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. 2023 Apr 5;13:5571. doi: 10.1038/s41598-023-32622-4

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Particular nonsynonymous mutations (identified in 5,248 viral genomes) are enriched in the S protein (A) and particular mutations (e.g., D614G) are frequent (occurring more than 20 times early in the pandemic) and retained in human, bat, and pangolin coronaviruses (B). None of the common variants are fixed in human populations. The tree of common variants is a maximum likelihood tree. The mutations are color coded by amino acid for taxa in the tree. Each colored tip in the tree is made up of one or more samples. The human samples are numerous, and the merging of many dots for many samples gives rise to the purple bar.