Alina Chan on SARS-CoV-2

May 21, 2020

J.C. on a Bike discussed a recent preprint of a paper by Alina Chan. Here is some of it:

“…Our observations suggest that by the time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV. However, no precursors or branches of evolution stemming from a less human-adapted SARS-CoV-2-like virus have been detected. The sudden appearance of a highly infectious SARS-CoV-2 presents a major cause for concern that should motivate stronger international efforts to identify the source and prevent near future re-emergence.”

“SARS-CoV was observed to adapt under selective pressure that was highest as it crossed from Himalayan palm civets (intermediate host species) to humans and diminished towards the end of the epidemic (15–18); this series of adaptations between species and in humans culminated in a highly infectious SARS-CoV that dominated the late epidemic phase. In comparison, SARS-CoV-2 exhibits genetic diversity that is more similar to that of late epidemic SARS-CoV (Figure 1, Supplementary Table). In fact, the exceedingly high level of identity shared among SARS-CoV-2 isolates makes it impractical to model site-wise selection pressure. As more mutations occur and, ideally, when SARS-CoV-2-like viruses from an intermediate host species are identified, it will become possible to model selection pressure as was done for SARS-CoV.”

A virus’s host environment tends to select against most random mutations. In other words, if it ain’t broke, don’t fix it. If a virus finds itself in a new host environment, it needs to change as was observed with SARS-CoV, or it can’t replicate. Ms. Chan’s findings suggest SARS-CoV-2 was already well “adapted” to human hosts and right now no one has identified the host that preceded humans. This suggests/supports the idea that SARS-CoV-2 came from GoF studies.

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