors of this review paper make a prediction and offer an explanation

a. There will be new coronaviruses in the future

b. The SARS coronavirus was a product of recombination of coronaviruses in bats that allowed it to go into either farmed civet cats or another animal, which occurred by these animals foraging for food in areas where bat faces containing the virus were. Infected civets were then taken to the Guandong market where the virus was continuing to mutate, because that’s what it does, that eventually allowed it to infect humans handling those cats in the butcher stands.

How can we be sure the COVID-19 coronavirus is not a bioweapon?

We can’t. Scientists don’t speak in absolute terms. They collect the available evidence and offer explanations that in this case:

1. Take into account as much of the available data as possible
2. Propose a mechanism
3. Allow us to make predictions based on this mechanism, which can be verified by collecting more data that can then used to test the validity of the original explanation and mechanism we hypothesized

The more time spent and data collected that is found to be supportive of the model, the more trust we place in it. Technically, when you hear virologists say,

“This coronavirus came from bats. It wasn’t bioengineered.”

What they’re really saying is,

“All of our investigations comparing the genomic sequence of this coronavirus to the database of other coronaviruses we currently have, which entails comparisons between a number of genetically stable domains and analyses of receptors, carry the same features we’ve seen before in natural recombination events that occurred with other coronaviruses.”

Origin of the COVID-19 Coronavirus

What virologists are offering is the most likely explanation based on available evidence and historical precedence they have about how coronaviruses behave in nature. Each paper published on this topic in scientific journals includes a number of approaches to analyze these viruses and experiments to demonstrate features in their genomic sequences and protein structures, which are then reviewed by other virologists before it’s approved by the editors of these journals.

Compare this with stories published in [insert website name] by authors who do none of this but instead, keep us mired in futile conversations that often require a suspension of disbelief but make some feel like they’re being “skeptical” and “scientific”.

Well, in the realm of empirical claims, skepticism, and being scientific: less rhetoric, more data.

1. Fan Y et al. Bat coronaviruses in China. Viruses 11(3), 210 (2019)
2. Cui, J., Li, F. & Shi, Z. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 17, 181–192 (2019)

Mohamed Ghilan earned a Ph.D. in Neuroscience in 2015 and is currently a 4th-year medical student. He is the founder of Al-Andalus Academy, an online learning platform delivering traditional Islamic teachings and an online book club where non-fiction books are explored and discussed through an Islamic lens during live webinars.

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