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. 2022 Mar 24;39(4):msac061. doi: 10.1093/molbev/msac061

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© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 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 protomer subunit interacting with human ACE2 is in the “up” configuration and the other two are in the “down” configuration (Xu et al. 2021). 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.