Detection of Inferred CCR5- and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing
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 PSSMNSI/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.