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In the original Wuhan genome the 501st position in the spike chain is occupied by an amino acid called asparagine. ….Mutations which cause just that substitution, known as n501y (or sometimes “Nelly”) subsequently turned up in the Alpha, Beta and Gamma variants. Another change they spotted, now called e484k (or “Eek”), was found in both Beta and Gamma.
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The rbd is not the only part of the spike protein where mutations matter. In a preprint published on June 22nd Ravindra Gupta, a molecular virologist at Cambridge University, and his colleagues put forward an argument as to why Delta is both more infectious and better at evading immunity than other variants. It is based on a substitution at site 681, which is at the point where, after the rbd meets ace2, the protein is cleft in two.
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Dr Gupta says p681r, helped by two shape-modifying mutations elsewhere, makes it easier for the protein to be cut up and thus get into cells. Its presence also means that, once a cell starts producing particles, their spike proteins can get on to the cell’s surface pre-cut.
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