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. 2018 May 15;9:1928. doi: 10.1038/s41467-018-04217-5

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© The Author(s) 2018

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. 8 — Sequence and neutralization analysis of viruses from homogeneously infected CH0505. a Syn/nonsyn highlighter plot shows the synonymous (green) and nonsynonymous (red) mutations compared to the T/F sequences. b Autologous neutralization analysis. Multiple Env pseudoviruses were generated from seven time points from CH0505 over 2 years of infection. Neutralization susceptibility of 123 pseudoviruses were determined with 13 CH103-lineage antibodies (right panel) and neutralization susceptibility of 33 pseudoviruses were determined were determined with 16 CH235-lineage antibodies (right panel). Neutralization magnitude is color coded by warm colors, with red being the strongest. Blue color indicates that no neutralization activities were detected with neutralizing antibodies at the 50 µg/ml concentration. c Recombinant env genes from days 538 and 692 after infection. Recombinants and their breakpoints, as determined by RAPR, are shown. Recombination breakpoints are shown as black boxes, and they are filled when the breakpoints are significant

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