SUPPLEMENTARY MATERIAL

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Supplementary Material The Open AIDS Journal, 2012, Volume 6 i SUPPLEMENTARY MATERIAL Immune Reconstitution During the First Year of Antiretroviral Therapy of HIV-1-Infected Adults in Rural Burkina Faso Fabrice Tiba 1, Frans Nauwelaers 2, Siaka Traoré 3, Boubacar Coulibaly 3, Thierry Ouedraogo 3, Adama Compaoré 3, Hans-Georg Kräusslich 1 and Thomas Böhler *,1 1 Department of Infectious Diseases, Virology, University of Heidelberg, INF324, D-69120 Heidelberg, Germany 2 BD Biosciences, Erembodegem, Belgium 3 Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso Supplementary Table 1. Immunological and Virological Parameters in HIV-1 Infected Subjects at Baseline, i.e., Before Starting HAART IR (A) NIR (B) VR (C) NVR (D) n = 33 15 25 17 CD4 + T-cell count (cells/ l) 179 (41-318) 202 (7-316) 214 (13-340) 146 (49-265) HIV-1 plasma viral load (log 10 copies/ml) 5.7 (4.3-6.4) 4.9 (4.3-6.0)* 5.8 (4.9-6.0) 5.7 (5.1-7.0) CD45RA + CCR7 + (% of CD4 + T-cells) 10 (3-32) 12.5 (3-28) 16 (3-32) 13 (3-32) CD45RA + CCR7 + CD4 + T-cell count (cells/ l) 23 (2-77) 18 (1-42) 18 (2-79) 28 (1-102) CD45RA + CCR7 + (% of CD8 + T-cells) 4 (1-9) 4 (0.4-14) 4 (1-9) 4 (3-9) CD45RA + CCR7 + CD8 + T-cell count (cells/ l) 25 (2-54) 6 (0.08-14) 14 (0.2-52) 28 (1-102) CD95 + (% of CD4 + T-cells) 97 (85-99) 97 (84-99) 96 (83-99) 98 (91-99) CD95 + CD4 + T-cells (cells/ l) 134 (37-306) 186 (7-305) 191 (12-315) 146 (47-239) CD95 + (% of CD4 neg T-cells) 98 (91-99) 96 (93-99) 97 (89-99) 99 (94-99) CD95 CD95 dim CD3 + CD4 + cells 16 (8-33) 22 (4-50) 19 (6-39) 26 (7-52) CD95 CD95 bright CD3 + CD4 + cells 307 (164-655) 349 (129-426) 279 (160-381) 337 (180-427)* CD95 + CD4 neg T-cells (cells/ l) 978 (501-1980) 532 (87-1762) 778 (489-1836) 855 (312-1981) CD95 CD95 bright CD3 + CD4 neg cells 126 (76-189) 141 (68-205) 125 (72-189) 150 (110-204) CD38 + (% of CD8 + T-cells) 97 (90-99) 98 (84-98) 95 (87-99) 99 (94-99) CD38 + CD8 + T-cells (cells/ l) 978 (501-1980) 688 (254-1756) 831 (546-1747) 1011 (377-1979) CD38 CD38 + CD3 + CD8 + cells 296 (149-827) 276 (184-890) 278 (126-701) 509 (241-890)* CD38 + (% of CD8 neg T-cells) 90 (81-95) 82 (75-94) 87 (80-96) 93 (82-96) CD38 + CD8 neg T-cells (cells/ l) 160 (40-243) 145 (6-258) 193 (34-274) 140 (43-206) CD38 CD38 + CD3 + CD8 neg cells 339 (209-655) 314 (205-781) 313 (205-667) 457 (231-781) Median values are shown with their 10 th - 90 th centile in parentheses. Patients with complete immunological follow-up (n=48) were grouped according to response to treatment: IR = good immunologic response, NIR = immunologic non-response. Patients with complete virologic follow-up (n=42) were divided into the following groups: VR = good virologic response, NVR = virologic non-response. The Mann-Whitney U-test was used to compare the IR vs NIR and VR vs NVR groups, respectively; asterisks indicate statistically significant differences: *p<0.05. Abbreviations: MFI = Median fluorescence intensity.

ii The Open AIDS Journal, 2012, Volume 6 Supplementary Material Supplementary Table 2. Immunological and Virological Parameters in HIV-1 Infected Subjects After 12 Months of HAART IR (A) NIR (B) VR (C) NVR (D) n = 33 15 25 17 CD4 + T-cell count (cells/ l) 418 (173-562) 254 (82-405)** 398 (151-576) 322 (185-563) HIV-1 plasma viral load (log 10 copies/ml) 1.6 (1.6-3.6) 1.6 (1.6-2.0) undetectable 2.0 (1.7-4.8) CD45RA + CCR7 + (% of CD4 + T-cells) 19 (4-38) 15 (4-26) 17 (3-38) 18 (5-37) CD45RA + CCR7 + CD4 + T-cell count (cells/ l) 72 (11-172) 30 (3-38) 41 (3-179) 72 (10-161) CD45RA + CCR7 + (% of CD8 + T-cells) 12 (2-22) 6 (5-7) 16 (2-28) 7 (3-14) CD45RA + CCR7 + CD8 + T-cell count (cells/ l) 95 (23-258) 25 (22-28)* 125 (19-318) 68 (26-158) CD95 + (% of CD4 + T-cells) 89 (75-96) 89 (69-98) 88 (70-98) 88 (78-99) CD95 + CD4 + T-cells (cells/ l) 312 (140-481) 135 (67-242)** 307 (102-480) 289 (102-487) CD95 + (% of CD4 neg T-cells) 87 (73-98) 83 (74-97) 85 (71-94) 92 (69-97) CD95 + CD4 neg T-cells (cells/ l) 742 (342-1841) 634 (312-1316) 846 (297-1492) 703 (363-1911) CD95 CD95 dim CD3 + CD4 + cells 12 (5-19) 9 (8-10) 12 (7-18) 10 (5-21) CD95 CD95 bright CD3 + CD4 + cells 150 (77-276) 78 (53-100)** 153 (63-278) 110 (70-316) CD95 CD95 bright CD3 + CD4 neg cells 74 (43-119) 48 (34-135) 69 (35-103) 85 (36-137) CD38 + (% of CD8 + T-cells) 87 (67-96) 73 (62-95) 83 (60-98) 86 (64-95) CD38 + CD8 + T-cells (cells/ l) 842 (404-1846) 395 (261-848) 846 (263-1524) 672 (405-1868) CD38 CD38 + CD3 + CD8 + cells 75 (50-186) 102 (88-218) 65 (40-196) 84 (56-180) CD38 + (% of CD8 neg T-cells) 78 (68-86) 67(67-77) 73 (61-87) 78 (69-83) CD38 + CD8 neg T-cells (cells/ l) 302 (132-497) 65 (63-174)*** 258 (102-437) 297 (101-577) CD38 CD38 + CD3 + CD8 neg cells 153 (83-262) 102 (89-218) 127 (82-210) 166 (83-280) Median values are shown with their 10 th - 90 th centile in parentheses. Patients with complete immunological follow-up (n=48) were grouped according to response to treatment: IR = good immunologic response, NIR = immunologic non-response. Patients with complete virologic follow-up (n=42) were divided into the following groups: VR = good virologic response, NVR = virologic non-response. The Mann-Whitney U-test was used to compare the IR vs NIR and VR vs NVR groups, respectively; asterisks indicate statistically significant differences: *p<0.05; **p<0.01; ***p<0.001. Abbreviations: MFI = Median fluorescence intensity.

Supplementary Material The Open AIDS Journal, 2012, Volume 6 iii Supplementary Table 3. Immunological and Virological Parameters in HIV-1 Infected Subjects at Baseline and After 12 Months of HAART IR and VR IR but NVR VR but NIR NIR and NVR n = 19 14 6 3 At baseline CD4 + T-cell count (cells/ l) 202 (13-412) 178 (63-251) 177 (7-316) 122 (7-256) HIV-1 plasma viral load (log 10 copies/ml) 5.3 (4.3-6.2) 5.8 (5.0-6.4) 5.1 (4.4-5.9) 5.8 (5.5-5.9) CD45RA + CCR7 + (% of CD4 + T-cells) 25 (1-32) 18 (8-35) 9 (3-27) 11 (9-13) CD45RA + CCR7 + CD4 + T-cell count (cells/ l) 31 (2-87) 18 (4-75) 13 (5-43) 6 (1-10) CD45RA + CCR7 + (% of CD8 + T-cells) 4 (1-10) 3 (1-7) 3 (0.4-7) 4 (0.5-9) CD45RA + CCR7 + CD8 + T-cell count (cells/ l) 12 (0.2-50) 33 (1-108) 3 (0-18) 8 (7-9) CD95 + (% of CD4 + T-cells) 97 (83-99) 99 (93-100)* 99 (92-100) 99 (99-100) CD95 + CD4 + T-cells (cells/ l) 195 (11-407) 175 (58-248) 208 (46-311) 119 (5-247) CD95 + (% of CD4 neg T-cells) 96 (83-100) 98 (92-100) 97 (94-100) 99 (99-100) CD95 CD95 dim CD3 + CD4 + cells 24 (7-43) 24 (5-155) 19 (8-59) 23 (9-33) CD95 CD95 bright CD3 + CD4 + cells 298 (159-442) 330 (204-427) 375 (215-523) 337 (264-425) CD95 + CD4 neg T-cells (cells/ l) 959 (489-1970) 1156 (515-1989) 747 (87-1762) 267 (260-381) CD95 CD95 bright CD3 + CD4 neg cells 126 (71-194) 151 (96-214) 160 (103-189) 159 (124-239) CD38 + (% of CD8 + T-cells) 96 (90-99) 98 (91-99) 92 (84-96) 93 (92-94) CD38 + CD8 + T-cells (cells/ l) 830 (499-1881) 1150 (498-1987) 1200 (688-1756) 315 (254-377) CD38 CD38 + CD3 + CD8 + cells 217 (123-1125) 509 (154-886)* 239 (184-276) 495 (259-781) CD38 + (% of CD8 neg T-cells) 88 (81-95) 93 (82-95) 95 (91-99) 98 (98-99) CD38 + CD8 neg T-cells (cells/ l) 181 (14-248) 157 (57-231) 200 (144-258) 61 (6-115) CD38 CD38 + CD3 + CD8 neg cells 292 (192-749) 482 (221-738)** 209 (205-313) 552 (449-890) After 12 months of HAART CD4 + T-cell count (cells/ l) 418 (162-653) 399 (187-562) 248 (96-405) 205 (82-296) HIV-1 plasma viral load (log 10 copies/ml) undetectable 1.9 (1.8-5.2) undetectable 1.7 (1.6-2.0) CD45RA + CCR7 + (% of CD4 + T-cells) 17 (2-38) 23 (5-38) 14 (3-25) 16 (4-36) CD45RA + CCR7 + CD4 + T-cell count (cells/ l) 69 (3-208) 72 (16-170) 35 (30-34) 20 (20-38) CD45RA + CCR7 + (% of CD8 + T-cells) 16 (2-28) 8 (2-17)* 11 (7-16) 10 (3-14) CD45RA + CCR7 + CD8 + T-cell count (cells/ l) 126 (19-319) 70 (26-159) 95 (28-128) 82 (25-160) CD95 + (% of CD4 + T-cells) 87 (70-97) 88 (78-99) 89 (74-95) 90 (79-100) CD95 + CD4 + T-cells (cells/ l) 398 (150-570) 439 (162-555) 154 (87-242) 184 (61-295) CD95 + (% of CD4 neg T-cells) 86 (74-96) 92 (67-97) 83 (74-92) 92 (87-97) CD95 CD95 dim CD3 + CD4 + cells 12 (8-19) 10 (8-22) 8 (8-9) 10 (6-22) CD95 CD95 bright CD3 + CD4 + cells 155 (114-260) 156 (74-304) 58 (53-64) 92 CD95 CD95 bright CD3 + CD4 neg cells 72 (56-106) 74 (37-125) 102 (64-135) 97 CD38 + (% of CD8 + T-cells) 87 (60-98) 88 (65-95) 62 94 CD38 + CD8 + T-cells (cells/ l) 842 (315-1549) 849 (427-1871) 261 395 CD38 CD38 + CD3 + CD8 + cells 65 (39-309) 83 (56-205) 74 125 CD38 + (% of CD8 neg T-cells) 77 (63-88) 79 (65-95) 67 77 CD38 + CD8 neg T-cells (cells/ l) 310 (124-582) 274 (134-436) 64 63 CD38 CD38 + CD3 + CD8 neg cells 133 (80-230) 166 (91-281) 89 267 *p<0.01 and **=p<0.001. Median values are shown with their 10th - 90th centile in parentheses. Patients (n=42) are grouped according to response to treatment: IR = good immunologic response, VR = good virologic response, NIR = immunologic non-response, NVR = virologic non-response. MFI = Median fluorescence intensity. Mann-Whitney U-test was used to compare the IR and VR vs. IR but NVR group.

iv The Open AIDS Journal, 2012, Volume 6 Supplementary Material Supplementary Table 4. Analysis of Individual Treatment Responses to HAART in Patients with Virological Treatment Failure During 12 Months of HAART VL 5.987478 3.754425 ND 2.09691 3.439964 2.591065 1.78533 CD4 7 ND 50 52 60 80 82 % Naive CD4 2.5 1.84 2.72 1.03 ND 1.62 3.51 % Naive CD8 0.46 1.48 1.25 1.37 3.6 3.2 7.01 MFI CD95dimCD4+ 4.18 6.79 4.53 8.35 8.35 15.75 8.94 MFI CD95dimCD4-12.1 8.9 8.66 5.7 6.49 8.54 12.19 MFI CD38CD8+ 889.65 777.37 577.72 858.21 162.53 121.88 124.09 MFI CD38CD8-780.87 922.24 511.66 713.7 201.69 406.79 218.7 VL 5.901261 3.792392 ND 2.706718 6.364538 3.371437 2.665581 CD4 59 ND 114 114 73 175 185 % Naive CD4 10.93 2.28 4.67 19.62 12.06 ND 10.37 % Naive CD8 1.06 1.46 1.7 1.92 1.01 ND 3.42 MFI CD95dimCD4+ 20.81 18.94 12.19 7.43 7.43 ND 22.17 MFI CD95dimCD4-11.76 21.97 11.34 17 20.35 ND 13.64 MFI CD38CD8+ 805.84 264.16 417.92 86.6 291.64 ND 60.16 MFI CD38CD8-482.61 271.39 302.32 132.16 187.69 ND 191.1 VL 5.237391 3.196453 ND 1.995635 1.863323 <1,591065 2.178977 CD4 132 ND 213 217 191 162 314 % Naive CD4 18.2 5.3 4.7 13.32 ND 8.9 29.19 % Naive CD8 3.88 3.54 4.77 6.74 8.37 6.15 7.99 MFI CD95dimCD4+ 6.26 13.76 13.1 8.58 9.65 ND 6.15 MFI CD95dimCD4-6.49 13.7 10.65 12.86 18.19 ND 15.96 MFI CD38CD8+ 495.81 339.82 179.43 72.99 65.52 49.58 224.68 MFI CD38CD8-421.7 299.61 213.83 86.99 93.9 72.34 226.71 VL 5.815216 3.408749 ND 2.217484 <1,591065 2.08636 2 CD4 198 ND 275 260 235 270 322 % Naive CD4 20.24 13.33 10.96 2.92 7.65 ND 19.27 % Naive CD8 7.43 2.3 2.29 4.62 5.42 ND ND MFI CD95dimCD4+ 72.34 20.17 13.4 8.47 8.1 ND 11.76 MFI CD95dimCD4-14.99 16.7 13.46 10.84 7.18 ND 3.29 MFI CD38CD8+ ND 327.81 213.83 144.6 130.97 ND 160.98 MFI CD38CD8- ND 294.27 228.76 189.38 105.54 ND 179.86 VL 5.409466 3.402605 ND 2.245513 <1,591065 <1,591065 1.94939 CD4 231 ND 219 244 248 249 360 % Naive CD4 5.44 4.64 5.35 13.48 7.11 ND 8.96 % Naive CD8 1.61 11.69 ND 22.96 4.22 ND 2.44 MFI CD95dimCD4+ 17.7 16.91 16.7 10.37 10.37 ND 12.63 MFI CD95dimCD4-20.44 20.08 19.63 14.14 9.37 ND 6.32 MFI CD38CD8+ ND 68.54 78.44 58.56 54.25 ND 79.15 MFI CD38CD8- ND 93.9 101.82 108.92 94.75 ND 110.9 ND = not determined VL= viral load (log10 copies/ml) M= months of treatment MFI = median fluorescence intensity Longitudinal data from 5 patients with CD4 counts ranging from 7 to 231 cells l -1 at baseline are shown. Abbreviations: M= months of treatment; MFI = median fluorescence intensity; ND = not determined; VL= viral load (log10 copies/ml).

Supplementary Material The Open AIDS Journal, 2012, Volume 6 v CD38 CD8+ CD38 CD8neg AUC=0.6218 AUC=0.7735 CD95 CD4neg CD95 CD95dim CD4+ AUC=0.4828 Supplementary Fig. (1). Receiver operating characteristics (ROC) curves of median fluorescence intensity of activation markers on peripheral blood T-cells show the lack of usefulness of these parameters as indicators of poor virologic treatment reponse at 12 months of HAART. ROC curves were generated using the MS Excel template of Marley W. Watkins available at http://www.public.asu.edu/~mw watkin/software/rocanalysis.xls. Abbreviation: AUC = area under the ROC curve.

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