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. 2011 Jun 23;7(6):e1002106. doi: 10.1371/journal.ppat.1002106

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Bunnik et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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An MST of all V3 sequences generated from PBMC and serum samples of all time points is shown. See the legend to Figure 3 for details regarding the layout of the figure. Nodes containing V3 sequences with an si phenotype as inferred by PSSM_NSI/SI and an x4 phenotype as inferred by geno2pheno_[coreceptor] are indicated in red, nodes containing discordant nsi/x4 variants are indicated in light blue, while all other sequences were predicted to be nsi/r5. As Dual-X clones were not detected in the Trofile assay until 18 months after the first MT-2⁺ time point, the V3 sequences of two Dual-X clones from this later time point are indicated in the top. These Dual-X sequences are closely related to the si/x4 sequences present at time point zero, suggesting that these si/x4 sequences indeed form the start of the major si/x4 branch in the tree. Mo, months; n.t., not tested.