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. 2021 Oct 26;11:21108. doi: 10.1038/s41598-021-00267-w

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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 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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Phylogenetic tree (December 2019–April 2020) colored by clades shows distribtution of West-African samples over all clades suggesting introductions from China and European countries. Patterns are country-specific, e.g. most Senegalese samples have close similarity with the French reference, most Nigerian samples cluster in early Chinese-based clade S and Ghanaian samples are spread over all clades. Within the clade S, there are putatively specific West-African mutations at the branches at C24370T and G22468T. G22486T may reflect migration routes because in the nextstrain analysis of Africa as a whole there are also Tunisian samples in this branch (https://nextstrain.org/ncov/africa?f_region=Africa, accessed Jun 26th, 2020). Two of the non-French related Senegalese samples come from these branches while the other (Senegal/136) has strong similarity with Spanish-end of February samples from the early clade S pointing at multiple introductions to Senegal from France, Spain and African countries. Graphics were generated using the software FigTree (version 1.4.4, http://tree.bio.ed.ac.uk/software/figtree/) for annotation of the phylogenetic tree and the nextstrain pipeline including software Augur (version 7.0.2, https://docs.nextstrain.org/projects/augur/en/stable/index.html) and TreeTime (version 0.7.6, https://github.com/neherlab/treetime)^28,31.