The coronavirus isolated from pangolin is similar at 99% in a specific region of the S protein, which corresponds to the 74 amino acids involved in the ACE (Angiotensin Converting Enzyme 2) receptor binding domain, the one that allows the virus to enter human cells to infect them.
By contrast, the virus RaTG13 isolated from bat R. affinis is highly divergent in this specific region (only 77 % of similarity). This means that the coronavirus isolated from pangolin is capable of entering human cells whereas the one isolated from bat R. affinis is not.
In addition, these genomic comparisons suggest that the SARS-Cov-2 virus is the result of a recombination between two different viruses, one close to RaTG13 and the other closer to the pangolin virus. In other words, it is a chimera between two pre-existing viruses.
This recombination mechanism had already been described in coronaviruses, in particular, to explain the origin of SARS-CoV. It is important to know that recombination results in a new virus potentially capable of infecting a new host species. For recombination to occur, the two divergent viruses must have infected the same organism simultaneously.
Two questions remain unanswered: in which organism did this recombination occur? (a bat, a pangolin or another species?) And above all, under what conditions did this recombination take place?
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