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. 2022 Jun 14;13:3416. doi: 10.1038/s41467-022-31147-0

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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 Creation of two dual-barcode libraries with distinct registration marks and uniquely addressable members. b Frequency of each lineage as a fraction of total population size. Colors indicate unique barcode identities. c Whole-genome sequencing identifies adaptive variants in HA. Individual single nucleotide variant (SNV) frequencies are indicated at each nucleotide position in a concatenated IAV genome for each library. d Long-read sequencing reveals selective sweeps by linking adaptive mutants in HA to single dominant barcodes. The frequencies of mutations coding for the indicated change that is linked to the dominant barcode are shown for both libraries (left). The actual frequency of K > Q and K > stop mutants versus the contribution from long-read sequencing errors to their appearance is unknown. The frequencies of all barcodes linked to the adaptive glutamic acid variant are indicated (right), with the dominant barcode in each library colored as in b. Source data are provided as a Source Data file.