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. 2021 Nov 24;6(12):1549–1560. doi: 10.1038/s41564-021-01000-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, Recombination-masked WGS phylogeny, highlighting the SS14 lineage (n = 426). b, Recombination-masked WGS phylogeny, highlighting the Nichols lineage (n = 102), including four outlying genomes (sublineages 6 and 7). For a and b, coloured strips show sublineage and country; tree tips show sublineage. Coloured triangle indicates node position of collapsed sister lineage. UltraFast bootstraps ≥95% are indicated with black diamond node marks. Note that sublineage 6 is shown in both trees (see main text). c, Temporal distribution of samples by sublineage (unrelated singleton genomes are grouped together). d, Total count of samples by sublineage. e, Relative proportion of each sublineage sample corresponding to country.