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. 2016 Aug 2;13:51. doi: 10.1186/s12977-016-0282-9

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© The Author(s) 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 4 — Viral diversity during active replication. Maximum likelihood phylogenetic trees (unrooted) of viral variants detected at virologic failure (just before treatment switch): a Patient 1; b Patient 2; c Patient 3. Plasma viremia sequences (gold) and episomal vDNA from PBMCS (violet) are highlighted; proviral DNA from the CD4⁺ T-cells (grey) is also included. Major plasma/episomal clusters are highlighted when clearly distinguished (Pt-1 and Pt-3), and the frequency of sequences included is color-coded at each tree (in percentages). In B (Pt-2), the overall result from the Env-tropism prediction is indicated