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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. Two distinct si/x4 branches and several minor si/x4 variants can be observed in this MST, which are described in more detail in the text. In addition, one branch contains V3 sequences with a predicted si/x4 phenotype which were reported R5 in the Trofile assay (indicated by dotted red oval). N.t., not tested; mo, months.