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There is no ‘standard’ colour scheme for amino acids in the sense of one recommended by a standards or professional organization for biochemists. There are several schemes used in practice — either by software applications or individuals — based on two main criteria:
The properties of the amino acid the colours are intended to indicate
The colour choice of ...
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In both infection by the virus and mRNA-mediated expression of the spike protein, spike proteins are produced in the host cell as membrane-bound proteins; they're not just separate particles floating around. Whether or not the rest of the viral machinery is present, these will end up displayed in the membrane of the infected cells. Here's a diagram showing ...
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