Figure 5. Positions on the three dimensional SARS-CoV-2 Spike trimer of amino acids encoded by three clusters of BA.1 codon sites that are evolving either neutrally or under negative selection in non-Omicron SARS-CoV-2 sequences.

The Spike subunit interacting with human ACE2 is in the “up” configuration and the other two are in the “down” configuration²³. The cluster region 1 and 2 encoded amino acid changes in BA.1 (in green and blue respectively) are within the receptor binding domain of Spike with the cluster 2 encoded changes located within the receptor binding motif. The cluster region 3 mutations are within the fusion domain of Spike. An interactive version of this figure can be found at https://observablehq.com/@stephenshank/sc2-omicron-clusters.