File S1 - HIV-1 Tropism Testing in Subjects Achieving Undetectable HIV-1 RNA: Diagnostic Accuracy, Viral Evolution and Compartmentalization

Phylogenetic relatedness of V3 forms before treatment initiation and after 2 years in each subject. Maximum-likelihood phylogenetic trees including V3-loop haplotypes present at a frequency ≥0.6% in the virus population in plasma (triangles), PBMCs before therapy initiation (circles) and PBMCs after persistent viremia suppression (squares). One tree is shown per each subject. Trees are rooted at the most frequent plasma sequence before antiretroviral treatment initiation. Filled symbols show predicted CXCR4-using viruses; open symbols show predicted CCR5-using viruses. Symbol size increases proportionally to the V3-loop haplotype frequency in the virus population in 10% intervals. Node reliability was tested using 1000 bootstraps; bootstrap values ≥50% are shown. A Geno2Pheno [coreceptor] false positive rate (FPR) equal or lower than 10% was used to define CXCR4 use.
(PDF)