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. 2023 Oct 6;14:6245. doi: 10.1038/s41467-023-41788-4

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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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Fig. 2 — A Single-cell transcriptomes were projected in UMAP space and colored by Leiden cluster. Leiden clusters were subsequently characterized by the mean viral fraction, the number of cells, and the cell cycle composition per cluster. Cluster T are all cells that could not be assigned an unambiguous infection state. B Differential expression of Leiden clusters revealed transcriptionally distinct subclusters of bystander cells, infected cells, and a small subset of interferon-producing cells. The color of each dot is pseudobulk gene expression of each gene per cluster, and the size of each dot is the expression normalized to the cluster with maximum expression of that gene. C–E Host transcriptional analysis revealed heterogeneity in infected and bystander populations, including differential gene expression in UMAP space of: C ISG15; D IFNL1; and E NFKBIA.