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. 2021 Aug 27;53(8):1229–1237. doi: 10.1038/s12276-021-00658-z

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© The Author(s) 2021

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a Phylogenetic tree constructed from 351,525 full-length SARS-CoV-2 genome sequences deposited in the GISAID database. Well-known named clades are indicated with light shades of color and labeled according to widely used nomenclature⁷⁵. Special sequences with prior knowledge: the Wuhan reference sequence (yellow), the sequence nearest to bat CoV RaTG13 (green) or RmYN02 (blue), and sequences sampled in December 2019 (gray) are marked with diamonds, and the presumed root (internal node with the maximum likelihood of being the root) is marked with a red square. The sequence data are constantly being updated on the GISAID website (https://www.gisaid.org/). b Detailed phylogenetic structure and associated substitutions between the presumed root (red square) and Wuhan-hu-1. c Boxplot showing the log-likelihood of being the root by collection time of the samples. Overall, likelihoods decrease steadily as collection time progresses. d Boxplot showing the edit distance from bat CoV RmYN02 by collection time of the samples. Overall, the edit distance does not significantly change over time.