Reply To: SARS cov2 and Covid 19


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#54356
Dr Edd
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Nope. Not fishy at all, Michael.

How “scientific” is this claim? Well for one thing it’s not an empirical finding. The claim is based on reasoning about scientific epistemology. Prof Petrovsky only claims we can’t say for certain that it came from animals – but that’s a very subjective claim for which he’s setting his own standards of proof. Presumably he would only concede the point if we found the animal it came from and tested it. But there are other ways we can deduce the origin.

To work on an RNA virus you must turn it into DNA and put it in a cloning vector so bacteria will grow it. This leaves traces: half restriction enzyme sites, for example. There are no such signs in the viral genomes of SARS-CoV-2. To assess the likelihood of synthesising it in a laboratory without leaving any traces, you’d have to quantify all the known synthetic RNA viruses and express those that show no signs of manipulation as a proportion of that total. But there aren’t any, to my knowledge. We can therefore deduce that the likelihood of the virus being synthetic is negligible.

But … but … it attaches so perfectly to human ACE2 (hACE2) receptors that it must have been designed specifically for humans – right? Wrong. It’s a product of natural selection rather than intelligent design.

“This is rather as if you imagine a puddle waking up one morning and thinking, ‘This is an interesting world I find myself in — an interesting hole I find myself in — fits me rather neatly, doesn’t it? In fact it fits me staggeringly well, must have been made to have me in it!'” (Douglas Adams, The Salmon of Doubt)

There are uncountable numbers of other novel viruses to which humans are exposed that are either blitzed by the immune system or cause no appreciable harm. This just happens to be a freak mutation that made it through all the obstacles. That’s why we’re talking about it. But don’t neglect all the other viruses that didn’t quite make it.

Bats have immensely strong immune systems which means they can host viruses but not get sick with them – which is what makes them powerful reservoirs of things like Ebola, SARS, MERS. So the fact that they are not as susceptible as humans to SARS-CoV-2 is hardly a surprise. Lots of mammals have ACE receptors in different configurations, and we don’t know how long this virus has been bouncing around between animals in the Wuhan wet markets and the hunters and market workers slowly getting adapted to people.

Thus Petrovsky’s musing may be derived from scientific fact, but the arguments based on it are epistemological – and philosophically ignorant. He fails to consider more plausible scenarios.

Here’s more information from Science Daily:

Possible origins of the virus

Based on their genomic sequencing analysis, Andersen and his collaborators concluded that the most likely origins for SARS-CoV-2 followed one of two possible scenarios.

In one scenario, the virus evolved to its current pathogenic state through natural selection in a non-human host and then jumped to humans. This is how previous coronavirus outbreaks have emerged, with humans contracting the virus after direct exposure to civets (SARS) and camels (MERS). The researchers proposed bats as the most likely reservoir for SARS-CoV-2 as it is very similar to a bat coronavirus. There are no documented cases of direct bat-human transmission, however, suggesting that an intermediate host was likely involved between bats and humans.

In this scenario, both of the distinctive features of SARS-CoV-2’s spike protein — the RBD portion that binds to cells and the cleavage site that opens the virus up — would have evolved to their current state prior to entering humans. In this case, the current epidemic would probably have emerged rapidly as soon as humans were infected, as the virus would have already evolved the features that make it pathogenic and able to spread between people.

In the other proposed scenario, a non-pathogenic version of the virus jumped from an animal host into humans and then evolved to its current pathogenic state within the human population. For instance, some coronaviruses from pangolins, armadillo-like mammals found in Asia and Africa, have an RBD structure very similar to that of SARS-CoV-2. A coronavirus from a pangolin could possibly have been transmitted to a human, either directly or through an intermediary host such as civets or ferrets.

Then the other distinct spike protein characteristic of SARS-CoV-2, the cleavage site, could have evolved within a human host, possibly via limited undetected circulation in the human population prior to the beginning of the epidemic. The researchers found that the SARS-CoV-2 cleavage site, appears similar to the cleavage sites of strains of bird flu that has been shown to transmit easily between people. SARS-CoV-2 could have evolved such a virulent cleavage site in human cells and soon kicked off the current epidemic, as the coronavirus would possibly have become far more capable of spreading between people.

If you’re scientifically literate, you can peruse this paper from the Scripps Research Institute – COVID-19 coronavirus epidemic has a natural origin – which debunks the rumours in more detail:

There are also rumours that the SARS-CoV-2 was artificially, or intentionally, made by humans in the lab, and this is highlighted in one manuscript submitted to BioRxiv (a manuscript sharing site prior to any peer review), claiming that SARS-CoV-2 has HIV sequence in it and was thus likely generated in the laboratory. In a rebuttal paper led by an HIV-1 virologist Dr. Feng Gao, they used careful bioinformatics analyses to demonstrate that the original claim of multiple HIV insertions into the SARS-CoV-2 is not HIV-1 specific but random [15]. Because of the many concerns raised by the international community, the authors who made the initial claim have already withdrawn this report.

Evolution is stepwise and accrues mutations gradually over time, whereas synthetic constructs would typically use a known backbone and introduce logical or targeted changes instead of the randomly occurring mutations that are present in naturally isolated viruses such as bat CoV RaTG13. In our view, there is currently no credible evidence to support the claim that SARS-CoV-2 originated from a laboratory-engineered CoV. It is more likely that SARS-CoV-2 is a recombinant CoV generated in nature between a bat CoV and another coronavirus in an intermediate animal host. More studies are needed to explore this possibility and resolve the natural origin of SARS-CoV-2. We should emphasize that, although SARS-CoV-2 shows no evidence of laboratory origin, viruses with such great public health threats must be handled properly in the laboratory and also properly regulated by the scientific community and governments.

I would advise people to perform basic checks before circulating rumours from conspiracy theory sites. Try a web search for counter-evidence. If the contrary arguments have more credible scientific support than the controversial claim, either mention that fact explicitly and give references – or even better, don’t post anything at all.