Origin of SARS-CoV-2 through recombination and purifying selection

An important new paper on the natural (not laboratory) origins of the SARS-CoV-2 virus. Interested to see that a number of the authors are based in Los Alamos National Lab, which is primarily known for its defense work.

Also, for those who don’t know or who deny the facts of natural selection, here’s a short explanation of negative or “purifying” selection from the Nature Education website:

Because more DNA changes are harmful than are beneficial, negative selection plays an important role in maintaining the long-term stability of biological structures by removing deleterious mutations. Thus, negative selection is sometimes also called purifying selection or background selection. One key reason why this form of selection is so prevalent is the success of evolution in optimizing biological structures: As soon as a system has been improved, there is the danger of losing that improvement by a deleterious mutation. Purifying selection makes sure that deleterious mutations cannot take over a population and that any improved structures—once fixed in a population—are maintained as long as they are needed. A dramatic example of such maintenance can be found in so-called “living fossils”: If a species’ ecological niche happens not to change for millions of years, fossil forms of the species can be almost indistinguishable from their present-day descendants.

COVID-19 has become a global pandemic caused by the novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis, discovering new drugs, and developing a vaccine. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike and other genes among bat, pangolin, and human coronaviruses, suggesting similar evolutionary constraints in different host species. We also demonstrate that SARS-CoV-2’s entire RBM was introduced through recombination with coronaviruses from pangolins, possibly a critical step in the evolution of SARS-CoV-2’s ability to infect humans. Similar purifying selection in different host species, together with frequent recombination among coronaviruses, suggests a common evolutionary mechanism that could lead to new emerging human coronaviruses.
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I’ve been rooting for team pangolin the whole time.

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Pangolin vs. Armadillo. My money’s on the 'dillo!

The observation that the crucial part of the Spike protein probably originates from pangolins has been kicking around since February.

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I’d never heard of a pangolin before coronavirus cropped up. I assumed it was related to the bat until I finally looked it up yesterday. Honestly, I was shocked that people ate them. Seeing too many dead armadillos on the side of the road would place it somewhere near last in the list of things I would eat, but still ahead of a bat. I guess if something moves, people will eat it.

I thought the last sentence of the article was provocative:

While the direct reservoir of SARS-CoV-2 is still being sought, one thing is clear: Reducing or eliminating direct human contact with wild animals is critical to preventing new CoV zoonosis in the future.

In Louisiana, I think armadillo is referred to as “possum on the half shell.” Seriously, armadillos are known to carry leprosy, so some parallels. Pangolin is also used in Chinese folk medicine,and apparently this crisis has taken a bit of pressure off this threatened species.

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