SUPPLEMENTARY FIG. S1. MVC inhibition curves in NP2-CD4/CCR5 cells. Luciferase reporter viruses pseudotyped with baseline (black solid lines) and MVC

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Meagan Wilson
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1 Supplementary Data

2 SUPPLEMENTARY FIG. S1. MVC inhibition curves in NP2-CD4/CCR5 cells. Luciferase reporter viruses pseudotyped with baseline (black solid lines) and MVC failure Envs (black dotted lines) were used to infect NP2-CD4/CCR5 cells in the presence of increasing concentrations of MVC, as described in the Materials and Methods section. Virus inhibition curves were generated as described previously. 2,3 The data shown are means of triplicates from three independent experiments. Error bars represent the SEM. Control Envs include MVC Res in a blue dotted line and JR-CSF in pink. 1 4 Env, envelope; MVC, Maraviroc; SEM, standard error of the mean.

3 SUPPLEMENTARY FIG. S2. MVC inhibition curves in 293-Affinofile cells. Luciferase reporter viruses pseudotyped with baseline (black solid lines) and MVC failure Envs (black dotted lines) were used to infect 293-Affinofile cells in the presence of increasing concentrations of MVC, as described in the Materials and Methods section. Expression of CD4 and CCR5 was induced on 293-Affinofile cells with 1.25 ng/ml minocycline and 2 lm Ponasterone A, respectively, as described in the Materials and Methods section. Virus inhibition curves were generated as described previously. 2,3 The data shown are means of triplicates from three independent experiments. Error bars represent the SEM. Control Envs include MVC Res blue dotted line and JR-CSF in pink. 1 4

5 SUPPLEMENTARY FIG. S3. Phylogenetic analysis of env genes isolated before MVC therapy and after failure confirmation in eight individuals. Neighbor-joining trees of clones isolated from the pretherapy time point (squares) and clones isolated from the failure confirmation time point (triangles) are shown. Subject 2 (blue); Subject 4 (magenta); Subject 5 (light blue); Subject 11 (green); Subject 17 (black); Subject 24 (yellow); Subject 26 (gray); and Subject 27 (red). The asterisk indicates clone MP Trees were constructed in MEGA (6.0) using the Tajima-Nei model of evolutionary distances and statistically supported by 100 bootstrap replicates. The scale is number of base substitutions per site.

6 SUPPLEMENTARY FIG. S4. CD4 and CCR5 expression levels on NP2-CD4/CCR5 cells and 293-Affinofile cells. The level of CD4 and CCR5 was measured on NP2-CD4/CCR5 cells and 293-Affinofile cells that were induced to express a moderate level of CD4 (with 1.25 ng/ml of minocycline) and a high level of CCR5 (with 2 lm of Ponasterone). The expression levels of CD4 and CCR5 were quantitated by quantitative flow cytometry. The histograms shown are representative of three independent experiments, and demonstrate the level of each receptor using phycoerythrin (PE)-conjugated flow cytometry antibodies. The table shows the mean and standard deviation of CD4 and CCR5 molecules per cell.

7 Supplementary Table S1. Optimized Background Therapy Patient ID Optimized background therapy Dose (mg) Delivery 2 EMTRICITABINE/TENOFOVIR DISOPROXIL 200/300 QD FUMARATE KALETRA 400/100 BID STAVUDINE 40 BID 4 EMTRICITABINE/TENOFOVIR DISOPROXIL 500 QD FUMARATE FOSAMPRENAVIR 700 BID RITONAVIR 100 BID ZIDOVUDINE 300 BID 5 EMTRICITABINE 200 QD ENFUVIRTIDE 90 BID KALETRA 3 Capsules BID TENOFOVIR 300 QD 11 DIDANOSINE 250 QD FOSAMPRENAVIR 700 BID RITONAVIR 100 BID 17 DIDANOSINE 250 QD ENFUVIRTIDE 90 BID (stopped study day 64) KALETRA 400/100 BID TENOFOVIR DISOPROXIL FUMARATE 300 QD 24 ATAZANAVIR 400 QD EMTRICITABINE 200 QD ENFUVIRTIDE 90 BID 26 EMTRICITABINE/TENOFOVIR DISOPROXIL 200/300 QD FUMARATE ENFUVIRTIDE 90 BID RITONAVIR 200 BID STAVUDINE 40 QD 27 DIDANOSINE 250 OD ENFUVIRTIDE 90 BD FOSAMPRENAVIR 700 BD LAMIVUDINE 300 OD (stopped study day 156) RITONAVIR 100 BD TENOFOVIR 300 OD Darunavir, raltegravir, and etravirine were not approved at the time of the study and were not allowed as optimal background therapy. BID, twice daily; OD, once daily; QD quarterly daily. References 1. Flynn JK, Paukovics G, Moore MS, et al.: The magnitude of HIV-1 resistance to the CCR5 antagonist maraviroc may impart a differential alteration in HIV-1 tropism for macrophages and T-cell subsets. Virology 2013;442: Roche M, Jakobsen MR, Ellett A, et al.: HIV-1 predisposed to acquiring resistance to maraviroc (MVC) and other CCR5 antagonists in vitro has an inherent, low-level ability to utilize MVC-bound CCR5 for entry. Retrovirology 2011; 8: Roche M, Jakobsen MR, Sterjovski J, et al.: HIV-1 escape from the CCR5 antagonist maraviroc associated with an altered and less efficient mechanism of gp120-ccr5 engagement that attenuates macrophage-tropism. J Virol 2011; 85: Roche M, Salimi H, Duncan R, et al.: A common mechanism of clinical HIV-1 resistance to the CCR5 antagonist maraviroc despite divergent resistance levels and lack of common gp120 resistance mutations. Retrovirology 2013; 10:43.

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