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. 2022 Jul 5;5:666. doi: 10.1038/s42003-022-03565-9

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© The Author(s) 2022

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 Subgenomic RNA data from most abundant ORFs for B.1.1.7 and respective ancestral lineages in Pillar 1 data (B_n = 51, B.1_n = 164, B.1.1_n = 302, B.1.1.7_n = 729). b Subgenomic RNA data from most highly expressed ORFs for B.1.177 and respective ancestral lineages in Pillar 1 data (B_n = 51, B.1_n = 164, B.1.177_n = 764). c Distribution of the reported days since symptom at the time of sampling for B (n = 40), B.1 (n = 133), B.1.1 (n = 248), B.1.177 (n = 398) and B.1.1.7 (n = 334) lineage infections. d Model estimates and 95% confidence intervals from generalised linear model comparing the effect of lineage and day of symptom onset on sgRNA abundance for most highly abundant ORFs. Reference lineage B.1. No interaction was observed between any lineage and the day of symptom onset. One B.1 sample with outlier N abundance (SHEF-CC370) was excluded. Error bars represent the standard error of the estimate. e Pseudo time course of RLU values for B.1.1.7 and B.1.177, plot restricted to 10 days. (0 Days; B.1.177_n = 92, B.1.1.7_n = 106. 1 Day; B.1.177_n = 52, B.1.1.7_n = 102. 2 Days; B.1.177_n = 28, B.1.1.7_n = 43. 3 Days; B.1.177_n = 31, B.1.1.7_n = 14. 4 Days; B.1.177_n = 17, B.1.1.7_n = 19.). f Normalised subgenomic RNA abundance for each of the most abundant ORFs stratified by the reported days since symptom onset and lineage, loess model. The plot is restricted to 10 days. (0 Days; B.1.177_n = 115, B.1.1.7_n = 93. 1 Day; B.1.177_n = 53, B.1.1.7_n = 93. 2 Days; B.1.177_n = 31, B.1.1.7_n = 47. 3 Days; B.1.177_n = 31, B.1.1.7_n = 12. 4 Days; B.1.177_n = 19, B.1.1.7_n = 18.). g Normalised sgRNA abundance for N and S is significantly increased at 0-4 days of infection. All p values calculated using an unpaired Wilcoxon signed-rank test, and adjusted for multiple testing with Holm (**** <0.0001, *** <0.001, ** <0.01, * <0.05, ns or blank = not significant). All boxplots depict the 25th, 50th (median), and 75th percentiles, and whiskers represent the most extreme datapoint which is no more than 1.5x the interquartile range. B.1.1.7 is represented in red, B.1.177 in teal, B in yellow, B.1 in green, B.1.1 in navy blue, B.1.1.1 in purple and other lineages in grey apart from D, S subgenomic RNA is teal, E is red, M is navy blue, N in green and ORF6 in yellow.