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. 2022 Mar 3;40(7):1123–1131. doi: 10.1038/s41587-022-01213-5

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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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Extended Data Fig. 1 — a, Diagnostic performance for influenza A virus subtyping may degrade over time, even considering conserved sites. At each year, we select the 15 most conserved 30-mers from recent sequences for segment 6 (N) for all N1 subtypes; each point is a 30-mer. Plotted value is the fraction of sequences in subsequent years (colored) that contain the 30-mer; bars are the mean. To aid visualization, only odd years are shown. 2007 N1 30-mers are absent following 2007 owing to antigenic shift during the 2009 H1N1 pandemic. b, Variation along the SARS-CoV-2 genome emerging over time during 2020. Bottom row (‘Combined’) shows all 1,131 single nucleotide polymorphisms, among 361,460 genomes, that crossed 0.1% or 1% frequency between February 1, 2020 and the end of 2020—i.e., (i) at <0.1% frequency in genomes collected before February 1 and 0.1–1% frequency by December 31 (light purple); or (ii) at <1% frequency before February 1 and at ≥1% frequency by December 31 (dark). Other rows show the month in which each polymorphism crosses the frequency threshold.