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. 2023 Dec 5;9(1):35–54. doi: 10.1038/s41564-023-01530-8

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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 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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Extended Data Fig. 4 — (a) Estimated infection times of the recipient in the n = 227 phylogenetically reconstructed source–recipient pairs from phyloTSI based on deep-sequence data alone (x-axis) against refined estimates accounting for sero-history and inferred direction of transmission (y-axis). Median estimates (dots) are shown along 95% uncertainty ranges (lines). (b) Histogram of absolute difference (bars) and mean absolute differences (triangle) between infection time estimates and the midpoint of seroconversion intervals in 98 source–recipient pairs in which the recipient had a last negative test, across the two methods (colour). (c) Histogram (bars) and median (triangle) age of the phylogenetically likely recipient, across the two methods (colours). (d) Histogram (bars) and median (triangle) age of the phylogenetically likely source, across the two methods (colours).